1
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Llorens-Giralt P, Ruiz-Romero M, Nurtdinov R, Herranz-Itúrbide M, Vicent GP, Serras F, Fabregat I, Corominas M. Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers. CELL GENOMICS 2025:100887. [PMID: 40409273 DOI: 10.1016/j.xgen.2025.100887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 03/10/2025] [Accepted: 04/28/2025] [Indexed: 05/25/2025]
Abstract
The mammalian liver exhibits remarkable regenerative capabilities after injury or resection. Central to this process is the precise modulation of gene expression, driven by changes in chromatin structure and the temporal activation of distal regulatory elements. In this study, we integrated chromatin accessibility and transcriptomic data after partial hepatectomy in mice. We show that the expression of crucial regeneration genes is orchestrated by a diverse array of cis-regulatory elements, including regeneration-specific enhancers and enhancers repurposed from various developmental stages. These enhancers collaborate to activate the transcriptional programs required for hepatocyte priming and proliferation, with their activity initially regulated by the activator protein-1 (AP-1) complex and ATF3, and subsequently by nuclear factor erythroid 2 (NFE2)-related factor 2 (NRF2) during proliferation. Our results also indicate that hepatic regeneration involves the repression of enhancers regulating liver-specific metabolic functions, particularly those involved in lipid metabolism. This study provides a genome-wide atlas of enhancer-gene interactions, offering new insights into the regulatory mechanisms underlying liver regeneration.
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Affiliation(s)
- Palmira Llorens-Giralt
- Department of Genetics, Microbiology and Statistics, Faculty of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Macarena Herranz-Itúrbide
- TGF-beta and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Av. Granvia de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain; Oncology Program, National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Guillermo P Vicent
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Baldiri Reixac 4-8, 08028 Barcelona, Spain
| | - Florenci Serras
- Department of Genetics, Microbiology and Statistics, Faculty of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - Isabel Fabregat
- TGF-beta and Cancer Group, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Av. Granvia de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain; Oncology Program, National Biomedical Research Institute on Liver and Gastrointestinal Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Corominas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology and Institute of Biomedicine (IBUB), University of Barcelona, Diagonal 643, 08028 Barcelona, Catalonia, Spain.
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2
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Wenlun W, Chaohang Y, Yan H, Wenbin L, Nanqing Z, Qianmin H, Shengcai W, Qing Y, Shirui Y, Feng Z, Lingyun Z. Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development. FRONTIERS IN BIOINFORMATICS 2025; 4:1494717. [PMID: 39882307 PMCID: PMC11774864 DOI: 10.3389/fbinf.2024.1494717] [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: 09/11/2024] [Accepted: 12/23/2024] [Indexed: 01/31/2025] Open
Abstract
The precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packages (limma et al.). LncRNA-miRNA relationships were predicted using miRcode and lncBaseV2, with miRNA-mRNA pairs identified via miRcode, miRDB, and Targetscan7. Based on the ceRNA theory, we constructed and visualized the lncRNA-miRNA-mRNA regulatory network using ggalluvial among other R packages. GO, Reactome, KEGG, and GSEA explored interactions in muscle development and regeneration. We identified five candidate lncRNAs (Xist, Gas5, Pvt1, Airn, and Meg3) as potential mediators in these processes and microgravity-induced muscle wasting. Additionally, we created a detailed lncRNA-miRNA-mRNA regulatory network, including interactions such as lncRNA Xist/miR-126/IRS1, lncRNA Xist/miR-486-5p/GAB2, lncRNA Pvt1/miR-148/RAB34, and lncRNA Gas5/miR-455-5p/SOCS3. Significant signaling pathway changes (PI3K/Akt, MAPK, NF-κB, cell cycle, AMPK, Hippo, and cAMP) were observed during muscle development, regeneration, and atrophy. Despite bioinformatics challenges, our research underscores the significant roles of lncRNAs in muscle protein synthesis, degradation, cell proliferation, differentiation, function, and metabolism under both normal and microgravity conditions. This study offers new insights into the molecular mechanisms governing skeletal muscle development and regeneration.
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Affiliation(s)
- Wang Wenlun
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan, China
| | - Yu Chaohang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Huang Yan
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Li Wenbin
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Zhou Nanqing
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Hu Qianmin
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Wu Shengcai
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Yuan Qing
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Yu Shirui
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Zhang Feng
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Zhu Lingyun
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan, China
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3
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Kim JW, Manickam R, Sinha P, Xuan W, Huang J, Awad K, Brotto M, Tipparaju SM. P7C3 ameliorates barium chloride-induced skeletal muscle injury activating transcriptomic and epigenetic modulation of myogenic regulatory factors. J Cell Physiol 2024; 239:e31346. [PMID: 38946152 DOI: 10.1002/jcp.31346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Skeletal muscle injury affects the quality of life in many pathologies, including volumetric muscle loss, contusion injury, and aging. We hypothesized that the nicotinamide phosphoribosyltransferase (Nampt) activator P7C3 improves muscle repair following injury. In the present study, we tested the effect of P7C3 (1-anilino-3-(3,6-dibromocarbazol-9-yl) propan-2-ol) on chemically induced muscle injury. Muscle injury was induced by injecting 50 µL 1.2% barium chloride (BaCl2) into the tibialis anterior (TA) muscle in C57Bl/6J wild-type male mice. Mice were then treated with either 10 mg/kg body weight of P7C3 or Vehicle intraperitoneally for 7 days and assessed for histological, biochemical, and molecular changes. In the present study, we show that the acute BaCl2-induced TA muscle injury was robust and the P7C3-treated mice displayed a significant increase in the total number of myonuclei and blood vessels, and decreased serum CK activity compared with vehicle-treated mice. The specificity of P7C3 was evaluated using Nampt+/- mice, which did not display any significant difference in muscle repair capacity among treated groups. RNA-sequencing analysis of the injured TA muscles displayed 368 and 212 genes to be exclusively expressed in P7C3 and Veh-treated mice, respectively. There was an increase in the expression of genes involved in cellular processes, inflammatory response, angiogenesis, and muscle development in P7C3 versus Veh-treated mice. Conversely, there is a decrease in muscle structure and function, myeloid cell differentiation, glutathione, and oxidation-reduction, drug metabolism, and circadian rhythm signaling pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction (qPCR) and reverse transcription-qPCR analyses identified increased Pax7, Myf5, MyoD, and Myogenin expression in P7C3-treated mice. Increased histone lysine (H3K) methylation and acetylation were observed in P7C3-treated mice, with significant upregulation in inflammatory markers. Moreover, P7C3 treatment significantly increased the myotube fusion index in the BaCl2-injured human skeletal muscle in vitro. P7C3 also inhibited the lipopolysaccharide-induced inflammatory response and mitochondrial membrane potential of RAW 264.7 macrophage cells. Overall, we demonstrate that P7C3 activates muscle stem cells and enhances muscle injury repair with increased angiogenesis.
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Affiliation(s)
- Joung W Kim
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Ravikumar Manickam
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Puja Sinha
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Wanling Xuan
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
| | - Jian Huang
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Kamal Awad
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Marco Brotto
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Srinivas M Tipparaju
- Department of Pharmaceutical Sciences, Taneja College of Pharmacy, University of South Florida, Tampa, Florida, USA
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4
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Duran P, Yang BA, Plaster E, Eiken M, Loebel C, Aguilar CA. Tracking of Nascent Matrix Deposition during Muscle Stem Cell Activation across Lifespan Using Engineered Hydrogels. Adv Biol (Weinh) 2024; 8:e2400091. [PMID: 38616175 DOI: 10.1002/adbi.202400091] [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: 02/18/2024] [Revised: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Adult stem cells occupy a niche that contributes to their function, but how stem cells rebuild their microenvironment after injury remains an open-ended question. Herein, biomaterial-based systems and metabolic labeling are utilized to evaluate how skeletal muscle stem cells deposit extracellular matrix. Muscle stem cells and committed myoblasts are observed to generate less nascent matrix than muscle resident fibro-adipogenic progenitors. When cultured on substrates that matched the stiffness of physiological uninjured and injured muscles, muscle stem cells increased nascent matrix deposition with activation kinetics. Reducing the ability to deposit nascent matrix by an inhibitor of vesicle trafficking (Exo-1) attenuated muscle stem cell function and mimicked impairments observed from muscle stem cells isolated from old muscles. Old muscle stem cells are observed to deposit less nascent matrix than young muscle stem cells, which is rescued with therapeutic supplementation of insulin-like growth factors. These results highlight the role of nascent matrix production with muscle stem cell activation.
