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Li J, Shen Z, Lin Y, Wang Z, Li M, Sun H, Wang Q, Zhao C, Xu J, Lu X, Gao W. DNA methylation of skeletal muscle function-related secretary factors identifies FGF2 as a potential biomarker for sarcopenia. J Cachexia Sarcopenia Muscle 2024; 15:1209-1217. [PMID: 38641928 PMCID: PMC11154778 DOI: 10.1002/jcsm.13472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Sarcopenia is characterized by progressive loss of muscle mass and function due to aging. DNA methylation has been identified to play important roles in the dysfunction of skeletal muscle. The aim of our present study was to explore the whole blood sample-based methylation changes of skeletal muscle function-related factors in patients with sarcopenia. METHODS The overall DNA methylation levels were analysed by using MethlTarget™ DNA Methylation Analysis platform in a discovery set consistent of 50 sarcopenic older adults (aged ≥65 years) and 50 age- and sex-matched non-sarcopenic individuals. The candidate differentially methylated regions (DMRs) were further validated by Methylation-specific PCR (MSP) in another two independent larger sets and confirmed by pyrosequencing. Receiver operating characteristic (ROC) curve analysis was used to determine the optimum cut-off levels of fibroblast growth factor 2 (FGF2)_30 methylation best predicting sarcopenia and area under the ROC curve (AUC) was measured. The correlation between candidate DMRs and the risk of sarcopenia was investigated by univariate analysis and multivariate logistic regression analysis. RESULTS Among 1149 cytosine-phosphate-guanine (CpG) sites of 27 skeletal muscle function-related secretary factors, 17 differentially methylated CpG sites and 7 differentially methylated regions (DMRs) were detected between patients with sarcopenia and control subjects in the discovery set. Further methylation-specific PCR identified that methylation of fibroblast growth factor 2 (FGF2)_30 was lower in patients with sarcopenia and the level was decreased as the severity of sarcopenia increased, which was confirmed by pyrosequencing. Correlation analysis demonstrated that the methylation level of FGF2_30 was positively correlated to ASMI (r = 0.372, P < 0.001), grip strength (r = 0.334, P < 0.001), and gait speed (r = 0.411, P < 0.001). ROC curve analysis indicated that the optimal cut-off value of FGF2_30 methylation level that predicted sarcopenia was 0.15 with a sensitivity of 84.6% and a specificity of 70.1% (AUC = 0.807, 95% CI = 0.756-0.858, P < 0.001). Multivariate logistic regression analyses showed that lower FGF2_30 methylation level (<0.15) was significantly associated with increased risk of sarcopenia even after adjustment for potential confounders including age, sex, and BMI (adjusted OR = 9.223, 95% CI: 6.614-12.861, P < 0.001). CONCLUSIONS Our results suggest that lower FGF2_30 methylation is correlated with the risk and severity of sarcopenia in the older adults, indicating that FGF2 methylation serve as a surrogate biomarker for the screening and evaluation of sarcopenia.
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Affiliation(s)
- Jia‐Wen Li
- Department of Geriatrics, Zhongda Hospital, School of MedicineSoutheast UniversityNanjingChina
| | - Zheng‐Kai Shen
- Jiangsu Province Center for Disease Control and PreventionNanjingChina
| | - Yu‐Shuang Lin
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Zhi‐Yue Wang
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Mei‐Lin Li
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Hui‐Xian Sun
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Quan Wang
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Can Zhao
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Jin‐Shui Xu
- Jiangsu Province Center for Disease Control and PreventionNanjingChina
| | - Xiang Lu
- Department of Geriatrics, Sir Run Run HospitalNanjing Medical UniversityNanjingChina
| | - Wei Gao
- Department of Geriatrics, Zhongda Hospital, School of MedicineSoutheast UniversityNanjingChina
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Prado CM, Batsis JA, Donini LM, Gonzalez MC, Siervo M. Sarcopenic obesity in older adults: a clinical overview. Nat Rev Endocrinol 2024; 20:261-277. [PMID: 38321142 DOI: 10.1038/s41574-023-00943-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/15/2023] [Indexed: 02/08/2024]
Abstract
Sarcopenic obesity is characterized by a concurrent decline in muscle mass and function, along with increased adipose tissue. Sarcopenic obesity is a growing concern in older adults owing to significant health consequences, including implications for mortality, comorbidities and risk of developing geriatric syndromes. A 2022 consensus statement established a new definition and diagnostic criteria for sarcopenic obesity. The pathophysiology of this condition involves a complex interplay between muscle, adipose tissue, hormonal changes, inflammation, oxidative stress and lifestyle factors, among others. Sarcopenic obesity is treated with a range of management approaches, such as lifestyle interventions, exercise, nutrition and medical therapies. Emerging therapies that were developed for treating other conditions may be relevant to sarcopenic obesity, including novel pharmacological agents and personalized approaches such as precision medicine. In this Review, we synthesize the current knowledge of the clinical importance of sarcopenic obesity, its assessment and diagnosis, along with current and emerging management strategies.
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Affiliation(s)
- Carla M Prado
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - John A Batsis
- Division of Geriatric Medicine, School of Medicine, and Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lorenzo M Donini
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - M Cristina Gonzalez
- Postgraduate Program in Nutrition and Food, Pelotas, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - Mario Siervo
- School of Population Health, Curtin University, Perth, Western Australia, Australia
- Curtin Dementia Centre of Excellence, enAble Institute, Curtin University, Perth, Western Australia, Australia
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3
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Ruple BA, Mattingly ML, Godwin JS, McIntosh MC, Kontos NJ, Agyin-Birikorang A, Michel JM, Plotkin DL, Chen SY, Ziegenfuss TN, Fruge AD, Gladden LB, Robinson AT, Mobley CB, Mackey AL, Roberts MD. The effects of resistance training on denervated myofibers, senescent cells, and associated protein markers in middle-aged adults. FASEB J 2024; 38:e23621. [PMID: 38651653 PMCID: PMC11047210 DOI: 10.1096/fj.202302103rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Denervated myofibers and senescent cells are hallmarks of skeletal muscle aging. However, sparse research has examined how resistance training affects these outcomes. We investigated the effects of unilateral leg extensor resistance training (2 days/week for 8 weeks) on denervated myofibers, senescent cells, and associated protein markers in apparently healthy middle-aged participants (MA, 55 ± 8 years old, 17 females, 9 males). We obtained dual-leg vastus lateralis (VL) muscle cross-sectional area (mCSA), VL biopsies, and strength assessments before and after training. Fiber cross-sectional area (fCSA), satellite cells (Pax7+), denervated myofibers (NCAM+), senescent cells (p16+ or p21+), proteins associated with denervation and senescence, and senescence-associated secretory phenotype (SASP) proteins were analyzed from biopsy specimens. Leg extensor peak torque increased after training (p < .001), while VL mCSA trended upward (interaction p = .082). No significant changes were observed for Type I/II fCSAs, NCAM+ myofibers, or senescent (p16+ or p21+) cells, albeit satellite cells increased after training (p = .037). While >90% satellite cells were not p16+ or p21+, most p16+ and p21+ cells were Pax7+ (>90% on average). Training altered 13 out of 46 proteins related to muscle-nerve communication (all upregulated, p < .05) and 10 out of 19 proteins related to cellular senescence (9 upregulated, p < .05). Only 1 out of 17 SASP protein increased with training (IGFBP-3, p = .031). In conclusion, resistance training upregulates proteins associated with muscle-nerve communication in MA participants but does not alter NCAM+ myofibers. Moreover, while training increased senescence-related proteins, this coincided with an increase in satellite cells but not alterations in senescent cell content or SASP proteins. These latter findings suggest shorter term resistance training is an unlikely inducer of cellular senescence in apparently healthy middle-aged participants. However, similar study designs are needed in older and diseased populations before definitive conclusions can be drawn.
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Affiliation(s)
| | | | | | | | | | | | - J. Max Michel
- School of Kinesiology, Auburn University, Auburn, AL, USA
| | | | | | | | | | | | | | | | - Abigail L. Mackey
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
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4
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Roberts MD, Ruple BA, Godwin JS, McIntosh MC, Chen SY, Kontos NJ, Agyin-Birikorang A, Michel M, Plotkin DL, Mattingly ML, Mobley B, Ziegenfuss TN, Fruge AD, Kavazis AN. A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training. Aging (Albany NY) 2024; 16:6631-6651. [PMID: 38643460 PMCID: PMC11087122 DOI: 10.18632/aging.205751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
The skeletal muscle proteome alterations to aging and resistance training have been reported in prior studies. However, conventional proteomics in skeletal muscle typically yields wide protein abundance ranges that mask the detection of lowly expressed proteins. Thus, we adopted a novel deep proteomics approach whereby myofibril (MyoF) and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS). Specifically, we investigated MyoF and non-MyoF proteomic profiles of the vastus lateralis muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6). Additionally, MA muscle was analyzed following eight weeks of resistance training (RT, 2d/week). Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteomes were evident between age cohorts, and most differentially expressed non-MyoF proteins (447/543) were more enriched in MA versus Y. Biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. RT in MA participants only altered ~0.3% of MyoF and ~1.0% of non-MyoF proteomes. In summary, aging and RT predominantly affect non-contractile proteins in skeletal muscle. Additionally, marginal proteome adaptations with RT suggest more rigorous training may stimulate more robust effects or that RT, regardless of age, subtly alters basal state skeletal muscle protein abundances.
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Affiliation(s)
| | | | | | | | | | | | | | - Max Michel
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | | | - Brooks Mobley
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | - Andrew D. Fruge
- College of Nursing, Auburn University, Auburn, AL 36849, USA
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5
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Luo J, Wang W, Li J, Duan H, Xu C, Tian X, Zhang D. Epigenome-wide association study identifies DNA methylation loci associated with handgrip strength in Chinese monozygotic twins. Front Cell Dev Biol 2024; 12:1378680. [PMID: 38633108 PMCID: PMC11021642 DOI: 10.3389/fcell.2024.1378680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Background: The decline in muscle strength and function with aging is well recognized, but remains poorly characterized at the molecular level. Here, we report the epigenetic relationship between genome-wide DNA methylation and handgrip strength (HGS) among Chinese monozygotic (MZ) twins. Methods: DNA methylation (DNAm) profiling was conducted in whole blood samples through Reduced Representation Bisulfite Sequencing method. Generalized estimating equation was applied to regress the DNAm of each CpG with HGS. The Genomic Regions Enrichment of Annotations Tool was used to perform enrichment analysis. Differentially methylated regions (DMRs) were detected using comb-p. Causal inference was performed using Inference about Causation through Examination of Familial Confounding method. Finally, we validated candidate CpGs in community residents. Results: We identified 25 CpGs reaching genome-wide significance level. These CpGs located in 9 genes, especially FBLN1, RXRA, and ABHD14B. Many enriched terms highlighted calcium channels, neuromuscular junctions, and skeletal muscle organ development. We identified 21 DMRs of HGS, with several DMRs within FBLN1, SLC30A8, CST3, and SOCS3. Causal inference indicated that the DNAm of 16 top CpGs within FBLN1, RXRA, ABHD14B, MFSD6, and TYW1B might influence HGS, while HGS influenced DNAm at two CpGs within FBLN1 and RXRA. In validation analysis, methylation levels of six CpGs mapped to FLBN1 and one CpG mapped to ABHD14B were negatively associated with HGS weakness in community population. Conclusion: Our study identified multiple DNAm variants potentially related to HGS, especially CpGs within FBLN1 and ABHD14B. These findings provide new clues to the epigenetic modification underlying muscle strength decline.
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Affiliation(s)
- Jia Luo
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Jingxian Li
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Haiping Duan
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong, China
- Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Chunsheng Xu
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong, China
- Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Xiaocao Tian
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong, China
- Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
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6
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Livshits G, Kalinkovich A. Restoration of epigenetic impairment in the skeletal muscle and chronic inflammation resolution as a therapeutic approach in sarcopenia. Ageing Res Rev 2024; 96:102267. [PMID: 38462046 DOI: 10.1016/j.arr.2024.102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Sarcopenia is an age-associated loss of skeletal muscle mass, strength, and function, accompanied by severe adverse health outcomes, such as falls and fractures, functional decline, high health costs, and mortality. Hence, its prevention and treatment have become increasingly urgent. However, despite the wide prevalence and extensive research on sarcopenia, no FDA-approved disease-modifying drugs exist. This is probably due to a poor understanding of the mechanisms underlying its pathophysiology. Recent evidence demonstrate that sarcopenia development is characterized by two key elements: (i) epigenetic dysregulation of multiple molecular pathways associated with sarcopenia pathogenesis, such as protein remodeling, insulin resistance, mitochondria impairments, and (ii) the creation of a systemic, chronic, low-grade inflammation (SCLGI). In this review, we focus on the epigenetic regulators that have been implicated in skeletal muscle deterioration, their individual roles, and possible crosstalk. We also discuss epidrugs, which are the pharmaceuticals with the potential to restore the epigenetic mechanisms deregulated in sarcopenia. In addition, we discuss the mechanisms underlying failed SCLGI resolution in sarcopenia and the potential application of pro-resolving molecules, comprising specialized pro-resolving mediators (SPMs) and their stable mimetics and receptor agonists. These compounds, as well as epidrugs, reveal beneficial effects in preclinical studies related to sarcopenia. Based on these encouraging observations, we propose the combination of epidrugs with SCLI-resolving agents as a new therapeutic approach for sarcopenia that can effectively attenuate of its manifestations.
