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Meyer DH, Schumacher B. Aging clocks based on accumulating stochastic variation. NATURE AGING 2024; 4:871-885. [PMID: 38724736 PMCID: PMC11186771 DOI: 10.1038/s43587-024-00619-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Aging clocks have provided one of the most important recent breakthroughs in the biology of aging, and may provide indicators for the effectiveness of interventions in the aging process and preventive treatments for age-related diseases. The reproducibility of accurate aging clocks has reinvigorated the debate on whether a programmed process underlies aging. Here we show that accumulating stochastic variation in purely simulated data is sufficient to build aging clocks, and that first-generation and second-generation aging clocks are compatible with the accumulation of stochastic variation in DNA methylation or transcriptomic data. We find that accumulating stochastic variation is sufficient to predict chronological and biological age, indicated by significant prediction differences in smoking, calorie restriction, heterochronic parabiosis and partial reprogramming. Although our simulations may not explicitly rule out a programmed aging process, our results suggest that stochastically accumulating changes in any set of data that have a ground state at age zero are sufficient for generating aging clocks.
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Affiliation(s)
- David H Meyer
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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2
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Okada D. Application of a mathematical model to clarify the statistical characteristics of a pan-tissue DNA methylation clock. GeroScience 2024; 46:2001-2015. [PMID: 37787856 PMCID: PMC10828133 DOI: 10.1007/s11357-023-00949-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023] Open
Abstract
DNA methylation clocks estimate biological age based on DNA methylation profiles. This study developed a mathematical model to describe DNA methylation aging and the establishment of a pan-tissue DNA methylation clock. The model simulates the aging dynamics of DNA methylation profiles based on passive demethylation as well as the process of cross-sectional bulk data acquisition. As a result, this study identified two conditions under which the pan-tissue DNA methylation clock can successfully predict biological age: one condition is that the target tissues are sufficiently well represented in the training dataset, and the other condition is that the target sample contains cell subsets that are common among different tissues. When either of these conditions is met, the clock performs well. It is also suggested that the epigenetic age of all samples in the target tissue tends to be either over or underestimated when biological age prediction fails. The model can reveal the statistical characteristics of DNA methylation clocks.
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Affiliation(s)
- Daigo Okada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, 53 Syogoin-Kawaramachi, Sakyo-ku, Kyoto, Kyoto, 606-8507, Japan.
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3
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Sarandy MM, Gonçalves RV, Valacchi G. Cutaneous Redox Senescence. Biomedicines 2024; 12:348. [PMID: 38397950 PMCID: PMC10886899 DOI: 10.3390/biomedicines12020348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Our current understanding of skin cell senescence involves the role of environmental stressors (UV, O3, cigarette smoke, particulate matter, etc.), lifestyle (diet, exercise, etc.) as well as genetic factors (metabolic changes, hormonal, etc.). The common mechanism of action of these stressors is the disturbance of cellular redox balance characterized by increased free radicals and reactive oxygen species (ROS), and when these overload the intrinsic antioxidant defense system, it can lead to an oxidative stress cellular condition. The main redox mechanisms that activate cellular senescence in the skin involve (1) the oxidative damage of telomeres causing their shortening; (2) the oxidation of proteomes and DNA damage; (3) an a in lysosomal mass through the increased activity of resident enzymes such as senescence-associated β-galactosidase (SA-β-gal) as well as other proteins that are products of lysosomal activity; (4) and the increased expression of SASP, in particular pro-inflammatory cytokines transcriptionally regulated by NF-κB. However, the main targets of ROS on the skin are the proteome (oxi-proteome), followed by telomeres, nucleic acids (DNAs), lipids, proteins, and cytoplasmic organelles. As a result, cell cycle arrest pathways, lipid peroxidation, increased lysosomal content and dysfunctional mitochondria, and SASP synthesis occur. Furthermore, oxidative stress in skin cells increases the activity of p16INK4A and p53 as inhibitors of Rb and CDks, which are important for maintaining the cell cycle. p53 also promotes the inactivation of mTOR-mediated autophagic and apoptotic pathways, leading to senescence. However, these markers alone cannot establish the state of cellular senescence, and multiple analyses are encouraged for confirmation. An updated and more comprehensive approach to investigating skin senescence should include further assays of ox-inflammatory molecular pathways that can consolidate the understanding of cutaneous redox senescence.