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Affiliation(s)
- Pamela Duran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleanor Plaster
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madeline Eiken
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science & Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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5
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Wubshet NH, Cai G, Chen SJ, Sullivan M, Reeves M, Mays D, Harrison M, Varnado P, Yang B, Arreguin-Martinez E, Qu Y, Lin SS, Duran P, Aguilar C, Giza S, Clements T, Liu AP. Cellular mechanotransduction of human osteoblasts in microgravity. NPJ Microgravity 2024; 10:35. [PMID: 38514677 PMCID: PMC10957960 DOI: 10.1038/s41526-024-00386-4] [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: 08/30/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Astronauts experience significant and rapid bone loss as a result of an extended stay in space, making the International Space Station (ISS) the perfect laboratory for studying osteoporosis due to the accelerated nature of bone loss on the ISS. This prompts the question, how does the lack of load due to zero-gravity propagate to bone-forming cells, human fetal osteoblasts (hFOBs), altering their maturation to mineralization? Here, we aim to study the mechanotransduction mechanisms by which bone loss occurs in microgravity. Two automated experiments, microfluidic chips capable of measuring single-cell mechanics via aspiration and cell spheroids incubated in pressure-controlled chambers, were each integrated into a CubeLab deployed to the ISS National Laboratory. For the first experiment, we report protrusion measurements of aspirated cells after exposure to microgravity at the ISS and compare these results to ground control conducted inside the CubeLab. We found slightly elongated protrusions for space samples compared to ground samples indicating softening of hFOB cells in microgravity. In the second experiment, we encapsulated osteoblast spheroids in collagen gel and incubated the samples in pressure-controlled chambers. We found that microgravity significantly reduced filamentous actin levels in the hFOB spheroids. When subjected to pressure, the spheroids exhibited increased pSMAD1/5/9 expression, regardless of the microgravity condition. Moreover, microgravity reduced YAP expression, while pressure increased YAP levels, thus restoring YAP expression for spheroids in microgravity. Our study provides insights into the influence of microgravity on the mechanical properties of bone cells and the impact of compressive pressure on cell signaling in space.
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Affiliation(s)
- Nadab H Wubshet
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Grace Cai
- Applied Physics Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samuel J Chen
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | | | | | | | | | - Benjamin Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Yunjia Qu
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shan-Shan Lin
- Applied Physics Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pamela Duran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carlos Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | | | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Applied Physics Program, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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6
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Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell 2024; 59:676-691.e5. [PMID: 38290519 PMCID: PMC10939760 DOI: 10.1016/j.devcel.2024.01.004] [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: 06/24/2023] [Revised: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Regeneration involves gene expression changes explained in part by context-dependent recruitment of transcriptional activators to distal enhancers. Silencers that engage repressive transcriptional complexes are less studied than enhancers and more technically challenging to validate, but they potentially have profound biological importance for regeneration. Here, we identified candidate silencers through a screening process that examined the ability of DNA sequences to limit injury-induced gene expression in larval zebrafish after fin amputation. A short sequence (s1) on chromosome 5 near several genes that reduce expression during adult fin regeneration could suppress promoter activity in stable transgenic lines and diminish nearby gene expression in knockin lines. High-resolution analysis of chromatin organization identified physical associations of s1 with gene promoters occurring preferentially during fin regeneration, and genomic deletion of s1 elevated the expression of these genes after fin amputation. Our study provides methods to identify "tissue regeneration silencer elements" (TRSEs) with the potential to reduce unnecessary or deleterious gene expression during regeneration.
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Affiliation(s)
- Kazunori Ando
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jianhong Ou
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John D Thompson
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John Welsby
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sushant Bangru
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingwen Shen
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaolin Wei
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yarui Diao
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA.
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7
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Wubshet NH, Cai G, Chen SJ, Sullivan M, Reeves M, Mays D, Harrison M, Varnado P, Yang B, Arreguin-Martinez E, Qu Y, Lin SS, Duran P, Aguilar C, Giza S, Clements T, Liu AP. Cellular mechanotransduction of human osteoblasts in microgravity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583164. [PMID: 38464311 PMCID: PMC10925314 DOI: 10.1101/2024.03.03.583164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Astronauts experience significant and rapid bone loss as a result of an extended stay in space, making the International Space Station (ISS) the perfect laboratory for studying osteoporosis due to the accelerated nature of bone loss on the ISS. This prompts the question, how does the lack of load due to zero-gravity propagate to bone-forming cells, human fetal osteoblasts (hFOBs), altering their maturation to mineralization? Here, we aim to study the mechanotransduction mechanisms by which bone loss occurs in microgravity. Two automated experiments, 4 microfluidic chips capable of measuring single-cell mechanics of hFOBs via aspiration and cell spheroids incubated in pressure-controlled chambers, were each integrated into a CubeLab deployed to the ISS National Laboratory. For the first experiment, we report protrusion measurements of aspirated cells after exposure to microgravity at the ISS and compare these results to ground control conducted inside the CubeLab. Our analysis revealed slightly elongated protrusions for space samples compared to ground samples indicating softening of hFOB cells in microgravity. In the second experiment, we encapsulated osteoblast spheroids in collagen gel and incubated the samples in pressure-controlled chambers. We found that microgravity significantly reduced filamentous actin levels in the hFOB spheroids. When subjected to pressure, the spheroids exhibited increased pSMAD1/5/9 expression, regardless of the microgravity condition. Moreover, microgravity reduced YAP expression, while pressure increased YAP levels, thus restoring YAP expression for spheroids in microgravity. Our study provides insights into the influence of microgravity on the mechanical properties of bone cells and the impact of compressive pressure on cell behavior and signaling in space.
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Affiliation(s)
- Nadab H. Wubshet
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Grace Cai
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
| | - Samuel J. Chen
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | - Benjamin Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Yunjia Qu
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Shan-Shan Lin
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Duran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Carlos Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
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8
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Duran P, Yang BA, Plaster E, Eiken M, Loebel C, Aguilar CA. Quantification of local matrix deposition during muscle stem cell activation using engineered hydrogels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576326. [PMID: 38328131 PMCID: PMC10849481 DOI: 10.1101/2024.01.20.576326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Adult stem cells occupy a niche that contributes to their function, but how stem cells remodel their microenvironment remains an open-ended question. Herein, biomaterials-based systems and metabolic labeling were utilized to evaluate how skeletal muscle stem cells deposit extracellular matrix. Muscle stem cells and committed myoblasts were observed to generate less nascent matrix than muscle resident fibro-adipogenic progenitors. When cultured on substrates that matched the stiffness of physiological uninjured and injured muscles, the increased nascent matrix deposition was associated with stem cell activation. Reducing the ability to deposit nascent matrix in muscle stem cells attenuated function and mimicked impairments observed from muscle stem cells isolated from old aged muscles, which could be rescued with therapeutic supplementation of insulin-like growth factors. These results highlight how nascent matrix production is critical for maintaining healthy stem cell function.
