151
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Sorting senescence, ageing, and ageism in the context of human reproduction. J Assist Reprod Genet 2021; 38:1-2. [PMID: 33420649 DOI: 10.1007/s10815-021-02060-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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152
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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153
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Ruano D. Proteostasis Dysfunction in Aged Mammalian Cells. The Stressful Role of Inflammation. Front Mol Biosci 2021; 8:658742. [PMID: 34222330 PMCID: PMC8245766 DOI: 10.3389/fmolb.2021.658742] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
Aging is a biological and multifactorial process characterized by a progressive and irreversible deterioration of the physiological functions leading to a progressive increase in morbidity. In the next decades, the world population is expected to reach ten billion, and globally, elderly people over 80 are projected to triple in 2050. Consequently, it is also expected an increase in the incidence of age-related pathologies such as cancer, diabetes, or neurodegenerative disorders. Disturbance of cellular protein homeostasis (proteostasis) is a hallmark of normal aging that increases cell vulnerability and might be involved in the etiology of several age-related diseases. This review will focus on the molecular alterations occurring during normal aging in the most relevant protein quality control systems such as molecular chaperones, the UPS, and the ALS. Also, alterations in their functional cooperation will be analyzed. Finally, the role of inflammation, as a synergistic negative factor of the protein quality control systems during normal aging, will also be addressed. A better comprehension of the age-dependent modifications affecting the cellular proteostasis, as well as the knowledge of the mechanisms underlying these alterations, might be very helpful to identify relevant risk factors that could be responsible for or contribute to cell deterioration, a fundamental question still pending in biomedicine.
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Affiliation(s)
- Diego Ruano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Sevilla, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
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154
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Richard D, Capellini TD. Shifting epigenetic contexts influence regulatory variation and disease risk. Aging (Albany NY) 2021; 13:15699-15749. [PMID: 34138751 PMCID: PMC8266365 DOI: 10.18632/aging.203194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 11/25/2022]
Abstract
Epigenetic shifts are a hallmark of aging that impact transcriptional networks at regulatory level. These shifts may modify the effects of genetic regulatory variants during aging and contribute to disease pathomechanism. However, these shifts occur on the backdrop of epigenetic changes experienced throughout an individual's development into adulthood; thus, the phenotypic, and ultimately fitness, effects of regulatory variants subject to developmental- versus aging-related epigenetic shifts may differ considerably. Natural selection therefore may act differently on variants depending on their changing epigenetic context, which we propose as a novel lens through which to consider regulatory sequence evolution and phenotypic effects. Here, we define genomic regions subjected to altered chromatin accessibility as tissues transition from their fetal to adult forms, and subsequently from early to late adulthood. Based on these epigenomic datasets, we examine patterns of evolutionary constraint and potential functional impacts of sequence variation (e.g., genetic disease risk associations). We find that while the signals observed with developmental epigenetic changes are consistent with stronger fitness consequences (i.e., negative selection pressures), they tend to have weaker effects on genetic risk associations for aging-related diseases. Conversely, we see stronger effects of variants with increased local accessibility in adult tissues, strongest in young adult when compared to old. We propose a model for how epigenetic status of a region may influence the effects of evolutionary relevant sequence variation, and suggest that such a perspective on gene regulatory networks may elucidate our understanding of aging biology.
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Affiliation(s)
- Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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155
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Zupkovitz G, Kabiljo J, Kothmayer M, Schlick K, Schöfer C, Lagger S, Pusch O. Analysis of Methylation Dynamics Reveals a Tissue-Specific, Age-Dependent Decline in 5-Methylcytosine Within the Genome of the Vertebrate Aging Model Nothobranchius furzeri. Front Mol Biosci 2021; 8:627143. [PMID: 34222326 PMCID: PMC8242171 DOI: 10.3389/fmolb.2021.627143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Erosion of the epigenetic DNA methylation landscape is a widely recognized hallmark of aging. Emerging advances in high throughput sequencing techniques, in particular DNA methylation data analysis, have resulted in the establishment of precise human and murine age prediction tools. In vertebrates, methylation of cytosine at the C5 position of CpG dinucleotides is executed by DNA methyltransferases (DNMTs) whereas the process of enzymatic demethylation is highly dependent on the activity of the ten-eleven translocation methylcytosine dioxygenase (TET) family of enzymes. Here, we report the identification of the key players constituting the DNA methylation machinery in the short-lived teleost aging model Nothobranchius furzeri. We present a comprehensive spatio-temporal expression profile of the methylation-associated enzymes from embryogenesis into late adulthood, thereby covering the complete killifish life cycle. Data mining of the N. furzeri genome produced five dnmt gene family orthologues corresponding to the mammalian DNMTs (DNMT1, 2, 3A, and 3B). Comparable to other teleost species, N. furzeri harbors multiple genomic copies of the de novo DNA methylation subfamily. A related search for the DNMT1 recruitment factor UHRF1 and TET family members resulted in the identification of N. furzeri uhrf1, tet1, tet2, and tet3. Phylogenetic analysis revealed high cross-species similarity on the amino acid level of all individual dnmts, tets, and uhrf1, emphasizing a high degree of functional conservation. During early killifish development all analyzed dnmts and tets showed a similar expression profile characterized by a strong increase in transcript levels after fertilization, peaking either at embryonic day 6 or at the black eye stage of embryonic development. In adult N. furzeri, DNA methylation regulating enzymes showed a ubiquitous tissue distribution. Specifically, we observed an age-dependent downregulation of dnmts, and to some extent uhrf1, which correlated with a significant decrease in global DNA methylation levels in the aging killifish liver and muscle. The age-dependent DNA methylation profile and spatio-temporal expression characteristics of its enzymatic machinery reported here may serve as an essential platform for the identification of an epigenetic aging clock in the new vertebrate model system N. furzeri.
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Affiliation(s)
- Gordin Zupkovitz
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of Life Science Engineering, University of Applied Sciences Technikum Wien, Vienna, Austria.,City of Vienna Competence Team Aging Tissue, Vienna, Austria
| | - Julijan Kabiljo
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Michael Kothmayer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Katharina Schlick
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Christian Schöfer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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156
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Alvarez-Franco A, Rouco R, Ramirez RJ, Guerrero-Serna G, Tiana M, Cogliati S, Kaur K, Saeed M, Magni R, Enriquez JA, Sanchez-Cabo F, Jalife J, Manzanares M. Transcriptome and proteome mapping in the sheep atria reveal molecular featurets of atrial fibrillation progression. Cardiovasc Res 2021; 117:1760-1775. [PMID: 33119050 PMCID: PMC8208739 DOI: 10.1093/cvr/cvaa307] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
AIMS Atrial fibrillation (AF) is a progressive cardiac arrhythmia that increases the risk of hospitalization and adverse cardiovascular events. There is a clear demand for more inclusive and large-scale approaches to understand the molecular drivers responsible for AF, as well as the fundamental mechanisms governing the transition from paroxysmal to persistent and permanent forms. In this study, we aimed to create a molecular map of AF and find the distinct molecular programmes underlying cell type-specific atrial remodelling and AF progression. METHODS AND RESULTS We used a sheep model of long-standing, tachypacing-induced AF, sampled right and left atrial tissue, and isolated cardiomyocytes (CMs) from control, intermediate (transition), and late time points during AF progression, and performed transcriptomic and proteome profiling. We have merged all these layers of information into a meaningful three-component space in which we explored the genes and proteins detected and their common patterns of expression. Our data-driven analysis points at extracellular matrix remodelling, inflammation, ion channel, myofibril structure, mitochondrial complexes, chromatin remodelling, and genes related to neural function, as well as critical regulators of cell proliferation as hallmarks of AF progression. Most important, we prove that these changes occur at early transitional stages of the disease, but not at later stages, and that the left atrium undergoes significantly more profound changes than the right atrium in its expression programme. The pattern of dynamic changes in gene and protein expression replicate the electrical and structural remodelling demonstrated previously in the sheep and in humans, and uncover novel mechanisms potentially relevant for disease treatment. CONCLUSIONS Transcriptomic and proteomic analysis of AF progression in a large animal model shows that significant changes occur at early stages, and that among others involve previously undescribed increase in mitochondria, changes to the chromatin of atrial CMs, and genes related to neural function and cell proliferation.
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Affiliation(s)
- Alba Alvarez-Franco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Raquel Rouco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Rafael J Ramirez
- Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, USA
| | - Guadalupe Guerrero-Serna
- Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, USA
| | - Maria Tiana
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Sara Cogliati
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Department of Physiology, Institute of Nutrition and Food Technology, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Kuljeet Kaur
- Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, USA
| | - Mohammed Saeed
- Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, USA
| | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Jose Antonio Enriquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Fatima Sanchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - José Jalife
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, USA
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
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157
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Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. SCIENCE ADVANCES 2021; 7:eabg6082. [PMID: 34172448 PMCID: PMC8232908 DOI: 10.1126/sciadv.abg6082] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
The notion that the germ line does not age goes back to the 19th-century ideas of August Weismann. However, being metabolically active, the germ line accumulates damage and other changes over time, i.e., it ages. For new life to begin in the same young state, the germ line must be rejuvenated in the offspring. Here, we developed a multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e., rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (ground zero) marks the beginning of organismal aging.