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Affiliation(s)
- Mariáurea Matias Sarandy
- Department of Animal Science, Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil
| | - Reggiani Vilela Gonçalves
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil
- Department of Animal Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil
| | - Giuseppe Valacchi
- Department of Animal Science, Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA
- Department of Environment and Prevention, University of Ferrara, 44121 Ferrara, Italy
- Department of Food and Nutrition, Kyung Hee University, Seoul 02447, Republic of Korea
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4
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Eremeev A, Pikina A, Ruchko Y, Bogomazova A. Clinical Potential of Cellular Material Sources in the Generation of iPSC-Based Products for the Regeneration of Articular Cartilage. Int J Mol Sci 2023; 24:14408. [PMID: 37833856 PMCID: PMC10572671 DOI: 10.3390/ijms241914408] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023] Open
Abstract
Inflammatory joint diseases, among which osteoarthritis and rheumatoid arthritis are the most common, are characterized by progressive degeneration of the cartilage tissue, resulting in the threat of limited or lost joint functionality in the absence of treatment. Currently, treating these diseases is difficult, and a number of existing treatment and prevention measures are not entirely effective and are complicated by the patients' conditions, the multifactorial nature of the pathology, and an incomplete understanding of the etiology. Cellular technologies based on induced pluripotent stem cells (iPSCs) can provide a vast cellular resource for the production of artificial cartilage tissue for replacement therapy and allow the possibility of a personalized approach. However, the question remains whether a number of etiological abnormalities associated with joint disease are transmitted from the source cell to iPSCs and their chondrocyte derivatives. Some data state that there is no difference between the iPSCs and their derivatives from healthy and sick donors; however, there are other data indicating a dissimilarity. Therefore, this topic requires a thorough study of the differentiation potential of iPSCs and the factors influencing it, the risk factors associated with joint diseases, and a comparative analysis of the characteristics of cells obtained from patients. Together with cultivation optimization methods, these measures can increase the efficiency of obtaining cell technology products and make their wide practical application possible.
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Affiliation(s)
- Artem Eremeev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435, Russia; (A.P.); (A.B.)
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, Moscow 119334, Russia;
| | - Arina Pikina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435, Russia; (A.P.); (A.B.)
- Department of Embryology, Faculty of Biology, Lomonosov Moscow State University, GSP-1 Leninskie Gory, Moscow 119991, Russia
| | - Yevgeny Ruchko
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, Moscow 119334, Russia;
| | - Alexandra Bogomazova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435, Russia; (A.P.); (A.B.)
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5
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Salz L, Seitz A, Schäfer D, Franzen J, Holzer T, Garcia-Prieto CA, Bürger I, Hardt O, Esteller M, Wagner W. Culture expansion of CAR T cells results in aberrant DNA methylation that is associated with adverse clinical outcome. Leukemia 2023; 37:1868-1878. [PMID: 37452103 PMCID: PMC10457202 DOI: 10.1038/s41375-023-01966-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Chimeric antigen receptor (CAR) T cells provide new perspectives for treatment of hematological malignancies. Manufacturing of these cellular products includes culture expansion procedures, which may affect cellular integrity and therapeutic outcome. In this study, we investigated culture-associated epigenetic changes in CAR T cells and found continuous gain of DNAm, particularly within genes that are relevant for T cell function. Hypermethylation in many genes, such as TCF7, RUNX1, and TOX, was reflected by transcriptional downregulation. 332 CG dinucleotides (CpGs) showed an almost linear gain in methylation with cell culture time, albeit neighboring CpGs were not coherently regulated on the same DNA strands. An epigenetic signature based on 14 of these culture-associated CpGs predicted cell culture time across various culture conditions. Notably, even in CAR T cell products of similar culture time higher DNAm levels at these CpGs were associated with significantly reduced long-term survival post transfusion. Our data demonstrate that cell culture expansion of CAR T cells evokes DNA hypermethylation at specific sites in the genome and the signature may also reflect loss of potential in CAR T cell products. Hence, reduced cultivation periods are beneficial to avoid dysfunctional methylation programs that seem to be associated with worse therapeutic outcome.
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Affiliation(s)
- Lucia Salz
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Alexander Seitz
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Daniel Schäfer
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Julia Franzen
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Tatjana Holzer
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Carlos A Garcia-Prieto
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Iris Bürger
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Olaf Hardt
- Miltenyi Biotec B.V. & Co. KG, Bergisch, Gladbach, Germany
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.