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Affiliation(s)
- Pamela Duran
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin A. Yang
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eleanor Plaster
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Madeline Eiken
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Loebel
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Dept. of Materials Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carlos A. Aguilar
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- BioInterfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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9
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Castor-Macias JA, Larouche JA, Wallace EC, Spence BD, Eames A, Duran P, Yang BA, Fraczek PM, Davis CA, Brooks SV, Maddipati KR, Markworth JF, Aguilar CA. Maresin 1 repletion improves muscle regeneration after volumetric muscle loss. eLife 2023; 12:e86437. [PMID: 38131691 PMCID: PMC10807862 DOI: 10.7554/elife.86437] [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: 01/26/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
The acute traumatic or surgical loss of skeletal muscle, known as volumetric muscle loss (VML), is a devastating type of injury that results in exacerbated and persistent inflammation followed by fibrosis. The mechanisms that mediate the magnitude and duration of the inflammatory response and ensuing fibrosis after VML remain understudied, and as such, the development of regenerative therapies has been limited. To address this need, we profiled how lipid mediators, which are potent regulators of the immune response after injury, varied with VML injuries that heal or result in fibrosis. We observed that non-healing VML injuries displayed increased pro-inflammatory eicosanoids and a lack of pro-resolving lipid mediators. Treatment of VML with a pro-resolving lipid mediator synthesized from docosahexaenoic acid, called Maresin 1, ameliorated fibrosis through reduction of neutrophils and macrophages and enhanced recovery of muscle strength. These results expand our knowledge of the dysregulated immune response that develops after VML and identify a novel immuno-regenerative therapeutic modality in Maresin 1.
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Affiliation(s)
- Jesus A Castor-Macias
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Jacqueline A Larouche
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Emily C Wallace
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Bonnie D Spence
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Alec Eames
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Pamela Duran
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Benjamin A Yang
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Paula M Fraczek
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Carol A Davis
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Susan V Brooks
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Krishna Rao Maddipati
- Department of Pathology, Lipidomics Core Facility, Wayne State UniversityDetroitUnited States
| | - James F Markworth
- Department of Animal Sciences, Purdue UniversityWest Lafayette, IndianaUnited States
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
- Program in Cellular and Molecular Biology, University of MichiganAnn ArborUnited States
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10
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Koopmans PJ, Ismaeel A, Goljanek-Whysall K, Murach KA. The roles of miRNAs in adult skeletal muscle satellite cells. Free Radic Biol Med 2023; 209:228-238. [PMID: 37879420 PMCID: PMC10911817 DOI: 10.1016/j.freeradbiomed.2023.10.403] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Satellite cells are bona fide muscle stem cells that are indispensable for successful post-natal muscle growth and regeneration after severe injury. These cells also participate in adult muscle adaptation in several capacities. MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA that are implicated in several aspects of stem cell function. There is evidence to suggest that miRNAs affect satellite cell behavior in vivo during development and myogenic progenitor behavior in vitro, but the role of miRNAs in adult skeletal muscle satellite cells is less studied. In this review, we provide evidence for how miRNAs control satellite cell function with emphasis on satellite cells of adult skeletal muscle in vivo. We first outline how miRNAs are indispensable for satellite cell viability and control the phases of myogenesis. Next, we discuss the interplay between miRNAs and myogenic cell redox status, senescence, and communication to other muscle-resident cells during muscle adaptation. Results from recent satellite cell miRNA profiling studies are also summarized. In vitro experiments in primary myogenic cells and cell lines have been invaluable for exploring the influence of miRNAs, but we identify a need for novel genetic tools to further interrogate how miRNAs control satellite cell behavior in adult skeletal muscle in vivo.
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Affiliation(s)
- Pieter Jan Koopmans
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ahmed Ismaeel
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Katarzyna Goljanek-Whysall
- School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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11
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Maehara H, Kokaji T, Hatano A, Suzuki Y, Matsumoto M, Nakayama KI, Egami R, Tsuchiya T, Ozaki H, Morita K, Shirai M, Li D, Terakawa A, Uematsu S, Hironaka KI, Ohno S, Kubota H, Araki H, Miura F, Ito T, Kuroda S. DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle. Sci Rep 2023; 13:19118. [PMID: 37926704 PMCID: PMC10625943 DOI: 10.1038/s41598-023-46393-5] [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: 08/18/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023] Open
Abstract
Each tissue has a dominant set of functional proteins required to mediate tissue-specific functions. Epigenetic modifications, transcription, and translational efficiency control tissue-dominant protein production. However, the coordination of these regulatory mechanisms to achieve such tissue-specific protein production remains unclear. Here, we analyzed the DNA methylome, transcriptome, and proteome in mouse liver and skeletal muscle. We found that DNA hypomethylation at promoter regions is globally associated with liver-dominant or skeletal muscle-dominant functional protein production within each tissue, as well as with genes encoding proteins involved in ubiquitous functions in both tissues. Thus, genes encoding liver-dominant proteins, such as those involved in glycolysis or gluconeogenesis, the urea cycle, complement and coagulation systems, enzymes of tryptophan metabolism, and cytochrome P450-related metabolism, were hypomethylated in the liver, whereas those encoding-skeletal muscle-dominant proteins, such as those involved in sarcomere organization, were hypomethylated in the skeletal muscle. Thus, DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins.
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Affiliation(s)
- Hideki Maehara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Toshiya Kokaji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916‑5 Takayama, Ikoma, Nara, Japan
| | - Atsushi Hatano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-Dori, Chuo-Ku, Niigata City, Niigata, 951-8510, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-Dori, Chuo-Ku, Niigata City, Niigata, 951-8510, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Riku Egami
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Takaho Tsuchiya
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Ibaraki, 305‑8575, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Ibaraki, 305‑8577, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Ibaraki, 305‑8575, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Ibaraki, 305‑8577, Japan
| | - Keigo Morita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Masaki Shirai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Dongzi Li
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Akira Terakawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Saori Uematsu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Ken-Ichi Hironaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Satoshi Ohno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, 7‑3‑1 Hongo, Bunkyo‑ku, Tokyo, 113‑0033, Japan
- Department of AI Systems Medicine, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiromitsu Araki
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
- Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, 7‑3‑1 Hongo, Bunkyo‑ku, Tokyo, 113‑0033, Japan.
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12
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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13
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Lim S, Lee DE, Morena da Silva F, Koopmans PJ, Vechetti IJ, von Walden F, Greene NP, Murach KA. MicroRNA control of the myogenic cell transcriptome and proteome: the role of miR-16. Am J Physiol Cell Physiol 2023; 324:C1101-C1109. [PMID: 36971422 PMCID: PMC10191132 DOI: 10.1152/ajpcell.00071.2023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
MicroRNAs (miRs) control stem cell biology and fate. Ubiquitously expressed and conserved miR-16 was the first miR implicated in tumorigenesis. miR-16 is low in muscle during developmental hypertrophy and regeneration. It is enriched in proliferating myogenic progenitor cells but is repressed during differentiation. The induction of miR-16 blocks myoblast differentiation and myotube formation, whereas knockdown enhances these processes. Despite a central role for miR-16 in myogenic cell biology, how it mediates its potent effects is incompletely defined. In this investigation, global transcriptomic and proteomic analyses after miR-16 knockdown in proliferating C2C12 myoblasts revealed how miR-16 influences myogenic cell fate. Eighteen hours after miR-16 inhibition, ribosomal protein gene expression levels were higher relative to control myoblasts and p53 pathway-related gene abundance was lower. At the protein level at this same time point, miR-16 knockdown globally upregulated tricarboxylic acid (TCA) cycle proteins while downregulating RNA metabolism-related proteins. miR-16 inhibition induced specific proteins associated with myogenic differentiation such as ACTA2, EEF1A2, and OPA1. We extend prior work in hypertrophic muscle tissue and show that miR-16 is lower in mechanically overloaded muscle in vivo. Our data collectively point to how miR-16 is implicated in aspects of myogenic cell differentiation. A deeper understanding of the role of miR-16 in myogenic cells has consequences for muscle developmental growth, exercise-induced hypertrophy, and regenerative repair after injury, all of which involve myogenic progenitors.
