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Sun L, Luan J, Wang J, Li X, Zhang W, Ji X, Liu L, Wang R, Xu B. GEPREP: A comprehensive data atlas of RNA-seq-based gene expression profiles of exercise responses. JOURNAL OF SPORT AND HEALTH SCIENCE 2024:100992. [PMID: 39341494 DOI: 10.1016/j.jshs.2024.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 06/11/2024] [Accepted: 07/31/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND Physical activity can regulate and affect gene expression in multiple tissues and cells. Recently, with the development of next-generation sequencing, a large number of RNA-sequencing (RNA-seq)-based gene expression profiles about physical activity have been shared in public resources; however, they are poorly curated and underutilized. To tackle this problem, we developed a data atlas of such data through comprehensive data collection, curation, and organization. METHODS The data atlas, termed gene expression profiles of RNA-seq-based exercise responses (GEPREP), was built on a comprehensive collection of high-quality RNA-seq data on exercise responses. The metadata of each sample were manually curated. Data were uniformly processed and batch effects corrected. All the information was well organized in an easy-to-use website for free search, visualization, and download. RESULTS GEPREP now includes 69 RNA-seq datasets of pre- and post-exercise, comprising 26 human datasets (1120 samples) and 43 mouse datasets (1006 samples). Specifically, there were 977 (87.2%) human samples of skeletal muscle and 143 (12.8%) human samples of blood. There were also samples across 9 mice tissues with skeletal muscle (359, 35.7%) and brain (280, 27.8%) accounting for the main fractions. Metadata-including subject, exercise interventions, sampling sites, and post-processing methods-are also included. The metadata and gene expression profiles are freely accessible at http://www.geprep.org.cn/. CONCLUSION GEPREP is a comprehensive data atlas of RNA-seq-based gene expression profiles responding to exercise. With its reliable annotations and user-friendly interfaces, it has the potential to deepen our understanding of exercise physiology.
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Affiliation(s)
- Lei Sun
- School of Information Engineering, Yangzhou University, Yangzhou, 225127, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China
| | - Jinwen Luan
- School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China
| | - Jinbiao Wang
- School of Information Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Xiaoli Li
- Laboratory of Developmental Biology, Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Wenqian Zhang
- School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China
| | - Xiaohui Ji
- School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China
| | - Longhua Liu
- School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China.
| | - Ru Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China.
| | - Bingxiang Xu
- School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China.
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2
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Bittel AJ, Chen YW. DNA Methylation in the Adaptive Response to Exercise. Sports Med 2024; 54:1419-1458. [PMID: 38561436 DOI: 10.1007/s40279-024-02011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Emerging evidence published over the past decade has highlighted the role of DNA methylation in skeletal muscle function and health, including as an epigenetic transducer of the adaptive response to exercise. In this review, we aim to synthesize the latest findings in this field to highlight: (1) the shifting understanding of the genomic localization of altered DNA methylation in response to acute and chronic aerobic and resistance exercise in skeletal muscle (e.g., promoter, gene bodies, enhancers, intergenic regions, un-annotated regions, and genome-wide methylation); (2) how these global/regional methylation changes relate to transcriptional activity following exercise; and (3) the factors (e.g., individual demographic or genetic features, dietary, training history, exercise parameters, local epigenetic characteristics, circulating hormones) demonstrated to alter both the pattern of DNA methylation after exercise, and the relationship between DNA methylation and gene expression. Finally, we discuss the changes in non-CpG methylation and 5-hydroxymethylation after exercise, as well as the importance of emerging single-cell analyses to future studies-areas of increasing focus in the field of epigenetics. We anticipate that this review will help generate a framework for clinicians and researchers to begin developing and testing exercise interventions designed to generate targeted changes in DNA methylation as part of a personalized exercise regimen.
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Affiliation(s)
- Adam J Bittel
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.
| | - Yi-Wen Chen
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Science, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St NW, Washington, DC, 20052, USA
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Roberts MD, McCarthy JJ, Hornberger TA, Phillips SM, Mackey AL, Nader GA, Boppart MD, Kavazis AN, Reidy PT, Ogasawara R, Libardi CA, Ugrinowitsch C, Booth FW, Esser KA. Mechanisms of mechanical overload-induced skeletal muscle hypertrophy: current understanding and future directions. Physiol Rev 2023; 103:2679-2757. [PMID: 37382939 PMCID: PMC10625844 DOI: 10.1152/physrev.00039.2022] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
Mechanisms underlying mechanical overload-induced skeletal muscle hypertrophy have been extensively researched since the landmark report by Morpurgo (1897) of "work-induced hypertrophy" in dogs that were treadmill trained. Much of the preclinical rodent and human resistance training research to date supports that involved mechanisms include enhanced mammalian/mechanistic target of rapamycin complex 1 (mTORC1) signaling, an expansion in translational capacity through ribosome biogenesis, increased satellite cell abundance and myonuclear accretion, and postexercise elevations in muscle protein synthesis rates. However, several lines of past and emerging evidence suggest that additional mechanisms that feed into or are independent of these processes are also involved. This review first provides a historical account of how mechanistic research into skeletal muscle hypertrophy has progressed. A comprehensive list of mechanisms associated with skeletal muscle hypertrophy is then outlined, and areas of disagreement involving these mechanisms are presented. Finally, future research directions involving many of the discussed mechanisms are proposed.
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Affiliation(s)
- Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
| | - Troy A Hornberger
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Stuart M Phillips
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Abigail L Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital-Bispebjerg and Frederiksberg, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gustavo A Nader
- Department of Kinesiology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States
| | - Marni D Boppart
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
| | - Andreas N Kavazis
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - Paul T Reidy
- Department of Kinesiology, Nutrition and Health, Miami University, Oxford, Ohio, United States
| | - Riki Ogasawara
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Cleiton A Libardi
- MUSCULAB-Laboratory of Neuromuscular Adaptations to Resistance Training, Department of Physical Education, Federal University of São Carlos, São Carlos, Brazil
| | - Carlos Ugrinowitsch
- School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil
| | - Frank W Booth
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Karyn A Esser
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, Florida, United States
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4
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Sexton CL, Godwin JS, McIntosh MC, Ruple BA, Osburn SC, Hollingsworth BR, Kontos NJ, Agostinelli PJ, Kavazis AN, Ziegenfuss TN, Lopez HL, Smith R, Young KC, Dwaraka VB, Frugé AD, Mobley CB, Sharples AP, Roberts MD. Skeletal Muscle DNA Methylation and mRNA Responses to a Bout of Higher versus Lower Load Resistance Exercise in Previously Trained Men. Cells 2023; 12:263. [PMID: 36672198 PMCID: PMC9856538 DOI: 10.3390/cells12020263] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
We sought to determine the skeletal muscle genome-wide DNA methylation and mRNA responses to one bout of lower load (LL) versus higher load (HL) resistance exercise. Trained college-aged males (n = 11, 23 ± 4 years old, 4 ± 3 years self-reported training) performed LL or HL bouts to failure separated by one week. The HL bout (i.e., 80 Fail) consisted of four sets of back squats and four sets of leg extensions to failure using 80% of participants estimated one-repetition maximum (i.e., est. 1-RM). The LL bout (i.e., 30 Fail) implemented the same paradigm with 30% of est. 1-RM. Vastus lateralis muscle biopsies were collected before, 3 h, and 6 h after each bout. Muscle DNA and RNA were batch-isolated and analyzed using the 850k Illumina MethylationEPIC array and Clariom S mRNA microarray, respectively. Performed repetitions were significantly greater during the 30 Fail versus 80 Fail (p < 0.001), although total training volume (sets × reps × load) was not significantly different between bouts (p = 0.571). Regardless of bout, more CpG site methylation changes were observed at 3 h versus 6 h post exercise (239,951 versus 12,419, respectively; p < 0.01), and nuclear global ten-eleven translocation (TET) activity, but not global DNA methyltransferase activity, increased 3 h and 6 h following exercise regardless of bout. The percentage of genes significantly altered at the mRNA level that demonstrated opposite DNA methylation patterns was greater 3 h versus 6 h following exercise (~75% versus ~15%, respectively). Moreover, high percentages of genes that were up- or downregulated 6 h following exercise also demonstrated significantly inversed DNA methylation patterns across one or more CpG sites 3 h following exercise (65% and 82%, respectively). While 30 Fail decreased DNA methylation across various promoter regions versus 80 Fail, transcriptome-wide mRNA and bioinformatics indicated that gene expression signatures were largely similar between bouts. Bioinformatics overlay of DNA methylation and mRNA expression data indicated that genes related to "Focal adhesion," "MAPK signaling," and "PI3K-Akt signaling" were significantly affected at the 3 h and 6 h time points, and again this was regardless of bout. In conclusion, extensive molecular profiling suggests that post-exercise alterations in the skeletal muscle DNA methylome and mRNA transcriptome elicited by LL and HL training bouts to failure are largely similar, and this could be related to equal volumes performed between bouts.