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6
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Rosa GP, Peixoto AF, Barreto MC, Seca AML, Pinto DCGA. Bio-Guided Optimization of Cystoseira abies-marina Cosmeceuticals Extraction by Advanced Technologies. Mar Drugs 2022; 21:35. [PMID: 36662208 PMCID: PMC9861939 DOI: 10.3390/md21010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/17/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Cystoseira abies-marina (reclassified as Gongolaria abies-marina) is a brown seaweed species rich in meroterpenoids, presenting interesting antioxidant, antitumor, and anti-inflammatory activities. However, there is still a lot to uncover regarding the bioactive potential of this species, as evidenced by the lack of records of antiaging activities from Cystoseira abies-marina, making this macroalga an excellent candidate for studies of its cosmeceutical potential. Ultrasound-(UAE) and microwave-assisted extraction (MAE) are advanced sustainable technologies that are very efficient in enhancing bioactive compound extraction. Applying these extraction techniques to a new biological matrix often calls for optimizing the parameters toward the best extraction yield. Since Cystoseira abies-marina is a new matrix for both UAE and MAE techniques, the present work proposes the optimization of the extraction process, using a novel approach: instead of only focusing on increasing the yield, the goal of this work is to determine the parameters for UAE and MAE that lead to extracts with better antiaging activities. For this bio-guided approach, several Cystoseira abies-marina extracts were prepared by UAE and MAE under varying conditions of solvent, time, and algae/solvent ratios. Their antiaging activities were then determined, and all the results combined to unveil the conditions yielding extracts with higher cosmeceutical potential. Using statistical tools, it was found that, for UAE, the best conditions were ethyl acetate, 15 min, and a ratio of 1:4, which led to an extract with high yield, and causing the strong inhibition of tyrosinase and elastase. In turn, ethanol, 10 min, and a ratio of 1:4 were the best conditions for MAE, leading to the extract with the best antioxidant activity. The results show that the proposed bio-guided approach was effective in obtaining extracts with high cosmeceutical potential, unveiling the possibility of modulating an extract's activity by changing the extraction method.
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Affiliation(s)
- Gonçalo P. Rosa
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE—Global Change and Sustainability Institute, Faculty of Sciences and Technology, University of the Azores, 9500-321 Ponta Delgada, Portugal
| | - Andreia F. Peixoto
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Maria Carmo Barreto
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE—Global Change and Sustainability Institute, Faculty of Sciences and Technology, University of the Azores, 9500-321 Ponta Delgada, Portugal
| | - Ana M. L. Seca
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE—Global Change and Sustainability Institute, Faculty of Sciences and Technology, University of the Azores, 9500-321 Ponta Delgada, Portugal
| | - Diana C. G. A. Pinto
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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7
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Fraile M, Eiro N, Costa LA, Martín A, Vizoso FJ. Aging and Mesenchymal Stem Cells: Basic Concepts, Challenges and Strategies. BIOLOGY 2022; 11:1678. [PMID: 36421393 PMCID: PMC9687158 DOI: 10.3390/biology11111678] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 08/27/2023]
Abstract
Aging and frailty are complex processes implicating multifactorial mechanisms, such as replicative senescence, oxidative stress, mitochondrial dysfunction, or autophagy disorder. All of these mechanisms drive dramatic changes in the tissue environment, such as senescence-associated secretory phenotype factors and inflamm-aging. Thus, there is a demand for new therapeutic strategies against the devastating effects of the aging and associated diseases. Mesenchymal stem cells (MSC) participate in a "galaxy" of tissue signals (proliferative, anti-inflammatory, and antioxidative stress, and proangiogenic, antitumor, antifibrotic, and antimicrobial effects) contributing to tissue homeostasis. However, MSC are also not immune to aging. Three strategies based on MSC have been proposed: remove, rejuvenate, or replace the senescent MSC. These strategies include the use of senolytic drugs, antioxidant agents and genetic engineering, or transplantation of younger MSC. Nevertheless, these strategies may have the drawback of the adverse effects of prolonged use of the different drugs used or, where appropriate, those of cell therapy. In this review, we propose the new strategy of "Exogenous Restitution of Intercellular Signalling of Stem Cells" (ERISSC). This concept is based on the potential use of secretome from MSC, which are composed of molecules such as growth factors, cytokines, and extracellular vesicles and have the same biological effects as their parent cells. To face this cell-free regenerative therapy challenge, we have to clarify key strategy aspects, such as establishing tools that allow us a more precise diagnosis of aging frailty in order to identify the therapeutic requirements adapted to each case, identify the ideal type of MSC in the context of the functional heterogeneity of these cellular populations, to optimize the mass production and standardization of the primary materials (cells) and their secretome-derived products, to establish the appropriate methods to validate the anti-aging effects and to determine the most appropriate route of administration for each case.