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Affiliation(s)
- Gregory Livshits
- Department of Morphological Sciences, Adelson School of Medicine, Ariel University, Ariel 4077625, Israel; Department of Anatomy and Anthropology, Faculty of Medical and Health Sciences, School of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel.
| | - Alexander Kalinkovich
- Department of Anatomy and Anthropology, Faculty of Medical and Health Sciences, School of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel
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7
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Cisterna B, Malatesta M. Molecular and Structural Alterations of Skeletal Muscle Tissue Nuclei during Aging. Int J Mol Sci 2024; 25:1833. [PMID: 38339110 PMCID: PMC10855217 DOI: 10.3390/ijms25031833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Aging is accompanied by a progressive loss of skeletal muscle mass and strength. The mechanisms underlying this phenomenon are certainly multifactorial and still remain to be fully elucidated. Changes in the cell nucleus structure and function have been considered among the possible contributing causes. This review offers an overview of the current knowledge on skeletal muscle nuclei in aging, focusing on the impairment of nuclear pathways potentially involved in age-related muscle decline. In skeletal muscle two types of cells are present: fiber cells, constituting the contractile muscle mass and containing hundreds of myonuclei, and the satellite cells, i.e., the myogenic mononuclear stem cells occurring at the periphery of the fibers and responsible for muscle growth and repair. Research conducted on different experimental models and with different methodological approaches demonstrated that both the myonuclei and satellite cell nuclei of aged skeletal muscles undergo several structural and molecular alterations, affecting chromatin organization, gene expression, and transcriptional and post-transcriptional activities. These alterations play a key role in the impairment of muscle fiber homeostasis and regeneration, thus contributing to the age-related decrease in skeletal muscle mass and function.
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Affiliation(s)
| | - Manuela Malatesta
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
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8
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Granic A, Suetterlin K, Shavlakadze T, Grounds M, Sayer A. Hallmarks of ageing in human skeletal muscle and implications for understanding the pathophysiology of sarcopenia in women and men. Clin Sci (Lond) 2023; 137:1721-1751. [PMID: 37986616 PMCID: PMC10665130 DOI: 10.1042/cs20230319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Ageing is a complex biological process associated with increased morbidity and mortality. Nine classic, interdependent hallmarks of ageing have been proposed involving genetic and biochemical pathways that collectively influence ageing trajectories and susceptibility to pathology in humans. Ageing skeletal muscle undergoes profound morphological and physiological changes associated with loss of strength, mass, and function, a condition known as sarcopenia. The aetiology of sarcopenia is complex and whilst research in this area is growing rapidly, there is a relative paucity of human studies, particularly in older women. Here, we evaluate how the nine classic hallmarks of ageing: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication contribute to skeletal muscle ageing and the pathophysiology of sarcopenia. We also highlight five novel hallmarks of particular significance to skeletal muscle ageing: inflammation, neural dysfunction, extracellular matrix dysfunction, reduced vascular perfusion, and ionic dyshomeostasis, and discuss how the classic and novel hallmarks are interconnected. Their clinical relevance and translational potential are also considered.
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Affiliation(s)
- Antoneta Granic
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, U.K
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, U.K
| | - Karen Suetterlin
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, U.K
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, U.K
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle upon Tyne, U.K
| | - Tea Shavlakadze
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, NY, U.S.A
| | - Miranda D. Grounds
- Department of Anatomy, Physiology and Human Biology, School of Human Sciences, the University of Western Australia, Perth, WA 6009, Australia
| | - Avan A. Sayer
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, U.K
- NIHR Newcastle Biomedical Research Centre, Newcastle University and Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, U.K
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Kmiołek T, Filipowicz G, Bogucka D, Wajda A, Ejma-Multański A, Stypińska B, Modzelewska E, Kaliberda Y, Radkowski M, Targowski T, Wrona J, Paradowska-Gorycka A. Aging and the impact of global DNA methylation, telomere shortening, and total oxidative status on sarcopenia and frailty syndrome. Immun Ageing 2023; 20:61. [PMID: 37964387 PMCID: PMC10644469 DOI: 10.1186/s12979-023-00384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023]
Abstract
Aging is a biological event that influences many organs and systems. Both sarcopenia and frailty syndrome refer to geriatric conditions with overlapping phenotypes. Many mechanisms are involved in the aging process such as DNA methylation telomeres which are susceptible to oxidative stress, and inflammations which result in telomere shortening, leading to chromosomal instability. The study aimed to determine the associations between these processes, frailty and sarcopenia syndrome. Global DNA methylation was analyzed using the ELISA method. Telomere length was analyzed using qPCR. Total oxidative status (TOS) was analyzed using a colorimetric method. The present study revealed that the main factor affecting methylation, telomeres length and level of total oxidant stress was age.
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Affiliation(s)
- Tomasz Kmiołek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland.
| | - Gabriela Filipowicz
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Diana Bogucka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Adam Ejma-Multański
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Barbara Stypińska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Ewa Modzelewska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Yana Kaliberda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
| | - Marcin Radkowski
- Department of Pathophysiology and Immunology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsaw, Poland
| | - Tomasz Targowski
- Department of Pathophysiology and Immunology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsaw, Poland
| | - Julia Wrona
- Collegium Medicum University of Jan Kochanowski, 25-317, Kielce, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637, Warsawm, Poland
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10
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Patnaik E, Madu C, Lu Y. Epigenetic Modulators as Therapeutic Agents in Cancer. Int J Mol Sci 2023; 24:14964. [PMID: 37834411 PMCID: PMC10573652 DOI: 10.3390/ijms241914964] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetics play a crucial role in gene regulation and cellular processes. Most importantly, its dysregulation can contribute to the development of tumors. Epigenetic modifications, such as DNA methylation and histone acetylation, are reversible processes that can be utilized as targets for therapeutic intervention. DNA methylation inhibitors disrupt DNA methylation patterns by inhibiting DNA methyltransferases. Such inhibitors can restore normal gene expression patterns, and they can be effective against various forms of cancer. Histone deacetylase inhibitors increase histone acetylation levels, leading to altered gene expressions. Like DNA methylation inhibitors, histone methyltransferase inhibitors target molecules involved in histone methylation. Bromodomain and extra-terminal domain inhibitors target proteins involved in gene expression. They can be effective by inhibiting oncogene expression and inducing anti-proliferative effects seen in cancer. Understanding epigenetic modifications and utilizing epigenetic inhibitors will offer new possibilities for cancer research.
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Affiliation(s)
- Eshaan Patnaik
- Department of Biology, Memphis University School, Memphis, TN 38119, USA;
| | - Chikezie Madu
- Departments of Biological Sciences, University of Memphis, Memphis, TN 38152, USA;
| | - Yi Lu
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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11
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Gim JA, Lee SY, Kim SC, Baek KW, Seo SH, Yoo JI. Relationship between DNA methylation changes and skeletal muscle mass. BMC Genom Data 2023; 24:48. [PMID: 37653517 PMCID: PMC10472633 DOI: 10.1186/s12863-023-01152-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Sarcopenia is a disease diagnosed in the elderly. In patients with sarcopenia, the muscle mass decreases every year. The occurrence of sarcopenia is greatly affected by extrinsic factors such as eating habits, exercise, and lifestyle. The present study aimed to determine the relationship between muscle mass traits and genes affected by epigenetic factors with three different adjustment methods using Korean Genome and Epidemiology Study (KOGES) data. RESULTS We conducted a demographic study and DNA methylation profiling by three studies according to the muscle mass index (MMI) adjustment methods: appendicular skeletal muscle mass divided by body weight (MMI1); appendicular skeletal muscle mass divided by square of height (MMI2); appendicular skeletal muscle mass divided by BMI (MMI3). We analyzed differentially methylated regions (DMRs) for each group. We then restricted our subjects to be top 30% (T30) and bottom 30% (B30) based on each MMI adjustment method. Additionally, we performed enrichment analysis using PathfindR to evaluate the relationship between identified DMRs and sarcopenia. A total of 895 subjects were included in the demographic study. The values of BMI, waist, and hip showed a significant difference in all three groups. Among 446 participants, 44 subjects whose DNA methylation profiles were investigated were included for DNA methylation analysis. The results of enrichment analysis showed differences between groups. In the women group through MMI1 method, only the glutamatergic synapse pathway showed a significant result. In the men group through MMI2 method, the adherens junction pathway was the most significant. Women group through MMI2 method showed similar results, having an enriched Rap1 signaling pathway. In men group through MMI3 method, the Fc epsilon RI signaling pathway was the most enriched. Particularly, the notch signaling pathway was significantly enriched in women group through MMI3 method. CONCLUSION This study presents results about which factor should be concerned first in muscle mass index (MMI) adjustment. The present study suggested that GAB2 and JPH3 in MMI1 method, HLA-DQB1 and TBCD in MMI2 method, GAB2, NDUFB4 and ISPD in MMI3 method are potential genes that can have an impact on muscle mass. It could enable future epigenetic studies of genes based on annotation results. The present study is a nationwide study in Korea with the largest size up to date that compares adjustment indices for MMI in epigenetic research.
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Affiliation(s)
- Jeong-An Gim
- Department of Medical Science Research Center, College of Medicine, Korea University, Seoul, South Korea
| | - Sang-Yeob Lee
- Department of Biomedical Research Institute, Gyeongsang National University Hospital, Jinju, South Korea
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Seung Chan Kim
- Department of Biostatistics Cooperation Center, Gyeongsang National University Hospital, Jinju, South Korea
| | - Kyung-Wan Baek
- Department of Physical Education, Gyeongsang National University, Jinju, South Korea
- Department of Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju, South Korea
| | - Sung Hyo Seo
- Department of Biomedical Research Institute, Gyeongsang National University Hospital, Jinju, South Korea
| | - Jun-Il Yoo
- Department of Orthopaedic Surgery, Inha University Hospital, 27 Inhang-ro, Jung-gu, Incheon, 22332, Republic of Korea.
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Reece AS, Bennett K, Hulse GK. Cannabis- and Substance-Related Carcinogenesis in Europe: A Lagged Causal Inferential Panel Regression Study. J Xenobiot 2023; 13:323-385. [PMID: 37489337 PMCID: PMC10366890 DOI: 10.3390/jox13030024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
Recent European data facilitate an epidemiological investigation of the controversial cannabis-cancer relationship. Of particular concern were prior findings associating high-dose cannabis use with reproductive problems and potential genetic impacts. Cancer incidence data age-standardised to the world population was obtained from the European Cancer Information System 2000-2020 and many European national cancer registries. Drug use data were obtained from the European Monitoring Centre for Drugs and Drug Addiction. Alcohol and tobacco consumption was sourced from the WHO. Median household income was taken from the World bank. Cancer rates in high-cannabis-use countries were significantly higher than elsewhere (β-estimate = 0.4165, p = 3.54 × 10-115). Eighteen of forty-one cancers (42,675 individual rates) were significantly associated with cannabis exposure at bivariate analysis. Twenty-five cancers were linked in inverse-probability-weighted multivariate models. Temporal lagging in panel models intensified these effects. In multivariable models, cannabis was a more powerful correlate of cancer incidence than tobacco or alcohol. Reproductive toxicity was evidenced by the involvement of testis, ovary, prostate and breast cancers and because some of the myeloid and lymphoid leukaemias implicated occur in childhood, indicating inherited intergenerational genotoxicity. Cannabis is a more important carcinogen than tobacco and alcohol and fulfills epidemiological qualitative and quantitative criteria for causality for 25/41 cancers. Reproductive and transgenerational effects are prominent. These findings confirm the clinical and epidemiological salience of cannabis as a major multigenerational community carcinogen.
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Affiliation(s)
- Albert Stuart Reece
- Division of Psychiatry, University of Western Australia, Crawley, WA 6009, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Kellie Bennett
- Division of Psychiatry, University of Western Australia, Crawley, WA 6009, Australia
- Faculty of Health Sciences, Curtin University, 208 Kent St., Bentley, Perth, WA 6102, Australia
| | - Gary Kenneth Hulse
- Division of Psychiatry, University of Western Australia, Crawley, WA 6009, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
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Roberts MD, Ruple BA, Godwin JS, McIntosh MC, Chen SY, Kontos NJ, Agyin-Birikorang A, Max Michel J, Plotkin DL, Mattingly ML, Brooks Mobley C, Ziegenfuss TN, Fruge AD, Kavazis AN. A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543459. [PMID: 37333259 PMCID: PMC10274632 DOI: 10.1101/2023.06.02.543459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We examined the myofibrillar (MyoF) and non-myofibrillar (non-MyoF) proteomic profiles of the vastus lateralis (VL) muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6), and MA following eight weeks of knee extensor resistance training (RT, 2d/week). Shotgun/bottom-up proteomics in skeletal muscle typically yields wide protein abundance ranges that mask lowly expressed proteins. Thus, we adopted a novel approach whereby the MyoF and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS) analysis. A total of 10,866 proteins (4,421 MyoF and 6,445 non-MyoF) were identified. Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteome were evident between age cohorts. Further, most of these age-related non-MyoF proteins (447/543) were more enriched in MA versus Y. Several biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including (but not limited to) increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. Non-MyoF proteins associated with splicing and proteostasis were further interrogated, and in agreement with bioinformatics, alternative protein variants, spliceosome-associated proteins (snRNPs), and proteolysis-related targets were more abundant in MA versus Y. RT in MA non-significantly increased VL muscle cross-sectional area (+6.5%, p=0.066) and significantly increased knee extensor strength (+8.7%, p=0.048). However, RT modestly altered the MyoF (~0.3%, 11 upregulated and two downregulated proteins) and non-MyoF proteomes (~1.0%, 56 upregulated and eight downregulated proteins, p<0.01). Further, RT did not affect predicted biological processes in either fraction. Although participant numbers were limited, these preliminary results using a novel deep proteomic approach in skeletal muscle suggest that aging and RT predominantly affects protein abundances in the non-contractile protein pool. However, the marginal proteome adaptations occurring with RT suggest either: a) this may be an aging-associated phenomenon, b) more rigorous RT may stimulate more robust effects, or c) RT, regardless of age, subtly affects skeletal muscle protein abundances in the basal state.