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Affiliation(s)
- Casey L. Sexton
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | | | | | | | | | | | | | | | | | - Hector L. Lopez
- The Center for Applied Health Sciences, Canfield, OH 44406, USA
| | | | - Kaelin C. Young
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
- Edward Via College of Osteopathic Medicine, Auburn, AL 24060, USA
| | | | - Andrew D. Frugé
- College of Nursing, Auburn University, Auburn, AL 36849, USA
| | | | - Adam P. Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences, 0863 Oslo, Norway
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
- Edward Via College of Osteopathic Medicine, Auburn, AL 24060, USA
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Muroya S. An insight into farm animal skeletal muscle metabolism based on a metabolomics approach. Meat Sci 2022; 195:108995. [DOI: 10.1016/j.meatsci.2022.108995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 01/10/2023]
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6
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Hansen PB, Ruud AK, de los Campos G, Malinowska M, Nagy I, Svane SF, Thorup-Kristensen K, Jensen JD, Krusell L, Asp T. Integration of DNA Methylation and Transcriptome Data Improves Complex Trait Prediction in Hordeum vulgare. PLANTS 2022; 11:plants11172190. [PMID: 36079572 PMCID: PMC9459846 DOI: 10.3390/plants11172190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022]
Abstract
Whole-genome multi-omics profiles contain valuable information for the characterization and prediction of complex traits in plants. In this study, we evaluate multi-omics models to predict four complex traits in barley (Hordeum vulgare); grain yield, thousand kernel weight, protein content, and nitrogen uptake. Genomic, transcriptomic, and DNA methylation data were obtained from 75 spring barley lines tested in the RadiMax semi-field phenomics facility under control and water-scarce treatment. By integrating multi-omics data at genomic, transcriptomic, and DNA methylation regulatory levels, a higher proportion of phenotypic variance was explained (0.72–0.91) than with genomic models alone (0.55–0.86). The correlation between predictions and phenotypes varied from 0.17–0.28 for control plants and 0.23–0.37 for water-scarce plants, and the increase in accuracy was significant for nitrogen uptake and protein content compared to models using genomic information alone. Adding transcriptomic and DNA methylation information to the prediction models explained more of the phenotypic variance attributed to the environment in grain yield and nitrogen uptake. It furthermore explained more of the non-additive genetic effects for thousand kernel weight and protein content. Our results show the feasibility of multi-omics prediction for complex traits in barley.
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Affiliation(s)
- Pernille Bjarup Hansen
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
- Correspondence: (P.B.H.); (T.A.); Tel.: +45-87158243 (T.A.)
| | - Anja Karine Ruud
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
| | - Gustavo de los Campos
- Departments of Epidemiology & Biostatistics and Statistics & Probability, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Marta Malinowska
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
| | - Simon Fiil Svane
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Copenhagen University, 2630 Taastrup, Denmark
| | - Kristian Thorup-Kristensen
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Copenhagen University, 2630 Taastrup, Denmark
| | | | - Lene Krusell
- Sejet Plant Breeding, Nørremarksvej 67, 8700 Horsens, Denmark
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, 4200 Slagelse, Denmark
- Correspondence: (P.B.H.); (T.A.); Tel.: +45-87158243 (T.A.)
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7
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Ling C, Bacos K, Rönn T. Epigenetics of type 2 diabetes mellitus and weight change - a tool for precision medicine? Nat Rev Endocrinol 2022; 18:433-448. [PMID: 35513492 DOI: 10.1038/s41574-022-00671-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
Pioneering studies performed over the past few decades demonstrate links between epigenetics and type 2 diabetes mellitus (T2DM), the metabolic disorder with the most rapidly increasing prevalence in the world. Importantly, these studies identified epigenetic modifications, including altered DNA methylation, in pancreatic islets, adipose tissue, skeletal muscle and the liver from individuals with T2DM. As non-genetic factors that affect the risk of T2DM, such as obesity, unhealthy diet, physical inactivity, ageing and the intrauterine environment, have been associated with epigenetic modifications in healthy individuals, epigenetics probably also contributes to T2DM development. In addition, genetic factors associated with T2DM and obesity affect the epigenome in human tissues. Notably, causal mediation analyses found DNA methylation to be a potential mediator of genetic associations with metabolic traits and disease. In the past few years, translational studies have identified blood-based epigenetic markers that might be further developed and used for precision medicine to help patients with T2DM receive optimal therapy and to identify patients at risk of complications. This Review focuses on epigenetic mechanisms in the development of T2DM and the regulation of body weight in humans, with a special focus on precision medicine.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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Mahatme S, K V, Kumar N, Rao V, Kovela RK, Sinha MK. Impact of high-intensity interval training on cardio-metabolic health outcomes and mitochondrial function in older adults: a review. Med Pharm Rep 2022; 95:115-130. [PMID: 35721039 PMCID: PMC9176307 DOI: 10.15386/mpr-2201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 11/27/2022] Open
Abstract
Exercise being a potent stimulator of mitochondrial biogenesis, there is a need to investigate the effects of high-intensity interval training (HIIT) among older adults. This review explores and summarizes the impact of HIIT on mitochondria and various cardio-metabolic health outcomes among older adults, healthy and with comorbid conditions. Electronic databases were scrutinized for literature using permutations of keywords related to (i) Elderly population (ii) HIIT (iii) Mitochondria, cell organelles, and (iv) cardio-metabolic health outcomes. Twenty-one studies that met the inclusion criteria are included in this review. HIIT is an innovative therapeutic modality in preserving mitochondrial quality with age and serves to be a viable, safe, and beneficial exercise alternative in both ill and healthy older adults.
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Affiliation(s)
- Simran Mahatme
- Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vaishali K
- Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, Bihar, India
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of higher Education, Manipal, Karnataka, India
| | - Vanishree Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of higher Education, Manipal, Karnataka, India
| | - Rakesh Krishna Kovela
- Department of Neurophysiotherapy, Ravi Nair Physiotherapy College, Datta Meghe Institute of Medical Sciences, Sawangi (Meghe), Wardha, Maharashtra India
| | - Mukesh Kumar Sinha
- Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, Karnataka, India
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9
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Gabriel BM, Altıntaş A, Smith JAB, Sardon-Puig L, Zhang X, Basse AL, Laker RC, Gao H, Liu Z, Dollet L, Treebak JT, Zorzano A, Huo Z, Rydén M, Lanner JT, Esser KA, Barrès R, Pillon NJ, Krook A, Zierath JR. Disrupted circadian oscillations in type 2 diabetes are linked to altered rhythmic mitochondrial metabolism in skeletal muscle. SCIENCE ADVANCES 2021; 7:eabi9654. [PMID: 34669477 PMCID: PMC8528429 DOI: 10.1126/sciadv.abi9654] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/25/2021] [Indexed: 05/03/2023]
Abstract
Circadian rhythms are generated by an autoregulatory feedback loop of transcriptional activators and repressors. Circadian rhythm disruption contributes to type 2 diabetes (T2D) pathogenesis. We elucidated whether altered circadian rhythmicity of clock genes is associated with metabolic dysfunction in T2D. Transcriptional cycling of core-clock genes BMAL1, CLOCK, and PER3 was altered in skeletal muscle from individuals with T2D, and this was coupled with reduced number and amplitude of cycling genes and disturbed circadian oxygen consumption. Inner mitochondria–associated genes were enriched for rhythmic peaks in normal glucose tolerance, but not T2D, and positively correlated with insulin sensitivity. Chromatin immunoprecipitation sequencing identified CLOCK and BMAL1 binding to inner-mitochondrial genes associated with insulin sensitivity, implicating regulation by the core clock. Inner-mitochondria disruption altered core-clock gene expression and free-radical production, phenomena that were restored by resveratrol treatment. We identify bidirectional communication between mitochondrial function and rhythmic gene expression, processes that are disturbed in diabetes.