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Affiliation(s)
- Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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158
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McCauley BS, Dang W. Loosening chromatin and dysregulated transcription: a perspective on cryptic transcription during mammalian aging. Brief Funct Genomics 2021; 21:56-61. [PMID: 34050364 DOI: 10.1093/bfgp/elab026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
Cryptic transcription, the initiation of transcription from non-promoter regions within a gene body, is a type of transcriptional dysregulation that occurs throughout eukaryotes. In mammals, cryptic transcription is normally repressed at the level of chromatin, and this process is increased upon perturbation of complexes that increase intragenic histone H3 lysine 4 methylation or decrease intragenic H3 lysine 36 methylation, DNA methylation, or nucleosome occupancy. Significantly, similar changes to chromatin structure occur during aging, and, indeed, recent work indicates that cryptic transcription is elevated during aging in mammalian stem cells. Although increased cryptic transcription is known to promote aging in yeast, whether elevated cryptic transcription also contributes to mammalian aging is unclear. There is ample evidence that perturbations known to increase cryptic transcription are deleterious in embryonic and adult stem cells, and in some cases phenocopy certain aging phenotypes. Furthermore, an increase in cryptic transcription requires or impedes pathways that are known to have reduced function during aging, potentially exacerbating other aging phenotypes. Thus, we propose that increased cryptic transcription contributes to mammalian stem cell aging.
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159
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Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
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Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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160
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Acton RJ, Yuan W, Gao F, Xia Y, Bourne E, Wozniak E, Bell J, Lillycrop K, Wang J, Dennison E, Harvey NC, Mein CA, Spector TD, Hysi PG, Cooper C, Bell CG. The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation. Nat Commun 2021; 12:2655. [PMID: 33976121 PMCID: PMC8113476 DOI: 10.1038/s41467-021-22639-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/05/2021] [Indexed: 02/03/2023] Open
Abstract
The epigenome has been shown to deteriorate with age, potentially impacting on ageing-related disease. tRNA, while arising from only ˜46 kb (<0.002% genome), is the second most abundant cellular transcript. tRNAs also control metabolic processes known to affect ageing, through core translational and additional regulatory roles. Here, we interrogate the DNA methylation state of the genomic loci of human tRNA. We identify a genomic enrichment for age-related DNA hypermethylation at tRNA loci. Analysis in 4,350 MeDIP-seq peripheral-blood DNA methylomes (16-82 years), identifies 44 and 21 hypermethylating specific tRNAs at study-and genome-wide significance, respectively, contrasting with none hypomethylating. Validation and replication (450k array and independent targeted Bisuphite-sequencing) supported the hypermethylation of this functional unit. Tissue-specificity is a significant driver, although the strongest consistent signals, also independent of major cell-type change, occur in tRNA-iMet-CAT-1-4 and tRNA-Ser-AGA-2-6. This study presents a comprehensive evaluation of the genomic DNA methylation state of human tRNA genes and reveals a discreet hypermethylation with advancing age.
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Affiliation(s)
- Richard J Acton
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Charterhouse Square, Queen Mary University of London, London, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
- Institute of Cancer Research, Sutton, UK
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, China
| | | | - Emma Bourne
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eva Wozniak
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Karen Lillycrop
- Human Development and Health, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Jun Wang
- Shenzhen Digital Life Institute, Shenzhen, Guangdong, China
- iCarbonX, Zhuhai, Guangdong, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
| | - Elaine Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Charles A Mein
- Barts & The London Genome Centre, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, King's College London, London, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Charterhouse Square, Queen Mary University of London, London, UK.
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161
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Lee EJ, Neppl RL. Influence of Age on Skeletal Muscle Hypertrophy and Atrophy Signaling: Established Paradigms and Unexpected Links. Genes (Basel) 2021; 12:genes12050688. [PMID: 34063658 PMCID: PMC8147613 DOI: 10.3390/genes12050688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Skeletal muscle atrophy in an inevitable occurrence with advancing age, and a consequence of disease including cancer. Muscle atrophy in the elderly is managed by a regimen of resistance exercise and increased protein intake. Understanding the signaling that regulates muscle mass may identify potential therapeutic targets for the prevention and reversal of muscle atrophy in metabolic and neuromuscular diseases. This review covers the major anabolic and catabolic pathways that regulate skeletal muscle mass, with a focus on recent progress and potential new players.
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162
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Pasyukova EG, Symonenko AV, Rybina OY, Vaiserman AM. Epigenetic enzymes: A role in aging and prospects for pharmacological targeting. Ageing Res Rev 2021; 67:101312. [PMID: 33657446 DOI: 10.1016/j.arr.2021.101312] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
The development of interventions aimed at improving healthspan is one of the priority tasks for the academic and public health authorities. It is also the main objective of a novel branch in biogerontological research, geroscience. According to the geroscience concept, targeting aging is an effective way to combat age-related disorders. Since aging is an exceptionally complex process, system-oriented integrated approaches seem most appropriate for such an interventional strategy. Given the high plasticity and adaptability of the epigenome, epigenome-targeted interventions appear highly promising in geroscience research. Pharmaceuticals targeted at mechanisms involved in epigenetic control of gene activity are actively developed and implemented to prevent and treat various aging-related conditions such as cardiometabolic, neurodegenerative, inflammatory disorders, and cancer. In this review, we describe the roles of epigenetic mechanisms in aging; characterize enzymes contributing to the regulation of epigenetic processes; particularly focus on epigenetic drugs, such as inhibitors of DNA methyltransferases and histone deacetylases that may potentially affect aging-associated diseases and longevity; and discuss possible caveats associated with the use of epigenetic drugs.
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Affiliation(s)
- Elena G Pasyukova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Alexander V Symonenko
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Olga Y Rybina
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia; Federal State Budgetary Educational Institution of Higher Education «Moscow Pedagogical State University», M. Pirogovskaya Str. 1/1, Moscow, 119991, Russia
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163
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Schwender K, Holländer O, Klopfleisch S, Eveslage M, Danzer MF, Pfeiffer H, Vennemann M. Development of two age estimation models for buccal swab samples based on 3 CpG sites analyzed with pyrosequencing and minisequencing. Forensic Sci Int Genet 2021; 53:102521. [PMID: 33933877 DOI: 10.1016/j.fsigen.2021.102521] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/07/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
The analysis of DNA methylation levels of specific CpG sites is one of the most promising molecular techniques to estimate an individual's age. Numerous studies were published recently presenting age estimation models based on DNA methylation patterns from blood samples, with only a few using saliva or buccal swabs. The aim of this study was to identify age-dependent methylation of 88 CpG sites in eight different marker regions (PDE4C, ELOVL2, ITGA2B, ASPA, EDARADD, SST, KLF14 and SLC12A5) in buccal swab samples. A total of 141 buccal swabs from individuals with age ranging from 21 to 69 years were split into a training set (n = 95) and a validation set (n = 46). Samples of the training set were analyzed by pyrosequencing and markers with best age correlation were identified. Stepwise linear regression analysis was performed resulting in an age estimation model including three of the examined CpG sites and showing a mean absolute deviation of estimated from chronological age of 5.11 years. To allow easy implementation into forensic laboratories without the need for pyrosequencing equipment, a multiplex minisequencing reaction was developed, including the same CpG sites previously identified by pyrosequencing. An adjusted age estimation model was evaluated with a mean absolute deviation of estimated from chronological age of 5.16 years. The independent validation set of 46 buccal swab samples was used to test model performances. Mean absolute deviation of estimated from chronological age was 5.33 years and 6.44 years for the pyrosequencing model and the minisequencing model, respectively. Comparison of the two methods showed a high concordance of results, both, qualitatively and quantitatively. In conclusion, buccal swabs offer a suitable alternative to blood samples for molecular age estimation with the additional advantage of being collected non-invasively. Furthermore we showed that minisequencing offers a cost-effective and easy-to-integrate alternative to pyrosequencing for the analysis of methylation status of individual CpG sites.
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Affiliation(s)
- Kristina Schwender
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany; Institute of Legal Medicine, University of Munich, Nußbaumstraße 26, 80336 Munich, Germany
| | - Olivia Holländer
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany
| | | | - Maria Eveslage
- Institute of Biostatistics and Clinical Research, University of Münster, Schmeddingstraße 56, 48149 Münster, Germany
| | - Moritz Fabian Danzer
- Institute of Biostatistics and Clinical Research, University of Münster, Schmeddingstraße 56, 48149 Münster, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany.
