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Wang Y, Zhao J, Chen S, Li D, Yang J, Zhao X, Qin M, Guo M, Chen C, He Z, Zhou Y, Xu L. Let-7 as a Promising Target in Aging and Aging-Related Diseases: A Promise or a Pledge. Biomolecules 2022; 12:biom12081070. [PMID: 36008964 PMCID: PMC9406090 DOI: 10.3390/biom12081070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
The abnormal regulation and expression of microRNA (miRNA) are closely related to the aging process and the occurrence and development of aging-related diseases. Lethal-7 (let-7) was discovered in Caenorhabditis elegans (C. elegans) and plays an important role in development by regulating cell fate regulators. Accumulating evidence has shown that let-7 is elevated in aging tissues and participates in multiple pathways that regulate the aging process, including affecting tissue stem cell function, body metabolism, and various aging-related diseases (ARDs). Moreover, recent studies have found that let-7 plays an important role in the senescence of B cells, suggesting that let-7 may also participate in the aging process by regulating immune function. Therefore, these studies show the diversity and complexity of let-7 expression and regulatory functions during aging. In this review, we provide a detailed overview of let-7 expression regulation as well as its role in different tissue aging and aging-related diseases, which may provide new ideas for enriching the complex expression regulation mechanism and pathobiological function of let-7 in aging and related diseases and ultimately provide help for the development of new therapeutic strategies.
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Affiliation(s)
- Ya Wang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Shipeng Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Dongmei Li
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Jing Yang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Xu Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Ming Qin
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Zhixu He
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi 563000, China;
| | - Ya Zhou
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Medical Physics, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (L.X.)
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (L.X.)
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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Rubanova N, Pinna G, Kropp J, Campalans A, Radicella JP, Polesskaya A, Harel-Bellan A, Morozova N. MasterPATH: network analysis of functional genomics screening data. BMC Genomics 2020; 21:632. [PMID: 32928103 PMCID: PMC7491077 DOI: 10.1186/s12864-020-07047-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Background Functional genomics employs several experimental approaches to investigate gene functions. High-throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of genes potentially involved in biological processes of interest (so called hit list). Several computational methods exist to analyze and interpret such lists, the most widespread of which aim either at investigating of significantly enriched biological processes, or at extracting significantly represented subnetworks. Results Here we propose a novel network analysis method and corresponding computational software that employs the shortest path approach and centrality measure to discover members of molecular pathways leading to the studied phenotype, based on functional genomics screening data. The method works on integrated interactomes that consist of both directed and undirected networks – HIPPIE, SIGNOR, SignaLink, TFactS, KEGG, TransmiR, miRTarBase. The method finds nodes and short simple paths with significant high centrality in subnetworks induced by the hit genes and by so-called final implementers – the genes that are involved in molecular events responsible for final phenotypic realization of the biological processes of interest. We present the application of the method to the data from miRNA loss-of-function screen and transcriptome profiling of terminal human muscle differentiation process and to the gene loss-of-function screen exploring the genes that regulates human oxidative DNA damage recognition. The analysis highlighted the possible role of several known myogenesis regulatory miRNAs (miR-1, miR-125b, miR-216a) and their targets (AR, NR3C1, ARRB1, ITSN1, VAV3, TDGF1), as well as linked two major regulatory molecules of skeletal myogenesis, MYOD and SMAD3, to their previously known muscle-related targets (TGFB1, CDC42, CTCF) and also to a number of proteins such as C-KIT that have not been previously studied in the context of muscle differentiation. The analysis also showed the role of the interaction between H3 and SETDB1 proteins for oxidative DNA damage recognition. Conclusion The current work provides a systematic methodology to discover members of molecular pathways in integrated networks using functional genomics screening data. It also offers a valuable instrument to explain the appearance of a set of genes, previously not associated with the process of interest, in the hit list of each particular functional genomics screening.