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Affiliation(s)
- Brendan M. Gabriel
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
- Aberdeen Cardiovascular and Diabetes Centre, The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonathon A. B. Smith
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sardon-Puig
- Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Xiping Zhang
- Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Astrid L. Basse
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rhianna C. Laker
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hui Gao
- Department of Biosciences and Nutrition (BioNut), Karolinska Institutet, Stockholm, Sweden
| | - Zhengye Liu
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Lucile Dollet
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas T. Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- Departament de Bioquímica y Biomedicina Molecular, Facultat de Biologia, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Spain
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Mikael Rydén
- Department of Medicine (H7), Unit for Endocrinology and Diabetes, Karolinska Institutet, Stockholm, Sweden
| | - Johanna T. Lanner
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Karyn A. Esser
- Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas J. Pillon
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Krook
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R. Zierath
- Department of Physiology and Pharmacology, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Molecular Medicine and Surgery, Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
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10
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McKendry J, Stokes T, Mcleod JC, Phillips SM. Resistance Exercise, Aging, Disuse, and Muscle Protein Metabolism. Compr Physiol 2021; 11:2249-2278. [PMID: 34190341 DOI: 10.1002/cphy.c200029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Skeletal muscle is the organ of locomotion, its optimal function is critical for athletic performance, and is also important for health due to its contribution to resting metabolic rate and as a site for glucose uptake and storage. Numerous endogenous and exogenous factors influence muscle mass. Much of what is currently known regarding muscle protein turnover is owed to the development and use of stable isotope tracers. Skeletal muscle mass is determined by the meal- and contraction-induced alterations of muscle protein synthesis and muscle protein breakdown. Increased loading as resistance training is the most potent nonpharmacological strategy by which skeletal muscle mass can be increased. Conversely, aging (sarcopenia) and muscle disuse lead to the development of anabolic resistance and contribute to the loss of skeletal muscle mass. Nascent omics-based technologies have significantly improved our understanding surrounding the regulation of skeletal muscle mass at the gene, transcript, and protein levels. Despite significant advances surrounding the mechanistic intricacies that underpin changes in skeletal muscle mass, these processes are complex, and more work is certainly needed. In this article, we provide an overview of the importance of skeletal muscle, describe the influence that resistance training, aging, and disuse exert on muscle protein turnover and the molecular regulatory processes that contribute to changes in muscle protein abundance. © 2021 American Physiological Society. Compr Physiol 11:2249-2278, 2021.
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Affiliation(s)
- James McKendry
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Tanner Stokes
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan C Mcleod
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Stuart M Phillips
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
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11
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Targets identified from exercised heart: killing multiple birds with one stone. NPJ Regen Med 2021; 6:23. [PMID: 33837221 PMCID: PMC8035363 DOI: 10.1038/s41536-021-00128-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular diseases (CVDs) are a major cause of mortality worldwide, which are mainly driven by factors such as aging, sedentary lifestyle, and excess alcohol use. Exercise targets several molecules and protects hearts against many of these physiological and pathological stimuli. Accordingly, it is widely recognized as an effective therapeutic strategy for CVD. To investigate the molecular mechanism of exercise in cardiac protection, we identify and describe several crucial targets identified from exercised hearts. These targets include insulin-like growth factor 1 (IGF1)-phosphatidylinositol 3 phosphate kinase (PI3K)/protein kinase B (AKT), transcription factor CCAAT/enhancer-binding protein β (C/EBPβ), cardiac microRNAs (miRNAs, miR-222 and miR-17-3p etc.), exosomal-miRNAs (miR-342, miR-29, etc.), Sirtuin 1 (SIRT1), and nuclear factor erythroid 2‑related factor/metallothioneins (Nrf2/Mts). Targets identified from exercised hearts can alleviate injury via multiple avenues, including: (1) promoting cardiomyocyte proliferation; (2) facilitating cardiomyocyte growth and physiologic hypertrophy; (3) elevating the anti-apoptotic capacity of cardiomyocytes; (4) improving vascular endothelial function; (5) inhibiting pathological remodeling and fibrosis; (6) promoting extracellular vesicles (EVs) production and exosomal-molecules transfer. Exercise is one treatment (‘stone’), which is cardioprotective via multiple avenues (‘birds’), and is considered ‘killing multiple birds with one stone’ in this review. Further, we discuss the potential application of EV cargos in CVD treatment. We provide an outline of targets identified from the exercised heart and their mechanisms, as well as novel ideas for CVD treatment, which may provide novel direction for preclinical trials in cardiac rehabilitation.
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12
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Small L, Ingerslev LR, Manitta E, Laker RC, Hansen AN, Deeney B, Carrié A, Couvert P, Barrès R. Ablation of DNA-methyltransferase 3A in skeletal muscle does not affect energy metabolism or exercise capacity. PLoS Genet 2021; 17:e1009325. [PMID: 33513138 PMCID: PMC7875352 DOI: 10.1371/journal.pgen.1009325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/10/2021] [Accepted: 01/04/2021] [Indexed: 02/03/2023] Open
Abstract
In response to physical exercise and diet, skeletal muscle adapts to energetic demands through large transcriptional changes. This remodelling is associated with changes in skeletal muscle DNA methylation which may participate in the metabolic adaptation to extracellular stimuli. Yet, the mechanisms by which muscle-borne DNA methylation machinery responds to diet and exercise and impacts muscle function are unknown. Here, we investigated the function of de novo DNA methylation in fully differentiated skeletal muscle. We generated muscle-specific DNA methyltransferase 3A (DNMT3A) knockout mice (mD3AKO) and investigated the impact of DNMT3A ablation on skeletal muscle DNA methylation, exercise capacity and energy metabolism. Loss of DNMT3A reduced DNA methylation in skeletal muscle over multiple genomic contexts and altered the transcription of genes known to be influenced by DNA methylation, but did not affect exercise capacity and whole-body energy metabolism compared to wild type mice. Loss of DNMT3A did not alter skeletal muscle mitochondrial function or the transcriptional response to exercise however did influence the expression of genes involved in muscle development. These data suggest that DNMT3A does not have a large role in the function of mature skeletal muscle although a role in muscle development and differentiation is likely. Skeletal muscle is a plastic tissue able to adapt to environmental stimuli such as exercise and diet in order to respond to energetic demand. One of the ways in which skeletal muscle can rapidly react to these stimuli is DNA methylation. This is when chemical groups are attached to DNA, potentially influencing the transcription of genes. We investigated the function of DNA methylation in skeletal muscle by generating mice that lacked one of the main enzymes responsible for de novo DNA methylation, DNA methyltransferase 3A (DNMT3A), specifically in muscle. We found that loss of DNMT3A reduced DNA methylation in muscle however this did not lead to differences in exercise capacity or energy metabolism. This suggests that DNMT3a is not involved in the adaptation of skeletal muscle to diet or exercise.
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Affiliation(s)
- Lewin Small
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R. Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eleonora Manitta
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rhianna C. Laker
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ann N. Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brendan Deeney
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alain Carrié
- Sorbonne Université-INSERM UMR_S 1166 ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Philippe Couvert
- Sorbonne Université-INSERM UMR_S 1166 ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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13
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Decoding personal biotic and abiotic airborne exposome. Nat Protoc 2021; 16:1129-1151. [PMID: 33437065 DOI: 10.1038/s41596-020-00451-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/20/2020] [Indexed: 11/08/2022]
Abstract
The complexity and dynamics of human diseases are driven by the interactions between internal molecular activities and external environmental exposures. Although advances in omics technology have dramatically broadened the understanding of internal molecular and cellular mechanisms, understanding of the external environmental exposures, especially at the personal level, is still rudimentary in comparison. This is largely owing to our limited ability to efficiently collect the personal environmental exposome (PEE) and extract the nucleic acids and chemicals from PEE. Here we describe a protocol that integrates hardware and experimental pipelines to collect and decode biotic and abiotic external exposome at the individual level. The described protocol has several advantages over conventional approaches, such as exposome monitoring at the personal level, decontamination steps to increase sensitivity and simultaneous capture and high-throughput profiling of biotic and abiotic exposures. The protocol takes ~18 h of bench time over 2-3 d to prepare samples for high-throughput profiling and up to a couple of weeks of instrumental time to analyze, depending on the number of samples. Hundreds to thousands of species and organic compounds could be detected in the airborne particulate samples using this protocol. The composition and complexity of the biotic and abiotic substances are heavily influenced by the sampling spatiotemporal factors. Basic skillsets in molecular biology and analytical chemistry are required to carry out this protocol. This protocol could be modified to decode biotic and abiotic substances in other types of low or ultra-low input samples.
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14
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Laker RC, Altıntaş A, Lillard TS, Zhang M, Connelly JJ, Sabik OL, Onengut S, Rich SS, Farber CR, Barrès R, Yan Z. Exercise during pregnancy mitigates negative effects of parental obesity on metabolic function in adult mouse offspring. J Appl Physiol (1985) 2020; 130:605-616. [PMID: 33332990 DOI: 10.1152/japplphysiol.00641.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Parental health influences embryonic development and susceptibility to disease in the offspring. We investigated whether maternal voluntary running during gestation could protect the offspring from the adverse effects of maternal or paternal high-fat diet (HF) in mice. We performed transcriptomic and whole-genome DNA methylation analyses in female offspring skeletal muscle and targeted DNA methylation analysis of the peroxisome proliferator-activated receptor-γ coactivator-1α (Pgc-1α) promoter in both male and female adult offspring. Maternal HF resulted in impaired metabolic homeostasis in male offspring at 9 mo of age, whereas both male and female offspring were negatively impacted by paternal HF. Maternal exercise during gestation completely mitigated these metabolic impairments. Female adult offspring from obese male or female parent had skeletal muscle transcriptional profiles enriched in genes regulating inflammation and immune responses, whereas maternal exercise resulted in a transcriptional profile similar to offspring from normal chow (NC)-fed parents. Maternal HF, but not paternal HF, resulted in hypermethylation of the Pgc-1α promoter at CpG-260, which was abolished by maternal exercise. These findings demonstrate the negative consequences of maternal and paternal HF for the offspring's metabolic outcomes later in life possibly through different epigenetic mechanisms, and maternal exercise during gestation mitigates the negative consequences.NEW & NOTEWORTHY Maternal or paternal obesity causes metabolic impairment in adult offspring in mice. Maternal exercise during gestation can completely mitigate metabolic impairment. Maternal obesity, but not paternal obesity, results in hypermethylation of the Pgc-1α promoter at CpG-260, which can be abolished by maternal exercise.