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164
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Yu J, Wu Y, Li H, Zhou H, Shen C, Gao T, Lin M, Dai X, Ou J, Liu M, Huang X, Zheng B, Sun F. BMI1 Drives Steroidogenesis Through Epigenetically Repressing the p38 MAPK Pathway. Front Cell Dev Biol 2021; 9:665089. [PMID: 33928089 PMCID: PMC8076678 DOI: 10.3389/fcell.2021.665089] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/22/2021] [Indexed: 11/18/2022] Open
Abstract
Testosterone biosynthesis progressively decreases in aging males primarily as a result of functional changes to Leydig cells. Despite this, the mechanisms underlying steroidogenesis remain largely unclear. Using gene knock-out approaches, we and others have recently identified Bmi1 as an anti-aging gene. Herein, we investigate the role of BMI1 in steroidogenesis using mouse MLTC-1 and primary Leydig cells. We show that BMI1 can positively regulate testosterone production. Mechanistically, in addition to its known role in antioxidant activity, we also report that p38 mitogen-activated protein kinase (MAPK) signaling is activated, and testosterone levels reduced, in BMI1-deficient cells; however, the silencing of the p38 MAPK pathway restores testosterone production. Furthermore, we reveal that BMI1 directly binds to the promoter region of Map3k3, an upstream activator of p38, thereby modulating its chromatin status and repressing its expression. Consequently, this results in the inhibition of the p38 MAPK pathway and the promotion of steroidogenesis. Our study uncovered a novel epigenetic mechanism in steroidogenesis involving BMI1-mediated gene silencing and provides potential therapeutic targets for the treatment of hypogonadism.
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Affiliation(s)
- Jun Yu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, China
| | - Yibo Wu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Hong Li
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Hui Zhou
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Tingting Gao
- Center of Clinical Reproductive Medicine, The Affiliated Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University, Changzhou, China
| | - Meng Lin
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xiuliang Dai
- Center of Clinical Reproductive Medicine, The Affiliated Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University, Changzhou, China
| | - Jian Ou
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Meiling Liu
- National Health Commission Key Laboratory of Male Reproductive Health, National Research Institute for Family Planning, Beijing, China
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China.,National Health Commission Key Laboratory of Male Reproductive Health, National Research Institute for Family Planning, Beijing, China
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, China
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165
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Zhu Y, Ge J, Huang C, Liu H, Jiang H. Application of mesenchymal stem cell therapy for aging frailty: from mechanisms to therapeutics. Theranostics 2021; 11:5675-5685. [PMID: 33897874 PMCID: PMC8058725 DOI: 10.7150/thno.46436] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 03/15/2021] [Indexed: 12/20/2022] Open
Abstract
Aging frailty is a complex geriatric syndrome that becomes more prevalent with advancing age. It constitutes a major health problem due to frequent adverse outcomes. Frailty is characterized by disruption of physiological homeostasis and progressive decline of health status. Multiple factors contribute to development of frailty with advancing age, including genome instability, DNA damage, epigenetic alternations, stem cell exhaustion, among others. These interrelated factors comprehensively result in loss of tissue homeostasis and diminished reserve capacity in frailty. Therefore, the aged organism gradually represents symptoms of frailty with decline in physiological functions of organs. Notably, the brain, cardiovascular system, skeletal muscle, and endocrine system are intrinsically interrelated to frailty. The patients with frailty may display the diminished reserves capacity of organ systems. Due to the complex pathophysiology, no specific treatments have been approved for prevention of this syndrome. At such, effective strategies for intervening in pathogenic process to improve health status of frail patients are highly needed. Recent progress in cell-based therapy has greatly contributed to the amelioration of degenerative diseases related to age. Mesenchymal stem cells (MSCs) can exert regenerative effects and possess anti-inflammatory properties. Transplantation of MSCs represents as a promising therapeutic strategy to address the pathophysiologic problems of frail syndrome. Currently, MSC therapy have undergone the phase I and II trials in human subjects that have endorsed the safety and efficacy of MSCs for aging frailty. However, despite these positive results, caution is still needed with regard to potential to form tumors, and further large-scale studies are warranted to confirm the therapeutic efficacy of MSC therapy.
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166
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Guillermo ARR, Chocian K, Gavriilidis G, Vandamme J, Salcini AE, Mellor J, Woollard A. H3K27 modifiers regulate lifespan in C. elegans in a context-dependent manner. BMC Biol 2021; 19:59. [PMID: 33766022 PMCID: PMC7995591 DOI: 10.1186/s12915-021-00984-8] [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] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/16/2021] [Indexed: 11/30/2022] Open
Abstract
Background Evidence of global heterochromatin decay and aberrant gene expression in models of physiological and premature ageing have long supported the “heterochromatin loss theory of ageing”, which proposes that ageing is aetiologically linked to, and accompanied by, a progressive, generalised loss of repressive epigenetic signatures. However, the remarkable plasticity of chromatin conformation suggests that the re-establishment of such marks could potentially revert the transcriptomic architecture of animal cells to a “younger” state, promoting longevity and healthspan. To expand our understanding of the ageing process and its connection to chromatin biology, we screened an RNAi library of chromatin-associated factors for increased longevity phenotypes. Results We identified the lysine demethylases jmjd-3.2 and utx-1, as well as the lysine methyltransferase mes-2 as regulators of both lifespan and healthspan in C. elegans. Strikingly, we found that both overexpression and loss of function of jmjd-3.2 and utx-1 are all associated with enhanced longevity. Furthermore, we showed that the catalytic activity of UTX-1, but not JMJD-3.2, is critical for lifespan extension in the context of overexpression. In attempting to reconcile the improved longevity associated with both loss and gain of function of utx-1, we investigated the alternative lifespan pathways and tissue specificity of longevity outcomes. We demonstrated that lifespan extension caused by loss of utx-1 function is daf-16 dependent, while overexpression effects are partially independent of daf-16. In addition, lifespan extension was observed when utx-1 was knocked down or overexpressed in neurons and intestine, whereas in the epidermis, only knockdown of utx-1 conferred improved longevity. Conclusions We show that the regulation of longevity by chromatin modifiers can be the result of the interaction between distinct factors, such as the level and tissue of expression. Overall, we suggest that the heterochromatin loss model of ageing may be too simplistic an explanation of organismal ageing when molecular and tissue-specific effects are taken into account. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00984-8.
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Affiliation(s)
- Abigail R R Guillermo
- Department of Biochemistry, University of Oxford, Oxford, UK.,Present Address: Department of Physiology, National University of Singapore, Singapore, Singapore
| | | | | | - Julien Vandamme
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Present Address: Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Elisabetta Salcini
- Present Address: Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alison Woollard
- Department of Biochemistry, University of Oxford, Oxford, UK.
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167
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The Therapeutic Potential of Epigenome-Modifying Drugs in Cardiometabolic Disease. CURRENT GENETIC MEDICINE REPORTS 2021. [DOI: 10.1007/s40142-021-00198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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168
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Ansere VA, Ali-Mondal S, Sathiaseelan R, Garcia DN, Isola JVV, Henseb JD, Saccon TD, Ocañas SR, Tooley KB, Stout MB, Schneider A, Freeman WM. Cellular hallmarks of aging emerge in the ovary prior to primordial follicle depletion. Mech Ageing Dev 2021; 194:111425. [PMID: 33383072 PMCID: PMC8279026 DOI: 10.1016/j.mad.2020.111425] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 01/10/2023]
Abstract
Decline in ovarian reserve with advancing age is associated with reduced fertility and the emergence of metabolic disturbances, osteoporosis, and neurodegeneration. Recent studies have provided insight into connections between ovarian insufficiency and systemic aging, although the basic mechanisms that promote ovarian reserve depletion remain unknown. Here, we sought to determine if chronological age is linked to changes in ovarian cellular senescence, transcriptomic, and epigenetic mechanisms in a mouse model. Histological assessments and transcriptional analyses revealed the accumulation of lipofuscin aggresomes and senescence-related transcripts (Cdkn1a, Cdkn2a, Pai-1 and Hmgb1) significantly increased with advancing age. Transcriptomic profiling and pathway analyses following RNA sequencing, revealed an upregulation of genes related to pro-inflammatory stress and cell-cycle inhibition, whereas genes involved in cell-cycle progression were downregulated; which could be indicative of senescent cell accumulation. The emergence of these senescence-related markers preceded the dramatic decline in primordial follicle reserve observed. Whole Genome Oxidative Bisulfite Sequencing (WGoxBS) found no genome-wide or genomic context-specific DNA methylation and hydroxymethylation changes with advancing age. These findings suggest that cellular senescence may contribute to ovarian aging, and thus, declines in ovarian follicular reserve. Cell-type-specific analyses across the reproductive lifespan are needed to fully elucidate the mechanisms that promote ovarian insufficiency.
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Affiliation(s)
- Victor A Ansere
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Samim Ali-Mondal
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Roshini Sathiaseelan
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Driele N Garcia
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - José V V Isola
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jéssica D Henseb
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Tatiana D Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael B Stout
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Willard M Freeman
- Oklahoma Center for Geroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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169
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Zhou X, Sun H, Tan F, Yi R, Zhou C, Deng Y, Mu J, Zhao X. Anti-aging effect of Lactobacillus plantarum HFY09-fermented soymilk on D-galactose-induced oxidative aging in mice through modulation of the Nrf2 signaling pathway. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104386] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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170
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Erez N, Israitel L, Bitman-Lotan E, Wong WH, Raz G, Cornelio-Parra DV, Danial S, Flint Brodsly N, Belova E, Maksimenko O, Georgiev P, Druley T, Mohan RD, Orian A. A Non-stop identity complex (NIC) supervises enterocyte identity and protects from premature aging. eLife 2021; 10:62312. [PMID: 33629655 PMCID: PMC7936876 DOI: 10.7554/elife.62312] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
A hallmark of aging is loss of differentiated cell identity. Aged Drosophila midgut differentiated enterocytes (ECs) lose their identity, impairing tissue homeostasis. To discover identity regulators, we performed an RNAi screen targeting ubiquitin-related genes in ECs. Seventeen genes were identified, including the deubiquitinase Non-stop (CG4166). Lineage tracing established that acute loss of Non-stop in young ECs phenocopies aged ECs at cellular and tissue levels. Proteomic analysis unveiled that Non-stop maintains identity as part of a Non-stop identity complex (NIC) containing E(y)2, Sgf11, Cp190, (Mod) mdg4, and Nup98. Non-stop ensured chromatin accessibility, maintaining the EC-gene signature, and protected NIC subunit stability. Upon aging, the levels of Non-stop and NIC subunits declined, distorting the unique organization of the EC nucleus. Maintaining youthful levels of Non-stop in wildtype aged ECs safeguards NIC subunits, nuclear organization, and suppressed aging phenotypes. Thus, Non-stop and NIC, supervise EC identity and protects from premature aging.