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Affiliation(s)
- Natalia Rubanova
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France. .,Université Paris Diderot, Paris, France. .,Skolkovo Institute of Science and Technology, Skolkovo, Russia.
| | - Guillaume Pinna
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Jeremie Kropp
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France
| | - Anna Campalans
- Institute of Molecular and Cellular Radiobiology, Institut François Jacob, CEA, F-92265, Fontenay-aux-Roses, France.,INSERM, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.,Université Paris Sud, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France
| | - Juan Pablo Radicella
- Institute of Molecular and Cellular Radiobiology, Institut François Jacob, CEA, F-92265, Fontenay-aux-Roses, France.,INSERM, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.,Université Paris Sud, U967, bâtiment 56 PC 103 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France
| | - Anna Polesskaya
- Ecole Polytechnique, Université Paris-Saclay, CNRS UMR 7654, Laboratoire de Biochimie, Ecole Polytechnique, 91128, Palaiseau, France
| | - Annick Harel-Bellan
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France
| | - Nadya Morozova
- Institut des Hautes Etudes Scientifiques, Le Bois-Marie 35 rte de Chartres, 91440, Bures-sur-Yvette, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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4
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Luca E, Turcekova K, Hartung A, Mathes S, Rehrauer H, Krützfeldt J. Genetic deletion of microRNA biogenesis in muscle cells reveals a hierarchical non-clustered network that controls focal adhesion signaling during muscle regeneration. Mol Metab 2020; 36:100967. [PMID: 32240622 PMCID: PMC7139120 DOI: 10.1016/j.molmet.2020.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Decreased muscle mass is a major contributor to age-related morbidity, and strategies to improve muscle regeneration during ageing are urgently needed. Our aim was to identify the subset of relevant microRNAs (miRNAs) that partake in critical aspects of muscle cell differentiation, irrespective of computational predictions, genomic clustering or differential expression of the miRNAs. METHODS miRNA biogenesis was deleted in primary myoblasts using a tamoxifen-inducible CreLox system and combined with an add-back miRNA library screen. RNA-seq experiments, cellular signalling events, and glycogen synthesis, along with miRNA inhibitors, were performed in human primary myoblasts. Muscle regeneration in young and aged mice was assessed using the cardiotoxin (CTX) model. RESULTS We identified a hierarchical non-clustered miRNA network consisting of highly (miR-29a), moderately (let-7) and mildly active (miR-125b, miR-199a, miR-221) miRNAs that cooperate by directly targeting members of the focal adhesion complex. Through RNA-seq experiments comparing single versus combinatorial inhibition of the miRNAs, we uncovered a fundamental feature of this network, that miRNA activity inversely correlates to miRNA cooperativity. During myoblast differentiation, combinatorial inhibition of the five miRNAs increased activation of focal adhesion kinase (FAK), AKT, and p38 mitogen-activated protein kinase (MAPK), and improved myotube formation and insulin-dependent glycogen synthesis. Moreover, antagonizing the miRNA network in vivo following CTX-induced muscle regeneration enhanced muscle mass and myofiber formation in young and aged mice. CONCLUSION Our results provide novel insights into the dynamics of miRNA cooperativity and identify a miRNA network as therapeutic target for impaired focal adhesion signalling and muscle regeneration during ageing.
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Affiliation(s)
- Edlira Luca
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Switzerland
| | - Katarina Turcekova
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Switzerland; Competence Center Personalized Medicine UZH/ETH, ETH Zurich and University of Zurich, 8091, Switzerland
| | - Angelika Hartung
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Switzerland
| | - Sebastian Mathes
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Switzerland; Zurich Center for Integrative Human Physiology, University of Zurich, 8091, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich UZH/ETH, ETH Zurich and University of Zurich, 8091, Switzerland
| | - Jan Krützfeldt
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Switzerland; Competence Center Personalized Medicine UZH/ETH, ETH Zurich and University of Zurich, 8091, Switzerland; Zurich Center for Integrative Human Physiology, University of Zurich, 8091, Switzerland.