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Affiliation(s)
| | | | | | | | | | | | | | - J. Max Michel
- School of Kinesiology, Auburn University, Auburn, AL USA
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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15
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Gerovska D, Araúzo-Bravo MJ. Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles. Int J Mol Sci 2023; 24:ijms24032736. [PMID: 36769072 PMCID: PMC9917053 DOI: 10.3390/ijms24032736] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
To bring new extrachromosomal circular DNA (eccDNA) enrichment technologies closer to the clinic, specifically for screening, early diagnosis, and monitoring of diseases or lifestyle conditions, it is paramount to identify the differential pattern of the genic eccDNA signal between two states. Current studies using short-read sequenced purified eccDNA data are based on absolute numbers of unique eccDNAs per sample or per gene, length distributions, or standard methods for RNA-seq differential analysis. Previous analyses of RNA-seq data found significant transcriptomics difference between sedentary and active life style skeletal muscle (SkM) in young people but very few in old. The first attempt using circulomics data from SkM and blood of aged lifelong sedentary and physically active males found no difference at eccDNA level. To improve the capability of finding differences between circulomics data groups, we designed a computational method to identify Differentially Produced per Gene Circles (DPpGCs) from short-read sequenced purified eccDNA data based on the circular junction, split-read signal, of the eccDNA, and implemented it into a software tool DifCir in Matlab. We employed DifCir to find to the distinctive features of the influence of the physical activity or inactivity in the aged SkM that would have remained undetected by transcriptomics methods. We mapped the data from tissue from SkM and blood from two groups of aged lifelong sedentary and physically active males using Circle_finder and subsequent merging and filtering, to find the number and length distribution of the unique eccDNA. Next, we used DifCir to find up-DPpGCs in the SkM of the sedentary and active groups. We assessed the functional enrichment of the DPpGCs using Disease Gene Network and Gene Set Enrichment Analysis. To find genes that produce eccDNA in a group without comparison with another group, we introduced a method to find Common PpGCs (CPpGCs) and used it to find CPpGCs in the SkM of the sedentary and active group. Finally, we found the eccDNA that carries whole genes. We discovered that the eccDNA in the SkM of the sedentary group is not statistically different from that of physically active aged men in terms of number and length distribution of eccDNA. In contrast, with DifCir we found distinctive gene-associated eccDNA fingerprints. We identified statistically significant up-DPpGCs in the two groups, with the top up-DPpGCs shed by the genes AGBL4, RNF213, DNAH7, MED13, and WWTR1 in the sedentary group, and ZBTB7C, TBCD, ITPR2, and DDX11-AS1 in the active group. The up-DPpGCs in both groups carry mostly gene fragments rather than whole genes. Though the subtle transcriptomics difference, we found RYR1 to be both transcriptionally up-regulated and up-DPpGCs gene in sedentary SkM. DifCir emphasizes the high sensitivity of the circulome compared to the transcriptome to detect the molecular fingerprints of exercise in aged SkM. It allows efficient identification of gene hotspots that excise more eccDNA in a health state or disease compared to a control condition.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain
- Correspondence: (D.G.); (M.J.A.-B.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- CIBER of Frailty and Healthy Aging (CIBERfes), 28029 Madrid, Spain
- Max Planck Institute for Molecular Biomedicine, Computational Biology and Bioinformatics, Röntgenstr. 20, 48149 Münster, Germany
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
- Correspondence: (D.G.); (M.J.A.-B.)
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16
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Correia IM, da Silva Rodrigues G, Noronha NY, Watanabe LM, Luciano de Almeida M, Sobrinho ACDS, Nonino CB, Bueno Júnior CR. Older postmenopausal women with lower lean mass have hypermethylated sites in the PI3K-Akt pathway. Front Physiol 2023; 14:1150821. [PMID: 37123284 PMCID: PMC10143498 DOI: 10.3389/fphys.2023.1150821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction: The decrease in lean mass is directly related to the loss of independence, muscle strength, and worse quality of life over the years. Although the genetic determinants of muscle mass were well recognized, recent literature has been uncovering new epigenetic factors affecting the state of muscular tissue. This study aimed to verify differences in the DNA methylation profile among Brazilian postmenopausal women aged 50-70 years according to the lean mass evaluation. Methods: A cross-sectional study comprised 40 women aged 50-70 years. After K-means cluster analysis the 40 participants were divided into two groups, the Lower Lean Mass group with 20 participants (61.1 ± 4.6 years) and the Higher Lean Mass group with 20 participants (60.7 ± 3.2 years). Lean mass was measured by dual-energy X-ray emission densitometry (DEXA). The participants' DNA was extracted using the Salting Out technique and subsequently, the Illumina 850k EPIC Infinium Methylation BeadChip was performed to obtain methylation data. Results: We obtained 1,913 differentially methylated sites (p ≤ 0.005 of β > 5% and β < -5%) in a total of 979 genes between groups (p ≤ 0.005; -5% > β > 5%). In addition, the PI3K-Akt pathway had the greatest power of significance with an FDR of 4.6 × 10-3. Conclusion: Our results demonstrate a differentiation between specific sites of different genes, which have essential functions in body composition and energy metabolism, supporting future studies that aim to relate lean mass with epigenetics.
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Affiliation(s)
- Igor Massari Correia
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Guilherme da Silva Rodrigues
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- *Correspondence: Guilherme da Silva Rodrigues,
| | - Natália Yumi Noronha
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Lígia Moriguchi Watanabe
- Department of Health Sciences, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | | | - Carla Barbosa Nonino
- College of Nursing of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Carlos Roberto Bueno Júnior
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- College of Nursing of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
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Gorski PP, Raastad T, Ullrich M, Turner DC, Hallén J, Savari SI, Nilsen TS, Sharples AP. Aerobic exercise training resets the human skeletal muscle methylome 10 years after breast cancer treatment and survival. FASEB J 2023; 37:e22720. [PMID: 36542473 DOI: 10.1096/fj.202201510rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Cancer survivors suffer impairments in skeletal muscle in terms of reduced mass and function. Interestingly, human skeletal muscle possesses an epigenetic memory of earlier stimuli, such as exercise. Long-term retention of epigenetic changes in skeletal muscle following cancer survival and/or exercise training has not yet been studied. We, therefore, investigated genome-wide DNA methylation (methylome) in skeletal muscle following a 5-month, 3/week aerobic-training intervention in breast cancer survivors 10-14 years after diagnosis and treatment. These results were compared to breast cancer survivors who remained untrained and to age-matched controls with no history of cancer, who undertook the same training intervention. Skeletal muscle biopsies were obtained from 23 females before(pre) and after(post) the 5-month training period. InfiniumEPIC 850K DNA methylation arrays and RT-PCR for gene expression were performed. The breast cancer survivors displayed a significant retention of increased DNA methylation (i.e., hypermethylation) at a larger number of differentially methylated positions (DMPs) compared with healthy age-matched controls pre training. Training in cancer survivors led to an exaggerated number of DMPs with a hypermethylated signature occurring at non-regulatory regions compared with training in healthy age-matched controls. However, the opposite occurred in important gene regulatory regions, where training in cancer survivors elicited a considerable reduction in methylation (i.e., hypomethylation) in 99% of the DMPs located in CpG islands within promoter regions. Importantly, training was able to reverse the hypermethylation identified in cancer survivors back toward a hypomethylated signature that was observed pre training in healthy age-matched controls at 300 (out of 881) of these island/promoter-associated CpGs. Pathway enrichment analysis identified training in cancer survivors evoked a predominantly hypomethylated signature in pathways associated with cell cycle, DNA replication/repair, transcription, translation, mTOR signaling, and the proteosome. Differentially methylated region (DMR) analysis also identified genes: BAG1, BTG2, CHP1, KIFC1, MKL2, MTR, PEX11B, POLD2, S100A6, SNORD104, and SPG7 as hypermethylated in breast cancer survivors, with training reversing these CpG island/promoter-associated DMRs toward a hypomethylated signature. Training also elicited a largely different epigenetic response in healthy individuals than that observed in cancer survivors, with very few overlapping changes. Only one gene, SIRT2, was identified as having altered methylation in cancer survivors at baseline and after training in both the cancer survivors and healthy controls. Overall, human skeletal muscle may retain a hypermethylated signature as long as 10-14 years after breast cancer treatment/survival. Five months of aerobic training reset the skeletal muscle methylome toward signatures identified in healthy age-matched individuals in gene regulatory regions.
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Affiliation(s)
- Piotr P Gorski
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
| | - Truls Raastad
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
| | - Max Ullrich
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
| | - Daniel C Turner
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
| | - Jostein Hallén
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
| | - Sebastian Imre Savari
- Department of Cardiology, Oslo University Hospital, Oslo, Norway.,Precision Health Center for Optimized Cardiac Care, Oslo University Hospital, Oslo, Norway
| | - Tormod S Nilsen
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
| | - Adam P Sharples
- Institute for Physical Performance (IFP), Norwegian School of Sport Sciences, Oslo, Norway
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Ageing Skeletal Muscle: The Ubiquitous Muscle Stem Cell. Subcell Biochem 2023; 102:365-377. [PMID: 36600140 DOI: 10.1007/978-3-031-21410-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In 1999, in a review by Beardsley, the potential of adult stem cells, in repair and regeneration was heralded (Beardsley Sci Am 281:30-31, 1999). Since then, the field of regenerative medicine has grown exponentially, with the capability of restoring or regenerating the function of damaged, diseased or aged human tissues being an underpinning motivation. If successful, stem cell therapies offer the potential to treat, for example degenerative diseases. In the subsequent 20 years, extensive progress has been made in the arena of adult stem cells (for a recent review see (Zakrzewski et al. Stem Cell Res Ther 10:68, 2019)). Prior to the growth of the adult stem cell research arena, much focus had been placed on the potential of embryonic stem cells (ESCs). The first research revealing the potential of these cells was published in 1981, when scientists reported the ability of cultured stem cells from murine embryos, to not only self-renew, but to also become all cells of the three germ layers of the developing embryo (Evans and Kaufman Nature 292:154-156, 1981), (Martin Proc Natl Acad Sci U S A 78:7634-7638, 1981). It took almost 20 years, following these discoveries, for this technology to translate to human ESCs, using donated human embryos. In 1998, Thomson et al. reported the creation of the first human embryonic cell line (Thomson et al. Science 282:1145-1147, 1998). However, research utilising human ESCs was hampered by ethical and religious constraints and indeed in 2001 George W. Bush restricted US research funding to human ESCs, which had already been banked. The contentious nature of this arena perhaps facilitated the use of and the research potential for adult stem cells. It is beyond the scope of this review to focus on ESCs, although their potential for enhancing our understanding of human development is huge (for a recent review see (Cyranoski Nature 555:428-430, 2018)). Rather, although ESCs and their epigenetic regulation will be introduced for background understanding, the focus will be on stem cells more generally, the role of epigenetics in stem cell fate, skeletal muscle, skeletal muscle stem cells, the impact of ageing on muscle wasting and the mechanisms underpinning loss, with a focus on epigenetic adaptation.
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He L, Liang X, Wang Q, Yang C, Li Y, Liao L, Zhu Z, Wang Y. Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp. Immun Ageing 2022; 19:28. [PMID: 35655223 PMCID: PMC9161582 DOI: 10.1186/s12979-022-00285-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
Background Grass carp are an important farmed fish in China that are infected by many pathogens, especially grass carp reovirus (GCRV). Notably, grass carp showed age-dependent susceptibility to GCRV; that is, grass carp not older than one year were sensitive to GCRV, while those over three years old were resistant to this virus. However, the underlying mechanism remains unclear. Herein, whole genome-wide DNA methylation and gene expression variations between susceptible five-month-old (FMO) and resistant three-year-old (TYO) grass carp were investigated aiming to uncover potential epigenetic mechanisms. Results Colorimetric quantification revealed that the global methylation level in TYO fish was higher than that in FMO fish. Whole-genome bisulfite sequencing (WGBS) of the two groups revealed 6214 differentially methylated regions (DMRs) and 4052 differentially methylated genes (DMGs), with most DMRs and DMGs showing hypermethylation patterns in TYO fish. Correlation analysis revealed that DNA hypomethylation in promoter regions and DNA hypermethylation in gene body regions were associated with gene expression. Enrichment analysis revealed that promoter hypo-DMGs in TYO fish were significantly enriched in typical immune response pathways, whereas gene body hyper-DMGs in TYO fish were significantly enriched in terms related to RNA transcription, biosynthesis, and energy production. RNA-seq analysis of the corresponding samples indicated that most of the genes in the above terms were upregulated in TYO fish. Moreover, gene function analysis revealed that the two genes involved in energy metabolism displayed antiviral effects. Conclusions Collectively, these results revealed genome-wide variations in DNA methylation between grass carp of different ages. DNA methylation and gene expression variations in genes involved in immune response, biosynthesis, and energy production may contribute to age-dependent susceptibility to GCRV in grass carp. Our results provide important information for disease-resistant breeding programs for grass carp and may also benefit research on age-dependent diseases in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-022-00285-w.