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Affiliation(s)
- Neta Erez
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lena Israitel
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Wing H Wong
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Gal Raz
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dayanne V Cornelio-Parra
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Salwa Danial
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Na'ama Flint Brodsly
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Todd Druley
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Ryan D Mohan
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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171
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Chikuma S, Yamanaka S, Nakagawa S, Ueda MT, Hayabuchi H, Tokifuji Y, Kanayama M, Okamura T, Arase H, Yoshimura A. TRIM28 Expression on Dendritic Cells Prevents Excessive T Cell Priming by Silencing Endogenous Retrovirus. THE JOURNAL OF IMMUNOLOGY 2021; 206:1528-1539. [PMID: 33619215 DOI: 10.4049/jimmunol.2001003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
Acquired immune reaction is initiated by dendritic cells (DCs), which present Ags to a few naive Ag-specific T cells. Deregulation of gene expression in DCs may alter the outcome of the immune response toward immunodeficiency and/or autoimmune diseases. Expression of TRIM28, a nuclear protein that mediates gene silencing through heterochromatin, decreased in DCs from old mice, suggesting alteration of gene regulation. Mice specifically lacking TRIM28 in DCs show increased DC population in the spleen and enhanced T cell priming toward inflammatory effector T cells, leading to acceleration and exacerbation in experimental autoimmune encephalomyelitis. TRIM28-deficient DCs were found to ectopically transcribe endogenous retrovirus (ERV) elements. Combined genome-wide analysis revealed a strong colocalization among the decreased repressive histone mark H3K9me3-transcribed ERV elements and the derepressed host genes that were related to inflammation in TRIM28-deficient DCs. This suggests that TRIM28 occupancy of ERV elements critically represses expression of proximal inflammatory genes on the genome. We propose that gene silencing through repressive histone modification by TRIM28 plays a role in maintaining the integrity of precise gene regulation in DCs, which prevents aberrant T cell priming to inflammatory effector T cells.
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Affiliation(s)
- Shunsuke Chikuma
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan.,Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hodaka Hayabuchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yukiko Tokifuji
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Kanayama
- Department of Biodefense Research, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.,Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Disease, Osaka University, Osaka 565-0871, Japan; and.,Laboratory of Immunochemistry, World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
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172
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Scialo F, Sanz A. Coenzyme Q redox signalling and longevity. Free Radic Biol Med 2021; 164:187-205. [PMID: 33450379 DOI: 10.1016/j.freeradbiomed.2021.01.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 12/29/2022]
Abstract
Mitochondria are the powerhouses of the cell. They produce a significant amount of the energy we need to grow, survive and reproduce. The same system that generates energy in the form of ATP also produces Reactive Oxygen Species (ROS). Mitochondrial Reactive Oxygen Species (mtROS) were considered for many years toxic by-products of metabolism, responsible for ageing and many degenerative diseases. Today, we know that mtROS are essential redox messengers required to determine cell fate and maintain cellular homeostasis. Most mtROS are produced by respiratory complex I (CI) and complex III (CIII). How and when CI and CIII produce ROS is determined by the redox state of the Coenzyme Q (CoQ) pool and the proton motive force (pmf) generated during respiration. During ageing, there is an accumulation of defective mitochondria that generate high levels of mtROS. This causes oxidative stress and disrupts redox signalling. Here, we review how mtROS are generated in young and old mitochondria and how CI and CIII derived ROS control physiological and pathological processes. Finally, we discuss why damaged mitochondria amass during ageing as well as methods to preserve mitochondrial redox signalling with age.
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Affiliation(s)
- Filippo Scialo
- Dipartimento di Scienze Mediche Traslazionali, Università della Campania "Luigi Vanvitelli", 80131, Napoli, Italy
| | - Alberto Sanz
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, Glasgow, United Kingdom.
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173
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Li TY, Sleiman MB, Li H, Gao AW, Mottis A, Bachmann AM, El Alam G, Li X, Goeminne LJE, Schoonjans K, Auwerx J. The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress. ACTA ACUST UNITED AC 2021; 1:165-178. [PMID: 33718883 PMCID: PMC7116894 DOI: 10.1038/s43587-020-00025-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Organisms respond to mitochondrial stress by activating multiple defense pathways including the mitochondrial unfolded protein response (UPRmt). However, how UPRmt regulators are orchestrated to transcriptionally activate stress responses remains largely unknown. Here we identified CBP-1, the worm ortholog of the mammalian acetyltransferases CBP/p300, as an essential regulator of the UPRmt, as well as mitochondrial stress-induced immune response, reduction of amyloid-β aggregation and lifespan extension in Caenorhabditis elegans. Mechanistically, CBP-1 acts downstream of histone demethylases, JMJD-1.2/JMJD-3.1, and upstream of UPRmt transcription factors including ATFS-1, to systematically induce a broad spectrum of UPRmt genes and execute multiple beneficial functions. In mouse and human populations, transcript levels of CBP/p300 positively correlate with UPRmt transcripts and longevity. Furthermore, CBP/p300 inhibition disrupts, while forced expression of p300 is sufficient to activate, the UPRmt in mammalian cells. These results highlight an evolutionarily conserved mechanism that determines mitochondrial stress response, and promotes health and longevity through CBP/p300.
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Affiliation(s)
- Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Laboratory of Metabolic Signaling, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arwen W Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrienne Mottis
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexis Maximilien Bachmann
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ludger J E Goeminne
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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174
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Principles of the Molecular and Cellular Mechanisms of Aging. J Invest Dermatol 2021; 141:951-960. [PMID: 33518357 DOI: 10.1016/j.jid.2020.11.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Aging can be defined as a state of progressive functional decline accompanied by an increase in mortality. Time-dependent accumulation of cellular damage, namely lesions and mutations in the DNA and misfolded proteins, impair organellar and cellular function. Ensuing cell fate alterations lead to the accumulation of dysfunctional cells and hamper homeostatic processes, thus limiting regenerative potential; trigger low-grade inflammation; and alter intercellular and intertissue communication. The accumulation of molecular damage together with modifications in the epigenetic landscape, dysregulation of gene expression, and altered endocrine communication, drive the aging process and establish age as the main risk factor for age-associated diseases and multimorbidity.
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175
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Bitman-Lotan E, Orian A. Nuclear organization and regulation of the differentiated state. Cell Mol Life Sci 2021; 78:3141-3158. [PMID: 33507327 PMCID: PMC8038961 DOI: 10.1007/s00018-020-03731-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Regulation of the differentiated identity requires active and continued supervision. Inability to maintain the differentiated state is a hallmark of aging and aging-related disease. To maintain cellular identity, a network of nuclear regulators is devoted to silencing previous and non-relevant gene programs. This network involves transcription factors, epigenetic regulators, and the localization of silent genes to heterochromatin. Together, identity supervisors mold and maintain the unique nuclear environment of the differentiated cell. This review describes recent discoveries regarding mechanisms and regulators that supervise the differentiated identity and protect from de-differentiation, tumorigenesis, and attenuate forced somatic cell reprograming. The review focuses on mechanisms involved in H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity. We outline how the biophysical properties of these factors are involved in self-compartmentalization of heterochromatin and cell identity. Finally, we discuss the relevance of these regulators to aging and age-related disease.
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Affiliation(s)
- Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel.