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Affiliation(s)
- Rhianna C Laker
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Travis S Lillard
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Mei Zhang
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jessica J Connelly
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Olivia L Sabik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.,Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Suna Onengut
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Charles R Farber
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.,Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Zhen Yan
- Center for Skeletal Muscle Research at Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia
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15
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Khan Y, Hammarström D, Rønnestad BR, Ellefsen S, Ahmad R. Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline. BMC Bioinformatics 2020; 21:548. [PMID: 33256614 PMCID: PMC7708234 DOI: 10.1186/s12859-020-03866-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Background Human skeletal muscle responds to weight-bearing exercise with significant inter-individual differences. Investigation of transcriptome responses could improve our understanding of this variation. However, this requires bioinformatic pipelines to be established and evaluated in study-specific contexts. Skeletal muscle subjected to mechanical stress, such as through resistance training (RT), accumulates RNA due to increased ribosomal biogenesis. When a fixed amount of total-RNA is used for RNA-seq library preparations, mRNA counts are thus assessed in different amounts of tissue, potentially invalidating subsequent conclusions. The purpose of this study was to establish a bioinformatic pipeline specific for analysis of RNA-seq data from skeletal muscles, to explore the effects of different normalization strategies and to identify genes responding to RT in a volume-dependent manner (moderate vs. low volume). To this end, we analyzed RNA-seq data derived from a twelve-week RT intervention, wherein 25 participants performed both low- and moderate-volume leg RT, allocated to the two legs in a randomized manner. Bilateral muscle biopsies were sampled from m. vastus lateralis before and after the intervention, as well as before and after the fifth training session (Week 2). Result Bioinformatic tools were selected based on read quality, observed gene counts, methodological variation between paired observations, and correlations between mRNA abundance and protein expression of myosin heavy chain family proteins. Different normalization strategies were compared to account for global changes in RNA to tissue ratio. After accounting for the amounts of muscle tissue used in library preparation, global mRNA expression increased by 43–53%. At Week 2, this was accompanied by dose-dependent increases for 21 genes in rested-state muscle, most of which were related to the extracellular matrix. In contrast, at Week 12, no readily explainable dose-dependencies were observed. Instead, traditional normalization and non-normalized models resulted in counterintuitive reverse dose-dependency for many genes. Overall, training led to robust transcriptome changes, with the number of differentially expressed genes ranging from 603 to 5110, varying with time point and normalization strategy. Conclusion Optimized selection of bioinformatic tools increases the biological relevance of transcriptome analyses from resistance-trained skeletal muscle. Moreover, normalization procedures need to account for global changes in rRNA and mRNA abundance.
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Affiliation(s)
- Yusuf Khan
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway.,Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| | - Daniel Hammarström
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway.,Swedish School of Sport and Health Sciences, Stockholm, Sweden
| | - Bent R Rønnestad
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway
| | - Stian Ellefsen
- Section for Health and Exercise Physiology, Department of Public Health and Sport Sciences, Inland Norway University of Applied Sciences, Lillehammer, Norway.,Innlandet Hospital Trust, Lillehammer, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317, Hamar, Norway. .,Faculty of Health Sciences, Institute of Clinical Medicine, UiT - The Arctic University of Norway, Hansine Hansens veg 18, 9019, Tromsø, Norway.
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16
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Keller M, Yaskolka Meir A, Bernhart SH, Gepner Y, Shelef I, Schwarzfuchs D, Tsaban G, Zelicha H, Hopp L, Müller L, Rohde K, Böttcher Y, Stadler PF, Stumvoll M, Blüher M, Kovacs P, Shai I. DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial. Genome Med 2020; 12:97. [PMID: 33198820 PMCID: PMC7670623 DOI: 10.1186/s13073-020-00794-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND One of the major challenges in obesity treatment is to explain the high variability in the individual's response to specific dietary and physical activity interventions. With this study, we tested the hypothesis that specific DNA methylation changes reflect individual responsiveness to lifestyle intervention and may serve as epigenetic predictors for a successful weight-loss. METHODS We conducted an explorative genome-wide DNA methylation analysis in blood samples from 120 subjects (90% men, mean ± SD age = 49 ± 9 years, body mass-index (BMI) = 30.2 ± 3.3 kg/m2) from the 18-month CENTRAL randomized controlled trial who underwent either Mediterranean/low-carbohydrate or low-fat diet with or without physical activity. RESULTS Analyses comparing male subjects with the most prominent body weight-loss (responders, mean weight change - 16%) vs. non-responders (+ 2.4%) (N = 10 each) revealed significant variation in DNA methylation of several genes including LRRC27, CRISP2, and SLFN12 (all adj. P < 1 × 10-5). Gene ontology analysis indicated that biological processes such as cell adhesion and molecular functions such as calcium ion binding could have an important role in determining the success of interventional therapies in obesity. Epigenome-wide association for relative weight-loss (%) identified 15 CpGs being negatively correlated with weight change after intervention (all combined P < 1 × 10- 4) including new and also known obesity candidates such as NUDT3 and NCOR2. A baseline DNA methylation score better predicted successful weight-loss [area under the curve (AUC) receiver operating characteristic (ROC) = 0.95-1.0] than predictors such as age and BMI (AUC ROC = 0.56). CONCLUSIONS Body weight-loss following 18-month lifestyle intervention is associated with specific methylation signatures. Moreover, methylation differences in the identified genes could serve as prognostic biomarkers to predict a successful weight-loss therapy and thus contribute to advances in patient-tailored obesity treatment.
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Affiliation(s)
- Maria Keller
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 19-21, 04103, Leipzig, Germany
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O.Box 653, 84105, Beer Sheva, Israel
| | - Stephan H Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, 04107, Leipzig, Germany
- Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, 04107, Leipzig, Germany
| | - Yftach Gepner
- Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O.Box 653, 84105, Beer Sheva, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine and Sylvan Adams Sports Institute, Tel Aviv University, 6997801, Ramat Aviv, Israel
| | - Ilan Shelef
- Soroka University Medical Center, 84101, Beer-Sheva, Israel
| | - Dan Schwarzfuchs
- Soroka University Medical Center, 84101, Beer-Sheva, Israel
- Nuclear Research Center-Negev, 84190, Dimona, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O.Box 653, 84105, Beer Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O.Box 653, 84105, Beer Sheva, Israel
| | - Lydia Hopp
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107, Leipzig, Germany
| | - Luise Müller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 19-21, 04103, Leipzig, Germany
| | - Kerstin Rohde
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 19-21, 04103, Leipzig, Germany
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway
- Medical Division, Akershus University Hospital, 1478, Lørenskog, Norway
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, 04107, Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, University of Leipzig, 04109, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, 04103, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, 04103, Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, 1090, Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, 1871, Frederiksberg, Denmark
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Michael Stumvoll
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 19-21, 04103, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung, Helmholtz Zentrum München, Neuherberg, 85764, USA
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany.
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O.Box 653, 84105, Beer Sheva, Israel.
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17
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Adams K, Weber KS, Johnson SM. Exposome and Immunity Training: How Pathogen Exposure Order Influences Innate Immune Cell Lineage Commitment and Function. Int J Mol Sci 2020; 21:ijms21228462. [PMID: 33187101 PMCID: PMC7697998 DOI: 10.3390/ijms21228462] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 01/02/2023] Open
Abstract
Immune memory is a defining characteristic of adaptive immunity, but recent work has shown that the activation of innate immunity can also improve responsiveness in subsequent exposures. This has been coined “trained immunity” and diverges with the perception that the innate immune system is primitive, non-specific, and reacts to novel and recurrent antigen exposures similarly. The “exposome” is the cumulative exposures (diet, exercise, environmental exposure, vaccination, genetics, etc.) an individual has experienced and provides a mechanism for the establishment of immune training or immunotolerance. It is becoming increasingly clear that trained immunity constitutes a delicate balance between the dose, duration, and order of exposures. Upon innate stimuli, trained immunity or tolerance is shaped by epigenetic and metabolic changes that alter hematopoietic stem cell lineage commitment and responses to infection. Due to the immunomodulatory role of the exposome, understanding innate immune training is critical for understanding why some individuals exhibit protective phenotypes while closely related individuals may experience immunotolerant effects (e.g., the order of exposure can result in completely divergent immune responses). Research on the exposome and trained immunity may be leveraged to identify key factors for improving vaccination development, altering inflammatory disease development, and introducing potential new prophylactic treatments, especially for diseases such as COVID-19, which is currently a major health issue for the world. Furthermore, continued exposome research may prevent many deleterious effects caused by immunotolerance that frequently result in host morbidity or mortality.