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Affiliation(s)
- Maria Fraile
- Research Unit, Fundación Hospital de Jove, Avda. Eduardo Castro, 161, 33920 Gijon, Spain
| | - Noemi Eiro
- Research Unit, Fundación Hospital de Jove, Avda. Eduardo Castro, 161, 33920 Gijon, Spain
| | - Luis A. Costa
- Research Unit, Fundación Hospital de Jove, Avda. Eduardo Castro, 161, 33920 Gijon, Spain
| | - Arancha Martín
- Research Unit, Fundación Hospital de Jove, Avda. Eduardo Castro, 161, 33920 Gijon, Spain
- Department of Emergency, Hospital Universitario de Cabueñes, Los Prados, 395, 33394 Gijon, Spain
| | - Francisco J. Vizoso
- Research Unit, Fundación Hospital de Jove, Avda. Eduardo Castro, 161, 33920 Gijon, Spain
- Department of Surgery, Fundación Hospital de Jove, Avda. Eduardo Castro, 161, 33920 Gijon, Spain
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8
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Li A, Koch Z, Ideker T. Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging. J Intern Med 2022; 292:733-744. [PMID: 35726002 DOI: 10.1111/joim.13533] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Numerous studies have shown that epigenetic age-an individual's degree of aging based on patterns of DNA methylation-can be computed and is associated with an array of factors including diet, lifestyle, genetics, and disease. One can expect that still further associations will emerge with additional aging research, but to what end? Prediction of age was an important first step, but-in our view-the focus must shift from chasing increasingly accurate age computations to understanding the links between the epigenome and the mechanisms and physiological changes of aging. Here, we outline emerging areas of epigenetic aging research that prioritize biological understanding and clinical application. First, we survey recent progress in epigenetic clocks, which are beginning to predict not only chronological age but aging outcomes such as all-cause mortality and onset of disease, or which integrate aging signals across multiple biological processes. Second, we discuss research that exemplifies how investigation of the epigenome is building a mechanistic theory of aging and informing clinical practice. Such examples include identifying methylation sites and the genes most strongly predictive of aging-a subset of which have shown strong potential as biomarkers of neurodegenerative disease and cancer; relating epigenetic clock predictions to hallmarks of aging; and using longitudinal studies of DNA methylation to characterize human disease, resulting in the discovery of epigenetic indications of type 1 diabetes and the propensity for psychotic experiences.
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Affiliation(s)
- Adam Li
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zane Koch
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California, USA
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9
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Abstract
Cellular senescence is implicated in a wide range of physiological and pathological conditions throughout an organism's entire lifetime. In particular, it has become evident that senescence plays a causative role in aging and age-associated disorders. This is not due simply to the loss of function of senescent cells. Instead, the substantial alterations of the cellular activities of senescent cells, especially the array of secretory factors, impact the surrounding tissues or even entire organisms. Such non-cell-autonomous functionality is largely coordinated by tissue-specific genes, constituting a cell fate-determining state. Senescence can be viewed as a gain-of-function phenotype or a process of cell identity shift. Cellular functionality or lineage-specific gene expression is tightly linked to the cell type-specific epigenetic landscape, reinforcing the heterogeneity of senescence across cell types. Here, we aim to define the senescence cellular functionality and epigenetic features that may contribute to the gain-of-function phenotype.
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Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom; ,
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10
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Xu J, Liu D, Zhao D, Jiang X, Meng X, Jiang L, Yu M, Zhang L, Jiang H. Role of low-dose radiation in senescence and aging: A beneficial perspective. Life Sci 2022; 302:120644. [PMID: 35588864 DOI: 10.1016/j.lfs.2022.120644] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023]
Abstract
Cellular senescence refers to the permanent arrest of cell cycle caused by intrinsic and/or extrinsic stressors including oncogene activation, irradiation, DNA damage, oxidative stress, and certain cytokines (including senescence associated secretory phenotype). Cellular senescence is an important factor in aging. Accumulation of senescent cells has been implicated in the causation of various age-related organ disorders, tissue dysfunction, and chronic diseases. It is widely accepted that the biological effects triggered by low-dose radiation (LDR) are different from those caused by high-dose radiation. Experimental evidence suggests that LDR may promote growth and development, enhance longevity, induce embryo production, and delay the progression of chronic diseases. The underlying mechanisms of these effects include modulation of immune response, stimulation of hematopoietic system, antioxidative effect, reduced DNA damage and improved ability for DNA damage repair. In this review, we discuss the possible mechanisms by which LDR prevents senescence and aging from the perspectives of inhibiting cellular senescence and promoting the removal of senescent cells. We review a wide broad of evidence about the beneficial impact of LDR in senescence and aging models (including cardiovascular diseases, neurological diseases, arthritis and osteoporosis, chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis) to highlight the potential value of LDR in preventing aging and age-related diseases. However, there is no consensus on the effect of LDR on human health, and several important aspects require further investigation.