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5
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Lavin KM, Sealfon SC, McDonald MLN, Roberts BM, Wilk K, Nair VD, Ge Y, Lakshman Kumar P, Windham ST, Bamman MM. Skeletal muscle transcriptional networks linked to type I myofiber grouping in Parkinson's disease. J Appl Physiol (1985) 2019; 128:229-240. [PMID: 31829804 DOI: 10.1152/japplphysiol.00702.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disorder impacting cognition, movement, and quality of life in >10 million individuals worldwide. We recently characterized and quantified a skeletal muscle pathology in PD represented by exaggerated type I myofiber grouping presumed to result from denervation-reinnervation processes. Our previous findings indicated that impaired neuromuscular junction integrity may be involved in type I grouping, which is associated with excessive motor unit activation during weight-bearing tasks. In this study, we performed transcriptional profiling to test the hypothesis that type I grouping severity would link to distinct gene expression networks. We generated transcriptome-wide poly(A) RNA-Seq data from skeletal muscle of individuals with PD [n = 12 (9 men, 3 women); 67 ± 2 yr], age- and sex-matched older adults (n = 12; 68 ± 2 yr), and sex-matched young adults (n = 12; 30 ± 1 yr). Differentially expressed genes were evaluated across cohorts. Weighted gene correlation network analysis (WGCNA) was performed to identify gene networks most correlated with indicators of abnormal type I grouping. Among coexpression networks mapping to phenotypes pathologically increased in PD muscle, one network was highly significantly correlated to type I myofiber group size and another to percentage of type I myofibers found in groups. Annotation of coexpressed networks revealed that type I grouping is associated with altered expression of genes involved in neural development, postsynaptic signaling, cell cycle regulation and cell survival, protein and energy metabolism, inflammation/immunity, and posttranscriptional regulation (microRNAs). These transcriptomic findings suggest that skeletal muscle may play an active role in signaling to promote myofiber survival, reinnervation, and remodeling, perhaps to an extreme in PD.NEW & NOTEWORTHY Despite our awareness of the impact of Parkinson's disease (PD) on motor function for over two centuries, limited attention has focused on skeletal muscle. We previously identified type I myofiber grouping, a novel indicator of muscle dysfunction in PD, presumably a result of heightened rates of denervation/reinnervation. Using transcriptional profiling to identify networks associated with this phenotype, we provide insight into potential mechanistic roles of skeletal muscle in signaling to promote its survival in PD.
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Affiliation(s)
- Kaleen M Lavin
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York.,Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Merry-Lynn N McDonald
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brandon M Roberts
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katarzyna Wilk
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York.,Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York.,Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York.,Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Preeti Lakshman Kumar
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Samuel T Windham
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama.,UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Marcas M Bamman
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama.,UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs Medical Center, Birmingham, Alabama
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6
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Rodrigues Lopes I, Silva RJ, Caramelo I, Eulalio A, Mano M. Shedding light on microRNA function via microscopy-based screening. Methods 2019; 152:55-64. [DOI: 10.1016/j.ymeth.2018.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/13/2018] [Accepted: 09/28/2018] [Indexed: 12/24/2022] Open
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miR-600 Acts as a Bimodal Switch that Regulates Breast Cancer Stem Cell Fate through WNT Signaling. Cell Rep 2017; 18:2256-2268. [PMID: 28249169 DOI: 10.1016/j.celrep.2017.02.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/15/2016] [Accepted: 02/02/2017] [Indexed: 02/07/2023] Open
Abstract
Breast cancer stem cells (bCSCs) have been implicated in tumor progression and therapeutic resistance; however, the molecular mechanisms that define this state are unclear. We have performed two microRNA (miRNA) gain- and loss-of-function screens to identify miRNAs that regulate the choice between bCSC self-renewal and differentiation. We find that micro-RNA (miR)-600 silencing results in bCSC expansion, while its overexpression reduces bCSC self-renewal, leading to decreased in vivo tumorigenicity. miR-600 targets stearoyl desaturase 1 (SCD1), an enzyme required to produce active, lipid-modified WNT proteins. In the absence of miR-600, WNT signaling is active and promotes self-renewal, whereas overexpression of miR-600 inhibits the production of active WNT and promotes bCSC differentiation. In a series of 120 breast tumors, we found that a low level of miR-600 is correlated with active WNT signaling and a poor prognosis. These findings highlight a miR-600-centered signaling network that governs bCSC-fate decisions and influences tumor progression.
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Ceccarelli G, Benedetti L, Arcari ML, Carubbi C, Galli D. Muscle Stem Cell and Physical Activity: What Point is the Debate at? Open Med (Wars) 2017; 12:144-156. [PMID: 28765836 PMCID: PMC5529938 DOI: 10.1515/med-2017-0022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/21/2017] [Indexed: 12/11/2022] Open
Abstract
In the last 15 years, it emerged that the practice of regular physical activity reduces the risks of many diseases (cardiovascular diseases, diabetes, etc.) and it is fundamental in weight control and energy consuming to contrast obesity. Different groups proposed many molecular mechanisms as responsible for the positive effects of physical activity in healthy life. However, many points remain to be clarified. In this mini-review we reported the latest observations on the effects of physical exercise on healthy skeletal and cardiac muscle focusing on muscle stem cells. The last ones represent the fundamental elements for muscle regeneration post injury, but also for healthy muscle homeostasis. Interestingly, in both muscle tissues the morphological consequence of physical activity is a physiological hypertrophy that depends on different phenomena both in differentiated cells and stem cells. The signaling pathways for physical exercise effects present common elements in skeletal and cardiac muscle, like activation of specific transcription factors, proliferative pathways, and cytokines. More recently, post translational (miRNAs) or epigenetic (DNA methylation) modifications have been demonstrated. However, several points remain unresolved thus requiring new research on the effect of exercise on muscle stem cells.