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176
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Millan-Ariño L, Yuan ZF, Oomen ME, Brandenburg S, Chernobrovkin A, Salignon J, Körner L, Zubarev RA, Garcia BA, Riedel CG. Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans. ACTA ACUST UNITED AC 2021; 102:e114. [PMID: 32997895 PMCID: PMC7583481 DOI: 10.1002/cpps.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Histones are the major proteinaceous component of chromatin in eukaryotic cells and an important part of the epigenome, affecting most DNA‐related events, including transcription, DNA replication, and chromosome segregation. The properties of histones are greatly influenced by their post‐translational modifications (PTMs), over 200 of which are known today. Given this large number, researchers need sophisticated methods to study histone PTMs comprehensively. In particular, mass spectrometry (MS)−based approaches have gained popularity, allowing for the quantification of dozens of histone PTMs at once. Using these approaches, even the study of co‐occurring PTMs and the discovery of novel PTMs become feasible. The success of MS‐based approaches relies substantially on obtaining pure and well‐preserved histones for analysis, which can be difficult depending on the source material. Caenorhabditis elegans has been a popular model organism to study the epigenome, but isolation of pure histones from these animals has been challenging. Here, we address this issue, presenting a method for efficient isolation of pure histone proteins from C. elegans at good yield. Further, we describe an MS pipeline optimized for accurate relative quantification of histone PTMs from C. elegans. We alkylate and tryptically digest the histones, analyze them by bottom‐up MS, and then evaluate the resulting data by a C. elegans−adapted version of the software EpiProfile 2.0. Finally, we show the utility of this pipeline by determining differences in histone PTMs between C. elegans strains that age at different rates and thereby achieve very different lifespans. © 2020 The Authors. Basic Protocol 1: Large‐scale growth and harvesting of synchronized C. elegans Basic Protocol 2: Nuclear preparation, histone extraction, and histone purification Basic Protocol 3: Bottom‐up mass spectrometry analysis of histone PTMs and histone variants
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Affiliation(s)
- Lluís Millan-Ariño
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Zuo-Fei Yuan
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marlies E Oomen
- European Research Institute for the Biology of Ageing, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Simone Brandenburg
- European Research Institute for the Biology of Ageing, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Alexey Chernobrovkin
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Jérôme Salignon
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Lioba Körner
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Roman A Zubarev
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christian G Riedel
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.,European Research Institute for the Biology of Ageing, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
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177
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Siametis A, Niotis G, Garinis GA. DNA Damage and the Aging Epigenome. J Invest Dermatol 2021; 141:961-967. [PMID: 33494932 DOI: 10.1016/j.jid.2020.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/29/2022]
Abstract
In mammals, genome instability and aging are intimately linked as illustrated by the growing list of patients with progeroid and animal models with inborn DNA repair defects. Until recently, DNA damage was thought to drive aging by compromising transcription or DNA replication, thereby leading to age-related cellular malfunction and somatic mutations triggering cancer. However, recent evidence suggests that DNA lesions also elicit widespread epigenetic alterations that threaten cell homeostasis as a function of age. In this review, we discuss the functional links of persistent DNA damage with the epigenome in the context of aging and age-related diseases.
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Affiliation(s)
- Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George Niotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece.
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178
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Proshkina EN, Solovev IA, Shaposhnikov MV, Moskalev AA. Key Molecular Mechanisms of Aging, Biomarkers, and Potential Interventions. Mol Biol 2021. [DOI: 10.1134/s0026893320060096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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179
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Anglada T, Genescà A, Martín M. Age-associated deficient recruitment of 53BP1 in G1 cells directs DNA double-strand break repair to BRCA1/CtIP-mediated DNA-end resection. Aging (Albany NY) 2020; 12:24872-24893. [PMID: 33361520 PMCID: PMC7803562 DOI: 10.18632/aging.202419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
DNA repair mechanisms play a crucial role in maintaining genome integrity. However, the increased frequency of DNA double-strand breaks (DSBs) and genome rearrangements in aged individuals suggests an age-associated DNA repair deficiency. Previous work from our group revealed a delayed firing of the DNA damage response in human mammary epithelial cells (HMECs) from aged donors. We now report a decreased activity of the main DSB repair pathways, the canonical non-homologous end-joining (c-NHEJ) and the homologous recombination (HR) in these HMECs from older individuals. We describe here a deficient recruitment of 53BP1 to DSB sites in G1 cells, probably influenced by an altered epigenetic regulation. 53BP1 absence at some DSBs is responsible for the age-associated DNA repair defect, as it permits the ectopic formation of BRCA1 foci while still in the G1 phase. CtIP and RPA foci are also formed in G1 cells from aged donors, but RAD51 is not recruited, thus indicating that extensive DNA-end resection occurs in these breaks although HR is not triggered. These results suggest an age-associated switch of DSB repair from canonical to highly mutagenic alternative mechanisms that promote the formation of genome rearrangements, a source of genome instability that might contribute to the aging process.
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Affiliation(s)
- Teresa Anglada
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anna Genescà
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marta Martín
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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180
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Mayne B, Korbie D, Kenchington L, Ezzy B, Berry O, Jarman S. A DNA methylation age predictor for zebrafish. Aging (Albany NY) 2020; 12:24817-24835. [PMID: 33353889 PMCID: PMC7803548 DOI: 10.18632/aging.202400] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
Changes in DNA methylation at specific CpG sites have been used to build predictive models to estimate animal age, predominantly in mammals. Little testing for this effect has been conducted in other vertebrate groups, such as bony fish, the largest vertebrate class. The development of most age-predictive models has relied on a genome-wide sequencing method to obtain a DNA methylation level, which makes it costly to deploy as an assay to estimate age in many samples. Here, we have generated a reduced representation bisulfite sequencing data set of caudal fin tissue from a model fish species, zebrafish (Danio rerio), aged from 11.9-60.1 weeks. We identified changes in methylation at specific CpG sites that correlated strongly with increasing age. Using an optimised unique set of 26 CpG sites we developed a multiplex PCR assay that predicts age with an average median absolute error rate of 3.2 weeks in zebrafish between 10.9-78.1 weeks of age. We also demonstrate the use of multiplex PCR as an efficient quantitative approach to measure DNA methylation for the use of age estimation. This study highlights the potential further use of DNA methylation as an age estimation method in non-mammalian vertebrate species.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Lisa Kenchington
- Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
| | - Ben Ezzy
- Western Australian Zebrafish Experimental Research Centre (WAZERC), University of Western Australia, Perth, Western Australia, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, Western Australia, Australia
| | - Simon Jarman
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
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181
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Aly J, Engmann O. The Way to a Human's Brain Goes Through Their Stomach: Dietary Factors in Major Depressive Disorder. Front Neurosci 2020; 14:582853. [PMID: 33364919 PMCID: PMC7750481 DOI: 10.3389/fnins.2020.582853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Globally, more than 250 million people are affected by depression (major depressive disorder; MDD), a serious and debilitating mental disorder. Currently available treatment options can have substantial side effects and take weeks to be fully effective. Therefore, it is important to find safe alternatives, which act more rapidly and in a larger number of patients. While much research on MDD focuses on chronic stress as a main risk factor, we here make a point of exploring dietary factors as a somewhat overlooked, yet highly promising approach towards novel antidepressant pathways. Deficiencies in various groups of nutrients often occur in patients with mental disorders. These include vitamins, especially members of the B-complex (B6, B9, B12). Moreover, an imbalance of fatty acids, such as omega-3 and omega-6, or an insufficient supply with minerals, including magnesium and zinc, are related to MDD. While some of them are relevant for the synthesis of monoamines, others play a crucial role in inflammation, neuroprotection and the synthesis of growth factors. Evidence suggests that when deficiencies return to normal, changes in mood and behavior can be, at least in some cases, achieved. Furthermore, supplementation with dietary factors (so called "nutraceuticals") may improve MDD symptoms even in the absence of a deficiency. Non-vital dietary factors may affect MDD symptoms as well. For instance, the most commonly consumed psychostimulant caffeine may improve behavioral and molecular markers of MDD. The molecular structure of most dietary factors is well known. Hence, dietary factors may provide important molecular tools to study and potentially help treat MDD symptoms. Within this review, we will discuss the role of dietary factors in MDD risk and symptomology, and critically discuss how they might serve as auxiliary treatments or preventative options for MDD.
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Affiliation(s)
- Janine Aly
- Faculty of Medicine, Friedrich Schiller Universität, Jena, Germany
| | - Olivia Engmann
- Institute for Human Genetics, Jena University Hospital, Jena, Germany
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182
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Lee JR, Choe SH, Kim YH, Cho HM, Park HR, Lee HE, Jin YB, Kim JS, Jeong KJ, Park SJ, Huh JW. Longitudinal profiling of the blood transcriptome in an African green monkey aging model. Aging (Albany NY) 2020; 13:846-864. [PMID: 33290253 PMCID: PMC7834999 DOI: 10.18632/aging.202190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
African green monkeys (AGMs, Chlorocebus aethiops) are Old World monkeys which are used as experimental models in biomedical research. Recent technological advances in next generation sequencing are useful for unraveling the genetic mechanisms underlying senescence, aging, and age-related disease. To elucidate the normal aging mechanisms in older age, the blood transcriptomes of nine healthy, aged AGMs (15‒23 years old), were analyzed over two years. We identified 910‒1399 accumulated differentially expressed genes (DEGs) in each individual, which increased with age. Aging-related DEGs were sorted across the three time points. A major proportion of the aging-related DEGs belonged to gene ontology (GO) categories involved in translation and rRNA metabolic processes. Next, we sorted common aging-related DEGs across three time points over two years. Common aging-related DEGs belonged to GO categories involved in translation, cellular component biogenesis, rRNA metabolic processes, cellular component organization, biogenesis, and RNA metabolic processes. Furthermore, we identified 29 candidate aging genes that were upregulated across the time series analysis. These candidate aging genes were linked to protein synthesis. This study describes a changing gene expression pattern in AGMs during aging using longitudinal transcriptome sequencing. The candidate aging genes identified here may be potential targets for the treatment of aging.