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Affiliation(s)
- Jing Xu
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Dandan Liu
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Di Zhao
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Xin Jiang
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Xinxin Meng
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Lili Jiang
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Meina Yu
- Department of Special Clinic, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Long Zhang
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China
| | - Hongyu Jiang
- Department of Health Examination Center, The First Hospital of Jilin University, Changchun 130001, Jilin, China.
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11
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Higgins-Chen AT, Thrush KL, Wang Y, Minteer CJ, Kuo PL, Wang M, Niimi P, Sturm G, Lin J, Moore AZ, Bandinelli S, Vinkers CH, Vermetten E, Rutten BPF, Geuze E, Okhuijsen-Pfeifer C, van der Horst MZ, Schreiter S, Gutwinski S, Luykx JJ, Picard M, Ferrucci L, Crimmins EM, Boks MP, Hägg S, Hu-Seliger TT, Levine ME. A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking. NATURE AGING 2022; 2:644-661. [PMID: 36277076 PMCID: PMC9586209 DOI: 10.1038/s43587-022-00248-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/08/2022] [Indexed: 01/09/2023]
Abstract
Epigenetic clocks are widely used aging biomarkers calculated from DNA methylation data, but this data can be surprisingly unreliable. Here we show technical noise produces deviations up to 9 years between replicates for six prominent epigenetic clocks, limiting their utility. We present a computational solution to bolster reliability, calculating principal components from CpG-level data as input for biological age prediction. Our retrained principal-component versions of six clocks show agreement between most replicates within 1.5 years, improved detection of clock associations and intervention effects, and reliable longitudinal trajectories in vivo and in vitro. This method entails only one additional step compared to traditional clocks, requires no replicates or prior knowledge of CpG reliabilities for training, and can be applied to any existing or future epigenetic biomarker. The high reliability of principal component-based clocks is critical for applications to personalized medicine, longitudinal tracking, in vitro studies, and clinical trials of aging interventions.
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Affiliation(s)
- Albert T Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Kyra L Thrush
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Pei-Lun Kuo
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Meng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Peter Niimi
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Gabriel Sturm
- Departments of Psychiatry and Neurology, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
- New York State Psychiatric Institute, New York, NY United States
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, United States
| | - Ann Zenobia Moore
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | | | - Christiaan H Vinkers
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Eric Vermetten
- Department Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Bart P F Rutten
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Elbert Geuze
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, The Netherlands
- Brain Research & Innovation Centre, Ministry of Defence, Utrecht, the Netherlands
| | - Cynthia Okhuijsen-Pfeifer
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Marte Z van der Horst
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, The Netherlands
- Second Opinion Outpatient Clinic, GGNet Mental Health, Warnsveld, The Netherlands
| | - Stefanie Schreiter
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Gutwinski
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jurjen J Luykx
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, The Netherlands
- Second Opinion Outpatient Clinic, GGNet Mental Health, Warnsveld, The Netherlands
| | - Martin Picard
- Departments of Psychiatry and Neurology, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, United States
- New York State Psychiatric Institute, New York, NY United States
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Eileen M Crimmins
- Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Morgan E Levine
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
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12
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Galow AM, Peleg S. How to Slow down the Ticking Clock: Age-Associated Epigenetic Alterations and Related Interventions to Extend Life Span. Cells 2022; 11:468. [PMID: 35159278 PMCID: PMC8915189 DOI: 10.3390/cells11030468] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic alterations pose one major hallmark of organismal aging. Here, we provide an overview on recent findings describing the epigenetic changes that arise during aging and in related maladies such as neurodegeneration and cancer. Specifically, we focus on alterations of histone modifications and DNA methylation and illustrate the link with metabolic pathways. Age-related epigenetic, transcriptional and metabolic deregulations are highly interconnected, which renders dissociating cause and effect complicated. However, growing amounts of evidence support the notion that aging is not only accompanied by epigenetic alterations, but also at least in part induced by those. DNA methylation clocks emerged as a tool to objectively determine biological aging and turned out as a valuable source in search of factors positively and negatively impacting human life span. Moreover, specific epigenetic signatures can be used as biomarkers for age-associated disorders or even as targets for therapeutic approaches, as will be covered in this review. Finally, we summarize recent potential intervention strategies that target epigenetic mechanisms to extend healthy life span and provide an outlook on future developments in the field of longevity research.