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Aging, Skeletal Muscle, and Epigenetics. Plast Reconstr Surg 2022; 150:27S-33S. [DOI: 10.1097/prs.0000000000009670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Romero MA, Mumford PW, Roberson PA, Osburn SC, Young KC, Sedivy JM, Roberts MD. Translational Significance of the LINE-1 Jumping Gene in Skeletal Muscle. Exerc Sport Sci Rev 2022; 50:185-193. [PMID: 35749745 PMCID: PMC9651911 DOI: 10.1249/jes.0000000000000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Retrotransposons are gene segments that proliferate in the genome, and the Long INterspersed Element 1 (LINE-1 or L1) retrotransposon is active in humans. Although older mammals show enhanced skeletal muscle L1 expression, exercise generally reverses this trend. We hypothesize skeletal muscle L1 expression influences muscle physiology, and additional innovative investigations are needed to confirm this hypothesis.
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Affiliation(s)
- Matthew A. Romero
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California USA
| | - Petey W. Mumford
- Department of Exercise Science, Lindenwood University, St. Charles, Missouri USA
| | - Paul A. Roberson
- Department of Cellular and Molecular Physiology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania USA
| | | | - Kaelin C. Young
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center on the Biology of Aging, Brown University, Providence, Rhode Island, USA
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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23
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Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions. Genes (Basel) 2022; 13:genes13071151. [PMID: 35885934 PMCID: PMC9319582 DOI: 10.3390/genes13071151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Rainbow trout, Oncorhynchus mykiss, is an important cool, freshwater aquaculture species used as a model for biological research. However, its genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke muscle atrophy in rainbow trout. We described DNA methylation and its associated gene expression in atrophying muscle by comparing gravid, diploid females to sterile, triploid females. Methyl Mini-seq and RNA-Seq were simultaneously used to characterize genome-wide DNA methylation and its association with gene expression in rainbow trout muscle. Genome-wide enrichment in the number of CpGs, accompanied by depleted methylation levels, was noticed around the gene transcription start site (TSS). Hypermethylation of CpG sites within ±1 kb on both sides of TSS (promoter and gene body) was weakly/moderately associated with reduced gene expression. Conversely, hypermethylation of the CpG sites in downstream regions of the gene body +2 to +10 kb was weakly associated with increased gene expression. Unlike mammalian genomes, rainbow trout gene promotors are poor in CpG islands, at <1% compared to 60%. No signs of genome-wide, differentially methylated (DM) CpGs were observed due to the polyploidy effect; only 1206 CpGs (0.03%) were differentially methylated, and these were primarily associated with muscle atrophy. Twenty-eight genes exhibited differential gene expression consistent with methylation levels of 31 DM CpGs. These 31 DM CpGs represent potential epigenetic markers of muscle atrophy in rainbow trout. The DM CpG-harboring genes are involved in apoptosis, epigenetic regulation, autophagy, collagen metabolism, cell membrane functions, and Homeobox proteins. Our study also identified genes explaining higher water content and modulated glycolysis previously shown as characteristic biochemical signs of rainbow trout muscle atrophy associated with sexual maturation. This study characterized DNA methylation in the rainbow trout genome and its correlation with gene expression. This work also identified novel epigenetic markers associated with muscle atrophy in fish/lower vertebrates.
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Wagner S, Manickam R, Brotto M, Tipparaju SM. NAD + centric mechanisms and molecular determinants of skeletal muscle disease and aging. Mol Cell Biochem 2022; 477:1829-1848. [PMID: 35334034 PMCID: PMC10065019 DOI: 10.1007/s11010-022-04408-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/03/2022] [Indexed: 12/20/2022]
Abstract
The nicotinamide adenine dinucleotide (NAD+) is an essential redox cofactor, involved in various physiological and molecular processes, including energy metabolism, epigenetics, aging, and metabolic diseases. NAD+ repletion ameliorates muscular dystrophy and improves the mitochondrial and muscle stem cell function and thereby increase lifespan in mice. Accordingly, NAD+ is considered as an anti-oxidant and anti-aging molecule. NAD+ plays a central role in energy metabolism and the energy produced is used for movements, thermoregulation, and defense against foreign bodies. The dietary precursors of NAD+ synthesis is targeted to improve NAD+ biosynthesis; however, studies have revealed conflicting results regarding skeletal muscle-specific effects. Recent advances in the activation of nicotinamide phosphoribosyltransferase in the NAD+ salvage pathway and supplementation of NAD+ precursors have led to beneficial effects in skeletal muscle pathophysiology and function during aging and associated metabolic diseases. NAD+ is also involved in the epigenetic regulation and post-translational modifications of proteins that are involved in various cellular processes to maintain tissue homeostasis. This review provides detailed insights into the roles of NAD+ along with molecular mechanisms during aging and disease conditions, such as the impacts of age-related NAD+ deficiencies on NAD+-dependent enzymes, including poly (ADP-ribose) polymerase (PARPs), CD38, and sirtuins within skeletal muscle, and the most recent studies on the potential of nutritional supplementation and distinct modes of exercise to replenish the NAD+ pool.
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Affiliation(s)
- Sabrina Wagner
- Department of Pharmaceutical Sciences, USF Health Taneja College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, MDC 030, Tampa, FL, 33612, USA
| | - Ravikumar Manickam
- Department of Pharmaceutical Sciences, USF Health Taneja College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, MDC 030, Tampa, FL, 33612, USA
| | - Marco Brotto
- Bone-Muscle Research Center, College of Nursing & Health Innovation, University of Texas-Arlington (UTA), Arlington, TX, USA
| | - Srinivas M Tipparaju
- Department of Pharmaceutical Sciences, USF Health Taneja College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, MDC 030, Tampa, FL, 33612, USA.
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25
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Van Dyck L, Güiza F, Derese I, Pauwels L, Casaer MP, Hermans G, Wouters PJ, Van den Berghe G, Vanhorebeek I. DNA methylation alterations in muscle of critically ill patients. J Cachexia Sarcopenia Muscle 2022; 13:1731-1740. [PMID: 35274472 PMCID: PMC9178166 DOI: 10.1002/jcsm.12970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/15/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Intensive care unit (ICU)-acquired weakness can persist beyond ICU stay and has been associated with long-term functional impairment of ICU survivors. Recently, DNA methylation alterations were found in the blood of ICU patients, partially explaining long-term developmental impairment of critically ill children. As illness-induced aberrant DNA methylation theoretically could also be involved in long-term weakness, we investigated whether the DNA methylation signature in muscle of adult critically ill patients differs from that in muscle of healthy controls. METHODS Genome-wide methylation was determined (Infinium® HumanMethylationEPIC BeadChips) in DNA extracted from skeletal muscle biopsies that had been collected on Day 8 ± 1 in ICU from 172 EPaNIC-trial patients [66% male sex, median age 62.7 years, median body mass index (BMI) 25.9 kg/m2 ] and 20 matched healthy controls (70% male sex, median age 58.0 years, median BMI 24.4 kg/m2 ). Methylation status of individual cytosine-phosphate-guanine (CpG) sites of patients and controls was compared with F-tests, using the Benjamini-Hochberg false discovery rate to correct for multiple comparisons. Differential methylation of DNA regions was assessed with bump hunting, with 1000 permutations assessing uncertainty, expressed as family-wise error rate. Gene expression was investigated for 10 representative affected genes. RESULTS In DNA from ICU patients, 565 CpG sites, associated with 400 unique genes, were differentially methylated as compared with controls (average difference 3.2 ± 0.1% ranging up to 16.9%, P < 0.00005). Many of the associated genes appeared highly relevant for muscle structure and function/weakness, including genes involved in myogenesis, muscle regeneration, nerve/muscle membrane excitability, muscle denervation/re-innervation, axon guidance/myelination/degeneration/regeneration, synapse function, ion channelling with especially calcium signalling, metabolism (glucose, protein, and fat), insulin signalling, neuroendocrine hormone regulation, mitochondrial function, autophagy, apoptosis, oxidative stress, Wnt signalling, transcription regulation, muscle fat infiltration during regeneration, and fibrosis. In patients as compared with controls, we also identified two hypomethylated regions, spanning 18 and 3 CpG sites in the promoters of the HIC1 and NADK2 genes, respectively (average differences 5.8 ± 0.01% and 12.1 ± 0.04%, family-wise error rate <0.05). HIC1 and NADK2 play important roles in muscle regeneration and postsynaptic acetylcholine receptors and in mitochondrial processes, respectively. Nine of 10 investigated genes containing DNA methylation alterations were differentially expressed in patients as compared with controls (P ≤ 0.03). CONCLUSIONS Critically ill patients present with a different DNA methylation signature in skeletal muscle as compared with healthy controls, which in theory could provide a biological basis for long-term persistence of weakness in ICU survivors. TRIAL REGISTRATION ClinicalTrials.gov: NCT00512122, registered on 31 July 2007.
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Affiliation(s)
- Lisa Van Dyck
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Fabian Güiza
- Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Inge Derese
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Lies Pauwels
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Michaël P Casaer
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Greet Hermans
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Medical Intensive Care Unit, Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Pieter J Wouters
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Greet Van den Berghe
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Clinical Division of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Ilse Vanhorebeek
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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26
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Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep. Animals (Basel) 2022; 12:ani12111399. [PMID: 35681863 PMCID: PMC9179529 DOI: 10.3390/ani12111399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary DNA methylation is an important epigenetic modification and plays an important role in the regulation of gene expression. The study of DNA methylation will help to explore the effects of epigenetic modifications, other than DNA sequence variation, on biological phenotypes and physiological functions, promoting the revolution of livestock selection and breeding practices. DairyMeade sheep (thin-tailed) and Mongolian sheep (fat-tailed) have large differences in their dairy and meat production performances, as well as their tail phenotype, thus providing us with good materials for genomic DNA methylation studies. The below results provided a genome-wide DNA methylation landscape of muscle and tail-fat tissues between DairyMeade sheep and Mongolian sheep and a series of differentiated methylation regions (DMRs) in which CAMK2D may play a crucial role in fat metabolism and meat quality traits. These results may help us to understand how DNA methylation affects the economic traits of domestic animals like sheep. Abstract This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement.
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27
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Antoun E, Garratt ES, Taddei A, Burton MA, Barton SJ, Titcombe P, Westbury LD, Baczynska A, Migliavacca E, Feige JN, Sydall HE, Dennison E, Dodds R, Roberts HC, Richardson P, Sayer AA, Shaw S, Cooper C, Holbrook JD, Patel HP, Godfrey KM, Lillycrop KA. Epigenome-wide association study of sarcopenia: findings from the Hertfordshire Sarcopenia Study (HSS). J Cachexia Sarcopenia Muscle 2022; 13:240-253. [PMID: 34862756 PMCID: PMC8818655 DOI: 10.1002/jcsm.12876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/15/2021] [Accepted: 10/29/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Sarcopenia is the age-related loss of muscle mass, strength, and function. Epigenetic processes such as DNA methylation, which integrate both genetic and environmental exposures, have been suggested to contribute to the development of sarcopenia. This study aimed to determine whether differences in the muscle methylome are associated with sarcopenia and its component measures: grip strength, appendicular lean mass index (ALMi), and gait speed. METHODS Using the Infinium Human MethylationEPIC BeadChip, we measured DNA methylation in vastus lateralis muscle biopsies of 83 male participants (12 with sarcopenia) with a mean (standard deviation) age of 75.7 (3.6) years from the Hertfordshire Sarcopenia Study (HSS) and Hertfordshire Sarcopenia Study extension (HSSe) and examined associations with sarcopenia and its components. Pathway, histone mark, and transcription factor enrichment of the differentially methylated CpGs (dmCpGs) were determined, and sodium bisulfite pyrosequencing was used to validate the sarcopenia-associated dmCpGs. Human primary myoblasts (n = 6) isolated from vastus lateralis muscle biopsies from male individuals from HSSe were treated with the EZH2 inhibitor GSK343 to assess how perturbations in epigenetic processes may impact myoblast differentiation and fusion, measured by PAX7 and MYHC immunocytochemistry, and mitochondrial bioenergetics determined using the Seahorse XF96. RESULTS Sarcopenia was associated with differential methylation at 176 dmCpGs (false discovery rate ≤ 0.05) and 141 differentially methylated regions (Stouffer ≤ 0.05). The sarcopenia-associated dmCpGs were enriched in genes associated with myotube fusion (P = 1.40E-03), oxidative phosphorylation (P = 2.78E-02), and voltage-gated calcium channels (P = 1.59E-04). ALMi was associated with 71 dmCpGs, grip strength with 49 dmCpGs, and gait speed with 23 dmCpGs (false discovery rate ≤ 0.05). There was significant overlap between the dmCpGs associated with sarcopenia and ALMi (P = 3.4E-35), sarcopenia and gait speed (P = 4.78E-03), and sarcopenia and grip strength (P = 7.55E-06). There was also an over-representation of the sarcopenia, ALMi, grip strength, and gait speed-associated dmCpGs with sites of H3K27 trimethylation (all P ≤ 0.05) and amongst EZH2 target genes (all P ≤ 0.05). Furthermore, treatment of human primary myoblasts with the EZH2 inhibitor GSK343 inhibitor led to an increase in PAX7 expression (P ≤ 0.05), decreased myotube fusion (P = 0.043), and an increase in ATP production (P = 0.008), with alterations in the DNA methylation of genes involved in oxidative phosphorylation and myogenesis. CONCLUSIONS These findings show that differences in the muscle methylome are associated with sarcopenia and individual measures of muscle mass, strength, and function in older individuals. This suggests that changes in the epigenetic regulation of genes may contribute to impaired muscle function in later life.