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18
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Von Walden F, Rea M, Mobley CB, Fondufe-Mittendorf Y, McCarthy JJ, Peterson CA, Murach KA. The myonuclear DNA methylome in response to an acute hypertrophic stimulus. Epigenetics 2020; 15:1151-1162. [PMID: 32281477 PMCID: PMC7595631 DOI: 10.1080/15592294.2020.1755581] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In addition to multi-nucleated muscle fibres, numerous resident and infiltrating mononuclear cells populate the muscle compartment. As most epigenetic assays in skeletal muscle are conducted on whole tissue homogenates, essentially nothing is known about regulatory processes exclusively within muscle fibres in vivo. Utilizing a novel genetically modified mouse model developed by our laboratory, we (1) outline a simple and rapid workflow for isolating pure myonuclei from small tissue samples via fluorescent activated cell sorting and extracting high-quality large-fragment DNA for downstream analyses, and (2) provide information on myonuclear and interstitial cell nuclear CpG DNA methylation via reduced representation bisulphite sequencing (RRBS) using mice that were subjected to an acute mechanical overload of the plantaris muscle. In 3-month-old mice, myonuclei are ~50% of total nuclei in sham and ~30% in 3-d overloaded muscle, the difference being attributable to mononuclear cell infiltration and proliferation with overload. In purified myonuclei, pathway analysis of hypomethylated promoter regions following overload was distinct from interstitial nuclei and revealed marked regulation of factors that converge on the master regulator of muscle growth mTOR, and on autophagy. Specifically, acute hypomethylation of Rheb, Rictor, Hdac1, and Hdac2, in addition to a major driver of ribosome biogenesis Myc, reveals the epigenetic regulation of hypertrophic signalling within muscle fibres that may underpin the long-term growth response to loading. This study provides foundational information on global myonuclear epigenetics in vivo using RRBS, and demonstrates the importance of isolating specific nuclear populations to study the epigenetic regulation of skeletal muscle fibre adaptation.
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Affiliation(s)
- Ferdinand Von Walden
- K6 Department of Women’s and Children’s Health, Karolinska Institute, Stockholm, Sweden
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Matthew Rea
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - C. Brooks Mobley
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | | | - John J. McCarthy
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
| | - Charlotte A. Peterson
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
| | - Kevin A. Murach
- The Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physical Therapy, University of Kentucky, Lexington, KY, USA
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19
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Hall ECR, Murgatroyd C, Stebbings GK, Cunniffe B, Harle L, Salter M, Ramadass A, Westra JW, Hunter E, Akoulitchev A, Williams AG. The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures. Genes (Basel) 2020; 11:E905. [PMID: 32784689 PMCID: PMC7464522 DOI: 10.3390/genes11080905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 01/09/2023] Open
Abstract
The integration of genetic and environmental factors that regulate the gene expression patterns associated with exercise adaptation is mediated by epigenetic mechanisms. The organisation of the human genome within three-dimensional space, known as chromosome conformation, has recently been shown as a dynamic epigenetic regulator of gene expression, facilitating the interaction of distal genomic regions due to tight and regulated packaging of chromosomes in the cell nucleus. Technological advances in the study of chromosome conformation mean a new class of biomarker-the chromosome conformation signature (CCS)-can identify chromosomal interactions across several genomic loci as a collective marker of an epigenomic state. Investigative use of CCSs in biological and medical research shows promise in identifying the likelihood that a disease state is present or absent, as well as an ability to prospectively stratify individuals according to their likely response to medical intervention. The association of CCSs with gene expression patterns suggests that there are likely to be CCSs that respond, or regulate the response, to exercise and related stimuli. The present review provides a contextual background to CCS research and a theoretical framework discussing the potential uses of this novel epigenomic biomarker within sport and exercise science and medicine.
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Affiliation(s)
- Elliott C. R. Hall
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK; (G.K.S.); (A.G.W.)
| | | | - Georgina K. Stebbings
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK; (G.K.S.); (A.G.W.)
| | - Brian Cunniffe
- English Institute of Sport, Nottingham NG12 2LU, UK;
- Institute of Sport, Exercise and Health, University College London, London W1T 7HA, UK
| | - Lee Harle
- Holos Life Sciences, Oxford OX1 3HA, UK;
| | - Matthew Salter
- Oxford BioDynamics, Oxford OX4 2JZ, UK; (M.S.); (A.R.); (J.W.W.); (E.H.); (A.A.)
| | - Aroul Ramadass
- Oxford BioDynamics, Oxford OX4 2JZ, UK; (M.S.); (A.R.); (J.W.W.); (E.H.); (A.A.)
| | - Jurjen W. Westra
- Oxford BioDynamics, Oxford OX4 2JZ, UK; (M.S.); (A.R.); (J.W.W.); (E.H.); (A.A.)
| | - Ewan Hunter
- Oxford BioDynamics, Oxford OX4 2JZ, UK; (M.S.); (A.R.); (J.W.W.); (E.H.); (A.A.)
| | | | - Alun G. Williams
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK; (G.K.S.); (A.G.W.)
- Institute of Sport, Exercise and Health, University College London, London W1T 7HA, UK
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20
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Abstract
The skeletal muscle is the largest organ in the body, by mass. It is also the regulator of glucose homeostasis, responsible for 80% of postprandial glucose uptake from the circulation. Skeletal muscle is essential for metabolism, both for its role in glucose uptake and its importance in exercise and metabolic disease. In this article, we give an overview of the importance of skeletal muscle in metabolism, describing its role in glucose uptake and the diseases that are associated with skeletal muscle metabolic dysregulation. We focus on the role of skeletal muscle in peripheral insulin resistance and the potential for skeletal muscle-targeted therapeutics to combat insulin resistance and diabetes, as well as other metabolic diseases like aging and obesity. In particular, we outline the possibilities and pitfalls of the quest for exercise mimetics, which are intended to target the molecular mechanisms underlying the beneficial effects of exercise on metabolic disease. We also provide a description of the molecular mechanisms that regulate skeletal muscle glucose uptake, including a focus on the SNARE proteins, which are essential regulators of glucose transport into the skeletal muscle. © 2020 American Physiological Society. Compr Physiol 10:785-809, 2020.
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Affiliation(s)
- Karla E. Merz
- Department of Molecular and Cellular Endocrinology, City of Hope Beckman Research Institute, Duarte, California, USA
- The Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, California, USA
| | - Debbie C. Thurmond
- Department of Molecular and Cellular Endocrinology, City of Hope Beckman Research Institute, Duarte, California, USA
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Abstract
Obesity is a worldwide epidemic and contributes to global morbidity and mortality mediated via the development of nonalcoholic fatty liver disease (NAFLD), type 2 diabetes (T2D), cardiovascular (CVD) and other diseases. It is a consequence of an elevated caloric intake, a sedentary lifestyle and a genetic as well as an epigenetic predisposition. This review summarizes changes in DNA methylation and microRNAs identified in blood cells and different tissues in obese human and rodent models. It includes information on epigenetic alterations which occur in response to fat-enriched diets, exercise and metabolic surgery and discusses the potential of interventions to reverse epigenetic modifications.
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Affiliation(s)
- Meriem Ouni
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany.
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22
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Gut microbiota and regulation of myokine-adipokine function. Curr Opin Pharmacol 2020; 52:9-17. [DOI: 10.1016/j.coph.2020.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 12/27/2022]
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23
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Widmann M, Nieß AM, Munz B. Physical Exercise and Epigenetic Modifications in Skeletal Muscle. Sports Med 2020; 49:509-523. [PMID: 30778851 DOI: 10.1007/s40279-019-01070-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Physical activity and sports play major roles in the overall health status of humans. It is well known that regular exercise helps to lower the risk for a broad variety of health problems, such as cardiovascular disease, type 2 diabetes, and cancer. Being physically active induces a wide variety of molecular adaptations, for example fiber type switches or other metabolic alterations, in skeletal muscle tissue. These adaptations are based on exercise-induced changes to the skeletal muscle transcriptome. Understanding their nature is crucial to improve the development of exercise-based therapeutic strategies. Recent research indicates that specifically epigenetic mechanisms, i.e., pathways that induce changes in gene expression patterns without altering the DNA base sequence, might play a major role in controlling skeletal muscle transcriptional patterns. Epigenetic mechanisms include DNA and histone modifications, as well as expression of specific microRNAs. They can be modulated by environmental factors or external stimuli, such as exercise, and eventually induce specific and fine-tuned changes to the transcriptional response. In this review, we highlight current knowledge on epigenetic changes induced in exercising skeletal muscle, their target genes, and resulting phenotypic changes. In addition, we raise the question of whether epigenetic modifications might serve as markers for the design and management of optimized and individualized training protocols, as prognostic tools to predict training adaptation, or even as targets for the design of "exercise mimics".