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Affiliation(s)
- Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56216, Republic of Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Ji-Su Kim
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56216, Republic of Korea
| | - Kang Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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183
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Kouidou S, Malousi A, Andreou AZ. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: Triggering a Lethal Fight to Keep Control of the Ten-Eleven Translocase (TET)-Associated DNA Demethylation? Pathogens 2020; 9:E1006. [PMID: 33266135 PMCID: PMC7760189 DOI: 10.3390/pathogens9121006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/15/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
The extended and diverse interference of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in multiple host functions and the diverse associated symptoms implicate its involvement in fundamental cellular regulatory processes. The activity of ten-eleven translocase 2 (TET2) responsible for selective DNA demethylation, has been recently identified as a regulator of endogenous virus inactivation and viral invasion, possibly by proteasomal deregulation of the TET2/TET3 activities. In a recent report, we presented a detailed list of factors that can be affected by TET activity, including recognition of zinc finger protein binding sites and bimodal promoters, by enhancing the flexibility of adjacent sequences. In this review, we summarize the TET-associated processes and factors that could account for SARS-CoV-2 diverse symptoms. Moreover, we provide a correlation for the observed virus-induced symptoms that have been previously associated with TET activities by in vitro and in vitro studies. These include early hypoxia, neuronal regulation, smell and taste development, liver, intestinal, and cardiomyocyte differentiation. Finally, we propose that the high mortality of SARS-CoV-2 among adult patients, the different clinical symptoms of adults compared to children, the higher risk of patients with metabolic deregulation, and the low mortality rates among women can all be accounted for by the complex balance of the three enzymes with TET activity, which is developmentally regulated. This activity is age-dependent, related to telomere homeostasis and integrity, and associated with X chromosome inactivation via (de)regulation of the responsible XIST gene expression.
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Affiliation(s)
- Sofia Kouidou
- Lab of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Andigoni Malousi
- Lab of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
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184
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p53: A Key Protein That Regulates Pulmonary Fibrosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6635794. [PMID: 33312337 PMCID: PMC7721501 DOI: 10.1155/2020/6635794] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Pulmonary fibrosis is a progressively aggravating lethal disease that is a serious public health concern. Although the incidence of this disease is increasing, there is a lack of effective therapies. In recent years, the pathogenesis of pulmonary fibrosis has become a research hotspot. p53 is a tumor suppressor gene with crucial roles in cell cycle, apoptosis, tumorigenesis, and malignant transformation. Previous studies on p53 have predominantly focused on its role in neoplastic disease. Following in-depth investigation, several studies have linked it to pulmonary fibrosis. This review covers the association between p53 and pulmonary fibrosis, with the aim of providing novel ideas to improve the clinical diagnosis, treatment, and prognosis of pulmonary fibrosis.
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185
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Fang Y, Gu Y, Li L, Zhu L, Qian J, Zhao C, Xu L, Wei W, Du Y, Yuan N, Zhang S, Yuan Y, Xu Y, Jiang C, Wang J. Loss of Atg7 causes chaotic nucleosome assembly of mouse bone marrow CD11b +Ly6G - myeloid cells. Aging (Albany NY) 2020; 12:25673-25683. [PMID: 33232280 PMCID: PMC7803583 DOI: 10.18632/aging.104176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/15/2020] [Indexed: 12/13/2022]
Abstract
Atg7, a critical component of autophagy machinery, is essential for counteracting hematopoietic aging. However, the non-autophagic role of Atg7 on hematopoietic cells remains fundamentally unclear. In this study, we found that loss of Atg7, but not Atg5, another autophagy-essential gene, in the hematopoietic system reduces CD11b myeloid cellularity including CD11b+Ly6G+ and CD11b+Ly6G- populations in mouse bone marrow. Surprisingly, Atg7 deletion causes abnormally accumulated histone H3.1 to be overwhelmingly trapped in the cytoplasm in the CD11b+Ly6G-, but not the CD11b+Ly6G+ compartment. RNA profiling revealed extensively chaotic expression of the genes required in nucleosome assembly. Functional assays further indicated upregulated aging markers in the CD11b+Ly6G- population. Therefore, our study suggests that Atg7 is essential for maintaining proper nucleosome assembly and limiting aging in the bone marrow CD11b+Ly6G- population.
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Affiliation(s)
- Yixuan Fang
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China.,Department of Hematopoietic Engineering, Susky Life SciTech (Suzhou) Co. Ltd., Suzhou 215124, China.,State Key Laboratory of Radiation Medicine and Radioprotection, Soochow University School of Medicine, Suzhou 215123, China
| | - Yue Gu
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Lei Li
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Lingjiang Zhu
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jiawei Qian
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China
| | - Chen Zhao
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Li Xu
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Wen Wei
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Yanhua Du
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Na Yuan
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China.,Department of Hematopoietic Engineering, Susky Life SciTech (Suzhou) Co. Ltd., Suzhou 215124, China.,State Key Laboratory of Radiation Medicine and Radioprotection, Soochow University School of Medicine, Suzhou 215123, China
| | - Suping Zhang
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China.,Department of Hematopoietic Engineering, Susky Life SciTech (Suzhou) Co. Ltd., Suzhou 215124, China.,State Key Laboratory of Radiation Medicine and Radioprotection, Soochow University School of Medicine, Suzhou 215123, China
| | - Ye Yuan
- Department of Orthopaedics, the Second Affiliated Hospital of Soochow University, Osteoporosis Institute of Soochow University, Suzhou 215004, China
| | - Youjia Xu
- Department of Orthopaedics, the Second Affiliated Hospital of Soochow University, Osteoporosis Institute of Soochow University, Suzhou 215004, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Jianrong Wang
- Hematology Center of Cyrus Tang Medical Institute, Soochow University School of Medicine, Suzhou 215123, China.,National Clinical Research Center for Hematologic Diseases, Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China.,Department of Hematopoietic Engineering, Susky Life SciTech (Suzhou) Co. Ltd., Suzhou 215124, China.,State Key Laboratory of Radiation Medicine and Radioprotection, Soochow University School of Medicine, Suzhou 215123, China
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186
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Wang A, Chiou J, Poirion OB, Buchanan J, Valdez MJ, Verheyden JM, Hou X, Kudtarkar P, Narendra S, Newsome JM, Guo M, Faddah DA, Zhang K, Young RE, Barr J, Sajti E, Misra R, Huyck H, Rogers L, Poole C, Whitsett JA, Pryhuber G, Xu Y, Gaulton KJ, Preissl S, Sun X, NHLBI LungMap Consortium. Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes. eLife 2020; 9:e62522. [PMID: 33164753 PMCID: PMC7688309 DOI: 10.7554/elife.62522] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022] Open
Abstract
Respiratory failure associated with COVID-19 has placed focus on the lungs. Here, we present single-nucleus accessible chromatin profiles of 90,980 nuclei and matched single-nucleus transcriptomes of 46,500 nuclei in non-diseased lungs from donors of ~30 weeks gestation,~3 years and ~30 years. We mapped candidate cis-regulatory elements (cCREs) and linked them to putative target genes. We identified distal cCREs with age-increased activity linked to SARS-CoV-2 host entry gene TMPRSS2 in alveolar type 2 cells, which had immune regulatory signatures and harbored variants associated with respiratory traits. At the 3p21.31 COVID-19 risk locus, a candidate variant overlapped a distal cCRE linked to SLC6A20, a gene expressed in alveolar cells and with known functional association with the SARS-CoV-2 receptor ACE2. Our findings provide insight into regulatory logic underlying genes implicated in COVID-19 in individual lung cell types across age. More broadly, these datasets will facilitate interpretation of risk loci for lung diseases.