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Affiliation(s)
- Gabriele Ceccarelli
- Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy.,Center of Health Technologies (CHT), University of Pavia, Pavia, Italy
| | - Laura Benedetti
- Department of Public Health, Experimental Medicine and Forensic, University of Pavia, Pavia, Italy.,Center of Health Technologies (CHT), University of Pavia, Pavia, Italy
| | - Maria Luisa Arcari
- Department of Medicine and Surgery, S.Bi.Bi.T. Unit, University of Parma, Parma, Italy
| | - Cecilia Carubbi
- Department of Medicine and Surgery, S.Bi.Bi.T. Unit, University of Parma, Parma, Italy
| | - Daniela Galli
- Department of Medicine and Surgery, S.Bi.Bi.T. Unit and Sport and Exercise Medicine Center (SEM)., University of Parma c/o Ospedale Maggiore, Via Gramsci, 14, 43126, Tel: +39-0521-036306, , Parma, Italy.,Department of Medicine and Surgery, S.Bi.Bi.T. Unit, University of Parma, Parma, Italy
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9
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Thorley M, Duguez S, Mazza EMC, Valsoni S, Bigot A, Mamchaoui K, Harmon B, Voit T, Mouly V, Duddy W. Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines. Skelet Muscle 2016; 6:43. [PMID: 27931240 PMCID: PMC5146814 DOI: 10.1186/s13395-016-0115-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/18/2016] [Indexed: 12/31/2022] Open
Abstract
Background hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether genetic modification related to the cell cycle results in secondary effects that could undermine the validity of these cell models. Results Here we subjected five healthy and disease muscle cell isolates to transcriptomic analysis, comparing immortalized lines with their parent primary populations in both differentiated and undifferentiated states, and testing their myogenic character by comparison with non-myogenic (CD56-negative) cells. Principal component analysis of global gene expression showed tight clustering of immortalized myoblasts to their parent primary populations, with clean separation from the non-myogenic reference. Comparison was made to publicly available transcriptomic data from studies of muscle human pathology, cell, and animal models, including to derive a consensus set of genes previously shown to have altered regulation during myoblast differentiation. Hierarchical clustering of samples based on gene expression of this consensus set showed that immortalized lines retained the myogenic expression patterns of their parent primary populations. Of 2784 canonical pathways and gene ontology terms tested by gene set enrichment analysis, none were significantly enriched in immortalized compared to primary cell populations. We observed, at the whole transcriptome level, a strong signature of cell cycle shutdown associated with senescence in one primary myoblast population, whereas its immortalized clone was protected. Conclusions Immortalization had no observed effect on the myogenic cascade or on any other cellular processes, and it was protective against the systems level effects of senescence that are observed at higher division counts of primary cells. Electronic supplementary material The online version of this article (doi:10.1186/s13395-016-0115-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew Thorley
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - Stéphanie Duguez
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France.,Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland UK
| | - Emilia Maria Cristina Mazza
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara Valsoni
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Anne Bigot
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - Kamel Mamchaoui
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - Brennan Harmon
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010 USA
| | - Thomas Voit
- NIHR Biomedical Research Centre, Institute of Child Health, University College London, 30 Guilford Street, London, UK
| | - Vincent Mouly
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France
| | - William Duddy
- INSERM, CNRS, Institute of Myology, Center of Research in Myology, Sorbonne Universities, UPMC Univ Paris 6, Paris, France.,Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland UK
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Trbp Is Required for Differentiation of Myoblasts and Normal Regeneration of Skeletal Muscle. PLoS One 2016; 11:e0155349. [PMID: 27159388 PMCID: PMC4861269 DOI: 10.1371/journal.pone.0155349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/27/2016] [Indexed: 12/19/2022] Open
Abstract
Global inactivation of Trbp, a regulator of miRNA pathways, resulted in developmental defects and postnatal lethality in mice. Recently, we showed that cardiac-specific deletion of Trbp caused heart failure. However, its functional role(s) in skeletal muscle has not been characterized. Using a conditional knockout model, we generated mice lacking Trbp in the skeletal muscle. Unexpectedly, skeletal muscle specific Trbp mutant mice appear to be phenotypically normal under normal physiological conditions. However, these mice exhibited impaired muscle regeneration and increased fibrosis in response to cardiotoxin-induced muscle injury, suggesting that Trbp is required for muscle repair. Using cultured myoblast cells we further showed that inhibition of Trbp repressed myoblast differentiation in vitro. The impaired myogenesis is associated with reduced expression of muscle-specific miRNAs, miR-1a and miR-133a. Together, our study demonstrated that Trbp participates in the regulation of muscle differentiation and regeneration.