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Affiliation(s)
- Elie Antoun
- Human Development and Health Academic Unit, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Emma S. Garratt
- Human Development and Health Academic Unit, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton & University Hospital Southampton NHS Foundation TrustSouthamptonUK
| | | | - Mark A. Burton
- Human Development and Health Academic Unit, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Sheila J. Barton
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Phil Titcombe
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Leo D. Westbury
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Alicia Baczynska
- Academic Geriatric Medicine, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | | | | | - Holly E. Sydall
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Elaine Dennison
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Richard Dodds
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NIHR Newcastle Biomedical Research CentreNewcastle University and Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Helen C. Roberts
- NIHR Southampton Biomedical Research CentreUniversity of Southampton & University Hospital Southampton NHS Foundation TrustSouthamptonUK
- Academic Geriatric Medicine, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | | | - Avan A. Sayer
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NIHR Newcastle Biomedical Research CentreNewcastle University and Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Sarah Shaw
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Cyrus Cooper
- NIHR Southampton Biomedical Research CentreUniversity of Southampton & University Hospital Southampton NHS Foundation TrustSouthamptonUK
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | | | - Harnish P. Patel
- NIHR Southampton Biomedical Research CentreUniversity of Southampton & University Hospital Southampton NHS Foundation TrustSouthamptonUK
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
- Academic Geriatric Medicine, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Keith M. Godfrey
- Human Development and Health Academic Unit, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton & University Hospital Southampton NHS Foundation TrustSouthamptonUK
- MRC Lifecourse Epidemiology CentreUniversity of SouthamptonSouthamptonUK
| | - Karen A. Lillycrop
- Human Development and Health Academic Unit, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
- Biological SciencesUniversity of SouthamptonSouthamptonUK
- NIHR Southampton Biomedical Research CentreUniversity of Southampton & University Hospital Southampton NHS Foundation TrustSouthamptonUK
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28
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Cai Z, Liu D, Yang Y, Xie W, He M, Yu D, Wu Y, Wang X, Xiao W, Li Y. The role and therapeutic potential of stem cells in skeletal muscle in sarcopenia. Stem Cell Res Ther 2022; 13:28. [PMID: 35073997 PMCID: PMC8785537 DOI: 10.1186/s13287-022-02706-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/05/2022] [Indexed: 01/23/2023] Open
Abstract
Sarcopenia is a common age-related skeletal muscle disorder featuring the loss of muscle mass and function. In regard to tissue repair in the human body, scientists always consider the use of stem cells. In skeletal muscle, satellite cells (SCs) are adult stem cells that maintain tissue homeostasis and repair damaged regions after injury to preserve skeletal muscle integrity. Muscle-derived stem cells (MDSCs) and SCs are the two most commonly studied stem cell populations from skeletal muscle. To date, considerable progress has been achieved in understanding the complex associations between stem cells in muscle and the occurrence and treatment of sarcopenia. In this review, we first give brief introductions to sarcopenia, SCs and MDSCs. Then, we attempt to untangle the differences and connections between these two types of stem cells and further elaborate on the interactions between sarcopenia and stem cells. Finally, our perspectives on the possible application of stem cells for the treatment of sarcopenia in future are presented. Several studies emerging in recent years have shown that changes in the number and function of stem cells can trigger sarcopenia, which in turn leads to adverse influences on stem cells because of the altered internal environment in muscle. A better understanding of the role of stem cells in muscle, especially SCs and MDSCs, in sarcopenia will facilitate the realization of novel therapy approaches based on stem cells to combat sarcopenia.
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Affiliation(s)
- Zijun Cai
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Di Liu
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yuntao Yang
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Wenqing Xie
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Miao He
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Dengjie Yu
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yuxiang Wu
- School of Kinesiology, Jianghan University, Wuhan, 430056, China
| | - Xiuhua Wang
- Xiang Ya Nursing School, Central South University, Changsha, 410008, Hunan, China
| | - Wenfeng Xiao
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yusheng Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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29
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He L. Editorial: Epigenetic Clock: A Novel Tool for Nutrition Studies of Healthy Ageing. J Nutr Health Aging 2022; 26:316-317. [PMID: 35450985 DOI: 10.1007/s12603-022-1773-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L He
- Lingxiao He, School of Public Health, Xiamen University, Xiang'an South Road, 361104 Xiamen, China
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30
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Dzobo K. The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery. COMPREHENSIVE PHARMACOLOGY 2022. [PMCID: PMC8016209 DOI: 10.1016/b978-0-12-820472-6.00041-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Emerging threats to human health require a concerted effort in search of both preventive and treatment strategies, placing natural products at the center of efforts to obtain new therapies and reduce disease spread and associated mortality. The therapeutic value of compounds found in plants has been known for ages, resulting in their utilization in homes and in clinics for the treatment of many ailments ranging from common headache to serious conditions such as wounds. Despite the advancement observed in the world, plant based medicines are still being used to treat many pathological conditions or are used as alternatives to modern medicines. In most cases, these natural products or plant-based medicines are used in an un-purified state as extracts. A lot of research is underway to identify and purify the active compounds responsible for the healing process. Some of the current drugs used in clinics have their origins as natural products or came from plant extracts. In addition, several synthetic analogues are natural product-based or plant-based. With the emergence of novel infectious agents such as the SARS-CoV-2 in addition to already burdensome diseases such as diabetes, cancer, tuberculosis and HIV/AIDS, there is need to come up with new drugs that can cure these conditions. Natural products offer an opportunity to discover new compounds that can be converted into drugs given their chemical structure diversity. Advances in analytical processes make drug discovery a multi-dimensional process involving computational designing and testing and eventual laboratory screening of potential drug candidates. Lead compounds will then be evaluated for safety, pharmacokinetics and efficacy. New technologies including Artificial Intelligence, better organ and tissue models such as organoids allow virtual screening, automation and high-throughput screening to be part of drug discovery. The use of bioinformatics and computation means that drug discovery can be a fast and efficient process and enable the use of natural products structures to obtain novel drugs. The removal of potential bottlenecks resulting in minimal false positive leads in drug development has enabled an efficient system of drug discovery. This review describes the biosynthesis and screening of natural products during drug discovery as well as methods used in studying natural products.
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31
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Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
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Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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32
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Ruple BA, Godwin JS, Mesquita PHC, Osburn SC, Vann CG, Lamb DA, Sexton CL, Candow DG, Forbes SC, Frugé AD, Kavazis AN, Young KC, Seaborne RA, Sharples AP, Roberts MD. Resistance training rejuvenates the mitochondrial methylome in aged human skeletal muscle. FASEB J 2021; 35:e21864. [PMID: 34423880 DOI: 10.1096/fj.202100873rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/11/2022]
Abstract
Resistance training (RT) dynamically alters the skeletal muscle nuclear DNA methylome. However, no study has examined if RT affects the mitochondrial DNA (mtDNA) methylome. Herein, ten older, Caucasian untrained males (65 ± 7 y.o.) performed six weeks of full-body RT (twice weekly). Body composition and knee extensor torque were assessed prior to and 72 h following the last RT session. Vastus lateralis (VL) biopsies were also obtained. VL DNA was subjected to reduced representation bisulfite sequencing providing excellent coverage across the ~16-kilobase mtDNA methylome (254 CpG sites). Biochemical assays were also performed, and older male data were compared to younger trained males (22 ± 2 y.o., n = 7, n = 6 Caucasian & n = 1 African American). RT increased whole-body lean tissue mass (p = .017), VL thickness (p = .012), and knee extensor torque (p = .029) in older males. RT also affected the mtDNA methylome, as 63% (159/254) of the CpG sites demonstrated reduced methylation (p < .05). Several mtDNA sites presented a more "youthful" signature in older males after RT in comparison to younger males. The 1.12 kilobase mtDNA D-loop/control region, which regulates replication and transcription, possessed enriched hypomethylation in older males following RT. Enhanced expression of mitochondrial H- and L-strand genes and complex III/IV protein levels were also observed (p < .05). While limited to a shorter-term intervention, this is the first evidence showing that RT alters the mtDNA methylome in skeletal muscle. Observed methylome alterations may enhance mitochondrial transcription, and RT evokes mitochondrial methylome profiles to mimic younger men. The significance of these findings relative to broader RT-induced epigenetic changes needs to be elucidated.
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Affiliation(s)
- Bradley A Ruple
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | - Joshua S Godwin
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | | | - Shelby C Osburn
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | | | - Donald A Lamb
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, Alabama, USA
| | - Casey L Sexton
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | - Darren G Candow
- Faculty of Kinesiology and Health Studies, University of Regina, Regina, Saskatchewan, Canada
| | - Scott C Forbes
- Faculty of Education, Department of Physical Education Studies, Brandon University, Brandon, Manitoba, Canada
| | - Andrew D Frugé
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, Alabama, USA
| | | | - Kaelin C Young
- School of Kinesiology, Auburn University, Auburn, Alabama, USA.,Edward Via College of Osteopathic Medicine, Auburn, Alabama, USA
| | - Robert A Seaborne
- Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences, Olso, Norway
| | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, USA.,Edward Via College of Osteopathic Medicine, Auburn, Alabama, USA
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Voisin S, Jacques M, Landen S, Harvey NR, Haupt LM, Griffiths LR, Gancheva S, Ouni M, Jähnert M, Ashton KJ, Coffey VG, Thompson JM, Doering TM, Gabory A, Junien C, Caiazzo R, Verkindt H, Raverdy V, Pattou F, Froguel P, Craig JM, Blocquiaux S, Thomis M, Sharples AP, Schürmann A, Roden M, Horvath S, Eynon N. Meta-analysis of genome-wide DNA methylation and integrative omics of age in human skeletal muscle. J Cachexia Sarcopenia Muscle 2021; 12:1064-1078. [PMID: 34196129 PMCID: PMC8350206 DOI: 10.1002/jcsm.12741] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/19/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Knowledge of age-related DNA methylation changes in skeletal muscle is limited, yet this tissue is severely affected by ageing in humans. METHODS We conducted a large-scale epigenome-wide association study meta-analysis of age in human skeletal muscle from 10 studies (total n = 908 muscle methylomes from men and women aged 18-89 years old). We explored the genomic context of age-related DNA methylation changes in chromatin states, CpG islands, and transcription factor binding sites and performed gene set enrichment analysis. We then integrated the DNA methylation data with known transcriptomic and proteomic age-related changes in skeletal muscle. Finally, we updated our recently developed muscle epigenetic clock (https://bioconductor.org/packages/release/bioc/html/MEAT.html). RESULTS We identified 6710 differentially methylated regions at a stringent false discovery rate <0.005, spanning 6367 unique genes, many of which related to skeletal muscle structure and development. We found a strong increase in DNA methylation at Polycomb target genes and bivalent chromatin domains and a concomitant decrease in DNA methylation at enhancers. Most differentially methylated genes were not altered at the mRNA or protein level, but they were nonetheless strongly enriched for genes showing age-related differential mRNA and protein expression. After adding a substantial number of samples from five datasets (+371), the updated version of the muscle clock (MEAT 2.0, total n = 1053 samples) performed similarly to the original version of the muscle clock (median of 4.4 vs. 4.6 years in age prediction error), suggesting that the original version of the muscle clock was very accurate. CONCLUSIONS We provide here the most comprehensive picture of DNA methylation ageing in human skeletal muscle and reveal widespread alterations of genes involved in skeletal muscle structure, development, and differentiation. We have made our results available as an open-access, user-friendly, web-based tool called MetaMeth (https://sarah-voisin.shinyapps.io/MetaMeth/).