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Affiliation(s)
- Seongkyun Lim
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
| | - David E Lee
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
| | - Francielly Morena da Silva
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
| | - Pieter J Koopmans
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
- Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, Arkansas, United States
| | - Ivan J Vechetti
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
| | - Ferdinand von Walden
- Neuropediatrics, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas P Greene
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
- Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, Arkansas, United States
| | - Kevin A Murach
- Department of Health, Human Performance, and Recreation, Exercise Science Research Center, University of Arkansas, Fayetteville, Arkansas, United States
- Cell and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, Arkansas, United States
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14
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Yang BA, Larouche JA, Sabin KM, Fraczek PM, Parker SCJ, Aguilar CA. Three-dimensional chromatin re-organization during muscle stem cell aging. Aging Cell 2023; 22:e13789. [PMID: 36727578 PMCID: PMC10086523 DOI: 10.1111/acel.13789] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world's population continues to increase. The regeneration of damaged skeletal muscle is mediated by muscle stem cells, but in old age muscle stem cells become functionally attenuated. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
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Affiliation(s)
- Benjamin A. Yang
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Jacqueline A. Larouche
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Kaitlyn M. Sabin
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Paula M. Fraczek
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Stephen C. J. Parker
- Program in Cellular and Molecular BiologyUniversity of MichiganAnn ArborMichiganUSA
- Department of Computational Medicine & BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
- Department of Human GeneticsUniversity of MichiganAnn ArborMichiganUSA
| | - Carlos A. Aguilar
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
- Program in Cellular and Molecular BiologyUniversity of MichiganAnn ArborMichiganUSA
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15
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Abstract
Injury to muscle brings about the activation of stem cells, which then generate new myocytes to replace damaged tissue. We demonstrate that this activation is accompanied by a dramatic change in the stem-cell methylation pattern that prepares them epigenetically for terminal myocyte differentiation. These de- and de novo methylation events occur at regulatory elements associated with genes involved in myogenesis and are necessary for activation and regeneration. Local injury of one muscle elicits an almost identical epigenetic change in satellite cells from other muscles in the body, in a process mediated by circulating factors. Furthermore, this same methylation state is also generated in muscle stem cells (MuSCs) of female animals following pregnancy, even in the absence of any injury. Unlike the activation-induced expression changes, which are transient, the induced methylation profile is stably maintained in resident MuSCs and thus represents a molecular memory of previous physiological events that is probably programmed to provide a mechanism for long-term adaptation.
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16
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Harris RE. Regeneration enhancers: a field in development. Am J Physiol Cell Physiol 2022; 323:C1548-C1554. [PMID: 36252130 PMCID: PMC9829460 DOI: 10.1152/ajpcell.00403.2022] [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] [Indexed: 01/21/2023]
Abstract
The ability to regenerate tissues and organs following damage is not equally distributed across metazoans, and even highly related species can vary considerably in their regenerative capacity. Studies of animals with high regenerative potential have shown that factors expressed during normal development are often reactivated upon damage and required for successful regeneration. As such, regenerative potential may not be dictated by the presence or absence of the necessary genes, but whether such genes are appropriately activated following injury. The identification of damage-responsive enhancers that regulate regenerative gene expression in multiple species and tissues provides possible mechanistic insight into this phenomenon. Enhancers that are reused from developmental programs, and those that are potentially unique to regeneration, have been characterized individually and at a genome-wide scale. A better understanding of the regulatory events that, direct and in some cases limit, regenerative capacity is an important step in developing new methods to manipulate and augment regeneration, particularly in tissues that do not have this ability, including those of humans.
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Affiliation(s)
- Robin E. Harris
- School of Life Sciences, Arizona State University, Tempe, Arizona
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17
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Barutcu AR, Elizalde G, Gonzalez AE, Soni K, Rinn JL, Wagers AJ, Almada AE. Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells. Skelet Muscle 2022; 12:20. [PMID: 35971133 PMCID: PMC9377060 DOI: 10.1186/s13395-022-00303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The AP-1 transcription factor, FBJ osteosarcoma oncogene (FOS), is induced in adult muscle satellite cells (SCs) within hours following muscle damage and is required for effective stem cell activation and muscle repair. However, why FOS is rapidly downregulated before SCs enter cell cycle as progenitor cells (i.e., transiently expressed) remains unclear. Further, whether boosting FOS levels in the proliferating progeny of SCs can enhance their myogenic properties needs further evaluation. METHODS We established an inducible, FOS expression system to evaluate the impact of persistent FOS activity in muscle progenitor cells ex vivo. We performed various assays to measure cellular proliferation and differentiation, as well as uncover changes in RNA levels and three-dimensional (3D) chromatin interactions. RESULTS Persistent FOS activity in primary muscle progenitor cells severely antagonizes their ability to differentiate and form myotubes within the first 2 weeks in culture. RNA-seq analysis revealed that ectopic FOS activity in muscle progenitor cells suppressed a global pro-myogenic transcriptional program, while activating a stress-induced, mitogen-activated protein kinase (MAPK) transcriptional signature. Additionally, we observed various FOS-dependent, chromosomal re-organization events in A/B compartments, topologically associated domains (TADs), and genomic loops near FOS-regulated genes. CONCLUSIONS Our results suggest that elevated FOS activity in recently activated muscle progenitor cells perturbs cellular differentiation by altering the 3D chromosome organization near critical pro-myogenic genes. This work highlights the crucial importance of tightly controlling FOS expression in the muscle lineage and suggests that in states of chronic stress or disease, persistent FOS activity in muscle precursor cells may disrupt the muscle-forming process.
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Affiliation(s)
- A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Gabriel Elizalde
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alfredo E Gonzalez
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kartik Soni
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: BioFrontiers and Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Albert E Almada
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA.
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA.
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18
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Larouche JA, Fraczek PM, Kurpiers SJ, Yang BA, Davis C, Castor-Macias JA, Sabin K, Anderson S, Harrer J, Hall M, Brooks SV, Jang YC, Willett N, Shea LD, Aguilar CA. Neutrophil and natural killer cell imbalances prevent muscle stem cell-mediated regeneration following murine volumetric muscle loss. Proc Natl Acad Sci U S A 2022; 119:e2111445119. [PMID: 35377804 PMCID: PMC9169656 DOI: 10.1073/pnas.2111445119] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
Volumetric muscle loss (VML) overwhelms the innate regenerative capacity of mammalian skeletal muscle (SkM), leading to numerous disabilities and reduced quality of life. Immune cells are critical responders to muscle injury and guide tissue resident stem cell– and progenitor-mediated myogenic repair. However, how immune cell infiltration and intercellular communication networks with muscle stem cells are altered following VML and drive pathological outcomes remains underexplored. Herein, we contrast the cellular and molecular mechanisms of VML injuries that result in the fibrotic degeneration or regeneration of SkM. Following degenerative VML injuries, we observed the heightened infiltration of natural killer (NK) cells as well as the persistence of neutrophils beyond 2 wk postinjury. Functional validation of NK cells revealed an antagonistic role in neutrophil accumulation in part via inducing apoptosis and CCR1-mediated chemotaxis. The persistent infiltration of neutrophils in degenerative VML injuries was found to contribute to impairments in muscle stem cell regenerative function, which was also attenuated by transforming growth factor beta 1 (TGFβ1). Blocking TGFβ signaling reduced neutrophil accumulation and fibrosis and improved muscle-specific force. Collectively, these results enhance our understanding of immune cell–stem cell cross talk that drives regenerative dysfunction and provide further insight into possible avenues for fibrotic therapy exploration.
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Affiliation(s)
- Jacqueline A. Larouche
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Paula M. Fraczek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Sarah J. Kurpiers
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Benjamin A. Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Carol Davis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
| | - Jesus A. Castor-Macias
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Kaitlyn Sabin
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Shannon Anderson
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332
| | - Julia Harrer
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332
| | - Matthew Hall
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Susan V. Brooks
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109
| | - Young C. Jang
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Nick Willett
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403
| | - Lonnie D. Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Carlos A. Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109
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19
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Yang BA, Castor-Macias J, Fraczek P, Cornett A, Brown LA, Kim M, Brooks SV, Lombaert IMA, Lee JH, Aguilar CA. Sestrins regulate muscle stem cell metabolic homeostasis. Stem Cell Reports 2021; 16:2078-2088. [PMID: 34388363 PMCID: PMC8452514 DOI: 10.1016/j.stemcr.2021.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/20/2023] Open
Abstract
The health and homeostasis of skeletal muscle are preserved by a population of tissue-resident muscle stem cells (MuSCs) that maintain a state of mitotic and metabolic quiescence in adult tissues. The capacity of MuSCs to preserve the quiescent state declines with aging and metabolic insults, promoting premature activation and stem cell exhaustion. Sestrins are a class of stress-inducible proteins that act as antioxidants and inhibit the activation of the mammalian target of rapamycin complex 1 (mTORC1) signaling complex. Despite these pivotal roles, the role of Sestrins has not been explored in adult stem cells. We show that SESTRIN1,2 loss results in hyperactivation of the mTORC1 complex, increased propensity to enter the cell cycle, and shifts in metabolic flux. Aged SESTRIN1,2 knockout mice exhibited loss of MuSCs and a reduced ability to regenerate injured muscle. These findings demonstrate that Sestrins help maintain metabolic pathways in MuSCs that protect quiescence against aging.