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Negative regulation of initial steps in skeletal myogenesis by mTOR and other kinases. Sci Rep 2016; 6:20376. [PMID: 26847534 PMCID: PMC4742887 DOI: 10.1038/srep20376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 12/31/2015] [Indexed: 11/08/2022] Open
Abstract
The transition from a committed progenitor cell to one that is actively differentiating represents a process that is fundamentally important in skeletal myogenesis. Although the expression and functional activation of myogenic regulatory transcription factors (MRFs) are well known to govern lineage commitment and differentiation, exactly how the first steps in differentiation are suppressed in a proliferating myoblast is much less clear. We used cultured mammalian myoblasts and an RNA interference library targeting 571 kinases to identify those that may repress muscle differentiation in proliferating myoblasts in the presence or absence of a sensitizing agent directed toward CDK4/6, a kinase previously established to impede muscle gene expression. We identified 55 kinases whose knockdown promoted myoblast differentiation, either independently or in conjunction with the sensitizer. A number of the hit kinases could be connected to known MRFs, directly or through one interaction node. Focusing on one hit, Mtor, we validated its role to impede differentiation in proliferating myoblasts and carried out mechanistic studies to show that it acts, in part, by a rapamycin-sensitive complex that involves Raptor. Our findings inform our understanding of kinases that can block the transition from lineage commitment to a differentiating state in myoblasts and offer a useful resource for others studying myogenic differentiation.
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Post-transcriptional modulation of interleukin 8 by CNOT6L regulates skeletal muscle differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:263-70. [PMID: 26608607 DOI: 10.1016/j.bbamcr.2015.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 11/23/2022]
Abstract
CNOT6L is a deadenylase subunit belonging to the CCR4-NOT complex, a major deadenylase complex in eukaryotes involved at multiple levels in regulation of gene expression. While CNOT6L is expressed in skeletal muscle cells, its specific functions in this tissue are still largely unknown. Our previous work highlighted the functional of CNOT6L in skeletal muscle cell differentiation. To further explore how CNOT6L regulates myogenesis, we used here gene expression analysis to identify CNOT6L mRNA targets in human myoblasts. Among these novel targets, IL-8 (interleukin 8) mRNA was the most upregulated in CNOT6L knock-down (KD) cells. Biochemical approaches and poly (A) tail length assays showed that IL-8 mRNA is a direct target of CNOT6L, and further investigations by loss- and gain-of-function assays pointed out that IL-8 is an important effector of myogenesis. Therefore, we have characterized CNOT6L-IL-8 as a new signaling axis that regulates myogenesis.