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Affiliation(s)
- Manuel Widmann
- Department of Sports Medicine, University Medicine Tübingen, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Andreas M Nieß
- Department of Sports Medicine, University Medicine Tübingen, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Barbara Munz
- Department of Sports Medicine, University Medicine Tübingen, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany.
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24
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Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity. Nat Commun 2020; 11:470. [PMID: 31980607 PMCID: PMC6981202 DOI: 10.1038/s41467-019-13869-w] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 11/29/2019] [Indexed: 12/26/2022] Open
Abstract
The molecular mechanisms underlying the response to exercise and inactivity are not fully understood. We propose an innovative approach to profile the skeletal muscle transcriptome to exercise and inactivity using 66 published datasets. Data collected from human studies of aerobic and resistance exercise, including acute and chronic exercise training, were integrated using meta-analysis methods (www.metamex.eu). Here we use gene ontology and pathway analyses to reveal selective pathways activated by inactivity, aerobic versus resistance and acute versus chronic exercise training. We identify NR4A3 as one of the most exercise- and inactivity-responsive genes, and establish a role for this nuclear receptor in mediating the metabolic responses to exercise-like stimuli in vitro. The meta-analysis (MetaMEx) also highlights the differential response to exercise in individuals with metabolic impairments. MetaMEx provides the most extensive dataset of skeletal muscle transcriptional responses to different modes of exercise and an online interface to readily interrogate the database. The pathways that underlie the effects of exercise on metabolism remain incompletely described. Here, the authors perform a meta-analysis of transcriptomic data from 66 published datasets of human skeletal muscle. They identify pathways selectively activated by inactivity, aerobic or resistance exercise, and characterize NR4A3 as one of the genes responsive to inactivity.
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25
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Zhang Y, Oliveira AN, Hood DA. The intersection of exercise and aging on mitochondrial protein quality control. Exp Gerontol 2020; 131:110824. [PMID: 31911185 DOI: 10.1016/j.exger.2019.110824] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 12/23/2022]
Abstract
Skeletal muscle quality and quantity are negatively impacted with age. Part of this decline in function can be attributed to alterations in mitochondrial turnover, and in the mechanisms that regulate mitochondrial homeostasis. Protein quality control within the mitochondria relies on a number of interconnected processes, namely the mitochondrial unfolded protein response (UPRmt), protein import and mitophagy. In particular, the post-transcriptional regulation of protein import into the organelle has generated considerable recent interest in view of its dynamic versatility. The capacity for import can be increased by chronic exercise, and diminished by muscle disuse, and defects in the import pathway can be rescued by exercise. Within mitochondria, the unfolded protein response (UPR) is activated if protein import is altered, or if protein misfolding takes place. This UPR generates retrograde signaling to the nucleus to activate compensatory gene expression and protein synthesis. Mitophagy is also elevated with age, contributing to the lower mitochondrial content in aging muscle. However, mitophagy is amenable to exercise adaptations, as it is activated with each exercise bout, presumably to mediate mitochondrial quality control. However, this response is attenuated in older subjects. Although not yet completely elucidated, numerous molecular processes involved in mitochondrial biogenesis and turnover are affected with age. The contrasting and often opposite consequences of exercise and age suggest that exercise can serve as non-pharmacological "mitochondrial medicine" for aging muscle to ameliorate mitochondrial content and function, via pathways that implicate organelle protein quality control mechanisms.
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Affiliation(s)
- Yuan Zhang
- School of Sports and Health, Nanjing Sport Institute, Nanjing, Jiangsu, China
| | - Ashley N Oliveira
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario M3J 1P3, Canada
| | - David A Hood
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario M3J 1P3, Canada.
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26
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Hiam D, Simar D, Laker R, Altıntaş A, Gibson-Helm M, Fletcher E, Moreno-Asso A, Trewin AJ, Barres R, Stepto NK. Epigenetic Reprogramming of Immune Cells in Women With PCOS Impact Genes Controlling Reproductive Function. J Clin Endocrinol Metab 2019; 104:6155-6170. [PMID: 31390009 DOI: 10.1210/jc.2019-01015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is a chronic disease affecting reproductive function and whole-body metabolism. Although the etiology is unclear, emerging evidence indicates that the epigenetics may be a contributing factor. OBJECTIVE To determine the role of global and genome-wide epigenetic modifications in specific immune cells in PCOS compared with controls and whether these could be related to clinical features of PCOS. DESIGN Cross-sectional study. PARTICIPANTS Women with (n = 17) or without PCOS (n = 17). SETTING Recruited from the general community. MAIN OUTCOME MEASURES Isolated peripheral blood mononuclear cells were analyzed using multicolor flow cytometry methods to determine global DNA methylation levels in a cell-specific fashion. Transcriptomic and genome-wide DNA methylation analyses were performed on T helper cells using RNA sequencing and reduced representation bisulfite sequencing. RESULTS Women with PCOS had lower global DNA methylation in monocytes (P = 0.006) and in T helper (P = 0.004), T cytotoxic (P = 0.004), and B cells (P = 0.03). Specific genome-wide DNA methylation analysis of T helper cells from women with PCOS identified 5581 differentially methylated CpG sites. Functional gene ontology enrichment analysis showed that genes located at the proximity of differentially methylated CpG sites belong to pathways related to reproductive function and immune cell function. However, these genes were not altered at the transcriptomic level. CONCLUSIONS It was shown that PCOS is associated with global and gene-specific DNA methylation remodeling in a cell type-specific manner. Further investigation is warranted to determine whether epigenetic reprogramming of immune cells is important in determining the different phenotypes of PCOS.
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Affiliation(s)
- Danielle Hiam
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - David Simar
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Rhianna Laker
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Melanie Gibson-Helm
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Elly Fletcher
- Baker Heart and Disease Institute, Melbourne, Victoria, Australia
| | - Alba Moreno-Asso
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Adam J Trewin
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Romain Barres
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Nigel K Stepto
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Medicine-Western Health, School of Medicine, Faculty of Medicine, Dentistry, and Health Science, Melbourne, Australia
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Georgia-Eirini D, Athina S, Wim VB, Christos K, Theodoros C. Natural Products from Mediterranean Diet: From Anti-hyperlipidemic Agents to Dietary Epigenetic Modulators. Curr Pharm Biotechnol 2019; 20:825-844. [DOI: 10.2174/1573407215666190628150921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/23/2018] [Accepted: 06/03/2019] [Indexed: 01/05/2023]
Abstract
Background:
Cardiovascular Diseases (CVD) are, currently, the major contributor to global
mortality and will continue to dominate mortality rates in the future. Hyperlipidemia refers to the elevated
levels of lipids and cholesterol in the blood, and is also identified as dyslipidemia, manifesting in
the form of different disorders of lipoprotein metabolism. These abnormalities may lead to the development
of atherosclerosis, which can lead to coronary artery disease and stroke. In recent years, there
is a growing interest in the quest for alternative therapeutic treatments based on natural products, offering
better recovery and the avoidance of side effects. Recent technological advances have further improved
our understanding of the role of epigenetic mechanisms in hyperlipidemic disorders and dietary
prevention strategies.
Objective:
This is a comprehensive overview of the anti-hyperlipidemic effects of plant extracts, vegetables,
fruits and isolated compounds thereof, with a focus on natural products from the Mediterranean
region as well as the possible epigenetic changes in gene expression or cardiometabolic signaling
pathways.
Methods:
For the purpose of this study, we searched the PubMed, Scopus and Google Scholar databases
for eligible articles and publications over the last five years. The keywords included: “hyperlipidemia”,
“plant extract”, “herbs”, “natural products”, “vegetables”, “cholesterol” and others. We initially
included all relevant articles referring to in vitro studies, animal studies, Randomized Controlled
Trials (RCTs) and previous reviews.
Conclusion:
Many natural products found in the Mediterranean diet have been studied for the treatment
of hyperlipidemia. The antihyperlipidemic effect seems to be dose and/or consumption frequency
related, which highlights the fact that a healthy diet can only be effective in reversing disease markers
if it is consistent and within the framework of a healthy lifestyle. Finally, epigenetic biomarkers are increasingly
recognized as new lifestyle management tools to monitor a healthy dietary lifestyle for the
prevention of hyperlipidaemic disorders and comorbidities to promote a healthy life.