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Affiliation(s)
- Allen Wang
- Center for Epigenomics & Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California San DiegoLa JollaUnited States
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Olivier B Poirion
- Center for Epigenomics & Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Justin Buchanan
- Center for Epigenomics & Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Michael J Valdez
- Biomedical Sciences Graduate Program, University of California San DiegoLa JollaUnited States
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Jamie M Verheyden
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Xiaomeng Hou
- Center for Epigenomics & Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Parul Kudtarkar
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Sharvari Narendra
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Jacklyn M Newsome
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Minzhe Guo
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States
- Divisions of Pulmonary Biology and Biomedical Informatics, University of Cincinnati College of MedicineCincinnatiUnited States
| | | | - Kai Zhang
- Ludwig Institute for Cancer ResearchLa JollaUnited States
| | - Randee E Young
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
- Laboratory of Genetics, Department of Medical Genetics, University of Wisconsin-MadisonMadisonUnited States
| | - Justinn Barr
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Eniko Sajti
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Ravi Misra
- Department of Pediatrics and Clinical & Translational Science Institute, University of Rochester Medical CenterRochesterUnited States
| | - Heidie Huyck
- Department of Pediatrics and Clinical & Translational Science Institute, University of Rochester Medical CenterRochesterUnited States
| | - Lisa Rogers
- Department of Pediatrics and Clinical & Translational Science Institute, University of Rochester Medical CenterRochesterUnited States
| | - Cory Poole
- Department of Pediatrics and Clinical & Translational Science Institute, University of Rochester Medical CenterRochesterUnited States
| | - Jeffery A Whitsett
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States
- Divisions of Pulmonary Biology and Biomedical Informatics, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Gloria Pryhuber
- Department of Pediatrics and Clinical & Translational Science Institute, University of Rochester Medical CenterRochesterUnited States
| | - Yan Xu
- Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical CenterCincinnatiUnited States
- Divisions of Pulmonary Biology and Biomedical Informatics, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Kyle J Gaulton
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
| | - Sebastian Preissl
- Center for Epigenomics & Department of Cellular & Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Xin Sun
- Department of Pediatrics, University of California-San DiegoLa JollaUnited States
- Department of Biological Sciences, University of California-San DiegoLa JollaUnited States
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187
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [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: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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188
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Wu Z, Shi Y, Lu M, Song M, Yu Z, Wang J, Wang S, Ren J, Yang YG, Liu GH, Zhang W, Ci W, Qu J. METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA. Nucleic Acids Res 2020; 48:11083-11096. [PMID: 33035345 PMCID: PMC7641765 DOI: 10.1093/nar/gkaa816] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/31/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
N6-Methyladenosine (m6A) messenger RNA methylation is a well-known epitranscriptional regulatory mechanism affecting central biological processes, but its function in human cellular senescence remains uninvestigated. Here, we found that levels of both m6A RNA methylation and the methyltransferase METTL3 were reduced in prematurely senescent human mesenchymal stem cell (hMSC) models of progeroid syndromes. Transcriptional profiling of m6A modifications further identified MIS12, for which m6A modifications were reduced in both prematurely senescent hMSCs and METTL3-deficient hMSCs. Knockout of METTL3 accelerated hMSC senescence whereas overexpression of METTL3 rescued the senescent phenotypes. Mechanistically, loss of m6A modifications accelerated the turnover and decreased the expression of MIS12 mRNA while knockout of MIS12 accelerated cellular senescence. Furthermore, m6A reader IGF2BP2 was identified as a key player in recognizing and stabilizing m6A-modified MIS12 mRNA. Taken together, we discovered that METTL3 alleviates hMSC senescence through m6A modification-dependent stabilization of the MIS12 transcript, representing a novel epitranscriptional mechanism in premature stem cell senescence.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Mingming Lu
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Moshi Song
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zihui Yu
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Jilu Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Si Wang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Jie Ren
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Yun-Gui Yang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Weimin Ci
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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189
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Yi SJ, Kim K. New Insights into the Role of Histone Changes in Aging. Int J Mol Sci 2020; 21:ijms21218241. [PMID: 33153221 PMCID: PMC7662996 DOI: 10.3390/ijms21218241] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area.
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190
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Levy O, Amit G, Vaknin D, Snir T, Efroni S, Castaldi P, Liu YY, Cohen HY, Bashan A. Age-related loss of gene-to-gene transcriptional coordination among single cells. Nat Metab 2020; 2:1305-1315. [PMID: 33139959 DOI: 10.1038/s42255-020-00304-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
A long-standing model holds that stochastic aberrations of transcriptional regulation play a key role in the process of ageing. While transcriptional dysregulation is observed in many cell types in the form of increased cell-to-cell variability, its generality to all cell types remains doubted. Here, we propose a new approach for analysing transcriptional regulation in single-cell RNA sequencing data by focusing on the global coordination between the genes rather than the variability of individual genes or correlations between pairs of genes. Consistently, across very different organisms and cell types, we find a decrease in the gene-to-gene transcriptional coordination in ageing cells. In addition, we find that loss of gene-to-gene transcriptional coordination is associated with high mutational load of a specific, age-related signature and with radiation-induced DNA damage. These observations suggest a general, potentially universal, stochastic attribute of transcriptional dysregulation in ageing.
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Affiliation(s)
- Orr Levy
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Guy Amit
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Dana Vaknin
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Tom Snir
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Primary Care and General Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Haim Y Cohen
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel
| | - Amir Bashan
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel.
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191
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Capp JP, Thomas F. Tissue-disruption-induced cellular stochasticity and epigenetic drift: Common origins of aging and cancer? Bioessays 2020; 43:e2000140. [PMID: 33118188 DOI: 10.1002/bies.202000140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 01/10/2023]
Abstract
Age-related and cancer-related epigenomic modifications have been associated with enhanced cell-to-cell gene expression variability that characterizes increased cellular stochasticity. Since gene expression variability appears to be highly reduced by-and epigenetic and phenotypic stability acquired through-direct or long-range cellular interactions during cell differentiation, we propose a common origin for aging and cancer in the failure to control cellular stochasticity by cell-cell interactions. Tissue-disruption-induced cellular stochasticity associated with epigenetic drift would be at the origin of organ dysfunction because of an increase in phenotypic variation among cells, ultimately leading to cell death and organ failure through a loss of coordination in cellular functions, and eventually to cancerization. We propose mechanistic research perspectives to corroborate this hypothesis and explore its evolutionary consequences, highlighting a positive correlation between the median age of mass loss onset (a proxy for the onset of organ aging) and the median age at cancer diagnosis.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC (CREES), UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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192
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Abstract
Frailty is a syndrome characterized by the decline in the physiologic reserve and function of several systems, leading to increased vulnerability and adverse health outcomes. While common in the elderly, recent studies have underlined the higher prevalence of frailty in chronic diseases, independent of age. The pathophysiological mechanisms that contribute to frailty have not been completely understood, although significant progresses have recently been made. In this context, chronic inflammation is likely to play a pivotal role, both directly and indirectly through other systems, such as the musculoskeletal, endocrine, and neurological systems. Rheumatic diseases are characterized by chronic inflammation and accumulation of deficits during time. Therefore, studies have recently started to explore the link between frailty and rheumatic diseases, and in this review, we report what has been described so far. Frailty is dynamic and potentially reversible with 8.3%-17.9% of older adults spontaneously improving their frailty status over time. Muscle strength is likely the most significant influencing factor which could be improved with training thus pointing at the need to maintain physical activity. Not surprisingly, frailty is more prevalent in patients affected by rheumatic diseases than in healthy controls, regardless of age and is associated with high disease activity to affect the clinical outcomes, largely due to chronic inflammation. More importantly, the treatment of the underlying condition may prevent frailty. Scales to assess frailty in patients affected by rheumatic diseases have been proposed, but larger casuistries are needed to validate disease-specific indexes, which could allow more accurate prognostic estimates than demographic and disease-related variables alone. Frail patients can be more vulnerable and more difficult to treat, due to the risk of side effects, therefore frailty should be taken into account in clinical decisions. Clinical trials addressing frailty could identify patients who are less likely to tolerate potentially toxic medications and might benefit from more conservative regimens. In conclusion, the implementation of the concept of frailty in rheumatology will allow a better understanding of the patient global health, a finest risk stratification and a more individualized management strategy.
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Affiliation(s)
- Francesca Motta
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center– IRCCS, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
| | - Antonio Sica
- Humanitas Clinical and Research Center - IRCCS - Laboratory of Molecular Immunology, Milan, Italy
- Department of Pharmaceutical Sciences, University of Piemonte Orientale “A. Avogadro”, Novara, Italy
| | - Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center– IRCCS, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
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193
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Al Zouabi L, Bardin AJ. Stem Cell DNA Damage and Genome Mutation in the Context of Aging and Cancer Initiation. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036210. [PMID: 31932318 DOI: 10.1101/cshperspect.a036210] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Adult stem cells fuel tissue homeostasis and regeneration through their unique ability to self-renew and differentiate into specialized cells. Thus, their DNA provides instructions that impact the tissue as a whole. Since DNA is not an inert molecule, but rather dynamic, interacting with a myriad of chemical and physical factors, it encounters damage from both endogenous and exogenous sources. Damage to DNA introduces deviations from its normal intact structure and, if left unrepaired, may result in a genetic mutation. In turn, mutant genomes of stem and progenitor cells are inherited in cells of the lineage, thus eroding the genetic information that maintains homeostasis of the somatic cell population. Errors arising in stem and progenitor cells will have a substantially larger impact on the tissue in which they reside than errors occurring in postmitotic differentiated cells. Therefore, maintaining the integrity of genomic DNA within our stem cells is essential to protect the instructions necessary for rebuilding healthy tissues during homeostatic renewal. In this review, we will first discuss DNA damage arising in stem cells and cell- and tissue-intrinsic mechanisms that protect against harmful effects of this damage. Secondly, we will examine how erroneous DNA repair and persistent DNA damage in stem and progenitor cells impact stem cells and tissues in the context of cancer initiation and aging. Finally, we will discuss the use of invertebrate and vertebrate model systems to address unanswered questions on the role that DNA damage and mutation may play in aging and precancerous conditions.
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Affiliation(s)
- Lara Al Zouabi
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
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194
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Sural S, Liang CY, Wang FY, Ching TT, Hsu AL. HSB-1/HSF-1 pathway modulates histone H4 in mitochondria to control mtDNA transcription and longevity. SCIENCE ADVANCES 2020; 6:eaaz4452. [PMID: 33087356 PMCID: PMC7577724 DOI: 10.1126/sciadv.aaz4452] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/08/2020] [Indexed: 06/02/2023]
Abstract
Heat shock factor-1 (HSF-1) is a master regulator of stress responses across taxa. Overexpression of HSF-1 or genetic ablation of its conserved negative regulator, heat shock factor binding protein 1 (HSB-1), results in robust life-span extension in Caenorhabditis elegans Here, we found that increased HSF-1 activity elevates histone H4 levels in somatic tissues during development, while knockdown of H4 completely suppresses HSF-1-mediated longevity. Moreover, overexpression of H4 is sufficient to extend life span. Ablation of HSB-1 induces an H4-dependent increase in micrococcal nuclease protection of both nuclear chromatin and mitochondrial DNA (mtDNA), which consequently results in reduced transcription of mtDNA-encoded complex IV genes, decreased respiratory capacity, and a mitochondrial unfolded protein response-dependent life-span extension. Collectively, our findings reveal a previously unknown role of HSB-1/HSF-1 signaling in modulation of mitochondrial function via mediating histone H4-dependent regulation of mtDNA gene expression and concomitantly acting as a determinant of organismal longevity.