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Affiliation(s)
- Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jesus Castor-Macias
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paula Fraczek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ashley Cornett
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA; Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lemuel A Brown
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Myungjin Kim
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Susan V Brooks
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Isabelle M A Lombaert
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA; Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jun Hee Lee
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Larouche JA, Mohiuddin M, Choi JJ, Ulintz PJ, Fraczek P, Sabin K, Pitchiaya S, Kurpiers SJ, Castor-Macias J, Liu W, Hastings RL, Brown LA, Markworth JF, De Silva K, Levi B, Merajver SD, Valdez G, Chakkalakal JV, Jang YC, Brooks SV, Aguilar CA. Murine muscle stem cell response to perturbations of the neuromuscular junction are attenuated with aging. eLife 2021; 10:e66749. [PMID: 34323217 PMCID: PMC8360658 DOI: 10.7554/elife.66749] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/28/2021] [Indexed: 01/29/2023] Open
Abstract
During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function impacting mobility and quality of life. Muscle loss is often associated with denervation and a loss of resident muscle stem cells (satellite cells or MuSCs); however, the relationship between MuSCs and innervation has not been established. Herein, we administered severe neuromuscular trauma to a transgenic murine model that permits MuSC lineage tracing. We show that a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ), the synapse between myofibers and motor neurons, in healthy young adult muscles. In aging and in a mouse model of neuromuscular degeneration (Cu/Zn superoxide dismutase knockout - Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ in a manner akin to young muscle and partially restored MuSC ability to engraft into positions proximal to the NMJ. Using single cell RNA-sequencing of MuSCs isolated from aged muscle, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury and share similarity to synaptic myonuclei. Collectively, these data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors.
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Affiliation(s)
- Jacqueline A Larouche
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Mahir Mohiuddin
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Wallace Coulter Departmentof Biomedical Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Jeongmoon J Choi
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Wallace Coulter Departmentof Biomedical Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter J Ulintz
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
- Internal Medicine-Hematology/Oncology, University of MichiganAnn ArborUnited States
| | - Paula Fraczek
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Kaitlyn Sabin
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | | | - Sarah J Kurpiers
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Jesus Castor-Macias
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Wenxuan Liu
- Department of Pharmacology and Physiology, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of Rochester Medical CenterRochesterUnited States
- Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical CenterRochesterUnited States
| | - Robert Louis Hastings
- Departmentof Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
- Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown UniversityProvidenceUnited States
| | - Lemuel A Brown
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - James F Markworth
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Kanishka De Silva
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
| | - Benjamin Levi
- Department of Surgery, University of Texas SouthwesternDallasUnited States
- Childrens Research Institute and Center for Mineral MetabolismDallasUnited States
- Program in Cellular and Molecular Biology, University of MichiganAnn ArborUnited States
| | - Sofia D Merajver
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Internal Medicine-Hematology/Oncology, University of MichiganAnn ArborUnited States
| | - Gregorio Valdez
- Departmentof Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
- Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown UniversityProvidenceUnited States
| | - Joe V Chakkalakal
- Department of Pharmacology and Physiology, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of Rochester Medical CenterRochesterUnited States
- Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical CenterRochesterUnited States
| | - Young C Jang
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Wallace Coulter Departmentof Biomedical Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Susan V Brooks
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Department of Molecular & Integrative Physiology, University of MichiganAnn ArborUnited States
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Biointerfaces Institute, University of MichiganAnn ArborUnited States
- Childrens Research Institute and Center for Mineral MetabolismDallasUnited States
- Program in Cellular and Molecular Biology, University of MichiganAnn ArborUnited States
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21
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Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis. Cell Rep 2021; 32:107964. [PMID: 32726628 PMCID: PMC8025697 DOI: 10.1016/j.celrep.2020.107964] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/12/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
During aging, there is a progressive loss of volume and function in skeletal muscle that impacts mobility and quality of life. The repair of skeletal muscle is regulated by tissue-resident stem cells called satellite cells (or muscle stem cells [MuSCs]), but in aging, MuSCs decrease in numbers and regenerative capacity. The transcriptional networks and epigenetic changes that confer diminished regenerative function in MuSCs as a result of natural aging are only partially understood. Herein, we use an integrative genomics approach to profile MuSCs from young and aged animals before and after injury. Integration of these datasets reveals aging impacts multiple regulatory changes through significant differences in gene expression, metabolic flux, chromatin accessibility, and patterns of transcription factor (TF) binding activities. Collectively, these datasets facilitate a deeper understanding of the regulation tissue-resident stem cells use during aging and healing.
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22
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Contreras O, Córdova-Casanova A, Brandan E. PDGF-PDGFR network differentially regulates the fate, migration, proliferation, and cell cycle progression of myogenic cells. Cell Signal 2021; 84:110036. [PMID: 33971280 DOI: 10.1016/j.cellsig.2021.110036] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022]
Abstract
Platelet-derived growth factors (PDGFs) regulate embryonic development, tissue regeneration, and wound healing through their binding to PDGF receptors, PDGFRα and PDGFRβ. However, the role of PDGF signaling in regulating muscle development and regeneration remains elusive, and the cellular and molecular responses of myogenic cells are understudied. Here, we explore the PDGF-PDGFR gene expression changes and their involvement in skeletal muscle myogenesis and myogenic fate. By surveying bulk RNA sequencing and single-cell profiling data of skeletal muscle stem cells, we show that myogenic progenitors and muscle stem cells differentially express PDGF ligands and PDGF receptors during myogenesis. Quiescent adult muscle stem cells and myoblasts preferentially express PDGFRβ over PDGFRα. Remarkably, cell culture- and injury-induced muscle stem cell activation altered PDGF family gene expression. In myoblasts, PDGF-AB and PDGF-BB treatments activate two pro-chemotactic and pro-mitogenic downstream transducers, RAS-ERK1/2 and PI3K-AKT. PDGFRs inhibitor AG1296 inhibited ERK1/2 and AKT activation, myoblast migration, proliferation, and cell cycle progression induced by PDGF-AB and PDGF-BB. We also found that AG1296 causes myoblast G0/G1 cell cycle arrest. Remarkably, PDGF-AA did not promote a noticeable ERK1/2 or AKT activation, myoblast migration, or expansion. Also, myogenic differentiation reduced the expression of both PDGFRα and PDGFRβ, whereas forced PDGFRα expression impaired myogenesis. Thus, our data highlight PDGF signaling pathway to stimulate satellite cell proliferation aiming to enhance skeletal muscle regeneration and provide a deeper understanding of the role of PDGF signaling in non-fibroblastic cells.
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Affiliation(s)
- Osvaldo Contreras
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington 2052, Australia; Departamento de Biología Celular y Molecular and Center for Aging and Regeneration (CARE-ChileUC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.
| | - Adriana Córdova-Casanova
- Departamento de Biología Celular y Molecular and Center for Aging and Regeneration (CARE-ChileUC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
| | - Enrique Brandan
- Departamento de Biología Celular y Molecular and Center for Aging and Regeneration (CARE-ChileUC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile; Fundación Ciencia & Vida, 7780272 Santiago, Chile
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23
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Yang BA, Westerhof TM, Sabin K, Merajver SD, Aguilar CA. Engineered Tools to Study Intercellular Communication. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002825. [PMID: 33552865 PMCID: PMC7856891 DOI: 10.1002/advs.202002825] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/10/2020] [Indexed: 05/08/2023]
Abstract
All multicellular organisms rely on intercellular communication networks to coordinate physiological functions. As members of a dynamic social network, each cell receives, processes, and redistributes biological information to define and maintain tissue homeostasis. Uncovering the molecular programs underlying these processes is critical for prevention of disease and aging and development of therapeutics. The study of intercellular communication requires techniques that reduce the scale and complexity of in vivo biological networks while resolving the molecular heterogeneity in "omic" layers that contribute to cell state and function. Recent advances in microengineering and high-throughput genomics offer unprecedented spatiotemporal control over cellular interactions and the ability to study intercellular communication in a high-throughput and mechanistic manner. Herein, this review discusses how salient engineered approaches and sequencing techniques can be applied to understand collective cell behavior and tissue functions.