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Affiliation(s)
- Deligiannidou Georgia-Eirini
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Sygkouna Athina
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Vanden Berghe Wim
- Lab of Protein Science, Proteomics & Epigenetic Signaling (PPES), Department of Biomedical sciences, University Antwerp, 2610, Wilrijk, Belgium
| | - Kontogiorgis Christos
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Constantinides Theodoros
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, 68100, Greece
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Hibler E, Huang L, Andrade J, Spring B. Impact of a diet and activity health promotion intervention on regional patterns of DNA methylation. Clin Epigenetics 2019; 11:133. [PMID: 31506096 PMCID: PMC6737702 DOI: 10.1186/s13148-019-0707-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Studies demonstrate the impact of diet and physical activity on epigenetic biomarkers, specifically DNA methylation. However, no intervention studies have examined the combined impact of dietary and activity changes on the blood epigenome. The objective of this study was to examine the impact of the Make Better Choices 2 (MBC2) healthy diet and activity intervention on patterns of epigenome-wide DNA methylation. The MBC2 study was a 9-month randomized controlled trial among adults aged 18-65 with non-optimal levels of health behaviors. The study compared three 12-week interventions to (1) simultaneously increase exercise and fruit/vegetable intake, while decreasing sedentary leisure screen time; (2) sequentially increase fruit/vegetable intake and decrease leisure screen time first, then increase exercise; (3) increase sleep and decrease stress (control). We collected blood samples at baseline, 3 and 9 months, and measured DNA methylation using the Illumina EPIC (850 k) BeadChip. We examined region-based differential methylation patterns using linear regression models with the false discovery rate of 0.05. We also conducted pathway analysis using gene ontology (GO), KEGG, and IPA canonical pathway databases. RESULTS We found no differences between the MBC2 population (n = 340) and the subsample with DNA methylation measured (n = 68) on baseline characteristics or the impact of the intervention on behavior change. We identified no differentially methylated regions at baseline between the control versus intervention groups. At 3 versus 9 months, we identified 154 and 298 differentially methylated regions, respectively, between controls compared to pooled samples from sequential and simultaneous groups. In the GO database, we identified two gene ontology terms related to hemophilic cell adhesion and cell-cell adhesion. In IPA analysis, we found pathways related to carcinogenesis including PI3K/AKT, Wnt/β-catenin, sonic hedgehog, and p53 signaling. We observed an overlap between 3 and 9 months, including the GDP-L-fucose biosynthesis I, methylmalonyl metabolism, and estrogen-mediated cell cycle regulation pathways. CONCLUSIONS The results demonstrate that the MBC2 diet and physical activity intervention impacts patterns of DNA methylation in gene regions related to cell cycle regulation and carcinogenesis. Future studies will examine DNA methylation as a biomarker to identify populations that may particularly benefit from incorporating health behavior change into plans for precision prevention.
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Affiliation(s)
- Elizabeth Hibler
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 North Lakeshore Drive, Chicago, IL, 60611, USA.
| | - Lei Huang
- Center for Research Informatics, Biological Sciences Division, University of Chicago, 900 E. 57th. Street, Chicago, IL, 60637, USA
| | - Jorge Andrade
- Center for Research Informatics, Biological Sciences Division, University of Chicago, 900 E. 57th. Street, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, 900 E. 57th. Street, Chicago, IL, 60637, USA
| | - Bonnie Spring
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 North Lakeshore Drive, Chicago, IL, 60611, USA
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Miro-Blanch J, Yanes O. Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism. Front Genet 2019; 10:638. [PMID: 31338107 PMCID: PMC6628876 DOI: 10.3389/fgene.2019.00638] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023] Open
Abstract
Gut microbiota communities have coevolved for millions of years in a symbiotic relationship with their mammalian hosts. Elucidating and understanding the molecular mechanisms by which microbiota interacts with its host and how this contributes to the homeostasis of the host is crucial. One of these molecular relationships is the so-called chemical crosstalk between microbiota and host metabolisms, including the poorly explored epigenetic regulation of host tissues by the metabolic activity of gut microbiota in response to changes in diet. DNA methylation and histone modifications are epigenetic marks partly regulated by enzymes such as methylases and acetylases, whose activity depend on host and microbiota metabolites that act as substrates and cofactors for these reactions. However, providing a complete mechanistic description of the regulatory interactions between both metabolisms and the impact on the expression of host genes through an epigenetic modulation, remains elusive. This article presents our perspective on how metabolomic, metagenomic, transcriptomic, and epigenomic data can be used to investigate the "microbiota-nutrient metabolism-epigenetics axis." We also discuss the implications and opportunities this knowledge may have for basic and applied science, such as the impact on the way we structure future research, understand, and prevent diseases like type 2 diabetes or obesity.
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Affiliation(s)
- Joan Miro-Blanch
- Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Oscar Yanes
- Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Jiang C, Wang X, Li X, Inlora J, Wang T, Liu Q, Snyder M. Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. Cell 2019; 175:277-291.e31. [PMID: 30241608 DOI: 10.1016/j.cell.2018.08.060] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/07/2018] [Accepted: 08/27/2018] [Indexed: 11/25/2022]
Abstract
Human health is dependent upon environmental exposures, yet the diversity and variation in exposures are poorly understood. We developed a sensitive method to monitor personal airborne biological and chemical exposures and followed the personal exposomes of 15 individuals for up to 890 days and over 66 distinct geographical locations. We found that individuals are potentially exposed to thousands of pan-domain species and chemical compounds, including insecticides and carcinogens. Personal biological and chemical exposomes are highly dynamic and vary spatiotemporally, even for individuals located in the same general geographical region. Integrated analysis of biological and chemical exposomes revealed strong location-dependent relationships. Finally, construction of an exposome interaction network demonstrated the presence of distinct yet interconnected human- and environment-centric clouds, comprised of interacting ecosystems such as human, flora, pets, and arthropods. Overall, we demonstrate that human exposomes are diverse, dynamic, spatiotemporally-driven interaction networks with the potential to impact human health.
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Affiliation(s)
- Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Xin Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Xiyan Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Jingga Inlora
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Ting Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Qing Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94304, USA.
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Piccirillo R. Exercise-Induced Myokines With Therapeutic Potential for Muscle Wasting. Front Physiol 2019; 10:287. [PMID: 30984014 PMCID: PMC6449478 DOI: 10.3389/fphys.2019.00287] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/04/2019] [Indexed: 12/26/2022] Open
Abstract
Skeletal muscle is a highly vascularized tissue that can secrete proteins called myokines. These muscle-secreted factors exert biological functions in muscle itself (autocrine effect) or on short- or long-distant organs (paracrine/endocrine effects) and control processes such as metabolism, angiogenesis, or inflammation. Widely differing diseases ranging from genetic myopathies to cancers are emerging as causing dysregulated secretion of myokines from skeletal muscles. Myokines are also involved in the control of muscle size and may be important to be restored to normal levels to alleviate muscle wasting in various conditions, such as cancer, untreated diabetes, chronic obstructive pulmonary disease, aging, or heart failure. Interestingly, many myokines are induced by exercise (muscle-derived exerkines) and some even by specific types of physical activity, but more studies are needed on this issue. Most exercise-induced myokines travel throughout the body by means of extracellular vesicles. Restoring myokines by physical activity may be added to the list of mechanisms by which exercise exerts preventative or curative effects against a large number of diseases, including the deleterious muscle wasting they may cause. Extending our understanding about which myokines could be usefully restored in certain diseases might help in prescribing more tailored exercise or myokine-based drugs.
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Affiliation(s)
- Rosanna Piccirillo
- Department of Neurosciences, Mario Negri Institute for Pharmacological Research IRCCS, Milan, Italy
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32
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Samblas M, Milagro FI, Martínez A. DNA methylation markers in obesity, metabolic syndrome, and weight loss. Epigenetics 2019; 14:421-444. [PMID: 30915894 DOI: 10.1080/15592294.2019.1595297] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The fact that not all individuals exposed to the same environmental risk factors develop obesity supports the hypothesis of the existence of underlying genetic and epigenetic elements. There is suggestive evidence that environmental stimuli, such as dietary pattern, particularly during pregnancy and early life, but also in adult life, can induce changes in DNA methylation predisposing to obesity and related comorbidities. In this context, the DNA methylation marks of each individual have emerged not only as a promising tool for the prediction, screening, diagnosis, and prognosis of obesity and metabolic syndrome features, but also for the improvement of weight loss therapies in the context of precision nutrition. The main objectives in this field are to understand the mechanisms involved in transgenerational epigenetic inheritance, and featuring the nutritional and lifestyle factors implicated in the epigenetic modifications. Likewise, DNA methylation modulation caused by diet and environment may be a target for newer therapeutic strategies concerning the prevention and treatment of metabolic diseases.