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Meyer SU, Sass S, Mueller NS, Krebs S, Bauersachs S, Kaiser S, Blum H, Thirion C, Krause S, Theis FJ, Pfaffl MW. Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1. PLoS One 2015; 10:e0135284. [PMID: 26270642 PMCID: PMC4536022 DOI: 10.1371/journal.pone.0135284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022] Open
Abstract
Introduction Skeletal muscle cell differentiation is impaired by elevated levels of the inflammatory cytokine tumor necrosis factor-α (TNF-α) with pathological significance in chronic diseases or inherited muscle disorders. Insulin like growth factor-1 (IGF1) positively regulates muscle cell differentiation. Both, TNF-α and IGF1 affect gene and microRNA (miRNA) expression in this process. However, computational prediction of miRNA-mRNA relations is challenged by false positives and targets which might be irrelevant in the respective cellular transcriptome context. Thus, this study is focused on functional information about miRNA affected target transcripts by integrating miRNA and mRNA expression profiling data. Methodology/Principal Findings Murine skeletal myocytes PMI28 were differentiated for 24 hours with concomitant TNF-α or IGF1 treatment. Both, mRNA and miRNA expression profiling was performed. The data-driven integration of target prediction and paired mRNA/miRNA expression profiling data revealed that i) the quantity of predicted miRNA-mRNA relations was reduced, ii) miRNA targets with a function in cell cycle and axon guidance were enriched, iii) differential regulation of anti-differentiation miR-155-5p and miR-29b-3p as well as pro-differentiation miR-335-3p, miR-335-5p, miR-322-3p, and miR-322-5p seemed to be of primary importance during skeletal myoblast differentiation compared to the other miRNAs, iv) the abundance of targets and affected biological processes was miRNA specific, and v) subsets of miRNAs may collectively regulate gene expression. Conclusions Joint analysis of mRNA and miRNA profiling data increased the process-specificity and quality of predicted relations by statistically selecting miRNA-target interactions. Moreover, this study revealed miRNA-specific predominant biological implications in skeletal muscle cell differentiation and in response to TNF-α or IGF1 treatment. Furthermore, myoblast differentiation-associated miRNAs are suggested to collectively regulate gene clusters and targets associated with enriched specific gene ontology terms or pathways. Predicted miRNA functions of this study provide novel insights into defective regulation at the transcriptomic level during myocyte proliferation and differentiation due to inflammatory stimuli.
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Affiliation(s)
- Swanhild U. Meyer
- Physiology Weihenstephan, Technische Universität München, Freising, Germany
- * E-mail:
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nikola S. Mueller
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Bauersachs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sebastian Kaiser
- Department of Statistics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Sabine Krause
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching, Germany
| | - Michael W. Pfaffl
- Physiology Weihenstephan, Technische Universität München, Freising, Germany
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A transgenic resource for conditional competitive inhibition of conserved Drosophila microRNAs. Nat Commun 2015; 6:7279. [PMID: 26081261 PMCID: PMC4471878 DOI: 10.1038/ncomms8279] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/26/2015] [Indexed: 12/11/2022] Open
Abstract
Although the impact of microRNAs (miRNAs) in development and disease is well established, understanding the function of individual miRNAs remains challenging. Development of competitive inhibitor molecules such as miRNA sponges has allowed the community to address individual miRNA function in vivo. However, the application of these loss-of-function strategies has been limited. Here we offer a comprehensive library of 141 conditional miRNA sponges targeting well-conserved miRNAs in Drosophila. Ubiquitous miRNA sponge delivery and consequent systemic miRNA inhibition uncovers a relatively small number of miRNA families underlying viability and gross morphogenesis, with false discovery rates in the 4-8% range. In contrast, tissue-specific silencing of muscle-enriched miRNAs reveals a surprisingly large number of novel miRNA contributions to the maintenance of adult indirect flight muscle structure and function. A strong correlation between miRNA abundance and physiological relevance is not observed, underscoring the importance of unbiased screens when assessing the contributions of miRNAs to complex biological processes.
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Abstract
A genome-wide screen had previously shown that knocking down miR-98 and let-7g, two miRNAs of the let-7 family, leads to a dramatic increase in terminal myogenic differentiation. In the present paper, we report that a transcriptomic analysis of human myoblasts, where miR-98 was knocked down, revealed that approximately 240 genes were sensitive to miR-98 depletion. Among these potential targets of miR-98, we identified the transcriptional repressor E2F5 and showed that it is a direct target of miR-98. Knocking down simultaneously E2F5 and miR-98 almost fully restored normal differentiation, indicating that E2F5 is involved in the regulation of skeletal muscle differentiation. We subsequently show that E2F5 can bind to the promoters of two inhibitors of terminal muscle differentiation, ID1 (inhibitor of DNA binding 1) and HMOX1 (heme oxygenase 1), which decreases their expression in skeletal myoblasts. We conclude that miR-98 regulates muscle differentiation by altering the expression of the transcription factor E2F5 and, in turn, of multiple E2F5 targets.