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Affiliation(s)
- Sarah Voisin
- Institute for Health and Sport (iHeS)Victoria University, FootscrayMelbourneVic.Australia
| | - Macsue Jacques
- Institute for Health and Sport (iHeS)Victoria University, FootscrayMelbourneVic.Australia
| | - Shanie Landen
- Institute for Health and Sport (iHeS)Victoria University, FootscrayMelbourneVic.Australia
| | - Nicholas R. Harvey
- Faculty of Health Sciences & MedicineBond UniversityGold CoastQldAustralia
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical InnovationQueensland University of Technology (QUT)Kelvin GroveQldAustralia
| | - Larisa M. Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical InnovationQueensland University of Technology (QUT)Kelvin GroveQldAustralia
| | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical InnovationQueensland University of Technology (QUT)Kelvin GroveQldAustralia
| | - Sofiya Gancheva
- German Center for Diabetes Research (DZD)München‐NeuherbergGermany
- Division of Endocrinology and Diabetology, Medical FacultyHeinrich Heine UniversityDüsseldorfGermany
| | - Meriem Ouni
- German Center for Diabetes Research (DZD)München‐NeuherbergGermany
- Department of Experimental DiabetologyGerman Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE)NuthetalGermany
| | - Markus Jähnert
- German Center for Diabetes Research (DZD)München‐NeuherbergGermany
- Department of Experimental DiabetologyGerman Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE)NuthetalGermany
| | - Kevin J. Ashton
- Faculty of Health Sciences & MedicineBond UniversityGold CoastQldAustralia
| | - Vernon G. Coffey
- Faculty of Health Sciences & MedicineBond UniversityGold CoastQldAustralia
| | | | - Thomas M. Doering
- School of Health, Medical and Applied SciencesCentral Queensland UniversityRockhamptonQldAustralia
| | - Anne Gabory
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Claudine Junien
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Robert Caiazzo
- Univ Lille, Inserm, CHU Lille, Pasteur Institute Lille, U1190 Translational Research for Diabetes, European Genomic Institute of DiabetesLilleFrance
| | - Hélène Verkindt
- Univ Lille, Inserm, CHU Lille, Pasteur Institute Lille, U1190 Translational Research for Diabetes, European Genomic Institute of DiabetesLilleFrance
| | - Violetta Raverdy
- Univ Lille, Inserm, CHU Lille, Pasteur Institute Lille, U1190 Translational Research for Diabetes, European Genomic Institute of DiabetesLilleFrance
| | - François Pattou
- Univ Lille, Inserm, CHU Lille, Pasteur Institute Lille, U1190 Translational Research for Diabetes, European Genomic Institute of DiabetesLilleFrance
| | - Philippe Froguel
- Univ Lille, Inserm, CHU Lille, Pasteur Institute Lille, U1190 Translational Research for Diabetes, European Genomic Institute of DiabetesLilleFrance
- Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Jeffrey M. Craig
- IMPACT InstituteDeakin University, Geelong Waurn Ponds CampusGeelongVic.Australia
- Epigenetics, Murdoch Children's Research InstituteRoyal Children's HospitalParkvilleVic.Australia
| | - Sara Blocquiaux
- Physical Activity, Sport & Health Research Group, Department of Movement SciencesKU LeuvenLeuvenBelgium
| | - Martine Thomis
- Physical Activity, Sport & Health Research Group, Department of Movement SciencesKU LeuvenLeuvenBelgium
| | - Adam P. Sharples
- Institute for Physical PerformanceNorwegian School of Sport SciencesOsloNorway
| | - Annette Schürmann
- German Center for Diabetes Research (DZD)München‐NeuherbergGermany
- Department of Experimental DiabetologyGerman Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE)NuthetalGermany
| | - Michael Roden
- German Center for Diabetes Research (DZD)München‐NeuherbergGermany
- Division of Endocrinology and Diabetology, Medical FacultyHeinrich Heine UniversityDüsseldorfGermany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes ResearchHeinrich Heine UniversityDüsseldorfGermany
| | - Steve Horvath
- Department of Human Genetics and Biostatistics, David Geffen School of MedicineUniversity of California Los AngelesLos AngelesCAUSA
| | - Nir Eynon
- Institute for Health and Sport (iHeS)Victoria University, FootscrayMelbourneVic.Australia
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Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
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35
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Liu C, Yin Q, Li M, Fan Y, Shen C, Yang R. ACTB Methylation in Blood as a Potential Marker for the Pre-clinical Detection of Stroke: A Prospective Nested Case-Control Study. Front Neurosci 2021; 15:644943. [PMID: 34054407 PMCID: PMC8160447 DOI: 10.3389/fnins.2021.644943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/26/2021] [Indexed: 01/07/2023] Open
Abstract
Background Stroke is the second leading cause of death worldwide. If risk of stroke could be evaluated early or even at a preclinical stage, the mortality rate could be reduced dramatically. However, the identified genetic factors only account for 5-10% of the risk of stroke. Studies on the risk factors of stroke are urgently needed. We investigated the correlation between blood-based β-actin (ACTB) methylation and the risk of stroke in a prospective nested case-control study. Methods The methylation level of ACTB was quantitatively determined by mass spectrometry in 139 stroke cases who developed stroke within 2 years after recruitment and 147 age- and sex-matched controls who remained stroke-free in a median follow-up of 2.71 years. Results We observed a highly significant correlation between hypomethylation of one CpG site of ACTB and increased risk of stroke in an onset-time-dependent manner (for onset time ≤ 1.5 years: odds ratio (OR) per + 10% methylation = 0.76, P = 0.001; for onset time ≤ 1.32 years: OR per + 10% methylation = 0.59, P = 7.82 × 10-7; for onset time ≤ 1 year: OR per + 10% methylation = 0.43, P = 3.00 × 10-6), and the increased cumulative incidence of stroke (log-rank P = 3.13 × 10-7). Neighboring CpG sites showed an inverse correlation with age and drinking status in controls (P < 0.05) but not in stroke cases. Conclusion We firstly reported the blood-based ACTB methylation as a marker for the risk evaluation and preclinical detection of stroke, which can be further modified by age and drinking.
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Affiliation(s)
- Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiming Yin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mengxia Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Fan
- Division of Clinical Epidemiology, Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Chong Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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36
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Maasar MF, Turner DC, Gorski PP, Seaborne RA, Strauss JA, Shepherd SO, Cocks M, Pillon NJ, Zierath JR, Hulton AT, Drust B, Sharples AP. The Comparative Methylome and Transcriptome After Change of Direction Compared to Straight Line Running Exercise in Human Skeletal Muscle. Front Physiol 2021; 12:619447. [PMID: 33679435 PMCID: PMC7933519 DOI: 10.3389/fphys.2021.619447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
The methylome and transcriptome signatures following exercise that are physiologically and metabolically relevant to sporting contexts such as team sports or health prescription scenarios (e.g., high intensity interval training/HIIT) has not been investigated. To explore this, we performed two different sport/exercise relevant high-intensity running protocols in five male sport team members using a repeated measures design of: (1) change of direction (COD) versus; (2) straight line (ST) running exercise with a wash-out period of at least 2 weeks between trials. Skeletal muscle biopsies collected from the vastus lateralis 30 min and 24 h post exercise, were assayed using 850K methylation arrays and a comparative analysis with recent (subject-unmatched) sprint and acute aerobic exercise meta-analysis transcriptomes was performed. Despite COD and ST exercise being matched for classically defined intensity measures (speed × distance and number of accelerations/decelerations), COD exercise elicited greater movement (GPS-Playerload), physiological (HR), metabolic (lactate) as well as central and peripheral (differential RPE) exertion measures compared with ST exercise, suggesting COD exercise evoked a higher exercise intensity. The exercise response alone across both conditions evoked extensive alterations in the methylome 30 min and 24 h post exercise, particularly in MAPK, AMPK and axon guidance pathways. COD evoked a considerably greater hypomethylated signature across the genome compared with ST exercise, particularly at 30 min post exercise, enriched in: Protein binding, MAPK, AMPK, insulin, and axon guidance pathways. Comparative methylome analysis with sprint running transcriptomes identified considerable overlap, with 49% of genes that were altered at the expression level also differentially methylated after COD exercise. After differential methylated region analysis, we observed that VEGFA and its downstream nuclear transcription factor, NR4A1 had enriched hypomethylation within their promoter regions. VEGFA and NR4A1 were also significantly upregulated in the sprint transcriptome and meta-analysis of exercise transcriptomes. We also confirmed increased gene expression of VEGFA, and considerably larger increases in the expression of canonical metabolic genes PPARGC1A (that encodes PGC1-α) and NR4A3 in COD vs. ST exercise. Overall, we demonstrate that increased physiological/metabolic load via COD exercise in human skeletal muscle evokes considerable epigenetic modifications that are associated with changes in expression of genes responsible for adaptation to exercise.
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Affiliation(s)
- Mohd-Firdaus Maasar
- Stem Cells, Aging and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Daniel C Turner
- Stem Cells, Aging and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Institute for Science and Technology in Medicine, School of Pharmacy and Bioengineering, Keele University, Staffordshire, United Kingdom
| | - Piotr P Gorski
- Institute for Science and Technology in Medicine, School of Pharmacy and Bioengineering, Keele University, Staffordshire, United Kingdom.,Institute for Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Robert A Seaborne
- Stem Cells, Aging and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Juliette A Strauss
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Sam O Shepherd
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Matt Cocks
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Andrew T Hulton
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Barry Drust
- School of Sport, Exercise and Rehabilitation Sciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adam P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
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37
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Massenet J, Gardner E, Chazaud B, Dilworth FJ. Epigenetic regulation of satellite cell fate during skeletal muscle regeneration. Skelet Muscle 2021; 11:4. [PMID: 33431060 PMCID: PMC7798257 DOI: 10.1186/s13395-020-00259-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
In response to muscle injury, muscle stem cells integrate environmental cues in the damaged tissue to mediate regeneration. These environmental cues are tightly regulated to ensure expansion of muscle stem cell population to repair the damaged myofibers while allowing repopulation of the stem cell niche. These changes in muscle stem cell fate result from changes in gene expression that occur in response to cell signaling from the muscle environment. Integration of signals from the muscle environment leads to changes in gene expression through epigenetic mechanisms. Such mechanisms, including post-translational modification of chromatin and nucleosome repositioning, act to make specific gene loci more, or less, accessible to the transcriptional machinery. In youth, the muscle environment is ideally structured to allow for coordinated signaling that mediates efficient regeneration. Both age and disease alter the muscle environment such that the signaling pathways that shape the healthy muscle stem cell epigenome are altered. Altered epigenome reduces the efficiency of cell fate transitions required for muscle repair and contributes to muscle pathology. However, the reversible nature of epigenetic changes holds out potential for restoring cell fate potential to improve muscle repair in myopathies. In this review, we will describe the current knowledge of the mechanisms allowing muscle stem cell fate transitions during regeneration and how it is altered in muscle disease. In addition, we provide some examples of how epigenetics could be harnessed therapeutically to improve regeneration in various muscle pathologies.
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Affiliation(s)
- Jimmy Massenet
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.,Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS 5310, INSERM U1217, 8 Rockefeller Ave, 69008, Lyon, France
| | - Edward Gardner
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS 5310, INSERM U1217, 8 Rockefeller Ave, 69008, Lyon, France
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada. .,LIFE Research Institute, University of Ottawa, Ottawa, ON, K1H 8L6, Canada.
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38
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Poljsak B, Dahmane R, Adamič M, Sotler R, Levec T, Pavan Jukić D, Rotim C, Jukić T, Starc A. THE (A)SYMMETRY OF THE MALE GRAYING BEARD HAIRS AS AN INDICATION OF THE PROGRAMMED AGING PROCESS. Acta Clin Croat 2020; 59:650-660. [PMID: 34456453 PMCID: PMC8253069 DOI: 10.20471/acc.2020.59.04.11] [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: 09/18/2018] [Accepted: 10/22/2018] [Indexed: 11/24/2022] Open
Abstract
Aging interventions will be ineffective if we do not understand the basic principles of aging. Currently, there is no consensus on the issue whether aging is programmed or not. The hypothesis presented in this article indicates that aging (at least graying of male hairs) is programmed. This hypothesis is supported by the symmetry of the graying of male beard hairs. According to stochastic theories of aging, aging is a passive non-programmed process where random dispersion of graying hairs should result. On the contrary, programmed theories of aging would predict that there should be symmetry on the left and right parts of the face showing the same proportion, pattern and time of appearance of graying hairs.