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Affiliation(s)
- Anne-Marie Galow
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Shahaf Peleg
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
- Institute of Neuroregeneration and Neurorehabilitation of Qingdao University, Qingdao 266071, China
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13
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LEMOS VANESSAP, PORTO MICHELE, CEZAR RAFAELDAS, SANTOS BRUNOPDOS, SOUZA MELISSARDE, SILVA JULIANADA, NARDI NANCEB, CAMASSOLA MELISSA. Comparison of senescence phenotype of short- and long- term cultured rat mesenchymal stem cells in vitro. AN ACAD BRAS CIENC 2022; 94:e20211246. [DOI: 10.1590/0001-3765202220211246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/12/2022] [Indexed: 11/22/2022] Open
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14
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Sahabi S, Jafari-Gharabaghlou D, Zarghami N. A new insight into cell biological and biochemical changes through aging. Acta Histochem 2022; 124:151841. [PMID: 34995929 DOI: 10.1016/j.acthis.2021.151841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022]
Abstract
After several years of extensive research, the main cause of aging is yet elusive. There are some theories about aging, such as stem cell aging, senescent cells accumulation, and neuro-endocrine theories. None of them is able to explain all changes that happen in cells and body through aging. By finding out the main cause of aging, it will be much easier to control, prevent and even reverse the aging process. Our cells, regardless of their replicative capacity, get old through aging and they have almost the same epigenetic age. Different cell signaling pathways contribute to aging. The most important one is mTORC1 that becomes hyperactive in cells that undergo aging. Other significant changes with age are lysosome accumulation, impaired autophagy, and mitophagy. Immune system undergoes gradual changes through aging including a shift from lymphoid to myeloid lineage production as well as increased IL-6 and TNF-α which lead to age-related weight loss and meta-inflammation. Additionally, our endocrine system also experiences some changes that should be taken into consideration when looking for the main cause of aging in the human body. In this review, we planned to summarize some of the changes that happen in cells and the body through aging.
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15
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Mesenchymal Stem Cell Senescence and Osteogenesis. Medicina (B Aires) 2021; 58:medicina58010061. [PMID: 35056369 PMCID: PMC8779043 DOI: 10.3390/medicina58010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are stem cells with the potential ability to differentiate into various cells and the ability to self-renew and resemble fibroblasts. These cells can adhere to plastic to facilitate the culture process. MSCs can be used in research into tissue biotechnology and rejuvenation medicine. MSCs are also beneficial in recipient tissue and differentiate as a breakthrough strategy through paracrine activity. Many databases have shown MSC-based treatment can be beneficial in the reduction of osteogenesis induced by senescence. In this article, we will discuss the potential effect of MSCs in senescence cells related to osteogenesis.
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16
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Wang J, Liu W, Yu D, Yang Z, Li S, Sun X. Research Progress on the Treatment of Premature Ovarian Failure Using Mesenchymal Stem Cells: A Literature Review. Front Cell Dev Biol 2021; 9:749822. [PMID: 34966738 PMCID: PMC8710809 DOI: 10.3389/fcell.2021.749822] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/29/2021] [Indexed: 12/31/2022] Open
Abstract
Premature ovarian failure (POF) has become one of the main causes of infertility in women of childbearing age and the incidence of POF is increasing year by year, seriously affecting the physical and mental health of patients and increasing the economic burden on families and society as a whole. The etiology and pathogenesis of POF are complex and not very clear at present. Currently, hormone replacement therapy is mainly used to improve the symptoms of low estrogen, but cannot fundamentally solve the fertility problem. In recent years, stem cell (SC) transplantation has become one of the research hotspots in the treatment of POF. The results from animal experiments bring hope for the recovery of ovarian function and fertility in patients with POF. In this article, we searched the published literature between 2000 and 2020 from the PubMed database (https://pubmed.ncbi.nlm.nih.gov), and summarized the preclinical research data and possible therapeutic mechanism of mesenchymal stem cells (MSCs) in the treatment of POF. Our aim is to provide useful information for understanding POF and reference for follow-up research and treatment of POF.