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Affiliation(s)
- Benjamin A. Yang
- Department of Biomedical Engineering and Biointerfaces Institute2800 Plymouth Road, North Campus Research ComplexAnn ArborMIA10‐183USA
| | - Trisha M. Westerhof
- Department of Biomedical Engineering and Biointerfaces Institute2800 Plymouth Road, North Campus Research ComplexAnn ArborMIA10‐183USA
- Department of Internal MedicineDivision of Hematology/Oncology and Rogel Cancer Center1500 East Medical Center Drive, Rogel Cancer CenterAnn ArborMI7314USA
| | - Kaitlyn Sabin
- Department of Biomedical Engineering and Biointerfaces Institute2800 Plymouth Road, North Campus Research ComplexAnn ArborMIA10‐183USA
| | - Sofia D. Merajver
- Department of Internal MedicineDivision of Hematology/Oncology and Rogel Cancer Center1500 East Medical Center Drive, Rogel Cancer CenterAnn ArborMI7314USA
| | - Carlos A. Aguilar
- Department of Biomedical Engineering and Biointerfaces Institute2800 Plymouth Road, North Campus Research ComplexAnn ArborMIA10‐183USA
- Program in Cellular and Molecular Biology2800 Plymouth Road, North Campus Research ComplexAnn ArborMIA10‐183USA
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24
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Blanc RS, Kallenbach JG, Bachman JF, Mitchell A, Paris ND, Chakkalakal JV. Inhibition of inflammatory CCR2 signaling promotes aged muscle regeneration and strength recovery after injury. Nat Commun 2020; 11:4167. [PMID: 32820177 PMCID: PMC7441393 DOI: 10.1038/s41467-020-17620-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023] Open
Abstract
Muscle regeneration depends on a robust albeit transient inflammatory response. Persistent inflammation is a feature of age-related regenerative deficits, yet the underlying mechanisms are poorly understood. Here, we find inflammatory-related CC-chemokine-receptor 2 (Ccr2) expression in non-hematopoietic myogenic progenitors (MPs) during regeneration. After injury, the expression of Ccr2 in MPs corresponds to the levels of its ligands, the chemokines Ccl2, 7, and 8. We find stimulation of Ccr2-activity inhibits MP fusion and contribution to myofibers. This occurs in association with increases in MAPKp38δ/γ signaling, MyoD phosphorylation, and repression of the terminal myogenic commitment factor Myogenin. High levels of Ccr2-chemokines are a feature of regenerating aged muscle. Correspondingly, deletion of Ccr2 in MPs is necessary for proper fusion into regenerating aged muscle. Finally, opportune Ccr2 inhibition after injury enhances aged regeneration and functional recovery. These results demonstrate that inflammatory-induced activation of Ccr2 signaling in myogenic cells contributes to aged muscle regenerative decline. Chronic inflammation is a feature of age-related regenerative decline in skeletal muscles, but how it directly affects resident muscle stem cell fate and function is unclear. Here, the authors show that Ccr2 signaling in muscle stem cell derived progenitors represses terminal myogenic differentiation, and that targeting Ccr2 on aged myogenic progenitors rejuvenates aged skeletal muscle healing and function.
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Affiliation(s)
- Roméo S Blanc
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA.,Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical Center, Rochester, NY, USA
| | - Jacob G Kallenbach
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA.,Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, USA
| | - John F Bachman
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA.,Department of Pathology and Laboratory Medicine, Cell Biology of Disease Graduate Program, University of Rochester Medical Center, Rochester, NY, USA
| | - Amanda Mitchell
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
| | - Nicole D Paris
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA.,Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical Center, Rochester, NY, USA
| | - Joe V Chakkalakal
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA. .,Wilmot Cancer Institute, Stem Cell and Regenerative Medicine Institute, and The Rochester Aging Research Center, University of Rochester Medical Center, Rochester, NY, USA. .,Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, USA.
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25
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Harris RE, Stinchfield MJ, Nystrom SL, McKay DJ, Hariharan IK. Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila. eLife 2020; 9:58305. [PMID: 32490812 PMCID: PMC7299344 DOI: 10.7554/elife.58305] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/28/2020] [Indexed: 12/31/2022] Open
Abstract
Like tissues of many organisms, Drosophila imaginal discs lose the ability to regenerate as they mature. This loss of regenerative capacity coincides with reduced damage-responsive expression of multiple genes needed for regeneration. We previously showed that two such genes, wg and Wnt6, are regulated by a single damage-responsive enhancer that becomes progressively inactivated via Polycomb-mediated silencing as discs mature (Harris et al., 2016). Here we explore the generality of this mechanism and identify additional damage-responsive, maturity-silenced (DRMS) enhancers, some near genes known to be required for regeneration such as Mmp1, and others near genes that we now show function in regeneration. Using a novel GAL4-independent ablation system we characterize two DRMS-associated genes, apontic (apt), which curtails regeneration and CG9752/asperous (aspr), which promotes it. This mechanism of suppressing regeneration by silencing damage-responsive enhancers at multiple loci can be partially overcome by reducing activity of the chromatin regulator extra sex combs (esc).
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Affiliation(s)
| | | | - Spencer L Nystrom
- University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Daniel J McKay
- University of North Carolina at Chapel Hill, Chapel Hill, United States
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26
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Kwon JB, Vankara A, Ettyreddy AR, Bohning JD, Gersbach CA. Myogenic Progenitor Cell Lineage Specification by CRISPR/Cas9-Based Transcriptional Activators. Stem Cell Reports 2020; 14:755-769. [PMID: 32330446 PMCID: PMC7221109 DOI: 10.1016/j.stemcr.2020.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Engineered CRISPR/Cas9-based transcriptional activators can potently and specifically activate endogenous fate-determining genes to direct differentiation of pluripotent stem cells. Here, we demonstrate that endogenous activation of the PAX7 transcription factor results in stable epigenetic remodeling and differentiates human pluripotent stem cells into skeletal myogenic progenitor cells. Compared with exogenous overexpression of PAX7 cDNA, we find that endogenous activation results in the generation of more proliferative myogenic progenitors that can maintain PAX7 expression over multiple passages in serum-free conditions while preserving the capacity for terminal myogenic differentiation. Transplantation of human myogenic progenitors derived from endogenous activation of PAX7 into immunodeficient mice resulted in a greater number of human dystrophin+ myofibers compared with exogenous PAX7 overexpression. RNA-sequencing analysis also revealed transcriptome-wide differences between myogenic progenitors generated via CRISPR-based endogenous activation of PAX7 and exogenous PAX7 cDNA overexpression. These studies demonstrate the utility of CRISPR/Cas9-based transcriptional activators for controlling cell-fate decisions.
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Affiliation(s)
- Jennifer B Kwon
- University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC 27710, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Ashish Vankara
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Adarsh R Ettyreddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Joel D Bohning
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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27
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Stepien DM, Hwang C, Marini S, Pagani CA, Sorkin M, Visser ND, Huber AK, Edwards NJ, Loder SJ, Vasquez K, Aguilar CA, Kumar R, Mascharak S, Longaker MT, Li J, Levi B. Tuning Macrophage Phenotype to Mitigate Skeletal Muscle Fibrosis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:2203-2215. [PMID: 32161098 PMCID: PMC8080967 DOI: 10.4049/jimmunol.1900814] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Myeloid cells are critical to the development of fibrosis following muscle injury; however, the mechanism of their role in fibrosis formation remains unclear. In this study, we demonstrate that myeloid cell-derived TGF-β1 signaling is increased in a profibrotic ischemia reperfusion and cardiotoxin muscle injury model. We found that myeloid-specific deletion of Tgfb1 abrogates the fibrotic response in this injury model and reduces fibro/adipogenic progenitor cell proliferation while simultaneously enhancing muscle regeneration, which is abrogated by adaptive transfer of normal macrophages. Similarly, a murine TGFBRII-Fc ligand trap administered after injury significantly reduced muscle fibrosis and improved muscle regeneration. This study ultimately demonstrates that infiltrating myeloid cell TGF-β1 is responsible for the development of traumatic muscle fibrosis, and its blockade offers a promising therapeutic target for preventing muscle fibrosis after ischemic injury.