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Affiliation(s)
| | - Raja Dahmane
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Metka Adamič
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Robert Sotler
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Tina Levec
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Doroteja Pavan Jukić
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Cecilija Rotim
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Tomislav Jukić
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
| | - Andrej Starc
- 1Laboratory for Oxidative Stress Research, Faculty of Health Sciences, University of Ljubljana, Ljubljana, Slovenia; 2Department of Biomedicine in Health Care Division, Faculty of Health Sciences, Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia; 3Metka Adamič Dermatology Clinic, Ljubljana, Slovenia; 4Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Gynecology and Obstetrics, Osijek, Croatia; 5Dr Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia; 6Josip Juraj Strossmayer University of Osijek, Faculty of Medicine, Department of Internal Medicine, Family Medicine and History of Medicine, Osijek, Croatia
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He L, Khanal P, Morse CI, Williams A, Thomis M. Associations of combined genetic and epigenetic scores with muscle size and muscle strength: a pilot study in older women. J Cachexia Sarcopenia Muscle 2020; 11:1548-1561. [PMID: 33058541 PMCID: PMC7749602 DOI: 10.1002/jcsm.12585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/08/2020] [Accepted: 02/24/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Inter-individual variance in skeletal muscle is closely related to genetic architecture and epigenetic regulation. Studies have examined genetic and epigenetic relationships with characteristics of ageing muscle separately, while no study has combined both genetic and epigenetic profiles in ageing muscle research. The aim of this study was to evaluate the association between combined genetic and methylation scores and skeletal muscle phenotypes in older women. METHODS Forty-eight older Caucasian women (aged 65-79 years) were included in this study. Biceps brachii thickness and vastus lateralis anatomical cross-sectional area (ACSAVL ) were measured by ultrasonography. Maximum isometric elbow flexion (MVCEF ) and knee extension (MVCKE ) torques were measured by a customized dynamometer. The muscle-driven genetic predisposition score (GPSSNP ) was calculated based on seven muscle-related single nucleotide polymorphisms (SNPs). DNA methylation levels of whole blood samples were analysed using Infinium MethylationEPIC BeadChip arrays. The DNA methylation score was calculated as a weighted sum of methylation levels of sarcopenia-driven CpG sites (MSSAR ) or an overall gene-wise methylation score (MSSNP , the mean methylation level of CpG sites located in muscle-related genes). Linear regression models were built to study genetic and epigenetic associations with muscle size and strength. Three models were built with both genetic and methylation scores: (1) MSSAR + GPSSNP , (2) MSSNP + GPSSNP , and (3) gene-wise combined scores which were calculated as the ratio of the SNP score to the mean methylation level of promoters in the corresponding gene. Additional models with only a genetic or methylation score were also built. All models were adjusted for age and BMI. RESULTS MSSAR was negatively associated with ACSAVL , MVCEF , and MVCKE and explained 10.1%, 35.5%, and 40.1% of the variance, respectively. MSSAR explained more variance in these muscular phenotypes than GPSSNP , MSSNP , and models including both genetic and methylation scores. MSSNP and GPSSNP accounted for less than 8% and 5% of the variance in all muscular phenotypes, respectively. The genotype and methylation level of CNTF was positively related to MVCKE (P = 0.03) and explained 12.2% of the variance. The adjusted R2 and Akaike information criterion showed that models with only a MSSAR performed the best in explaining inter-individual variance in muscular phenotypes. CONCLUSIONS Our results improve the understanding of inter-individual variance in muscular characteristics of older women and suggest a possible application of a sarcopenia-driven methylation score to muscle strength estimation in older women while the combination with a genetic score still needs to be further studied.
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Affiliation(s)
- Lingxiao He
- Department of Movement Sciences, Physical Activity, Sports & Health Research Group, KU Leuven, Leuven, Belgium.,Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester, UK
| | - Praval Khanal
- Department of Movement Sciences, Physical Activity, Sports & Health Research Group, KU Leuven, Leuven, Belgium.,Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester, UK
| | - Christopher I Morse
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester, UK
| | - Alun Williams
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Manchester, UK.,Institute of Sport, Exercise and Health, University College London, London, UK
| | - Martine Thomis
- Department of Movement Sciences, Physical Activity, Sports & Health Research Group, KU Leuven, Leuven, Belgium
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40
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Shi K, Lu Y, Chen X, Li D, Du W, Yu M. Effects of Ten-Eleven Translocation-2 (Tet2) on myogenic differentiation of chicken myoblasts. Comp Biochem Physiol B Biochem Mol Biol 2020; 252:110540. [PMID: 33242661 DOI: 10.1016/j.cbpb.2020.110540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Skeletal muscle development is an orchestrated progress that is primarily regulated by temporospatial expression of myogenic regulatory factors (MRFs). Recent studies demonstrated that DNA demethylation also exerted a critical role in myogenesis. However, the function of Tet2 in the regulation of chicken myogenesis still remains unknown. In the present study, the role of Tet2 in regulating myogenic differentiation was determined by using a model of primary myoblasts from chickens. The expression of Tet2 was significantly elevated during myoblast differentiation. Meanwhile, the level of 5hmC in genomic DNA was increased, but H3K9me2 and H3K27me3 were markedly reduced following differentiation. Knockdown of Tet2 significantly inhibited the formation of multinucleated myotubes, which was accompanied by a reduction of relevant pivotal MRFs. Moreover, the level of 5hmC decreased sharply in Tet2 knockdown myoblasts. Attenuated differentiated myoblasts that resulted from reduced Tet2 also demonstrated an increased level of H3K9me2 and H3K27me3. Collectively, these results indicated that Tet2 played an essential role during myogenesis, which affected demethylation of genomic DNA and histone to regulate expression of MRFs and therefore, contributed to myoblast differentiation.
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Affiliation(s)
- Kai Shi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Yingling Lu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Xiaolu Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Dongfeng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Wenxing Du
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Minli Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China.
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Turner DC, Gorski PP, Maasar MF, Seaborne RA, Baumert P, Brown AD, Kitchen MO, Erskine RM, Dos-Remedios I, Voisin S, Eynon N, Sultanov RI, Borisov OV, Larin AK, Semenova EA, Popov DV, Generozov EV, Stewart CE, Drust B, Owens DJ, Ahmetov II, Sharples AP. DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity. Sci Rep 2020; 10:15360. [PMID: 32958812 PMCID: PMC7506549 DOI: 10.1038/s41598-020-72730-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Skeletal muscle tissue demonstrates global hypermethylation with age. However, methylome changes across the time-course of differentiation in aged human muscle derived cells, and larger coverage arrays in aged muscle tissue have not been undertaken. Using 850K DNA methylation arrays we compared the methylomes of young (27 ± 4.4 years) and aged (83 ± 4 years) human skeletal muscle and that of young/aged heterogenous muscle-derived human primary cells (HDMCs) over several time points of differentiation (0, 72 h, 7, 10 days). Aged muscle tissue was hypermethylated compared with young tissue, enriched for; pathways-in-cancer (including; focal adhesion, MAPK signaling, PI3K-Akt-mTOR signaling, p53 signaling, Jak-STAT signaling, TGF-beta and notch signaling), rap1-signaling, axon-guidance and hippo-signalling. Aged cells also demonstrated a hypermethylated profile in pathways; axon-guidance, adherens-junction and calcium-signaling, particularly at later timepoints of myotube formation, corresponding with reduced morphological differentiation and reductions in MyoD/Myogenin gene expression compared with young cells. While young cells showed little alterations in DNA methylation during differentiation, aged cells demonstrated extensive and significantly altered DNA methylation, particularly at 7 days of differentiation and most notably in focal adhesion and PI3K-AKT signalling pathways. While the methylomes were vastly different between muscle tissue and HDMCs, we identified a small number of CpG sites showing a hypermethylated state with age, in both muscle tissue and cells on genes KIF15, DYRK2, FHL2, MRPS33, ABCA17P. Most notably, differential methylation analysis of chromosomal regions identified three locations containing enrichment of 6–8 CpGs in the HOX family of genes altered with age. With HOXD10, HOXD9, HOXD8, HOXA3, HOXC9, HOXB1, HOXB3, HOXC-AS2 and HOXC10 all hypermethylated in aged tissue. In aged cells the same HOX genes (and additionally HOXC-AS3) displayed the most variable methylation at 7 days of differentiation versus young cells, with HOXD8, HOXC9, HOXB1 and HOXC-AS3 hypermethylated and HOXC10 and HOXC-AS2 hypomethylated. We also determined that there was an inverse relationship between DNA methylation and gene expression for HOXB1, HOXA3 and HOXC-AS3. Finally, increased physical activity in young adults was associated with oppositely regulating HOXB1 and HOXA3 methylation compared with age. Overall, we demonstrate that a considerable number of HOX genes are differentially epigenetically regulated in aged human skeletal muscle and HDMCs and increased physical activity may help prevent age-related epigenetic changes in these HOX genes.
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Affiliation(s)
- D C Turner
- Institute for Physical Performance, Norwegian School of Sport Sciences (NiH), Oslo, Norway.,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK
| | - P P Gorski
- Institute for Physical Performance, Norwegian School of Sport Sciences (NiH), Oslo, Norway.,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK
| | - M F Maasar
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - R A Seaborne
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK.,Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - P Baumert
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Exercise Biology Group, Faculty of Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - A D Brown
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - M O Kitchen
- Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK
| | - R M Erskine
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute of Sport, Exercise and Health, University College London, London, UK
| | - I Dos-Remedios
- Orthopedics Department, University Hospitals of the North Midlands, Keele University, Staffordshire, UK
| | - S Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, Australia
| | - N Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, Australia
| | - R I Sultanov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - O V Borisov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - A K Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - E A Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - D V Popov
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - E V Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - C E Stewart
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - B Drust
- School of Sport, Exercise and Rehabilitation Sciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - D J Owens
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - I I Ahmetov
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK. .,Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia. .,Department of Physical Education, Plekhanov Russian University of Economics, Moscow, Russia.
| | - A P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences (NiH), Oslo, Norway. .,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK. .,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK.
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Gurung R, Choong AM, Woo CC, Foo R, Sorokin V. Genetic and Epigenetic Mechanisms Underlying Vascular Smooth Muscle Cell Phenotypic Modulation in Abdominal Aortic Aneurysm. Int J Mol Sci 2020; 21:ijms21176334. [PMID: 32878347 PMCID: PMC7504666 DOI: 10.3390/ijms21176334] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) refers to the localized dilatation of the infra-renal aorta, in which the diameter exceeds 3.0 cm. Loss of vascular smooth muscle cells, degradation of the extracellular matrix (ECM), vascular inflammation, and oxidative stress are hallmarks of AAA pathogenesis and contribute to the progressive thinning of the media and adventitia of the aortic wall. With increasing AAA diameter, and left untreated, aortic rupture ensues with high mortality. Collective evidence of recent genetic and epigenetic studies has shown that phenotypic modulation of smooth muscle cells (SMCs) towards dedifferentiation and proliferative state, which associate with the ECM remodeling of the vascular wall and accompanied with increased cell senescence and inflammation, is seen in in vitro and in vivo models of the disease. This review critically analyses existing publications on the genetic and epigenetic mechanisms implicated in the complex role of SMCs within the aortic wall in AAA formation and reflects the importance of SMCs plasticity in AAA formation. Although evidence from the wide variety of mouse models is convincing, how this knowledge is applied to human biology needs to be addressed urgently leveraging modern in vitro and in vivo experimental technology.
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Affiliation(s)
- Rijan Gurung
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 9, Singapore 119228, Singapore; (R.G.); (R.F.)
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome, Singapore 138672, Singapore
| | - Andrew Mark Choong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 8, Singapore 119228, Singapore; (A.M.C.); (C.C.W.)
- Department of Cardiac, Thoracic and Vascular Surgery, National University Hospital, National University Health System, 1E Kent Ridge Road, NUHS Tower Block, Level 9, Singapore 119228, Singapore
| | - Chin Cheng Woo
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 8, Singapore 119228, Singapore; (A.M.C.); (C.C.W.)
| | - Roger Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 9, Singapore 119228, Singapore; (R.G.); (R.F.)
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome, Singapore 138672, Singapore
| | - Vitaly Sorokin
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 8, Singapore 119228, Singapore; (A.M.C.); (C.C.W.)
- Department of Cardiac, Thoracic and Vascular Surgery, National University Hospital, National University Health System, 1E Kent Ridge Road, NUHS Tower Block, Level 9, Singapore 119228, Singapore
- Correspondence: ; Tel.: +65-6779-5555
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Voisin S, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Doering TM, Thompson JLM, Benedict C, Cedernaes J, Lindholm ME, Craig JM, Rowlands DS, Sharples AP, Horvath S, Eynon N. An epigenetic clock for human skeletal muscle. J Cachexia Sarcopenia Muscle 2020; 11:887-898. [PMID: 32067420 PMCID: PMC7432573 DOI: 10.1002/jcsm.12556] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ageing is associated with DNA methylation changes in all human tissues, and epigenetic markers can estimate chronological age based on DNA methylation patterns across tissues. However, the construction of the original pan-tissue epigenetic clock did not include skeletal muscle samples and hence exhibited a strong deviation between DNA methylation and chronological age in this tissue. METHODS To address this, we developed a more accurate, muscle-specific epigenetic clock based on the genome-wide DNA methylation data of 682 skeletal muscle samples from 12 independent datasets (18-89 years old, 22% women, 99% Caucasian), all generated with Illumina HumanMethylation (HM) arrays (HM27, HM450, or HMEPIC). We also took advantage of the large number of samples to conduct an epigenome-wide association study of age-associated DNA methylation patterns in skeletal muscle. RESULTS The newly developed clock uses 200 cytosine-phosphate-guanine dinucleotides to estimate chronological age in skeletal muscle, 16 of which are in common with the 353 cytosine-phosphate-guanine dinucleotides of the pan-tissue clock. The muscle clock outperformed the pan-tissue clock, with a median error of only 4.6 years across datasets (vs. 13.1 years for the pan-tissue clock, P < 0.0001) and an average correlation of ρ = 0.62 between actual and predicted age across datasets (vs. ρ = 0.51 for the pan-tissue clock). Lastly, we identified 180 differentially methylated regions with age in skeletal muscle at a false discovery rate < 0.005. However, gene set enrichment analysis did not reveal any enrichment for gene ontologies. CONCLUSIONS We have developed a muscle-specific epigenetic clock that predicts age with better accuracy than the pan-tissue clock. We implemented the muscle clock in an r package called Muscle Epigenetic Age Test available on Bioconductor to estimate epigenetic age in skeletal muscle samples. This clock may prove valuable in assessing the impact of environmental factors, such as exercise and diet, on muscle-specific biological ageing processes.