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Affiliation(s)
- Jing Wang
- Department of Reproductive Medicine, Department of Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, China
| | - Wanru Liu
- Department of Reproductive Medicine, Department of Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, China
| | - Dehai Yu
- The Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China
| | - Zongxing Yang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Sijie Li
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xiguang Sun
- Hand Surgery Department, The First Hospital of Jilin University, Changchun, China
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17
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Woodward K, Shirokikh NE. Translational control in cell ageing: an update. Biochem Soc Trans 2021; 49:2853-2869. [PMID: 34913471 PMCID: PMC8786278 DOI: 10.1042/bst20210844] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/28/2022]
Abstract
Cellular ageing is one of the main drivers of organismal ageing and holds keys towards improving the longevity and quality of the extended life. Elucidating mechanisms underlying the emergence of the aged cells as well as their altered responses to the environment will help understanding the evolutionarily defined longevity preferences across species with different strategies of survival. Much is understood about the role of alterations in the DNA, including many epigenetic modifications such as methylation, in relation to the aged cell phenotype. While transcriptomes of the aged cells are beginning to be better-characterised, their translational responses remain under active investigation. Many of the translationally controlled homeostatic pathways are centred around mitigation of DNA damage, cell stress response and regulation of the proliferative potential of the cells, and thus are critical for the aged cell function. Translation profiling-type studies have boosted the opportunities in discovering the function of protein biosynthesis control and are starting to be applied to the aged cells. Here, we provide a summary of the current knowledge about translational mechanisms considered to be commonly altered in the aged cells, including the integrated stress response-, mechanistic target of Rapamycin- and elongation factor 2 kinase-mediated pathways. We enlist and discuss findings of the recent works that use broad profiling-type approaches to investigate the age-related translational pathways. We outline the limitations of the methods and the remaining unknowns in the established ageing-associated translation mechanisms, and flag translational mechanisms with high prospective importance in ageing, for future studies.
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Affiliation(s)
- Katrina Woodward
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, ACT 2601, Australia
| | - Nikolay E. Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, ACT 2601, Australia
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18
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Chao CC, Shen PW, Tzeng TY, Kung HJ, Tsai TF, Wong YH. Human iPSC-Derived Neurons as A Platform for Deciphering the Mechanisms behind Brain Aging. Biomedicines 2021; 9:1635. [PMID: 34829864 PMCID: PMC8615703 DOI: 10.3390/biomedicines9111635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
With an increased life expectancy among humans, aging has recently emerged as a major focus in biomedical research. The lack of in vitro aging models-especially for neurological disorders, where access to human brain tissues is limited-has hampered the progress in studies on human brain aging and various age-associated neurodegenerative diseases at the cellular and molecular level. In this review, we provide an overview of age-related changes in the transcriptome, in signaling pathways, and in relation to epigenetic factors that occur in senescent neurons. Moreover, we explore the current cell models used to study neuronal aging in vitro, including immortalized cell lines, primary neuronal culture, neurons directly converted from fibroblasts (Fib-iNs), and iPSC-derived neurons (iPSC-iNs); we also discuss the advantages and limitations of these models. In addition, the key phenotypes associated with cellular senescence that have been observed by these models are compared. Finally, we focus on the potential of combining human iPSC-iNs with genome editing technology in order to further our understanding of brain aging and neurodegenerative diseases, and discuss the future directions and challenges in the field.
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Affiliation(s)
- Chuan-Chuan Chao
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Department of Neurology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Wen Shen
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan;
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tsai-Yu Tzeng
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California at Davis, Sacramento, CA 95817, USA
| | - Ting-Fen Tsai
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Hui Wong
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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19
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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20
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The Impact of Stress Within and Across Generations: Neuroscientific and Epigenetic Considerations. Harv Rev Psychiatry 2021; 29:303-317. [PMID: 34049337 DOI: 10.1097/hrp.0000000000000300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The impact of stress and trauma on biological systems in humans can be substantial. They can result in epigenetic changes, accelerated brain development and sexual maturation, and predisposition to psychopathology. Such modifications may be accompanied by behavioral, emotional, and cognitive overtones during one's lifetime. Exposure during sensitive periods of neural development may lead to long-lasting effects that may not be affected by subsequent environmental interventions. The cumulative effects of life stressors in an individual may affect offspring's methylome makeup and epigenetic clocks, neurohormonal modulation and stress reactivity, and physiological and reproductive development. While offspring may suffer deleterious effects from parental stress and their own early-life adversity, these factors may also confer traits that prove beneficial and enhance fitness to their own environment. This article synthesizes the data on how stress shapes biological and behavioral dimensions, drawing from preclinical and human models. Advances in this field of knowledge should potentially allow for an improved understanding of how interventions may be increasingly tailored according to individual biomarkers and developmental history.