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Affiliation(s)
- David M Stepien
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Charles Hwang
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Simone Marini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - Chase A Pagani
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Michael Sorkin
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Noelle D Visser
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Amanda K Huber
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Nicole J Edwards
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Shawn J Loder
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Kaetlin Vasquez
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Carlos A Aguilar
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
- Biomedical Engineering Department, Biointerfaces Institute and Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109
| | - Ravi Kumar
- Acceleron Pharmaceuticals, Cambridge MA 02139
| | - Shamik Mascharak
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford School of Medicine, Stanford University, Stanford, CA 94305; and
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford School of Medicine, Stanford University, Stanford, CA 94305; and
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford University, Stanford, CA 94305
| | - Jun Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - Benjamin Levi
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109;
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28
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Barruet E, Garcia SM, Striedinger K, Wu J, Lee S, Byrnes L, Wong A, Xuefeng S, Tamaki S, Brack AS, Pomerantz JH. Functionally heterogeneous human satellite cells identified by single cell RNA sequencing. eLife 2020; 9:51576. [PMID: 32234209 PMCID: PMC7164960 DOI: 10.7554/elife.51576] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cells is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (Hu-MuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the Hu-MuSC pool contains clusters of transcriptionally distinct cells with consistency across human individuals. New surface marker combinations were enriched in transcriptional subclusters, including a subpopulation of Hu-MuSCs marked by CXCR4/CD29/CD56/CAV1 (CAV1+). In vitro, CAV1+ Hu-MuSCs are morphologically distinct, and characterized by resistance to activation compared to CAV1- Hu-MuSCs. In vivo, CAV1+ Hu-MuSCs demonstrated increased engraftment after transplantation. Our findings provide a comprehensive transcriptional view of normal Hu-MuSCs and describe new heterogeneity, enabling separation of functionally distinct human satellite cell subpopulations.
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Affiliation(s)
- Emilie Barruet
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Steven M Garcia
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Katharine Striedinger
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Jake Wu
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Solomon Lee
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Lauren Byrnes
- University of California San Francisco, San Francisco, United States
| | - Alvin Wong
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Sun Xuefeng
- Department of Orthopedic Surgery, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Stanley Tamaki
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Andrew S Brack
- Department of Orthopedic Surgery, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
| | - Jason H Pomerantz
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California, San Francisco, San Francisco, United States
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29
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Chromatin dynamics in regeneration epithelia: Lessons from Drosophila imaginal discs. Semin Cell Dev Biol 2020; 97:55-62. [DOI: 10.1016/j.semcdb.2019.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022]
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Rodriguez AM, Kang J. Regeneration enhancers: Starting a journey to unravel regulatory events in tissue regeneration. Semin Cell Dev Biol 2020; 97:47-54. [PMID: 30953740 PMCID: PMC6783330 DOI: 10.1016/j.semcdb.2019.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
Regeneration, an ability to replace lost body parts, is widespread across animal species. While mammals poorly regenerate most tissues, teleost fish and urodele amphibians possess remarkable regenerative capacity. Earlier work demonstrated that genes driving regeneration are evolutionarily conserved, indicating that a key factor in diverse tissue regeneration is not the presence or absence of regeneration-driving genes but the mechanisms controlling activation of these genes after injury. Thus, understanding the regulatory events of tissue regeneration could provide the means for unlocking latent capacities for tissue regeneration. After injury, cells undergo extensive epigenetic changes to establish new transcriptional programs for tissue regeneration. Gene transcription in eukaryotes is a complicated process that requires specific interactions between trans-acting regulators and cis-regulatory DNA elements. Among cis-regulatory elements, enhancers are essential to control precise gene expression. Recently, multiple regeneration/injury-associated enhancers have been identified in several model organisms. In this review, we highlight recently discovered regeneration/injury enhancers and their specific characteristics. We also discuss how abnormal regulation of regeneration enhancers influences animal development and physiology. Investigation of regeneration enhancers potentially allows us to begin understanding the fundamental biology of tissue regeneration and inspires new solutions for manipulating regenerative ability.
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Affiliation(s)
- Anjelica M Rodriguez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA.
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Chen X, Du J, Zhu Y, Zhang C, Sun H. Comprehensive analysis of lncRNA and mRNA expression profiles in macrophages activated by Actinidia eriantha polysaccharide. Int J Biol Macromol 2019; 136:980-993. [DOI: 10.1016/j.ijbiomac.2019.06.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022]
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Myoferlin Contributes to the Metastatic Phenotype of Pancreatic Cancer Cells by Enhancing Their Migratory Capacity through the Control of Oxidative Phosphorylation. Cancers (Basel) 2019; 11:cancers11060853. [PMID: 31248212 PMCID: PMC6628295 DOI: 10.3390/cancers11060853] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/13/2019] [Accepted: 06/16/2019] [Indexed: 12/11/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignancies with an overall survival of 5% and is the second cause of death by cancer, mainly linked to its high metastatic aggressiveness. Accordingly, understanding the mechanisms sustaining the PDAC metastatic phenotype remains a priority. In this study, we generated and used a murine in vivo model to select clones from the human Panc-1 PDAC cell line that exhibit a high propensity to seed and metastasize into the liver. We showed that myoferlin, a protein previously reported to be overexpressed in PDAC, is significantly involved in the migratory abilities of the selected cells. We first report that highly metastatic Panc-1 clones expressed a significantly higher myoferlin level than the corresponding low metastatic ones. Using scratch wound and Boyden’s chamber assays, we show that cells expressing a high myoferlin level have higher migratory potential than cells characterized by a low myoferlin abundance. Moreover, we demonstrate that myoferlin silencing leads to a migration decrease associated with a reduction of mitochondrial respiration. Since mitochondrial oxidative phosphorylation has been shown to be implicated in the tumor progression and dissemination, our data identify myoferlin as a valid potential therapeutic target in PDAC.
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Dell'Orso S, Juan AH, Ko KD, Naz F, Perovanovic J, Gutierrez-Cruz G, Feng X, Sartorelli V. Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions. Development 2019; 146:dev.174177. [PMID: 30890574 DOI: 10.1242/dev.174177] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/07/2019] [Indexed: 12/15/2022]
Abstract
Dedicated stem cells ensure postnatal growth, repair and homeostasis of skeletal muscle. Following injury, muscle stem cells (MuSCs) exit from quiescence and divide to reconstitute the stem cell pool and give rise to muscle progenitors. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs of distinct static cell states; however, bulk microarray and RNA sequencing provide only averaged gene expression profiles, blurring the heterogeneity and developmental dynamics of asynchronous MuSC populations. Instead, the granularity required to identify distinct cell types, states, and their dynamics can be afforded by single cell analysis. We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single cell RNA sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states.
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Affiliation(s)
- Stefania Dell'Orso
- Genome Technology Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA stefania.dell'
| | - Aster H Juan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA
| | - Kyung-Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA
| | - Faiza Naz
- Genome Technology Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA
| | - Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA
| | - Gustavo Gutierrez-Cruz
- Genome Technology Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA
| | - Xuesong Feng
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 208292, USA stefania.dell'
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Verma M, Asakura Y, Asakura A. Inhibition of microRNA-92a increases blood vessels and satellite cells in skeletal muscle but does not improve duchenne muscular dystrophy-related phenotype in mdx mice. Muscle Nerve 2019; 59:594-602. [PMID: 30698289 DOI: 10.1002/mus.26433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 01/08/2019] [Accepted: 01/27/2019] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The vasculature and blood flow in muscle are perturbed in Duchenne muscular dystrophy (DMD) and its mdx mouse model. MicroRNA-92a (miR-92a) is enriched in endothelial cells, especially during ischemic injury. METHODS Because antagonizing miR-92a was shown to result in increased proliferation and migration of endothelial cells and recovery from ischemia, we assessed the effects of Antagomir-92a in vitro in muscle stem cell culture and in vivo in mdx mice. RESULTS miR-92a was found to be highly expressed in muscle endothelial cells and satellite cells. Treatment with Antagomir-92a increased capillary density and tissue perfusion, which was accompanied by an increase in satellite cells. However, Antagomir-92a-treated mdx mice showed no histological improvement and had worse muscle function. Antagomir-92a suppressed myogenic differentiation in satellite cell culture. DISCUSSION AntagomiR-92a improves the vasculature but not the muscle in mdx mice, possibly due to its side effects on satellite cell differentiation. Muscle Nerve 59:594-594, 2019.