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Affiliation(s)
- Sarah Voisin
- Institute for Health and Sport, Victoria University, Melbourne, Australia
| | - Nicholas R Harvey
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia.,Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kevin J Ashton
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia
| | - Vernon G Coffey
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia
| | - Thomas M Doering
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia.,School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Australia
| | | | - Christian Benedict
- Sleep Research Laboratory, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | | | - Malene E Lindholm
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jeffrey M Craig
- Centre for Molecular and Medical Research, Deakin University, Geelong, Australia.,Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - David S Rowlands
- School of Sport, Exercise and Nutrition, Massey University, Wellington, New Zealand
| | - Adam P Sharples
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway.,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Steve Horvath
- Department of Human Genetics and Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nir Eynon
- Institute for Health and Sport, Victoria University, Melbourne, Australia
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Wild or farmed? A pilot study on determining origin of wildlife meat using methylation rate of ACTN3 gene and American mink. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Fan Y, Liang Y, Deng K, Zhang Z, Zhang G, Zhang Y, Wang F. Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing. BMC Genomics 2020; 21:327. [PMID: 32349667 PMCID: PMC7191724 DOI: 10.1186/s12864-020-6751-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/21/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic regulatory form that plays an important role in regulating the gene expression and the tissues development.. However, DNA methylation regulators involved in sheep muscle development remain unclear. To explore the functional importance of genome-scale DNA methylation during sheep muscle growth, this study systematically investigated the genome-wide DNA methylation profiles at key stages of Hu sheep developmental (fetus and adult) using deep whole-genome bisulfite sequencing (WGBS). RESULTS Our study found that the expression levels of DNA methyltransferase (DNMT)-related genes were lower in fetal muscle than in the muscle of adults. The methylation levels in the CG context were higher than those in the CHG and CHH contexts, and methylation levels were highest in introns, followed by exons and downstream regions. Subsequently, we identified 48,491, 17, and 135 differentially methylated regions (DMRs) in the CG, CHG, and CHH sequence contexts and 11,522 differentially methylated genes (DMGs). The results of bisulfite sequencing PCR (BSP) correlated well with the WGBS-Seq data. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis revealed that some DMGs were involved in regulating skeletal muscle development and fatty acid metabolism. By combining the WGBS-Seq and previous RNA-Seq data, a total of 159 overlap genes were obtained between differentially expressed genes (DEGs) and DMGs (FPKM > 10 and fold change > 4). Finally, we found that 9 DMGs were likely to be involved in muscle growth and metabolism of Hu sheep. CONCLUSIONS We systemically studied the global DNA methylation patterns of fetal and adult muscle development in Hu sheep, which provided new insights into a better understanding of the epigenetic regulation of sheep muscle development.
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Affiliation(s)
- Yixuan Fan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaxu Liang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaiping Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guomin Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Min B, Jeon K, Park JS, Kang Y. Demethylation and derepression of genomic retroelements in the skeletal muscles of aged mice. Aging Cell 2019; 18:e13042. [PMID: 31560164 PMCID: PMC6826136 DOI: 10.1111/acel.13042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/07/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Changes in DNA methylation influence the aging process and contribute to aging phenotypes, but few studies have been conducted on DNA methylation changes in conjunction with skeletal muscle aging. We explored the DNA methylation changes in a variety of retroelement families throughout aging (at 2, 20, and 28 months of age) in murine skeletal muscles by methyl‐binding domain sequencing (MBD‐seq). The two following contrasting patterns were observed among the members of each repeat family in superaged mice: (a) hypermethylation in weakly methylated retroelement copies and (b) hypomethylation in copies with relatively stronger methylation levels, representing a pattern of “regression toward the mean” within a single retroelement family. Interestingly, these patterns depended on the sizes of the copies. While the majority of the elements showed a slight increase in methylation, the larger copies (>5 kb) displayed evident demethylation. All these changes were not observed in T cells. RNA sequencing revealed a global derepression of retroelements during the late phase of aging (between 20 and 28 months of age), which temporally coincided with retroelement demethylation. Following this methylation drift trend of “regression toward the mean,” aging tended to progressively lose the preexisting methylation differences and local patterns in the genomic regions that had been elaborately established during the early period of development.
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Affiliation(s)
- Byungkuk Min
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
- Department of Functional Genomics University of Science and Technology (UST) Daejeon Korea
| | - Jung Sun Park
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
| | - Yong‐Kook Kang
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
- Department of Functional Genomics University of Science and Technology (UST) Daejeon Korea
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He L, Khanal P, Morse CI, Williams A, Thomis M. Differentially methylated gene patterns between age-matched sarcopenic and non-sarcopenic women. J Cachexia Sarcopenia Muscle 2019; 10:1295-1306. [PMID: 31508907 PMCID: PMC6903450 DOI: 10.1002/jcsm.12478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/09/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sarcopenia is characterized by progressive decreases in muscle mass, muscle strength, and muscle function with ageing. Although many studies have investigated the mechanisms of sarcopenia, its connection with epigenetic factors, such as DNA methylation, still remains poorly understood. The aim of this study was to explore sarcopenia-related DNA methylation differences in blood samples between age-matched sarcopenic and non-sarcopenic older women. METHODS A sarcopenic group (n = 24) was identified and selected from a set of 247 older Caucasian women (aged 65-80 years) based on cut-off points of skeletal muscle index at 6.75 kg/m2 and grip strength at 26 kg (the lower quintile of grip strength in the set). A non-sarcopenic group (n = 24) was created with a similar age distribution as that of the sarcopenic group. DNA methylation patterns of whole blood samples from both groups were analysed using Infinium MethylationEPIC BeadChip arrays. Differentially methylated cytosin-phosphate-guanine sites (dmCpGs) were identified at a P value threshold of 0.01 by comparing methylation levels between the sarcopenic and non-sarcopenic groups at each CpG site. dmCpG-related genes were annotated based on Homo sapiens hg19 genome build. The functions of these genes were further examined by GO and KEGG pathway enrichment analysis. RESULTS The global methylation level of all analysed CpG sites (n = 788 074) showed no significant difference between the sarcopenic and non-sarcopenic groups (0.812), while the average methylation level of dmCpGs (n = 6258) was significantly lower in the sarcopenic group (0.004). The sarcopenic group had significantly higher methylation levels in TSS200 (the region from transcription start site to 200 nucleotides upstream of the site) and lower methylation levels in gene body and 3'UTR regions. In respect of CpG regions, CpG islands in promoters and some intragenic regions showed greater levels of methylation in the sarcopenic group. dmCpG-related KEGG pathways were mainly associated with muscle function, actin cytoskeleton regulation, and energy metabolism. Seven genes (HSPB1, PBX4, CNKSR3, ORMDL3, MIR10A, ZNF619, and CRADD) were found with the same methylation direction as previous studies of blood sample methylation during ageing. Fifty-four genes were shared with previous studies of resistance training. CONCLUSIONS Our results improve understanding of epigenetic mechanisms of sarcopenia by identifying sarcopenia-related DNA methylation differences in blood samples of older women. These methylation differences suggest underlying alterations of gene expression and pathway function, which can partially explain sarcopenia-related muscular changes.
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Affiliation(s)
- Lingxiao He
- Department of Movement Sciences, Physical Activity, Sports & Health Research GroupKU LeuvenLeuvenBelgium
- Department of Sport and Exercise SciencesManchester Metropolitan UniversityManchesterUK
| | - Praval Khanal
- Department of Movement Sciences, Physical Activity, Sports & Health Research GroupKU LeuvenLeuvenBelgium
- Department of Sport and Exercise SciencesManchester Metropolitan UniversityManchesterUK
| | - Christopher I. Morse
- Department of Sport and Exercise SciencesManchester Metropolitan UniversityManchesterUK
| | - Alun Williams
- Department of Sport and Exercise SciencesManchester Metropolitan UniversityManchesterUK
- Institute of Sport, Exercise and HealthUniversity College LondonLondonUK
| | - Martine Thomis
- Department of Movement Sciences, Physical Activity, Sports & Health Research GroupKU LeuvenLeuvenBelgium
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Hadad N, Masser DR, Blanco-Berdugo L, Stanford DR, Freeman WM. Early-life DNA methylation profiles are indicative of age-related transcriptome changes. Epigenetics Chromatin 2019; 12:58. [PMID: 31594536 PMCID: PMC6781367 DOI: 10.1186/s13072-019-0306-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/14/2019] [Indexed: 12/15/2022] Open
Abstract
Background Alterations to cellular and molecular programs with brain aging result in cognitive impairment and susceptibility to neurodegenerative disease. Changes in DNA methylation patterns, an epigenetic modification required for various CNS functions are observed with brain aging and can be prevented by anti-aging interventions, but the relationship of altered methylation to gene expression is poorly understood. Results Paired analysis of the hippocampal methylome and transcriptome with aging of male and female mice demonstrates that age-related differences in methylation and gene expression are anti-correlated within gene bodies and enhancers. Altered promoter methylation with aging was found to be generally un-related to altered gene expression. A more striking relationship was found between methylation levels at young age and differential gene expression with aging. Highly methylated gene bodies and promoters in early life were associated with age-related increases in gene expression even in the absence of significant methylation changes with aging. As well, low levels of methylation in early life were correlated to decreased expression with aging. This relationship was also observed in genes altered in two mouse Alzheimer’s models. Conclusion DNA methylation patterns established in youth, in combination with other epigenetic marks, were able to accurately predict changes in transcript trajectories with aging. These findings are consistent with the developmental origins of disease hypothesis and indicate that epigenetic variability in early life may explain differences in aging trajectories and age-related disease.
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Affiliation(s)
- Niran Hadad
- Oklahoma Center for Neuroscience, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,Department of Physiology, Oklahoma City, OK, USA
| | | | - David R Stanford
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,Department of Physiology, Oklahoma City, OK, USA.,Oklahoma Nathan Shock Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Oklahoma Center for Neuroscience, Oklahoma City, OK, USA. .,Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA. .,Department of Physiology, Oklahoma City, OK, USA. .,Oklahoma Nathan Shock Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma City VA Medical Center, Oklahoma City, OK, 73104, USA.
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49
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Zhou J, So KK, Li Y, Li Y, Yuan J, Ding Y, Chen F, Huang Y, Liu J, Lee W, Li G, Ju Z, Sun H, Wang H. Elevated H3K27ac in aged skeletal muscle leads to increase in extracellular matrix and fibrogenic conversion of muscle satellite cells. Aging Cell 2019; 18:e12996. [PMID: 31325224 PMCID: PMC6718601 DOI: 10.1111/acel.12996] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 01/22/2023] Open
Abstract
Epigenetic alterations occur in various cells and tissues during aging, but it is not known if such alterations are also associated with aging in skeletal muscle. Here, we examined the changes of a panel of histone modifications and found H3K27ac (an active enhancer mark) is markedly increased in aged human skeletal muscle tissues. Further analyses uncovered that the H3K27ac increase and enhancer activation are associated with the up‐regulation of extracellular matrix (ECM) genes; this may result in alteration of the niche environment for skeletal muscle stem cells, also called satellite cells (SCs), which causes decreased myogenic potential and fibrogenic conversion of SCs. In mice, treatment of aging muscles with JQ1, an inhibitor of enhancer activation, inhibited the ECM up‐regulation and fibrogenic conversion of SCs and restored their myogenic differentiation potential. Altogether, our findings not only uncovered a novel aspect of skeletal muscle aging that is associated with enhancer remodeling but also implicated JQ1 as a potential treatment approach for restoring SC function in aging muscle.
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Affiliation(s)
- Jiajian Zhou
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Karl K. So
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yuying Li
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yang Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Jie Yuan
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yingzhe Ding
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Fengyuan Chen
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yile Huang
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Jin Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan University Guangzhou China
| | - Wayne Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Gang Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan University Guangzhou China
| | - Hao Sun
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
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50
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Gensous N, Bacalini MG, Franceschi C, Meskers CGM, Maier AB, Garagnani P. Age-Related DNA Methylation Changes: Potential Impact on Skeletal Muscle Aging in Humans. Front Physiol 2019; 10:996. [PMID: 31427991 PMCID: PMC6688482 DOI: 10.3389/fphys.2019.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/18/2019] [Indexed: 12/27/2022] Open
Abstract
Human aging is accompanied by a decline in muscle mass and muscle function, which is commonly referred to as sarcopenia. Sarcopenia is associated with detrimental clinical outcomes, such as a reduced quality of life, frailty, an increased risk of falls, fractures, hospitalization, and mortality. The exact underlying mechanisms of sarcopenia are poorly delineated and the molecular mechanisms driving the development and progression of this disorder remain to be uncovered. Previous studies have described age-related differences in gene expression, with one study identifying an age-specific expression signature of sarcopenia, but little is known about the influence of epigenetics, and specially of DNA methylation, in its pathogenesis. In this review, we will focus on the available knowledge in literature on the characterization of DNA methylation profiles during skeletal muscle aging and the possible impact of physical activity and nutrition. We will consider the possible use of the recently developed DNA methylation-based biomarkers of aging called epigenetic clocks in the assessment of physical performance in older individuals. Finally, we will discuss limitations and future directions of this field.
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Affiliation(s)
- Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Carel G M Meskers
- Amsterdam UMC, Department of Rehabilitation Medicine, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Andrea B Maier
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy
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