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Affiliation(s)
- Mirian Samblas
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain
| | - Fermín I Milagro
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain.,b CIBERobn, CIBER Fisiopatología de la Obesidad y Nutrición , Instituto de Salud Carlos III. Madrid , Spain.,c IdiSNA, Instituto de Investigación Sanitaria de Navarra (IdiSNA) , Pamplona , Spain
| | - Alfredo Martínez
- a Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research , University of Navarra , Pamplona , Spain.,b CIBERobn, CIBER Fisiopatología de la Obesidad y Nutrición , Instituto de Salud Carlos III. Madrid , Spain.,c IdiSNA, Instituto de Investigación Sanitaria de Navarra (IdiSNA) , Pamplona , Spain.,d IMDEA, Research Institute on Food & Health Sciences , Madrid , Spain
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Budai Z, Balogh L, Sarang Z. Short-term high-fat meal intake alters the expression of circadian clock-, inflammation-, and oxidative stress-related genes in human skeletal muscle. Int J Food Sci Nutr 2019; 70:749-758. [PMID: 30764669 DOI: 10.1080/09637486.2018.1557607] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dietary food, depending on timing, amount and composition can influence gene expression in various tissues. Here, we investigated the effect of high-fat meal diets of different compositions on the gene expression pattern of human skeletal muscle. Gene expression data of skeletal muscle samples from human volunteers prior and 4 h after the consumption of high lipid-containing meal consisting of either saturated-, monounsaturated- or polyunsaturated fatty acids were downloaded from the public repository. List of 843 differently expressed genes (DEGs) was generated. Functional analysis revealed that circadian rhythm-, inflammation- and oxidative stress-related genes are highly overrepresented among the DEGs. The magnitude of gene expression changes significantly increases with the saturation level of the dietary fatty acids and the majority of the DEGs are upregulated. We propose that, by altering circadian clock gene expression and inducing inflammation and oxidative stress, high lipid intake can contribute to muscle function decay in the long run.
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Affiliation(s)
- Zsófia Budai
- a Department of Biochemistry and Molecular Biology Faculty of Medicine , University of Debrecen , Debrecen , Hungary
| | - László Balogh
- b Institute of Sport Sciences University of Debrecen , Debrecen , Hungary
| | - Zsolt Sarang
- a Department of Biochemistry and Molecular Biology Faculty of Medicine , University of Debrecen , Debrecen , Hungary
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Methylome of human skeletal muscle after acute & chronic resistance exercise training, detraining & retraining. Sci Data 2018; 5:180213. [PMID: 30375987 PMCID: PMC6207066 DOI: 10.1038/sdata.2018.213] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is an important epigenetic modification that can regulate gene expression following environmental encounters without changes to the genetic code. Using Infinium MethylationEPIC BeadChip Arrays (850,000 CpG sites) we analysed for the first time, DNA isolated from untrained human skeletal muscle biopsies (vastus lateralis) at baseline (rest) and immediately following an acute (single) bout of resistance exercise. In the same participants, we also analysed the methylome following a period of muscle growth (hypertrophy) evoked via chronic (repeated bouts-3 sessions/wk) resistance exercise (RE) (training) over 7-weeks, followed by complete exercise cessation for 7-weeks returning muscle back to baseline levels (detraining), and finally followed by a subsequent 7-week period of RE-induced hypertrophy (retraining). These valuable methylome data sets described in the present manuscript and deposited in an open-access repository can now be shared and re-used to enable the identification of epigenetically regulated genes/networks that are modified after acute anabolic stimuli and hypertrophy, and further investigate the phenomenon of epigenetic memory in skeletal muscle.
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Delezie J, Handschin C. Endocrine Crosstalk Between Skeletal Muscle and the Brain. Front Neurol 2018; 9:698. [PMID: 30197620 PMCID: PMC6117390 DOI: 10.3389/fneur.2018.00698] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
Skeletal muscle is an essential regulator of energy homeostasis and a potent coordinator of exercise-induced adaptations in other organs including the liver, fat or the brain. Skeletal muscle-initiated crosstalk with other tissues is accomplished though the secretion of myokines, protein hormones which can exert autocrine, paracrine and long-distance endocrine effects. In addition, the enhanced release or uptake of metabolites from and into contracting muscle cells, respectively, likewise can act as a powerful mediator of tissue interactions, in particular in regard to the central nervous system. The present review will discuss the current stage of knowledge regarding how exercise and the muscle secretome improve a broad range of brain functions related to vascularization, neuroplasticity, memory, sleep and mood. Even though the molecular and cellular mechanisms underlying the communication between muscle and brain is still poorly understood, physical activity represents one of the most effective strategies to reduce the prevalence and incidence of depression, cognitive, metabolic or degenerative neuronal disorders, and thus warrants further study.
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Dziewulska A, Dobosz AM, Dobrzyn A. High-Throughput Approaches onto Uncover (Epi)Genomic Architecture of Type 2 Diabetes. Genes (Basel) 2018; 9:E374. [PMID: 30050001 PMCID: PMC6115814 DOI: 10.3390/genes9080374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex disorder that is caused by a combination of genetic, epigenetic, and environmental factors. High-throughput approaches have opened a new avenue toward a better understanding of the molecular bases of T2D. A genome-wide association studies (GWASs) identified a group of the most common susceptibility genes for T2D (i.e., TCF7L2, PPARG, KCNJ1, HNF1A, PTPN1, and CDKAL1) and illuminated novel disease-causing pathways. Next-generation sequencing (NGS)-based techniques have shed light on rare-coding genetic variants that account for an appreciable fraction of T2D heritability (KCNQ1 and ADRA2A) and population risk of T2D (SLC16A11, TPCN2, PAM, and CCND2). Moreover, single-cell sequencing of human pancreatic islets identified gene signatures that are exclusive to α-cells (GCG, IRX2, and IGFBP2) and β-cells (INS, ADCYAP1, INS-IGF2, and MAFA). Ongoing epigenome-wide association studies (EWASs) have progressively defined links between epigenetic markers and the transcriptional activity of T2D target genes. Differentially methylated regions were found in TCF7L2, THADA, KCNQ1, TXNIP, SOCS3, SREBF1, and KLF14 loci that are related to T2D. Additionally, chromatin state maps in pancreatic islets were provided and several non-coding RNAs (ncRNA) that are key to T2D pathogenesis were identified (i.e., miR-375). The present review summarizes major progress that has been made in mapping the (epi)genomic landscape of T2D within the last few years.
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Affiliation(s)
- Anna Dziewulska
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.
| | - Aneta M Dobosz
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.
| | - Agnieszka Dobrzyn
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland.
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Hawley JA, Lundby C, Cotter JD, Burke LM. Maximizing Cellular Adaptation to Endurance Exercise in Skeletal Muscle. Cell Metab 2018; 27:962-976. [PMID: 29719234 DOI: 10.1016/j.cmet.2018.04.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The application of molecular techniques to exercise biology has provided novel insight into the complexity and breadth of intracellular signaling networks involved in response to endurance-based exercise. Here we discuss several strategies that have high uptake by athletes and, on mechanistic grounds, have the potential to promote cellular adaptation to endurance training in skeletal muscle. Such approaches are based on the underlying premise that imposing a greater metabolic load and provoking extreme perturbations in cellular homeostasis will augment acute exercise responses that, when repeated over months and years, will amplify training adaptation.
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Affiliation(s)
- John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC 3000, Australia.
| | - Carsten Lundby
- Centre for Physical Activity Research, Copenhagen University Hospital, Copenhagen, Denmark
| | - James D Cotter
- School of Physical Education, Sport and Exercise Sciences, University of Otago, Dunedin, New Zealand
| | - Louise M Burke
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC 3000, Australia; Department of Sport Nutrition, Australian Institute of Sport, Belconnen, ACT, Australia
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Fabre O, Ingerslev LR, Garde C, Donkin I, Simar D, Barrès R. Exercise training alters the genomic response to acute exercise in human adipose tissue. Epigenomics 2018; 10:1033-1050. [PMID: 29671347 PMCID: PMC6190185 DOI: 10.2217/epi-2018-0039] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: To determine the genomic mechanisms by which adipose tissue responds to acute and chronic exercise. Methods: We profiled the transcriptomic and epigenetic response to acute exercise in human adipose tissue collected before and after endurance training. Results: Although acute exercises were performed at same relative intensities, the magnitude of transcriptomic changes after acute exercise was reduced by endurance training. DNA methylation remodeling induced by acute exercise was more prominent in trained versus untrained state. We found an overlap between gene expression and DNA methylation changes after acute exercise for 32 genes pre-training and six post-training, notably at adipocyte-specific genes. Conclusion: Training status differentially affects the epigenetic and transcriptomic response to acute exercise in human adipose tissue.
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Affiliation(s)
- Odile Fabre
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Garde
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Donkin
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Simar
- Mechanisms of Disease & Translational Research, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Romain Barrès
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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