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Affiliation(s)
- Mayank Verma
- Medical Scientist Training Program, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Yoko Asakura
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Atsushi Asakura
- Department of Neurology, University of Minnesota Medical School, Minneapolis, Minnesota, 55455, USA
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Tran-Thi TN, Wang S, Adetula AA, Zou C, Omar AI, Han JL, Zhang DX, Zhao SH. Gene expression profiling of porcine skeletal muscle satellite cells after poly(I:C) stimulation. Gene 2019; 695:113-121. [PMID: 30633943 DOI: 10.1016/j.gene.2018.12.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 02/08/2023]
Abstract
Porcine satellite cells (PSCs) play a vital role in the construction, development and self-renewal of skeletal muscle. In this study, PSCs were exposed to poly(I:C) stimulation to mimic viral infection during the proliferation and differentiation phases at 0, 12, 24 and 48 hours (h) of the stimulation. The untreated and treated PSCs were analyzed by the RNA-Seq technology. There were 88, 119, 104 and 95 genes being differentially expressed in 0 h vs 12 h treated, 12 h vs 24 h treated, 0 h vs 24 h treated and 24 h vs 48 h untreated comparison libraries, respectively. The GO terms analysis results showed that during the proliferation phase of treated PSCs, the up-regulated genes related to the immune system were highly expressed. In addition, the gene expressions associated with muscle structure development in response to growth factor emerged during the differentiation phase of untreated PSCs. The biological pathways associated with Influenza A, Toll-like receptor and chemokine signaling were revealed in PSCs following poly(I:C) stimulation. The differentially expressed genes were confirmed by quantitative real-time PCR. These findings expanded our understanding of gene expressions and signaling pathways about the infiltrated mechanism of the virus into PSCs.
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Affiliation(s)
- Thuy-Nhien Tran-Thi
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Sheng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Adeyinka Abiola Adetula
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Abdullah Ibne Omar
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China; National Engineering Laboratory for Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China.
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, PR China; International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
| | - Ding-Xiao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Shu-Hong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Key Laboratory of Pig Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, PR China.
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Aguilar CA, Greising SM, Watts A, Goldman SM, Peragallo C, Zook C, Larouche J, Corona BT. Multiscale analysis of a regenerative therapy for treatment of volumetric muscle loss injury. Cell Death Discov 2018; 4:33. [PMID: 29531830 PMCID: PMC5841404 DOI: 10.1038/s41420-018-0027-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/22/2017] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle possesses a remarkable capacity to regenerate when injured, but when confronted with major traumatic injury resulting in volumetric muscle loss (VML), the regenerative process consistently fails. The loss of muscle tissue and function from VML injury has prompted development of a suite of therapeutic approaches but these strategies have proceeded without a comprehensive understanding of the molecular landscape that drives the injury response. Herein, we administered a VML injury in an established rodent model and monitored the evolution of the healing phenomenology over multiple time points using muscle function testing, histology, and expression profiling by RNA sequencing. The injury response was then compared to a regenerative medicine treatment using orthotopic transplantation of autologous minced muscle grafts (~1 mm3 tissue fragments). A chronic inflammatory and fibrotic response was observed at all time points following VML. These results suggest that the pathological response to VML injury during the acute stage of the healing response overwhelms endogenous and therapeutic regenerative processes. Overall, the data presented delineate key molecular characteristics of the pathobiological response to VML injury that are critical effectors of effective regenerative treatment paradigms.
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Affiliation(s)
- Carlos A. Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI USA
| | - Sarah M. Greising
- Extremity Trauma and Regenerative Medicine, United States Army Institute of Surgical Research, Fort Sam Houston, San Antonio, TX USA
| | - Alain Watts
- Massachusetts Institute of Technology - Lincoln Laboratory, Lexington, MA USA
| | - Stephen M. Goldman
- Extremity Trauma and Regenerative Medicine, United States Army Institute of Surgical Research, Fort Sam Houston, San Antonio, TX USA
| | - Chelsea Peragallo
- Massachusetts Institute of Technology - Lincoln Laboratory, Lexington, MA USA
| | - Christina Zook
- Massachusetts Institute of Technology - Lincoln Laboratory, Lexington, MA USA
| | - Jacqueline Larouche
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI USA
| | - Benjamin T. Corona
- Extremity Trauma and Regenerative Medicine, United States Army Institute of Surgical Research, Fort Sam Houston, San Antonio, TX USA
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Larouche J, Greising SM, Corona BT, Aguilar CA. Robust inflammatory and fibrotic signaling following volumetric muscle loss: a barrier to muscle regeneration. Cell Death Dis 2018. [PMID: 29540673 PMCID: PMC5851980 DOI: 10.1038/s41419-018-0455-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jacqueline Larouche
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Australian Regenerative Medicine Institute, Monash University, Melbourne, Australia
| | - Sarah M Greising
- School of Kinesiology, University of Minnesota, Minneapolis, MN, USA
| | | | - Carlos A Aguilar
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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Abstract
Skeletal muscle satellite cells are quiescent adult resident stem cells that activate, proliferate and differentiate to generate myofibres following injury. They harbour a robust proliferation potential and self-renewing capacity enabling lifelong muscle regeneration. Although several classes of microRNAs were shown to regulate adult myogenesis, systematic examination of stage-specific microRNAs during lineage progression from the quiescent state is lacking. Here we provide a genome-wide assessment of the expression of small RNAs during the quiescence/activation transition and differentiation by RNA-sequencing. We show that the majority of small RNAs present in quiescent, activated and differentiated muscle cells belong to the microRNA class. Furthermore, by comparing expression in distinct cell states, we report a massive and dynamic regulation of microRNAs, both in numbers and amplitude, highlighting their pivotal role in regulation of quiescence, activation and differentiation. We also identify a number of microRNAs with reliable and specific expression in quiescence including several maternally-expressed miRNAs generated at the imprinted Dlk1-Dio3 locus. Unexpectedly, the majority of class-switching miRNAs are associated with the quiescence/activation transition suggesting a poised program that is actively repressed. These data constitute a key resource for functional analyses of miRNAs in skeletal myogenesis, and more broadly, in the regulation of stem cell self-renewal and tissue homeostasis.
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Baghdadi MB, Tajbakhsh S. Regulation and phylogeny of skeletal muscle regeneration. Dev Biol 2018; 433:200-209. [DOI: 10.1016/j.ydbio.2017.07.026] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022]
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Abstract
Volumetric muscle loss (VML) resulting from extremity trauma presents chronic and persistent functional deficits which ultimately manifest disability. Acellular biological scaffolds, or decellularized extracellular matrices (ECMs), embody an ideal treatment platform due to their current clinical use for soft tissue repair, off-the-shelf availability, and zero autogenous donor tissue burden. ECMs have been reported to promote functional skeletal muscle tissue remodeling in small and large animal models of VML injury, and this conclusion was reached in a recent clinical trial that enrolled 13 patients. However, numerous other pre-clinical reports have not observed ECM-mediated skeletal muscle regeneration. The current study was designed to reconcile these discrepancies. The capacity of ECMs to orchestrate functional muscle tissue remodeling was interrogated in a porcine VML injury model using unbiased assessments of muscle tissue regeneration and functional recovery. Here, we show that VML injury incites an overwhelming inflammatory and fibrotic response that leads to expansive fibrous tissue deposition and chronic functional deficits, which ECM repair does not augment.
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