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Meyer SU, Thirion C, Polesskaya A, Bauersachs S, Kaiser S, Krause S, Pfaffl MW. TNF-α and IGF1 modify the microRNA signature in skeletal muscle cell differentiation. Cell Commun Signal 2015; 13:4. [PMID: 25630602 PMCID: PMC4325962 DOI: 10.1186/s12964-015-0083-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 01/03/2015] [Indexed: 12/13/2022] Open
Abstract
Background Elevated levels of the inflammatory cytokine TNF-α are common in chronic diseases or inherited or degenerative muscle disorders and can lead to muscle wasting. By contrast, IGF1 has a growth promoting effect on skeletal muscle. The molecular mechanisms mediating the effect of TNF-α and IGF1 on muscle cell differentiation are not completely understood. Muscle cell proliferation and differentiation are regulated by microRNAs (miRNAs) which play a dominant role in this process. This study aims at elucidating how TNF-α or IGF1 regulate microRNA expression to affect myoblast differentiation and myotube formation. Results In this study, we analyzed the impact of TNF-α or IGF1 treatment on miRNA expression in myogenic cells. Results reveal that i) TNF-α and IGF1 regulate miRNA expression during skeletal muscle cell differentiation in vitro, ii) microRNA targets can mediate the negative effect of TNF-α on fusion capacity of skeletal myoblasts by targeting genes associated with axon guidance, MAPK signalling, focal adhesion, and neurotrophin signalling pathway, iii) inhibition of miR-155 in combination with overexpression of miR-503 partially abrogates the inhibitory effect of TNF-α on myotube formation, and iv) MAPK/ERK inhibition might participate in modulating the effect of TNF-α and IGF1 on miRNA abundance. Conclusions The inhibitory effects of TNF-α or the growth promoting effects of IGF1 on skeletal muscle differentiation include the deregulation of known muscle-regulatory miRNAs as well as miRNAs which have not yet been associated with skeletal muscle differentiation or response to TNF-α or IGF1. This study indicates that miRNAs are mediators of the inhibitory effect of TNF-α on myoblast differentiation. We show that intervention at the miRNA level can ameliorate the negative effect of TNF-α by promoting myoblast differentiation. Moreover, we cautiously suggest that TNF-α or IGF1 modulate the miRNA biogenesis of some miRNAs via MAPK/ERK signalling. Finally, this study identifies indicative biomarkers of myoblast differentiation and cytokine influence and points to novel RNA targets. Electronic supplementary material The online version of this article (doi:10.1186/s12964-015-0083-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swanhild U Meyer
- Physiology Weihenstephan, ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany.
| | - Christian Thirion
- SIRION Biotech GmbH, Am Klopferspitz 19, 82152, Martinsried, Germany.
| | - Anna Polesskaya
- CNRS FRE 3377, Univ. Paris-Sud, CEA Saclay, iBiTec-S/ SBIGeM, F-91191, Gif-sur-Yvette, France.
| | - Stefan Bauersachs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany. .,Current address: ETH Zurich, Institute of Agricultural Sciences, Animal Physiology, Universitätstrasse 2 / LFW B 58.1, 8092, Zurich, Switzerland.
| | - Sebastian Kaiser
- Department of Statistics, Ludwig-Maximilians-Universität München, Ludwigstr. 33, 80539, Munich, Germany.
| | - Sabine Krause
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, Munich, Germany.
| | - Michael W Pfaffl
- Physiology Weihenstephan, ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany.
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MiRNA let-7g regulates skeletal myoblast motility via Pinch-2. FEBS Lett 2014; 588:1623-9. [PMID: 24613920 DOI: 10.1016/j.febslet.2014.02.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 12/30/2022]
Abstract
Post-transcriptional regulation of gene expression by RNA-binding proteins and by small non-coding RNAs plays an important role in cell biology. Our previous results show that in murine skeletal myoblasts, the expression of Pinch-2, a focal adhesion remodeling factor that regulates cell motility, is repressed by an RNA-binding protein IMP-2/Igf2bp2. We now show that the expression of Pinch-2 is also regulated by the miRNA let-7g. Let-7g and IMP-2 repress Pinch-2 expression independently of each other. A knock-down of let-7g leads to an increase in Pinch-2 expression, and to a decrease of cell motility, which can be reversed by a simultaneous knock-down of Pinch-2. We conclude that let-7g controls the motility of mouse myoblasts in cell culture by post-transcriptionally regulating the expression of Pinch-2.
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