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Affiliation(s)
- Surojit Sural
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chung-Yi Liang
- Research Center for Healthy Aging, China Medical University, Taichung, 404, Taiwan
| | - Feng-Yung Wang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Tsui-Ting Ching
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan.
| | - Ao-Lin Hsu
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
- Research Center for Healthy Aging, China Medical University, Taichung, 404, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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195
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Bou Sleiman M, Jha P, Houtkooper R, Williams RW, Wang X, Auwerx J. The Gene-Regulatory Footprint of Aging Highlights Conserved Central Regulators. Cell Rep 2020; 32:108203. [PMID: 32997995 PMCID: PMC7527782 DOI: 10.1016/j.celrep.2020.108203] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/31/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Many genes and pathways have been linked to aging, yet our understanding of underlying molecular mechanisms is still lacking. Here, we measure changes in the transcriptome, histone modifications, and DNA methylome in three metabolic tissues of adult and aged mice. Transcriptome and methylome changes dominate the liver aging footprint, whereas heart and muscle globally increase chromatin accessibility, especially in aging pathways. In mouse and human data from multiple tissues and regulatory layers, age-related transcription factor expression changes and binding site enrichment converge on putative aging modulators, including ZIC1, CXXC1, HMGA1, MECP2, SREBF1, SREBF2, ETS2, ZBTB7A, and ZNF518B. Using Mendelian randomization, we establish possible epidemiological links between expression of some of these transcription factors or their targets, including CXXC1, ZNF518B, and BBC3, and longevity. We conclude that conserved modulators are at the core of the molecular footprint of aging, and variation in tissue-specific expression of some may affect human longevity.
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Affiliation(s)
- Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Pooja Jha
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Riekelt Houtkooper
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee, Memphis, TN 38163, USA
| | - Xu Wang
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.
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196
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Nakao M, Tanaka H, Koga T. Cellular Senescence Variation by Metabolic and Epigenomic Remodeling. Trends Cell Biol 2020; 30:919-922. [PMID: 32978041 DOI: 10.1016/j.tcb.2020.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/19/2022]
Abstract
Cellular senescence is a state of permanent cell cycle arrest accompanied by unique secretory actions, which influences tissue formation, tumor suppression and aging in vivo. Recent evidences suggest that metabolic and epigenomic reprogram cooperatively creates phenotypic differences of senescent cells, which may provide new clues to control aging processes.
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Affiliation(s)
- Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Japan.
| | - Hiroshi Tanaka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Japan
| | - Tomoaki Koga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Japan
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197
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Samoylova EM, Baklaushev VP. Cell Reprogramming Preserving Epigenetic Age: Advantages and Limitations. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1035-1047. [PMID: 33050850 DOI: 10.1134/s0006297920090047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 11/23/2022]
Abstract
Our understanding of cell aging advanced significantly since the discovery of this phenomenon by Hayflick and Moorhead in 1961. In addition to the well-known shortening of telomeric regions of chromosomes, cell aging is closely associated with changes of the DNA methylation profile. Establishing, maintaining, or reversing epigenetic age of a cell is central to the technology of cell reprogramming. Two distinct approaches - iPSC- and transdifferentiation-based cell reprogramming - affect differently epigenetic age of the cells. The iPSC-based reprogramming protocols are generally believed to result in the reversion of DNA methylation profiles towards less differentiated states, while the original methylation profiles are preserved in the direct trans-differentiation protocols. Clearly, in order to develop adequate model of CNS pathologies, one has to have thorough understanding of the biological roles of DNA methylation in the development, maintenance of functional activity, tissue and cell diversity, restructuring of neural networks during learning, as well as in aging-associated neuronal decline. Direct cell reprogramming is an excellent alternative and a valuable supplement to the iPSC-based technologies both as a source of mature cells for modeling of neurodegenerative diseases, and as a novel powerful strategy for in vivo cell replacement therapy. Further advancement of the regenerative and personalized medicine will strongly depend on optimization of the production of patient-specific autologous cells involving alternative approaches of direct and indirect cell reprogramming that take into account epigenetic age of the starting cell material.
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Affiliation(s)
- E M Samoylova
- Federal Research Clinical Center, FMBA of Russia, Moscow, 115682, Russia.
| | - V P Baklaushev
- Federal Research Clinical Center, FMBA of Russia, Moscow, 115682, Russia
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198
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Li Q, Xiang YH, Liang XJ, Zhang Y, Zhao PP, Wang M, Bao XM, Zhu XB, Deng AC. Expression of G9a in Auditory Cortex Is Downregulated in a Rat Model of Age-Related Hearing Loss. J Mol Neurosci 2020; 71:409-418. [PMID: 32671696 DOI: 10.1007/s12031-020-01663-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/08/2020] [Indexed: 01/11/2023]
Abstract
G9a is essential for dendritic plasticity and is associated with neurological disorders. The possible relationship between age-related hearing loss and G9a expression in the auditory cortex has not been fully explored. This study aimed to understand the expression patterns of G9a-mediated histone methylations in the auditory cortex during aging. Using immunofluorescence and western blotting, we demonstrated that a significant reduction in G9a expression observed in the auditory cortex of 24-month-old rats compared to 3-month-old rats, was associated with remarkable hearing threshold elevation and hair cell loss. Correspondingly, histone H3 lysine 9 (H3K9) mono- and dimethylation (marked by H3K9me1 and H3K9me2, respectively), which were regulated by G9a activity, also evidently decreased during aging. These findings, which merit further investigation, suggest a possible association between G9a-mediated histone methylations and central age-related hearing disorders.
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Affiliation(s)
- Qian Li
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yang-Hong Xiang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xiao-Jun Liang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yun Zhang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Peng-Peng Zhao
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Min Wang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xiao-Min Bao
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xian-Bai Zhu
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - An-Chun Deng
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
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199
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Epigenetic Clock: DNA Methylation in Aging. Stem Cells Int 2020; 2020:1047896. [PMID: 32724310 PMCID: PMC7366189 DOI: 10.1155/2020/1047896] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/20/2020] [Indexed: 02/07/2023] Open
Abstract
Aging, which is accompanied by decreased organ function and increased disease incidence, limits human lifespan and has attracted investigators for thousands of years. In recent decades, with the rapid development of biology, scientists have shown that epigenetic modifications, especially DNA methylation, are key regulators involved in this process. Regular fluctuations in global DNA methylation levels have been shown to accurately estimate biological age and disease prognosis. In this review, we discuss recent findings regarding the relationship between variations in DNA methylation level patterns and aging. In addition, we introduce the known mechanisms by which DNA methylation regulators affect aging and related diseases. As more studies uncover the mechanisms by which DNA methylation regulates aging, antiaging interventions and treatments for related diseases may be developed that enable human life extension.
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200
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Walker C, Burggren W. Remodeling the epigenome and (epi)cytoskeleton: a new paradigm for co-regulation by methylation. ACTA ACUST UNITED AC 2020; 223:223/13/jeb220632. [PMID: 32620673 DOI: 10.1242/jeb.220632] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The epigenome determines heritable patterns of gene expression in the absence of changes in DNA sequence. The result is programming of different cellular-, tissue- and organ-specific phenotypes from a single organismic genome. Epigenetic marks that comprise the epigenome (e.g. methylation) are placed upon or removed from chromatin (histones and DNA) to direct the activity of effectors that regulate gene expression and chromatin structure. Recently, the cytoskeleton has been identified as a second target for the cell's epigenetic machinery. Several epigenetic 'readers, writers and erasers' that remodel chromatin have been discovered to also remodel the cytoskeleton, regulating structure and function of microtubules and actin filaments. This points to an emerging paradigm for dual-function remodelers with 'chromatocytoskeletal' activity that can integrate cytoplasmic and nuclear functions. For example, the SET domain-containing 2 methyltransferase (SETD2) has chromatocytoskeletal activity, methylating both histones and microtubules. The SETD2 methyl mark on chromatin is required for efficient DNA repair, and its microtubule methyl mark is required for proper chromosome segregation during mitosis. This unexpected convergence of SETD2 activity on histones and microtubules to maintain genomic stability suggests the intriguing possibility of an expanded role in the cell for chromatocytoskeletal proteins that read, write and erase methyl marks on the cytoskeleton as well as chromatin. Coordinated use of methyl marks to remodel both the epigenome and the (epi)cytoskeleton opens the possibility for integrated regulation (which we refer to as 'epiregulation') of other higher-level functions, such as muscle contraction or learning and memory, and could even have evolutionary implications.
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Affiliation(s)
- Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Warren Burggren
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
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