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21
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Steg LC, Shireby GL, Imm J, Davies JP, Franklin A, Flynn R, Namboori SC, Bhinge A, Jeffries AR, Burrage J, Neilson GWA, Walker EM, Perfect LW, Price J, McAlonan G, Srivastava DP, Bray NJ, Cope EL, Jones KM, Allen ND, Pishva E, Dempster EL, Lunnon K, Mill J, Hannon E. Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons. Mol Brain 2021; 14:98. [PMID: 34174924 PMCID: PMC8236187 DOI: 10.1186/s13041-021-00810-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.
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Affiliation(s)
- Leonard C Steg
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Gemma L Shireby
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jennifer Imm
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jonathan P Davies
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Alice Franklin
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Robert Flynn
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Seema C Namboori
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Akshay Bhinge
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Aaron R Jeffries
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Joe Burrage
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Grant W A Neilson
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Emma M Walker
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Leo W Perfect
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Grainne McAlonan
- Department of Forensic and Neurodevelopmental Sciences, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Behavioural and Developmental Psychiatry, South London and Maudsley NHS Foundation Trust, London, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Nicholas J Bray
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Emma L Cope
- School of Biosciences, Cardiff University, Cardiff, UK
| | | | | | - Ehsan Pishva
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Emma L Dempster
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Eilis Hannon
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK.
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22
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DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift. Commun Biol 2021; 4:598. [PMID: 34011964 PMCID: PMC8134454 DOI: 10.1038/s42003-021-02116-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/14/2021] [Indexed: 12/27/2022] Open
Abstract
Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift. Julia Franzen et al. investigate if changes in DNA methylation at specific genetic loci during cell culture expansion are due to a specific mechanism or gradual deregulation of an epigenetic state. Their results suggest that changes in CpG methylation are due to indirect epigenetic drift, rather than a consequence of targeting by DNA methyltransferases.
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23
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Hägg S, Jylhävä J. Sex differences in biological aging with a focus on human studies. eLife 2021; 10:e63425. [PMID: 33982659 PMCID: PMC8118651 DOI: 10.7554/elife.63425] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Aging is a complex biological process characterized by hallmark features accumulating over the life course, shaping the individual's aging trajectory and subsequent disease risks. There is substantial individual variability in the aging process between men and women. In general, women live longer than men, consistent with lower biological ages as assessed by molecular biomarkers, but there is a paradox. Women are frailer and have worse health at the end of life, while men still perform better in physical function examinations. Moreover, many age-related diseases show sex-specific patterns. In this review, we aim to summarize the current knowledge on sexual dimorphism in human studies, with support from animal research, on biological aging and illnesses. We also attempt to place it in the context of the theories of aging, as well as discuss the explanations for the sex differences, for example, the sex-chromosome linked mechanisms and hormonally driven differences.
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Affiliation(s)
- Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
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24
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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: 4.0] [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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25
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Larocca D, Lee J, West MD, Labat I, Sternberg H. No Time to Age: Uncoupling Aging from Chronological Time. Genes (Basel) 2021; 12:611. [PMID: 33919082 PMCID: PMC8143125 DOI: 10.3390/genes12050611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Multicellular life evolved from simple unicellular organisms that could replicate indefinitely, being essentially ageless. At this point, life split into two fundamentally different cell types: the immortal germline representing an unbroken lineage of cell division with no intrinsic endpoint and the mortal soma, which ages and dies. In this review, we describe the germline as clock-free and the soma as clock-bound and discuss aging with respect to three DNA-based cellular clocks (telomeric, DNA methylation, and transposable element). The ticking of these clocks corresponds to the stepwise progressive limitation of growth and regeneration of somatic cells that we term somatic restriction. Somatic restriction acts in opposition to strategies that ensure continued germline replication and regeneration. We thus consider the plasticity of aging as a process not fixed to the pace of chronological time but one that can speed up or slow down depending on the rate of intrinsic cellular clocks. We further describe how germline factor reprogramming might be used to slow the rate of aging and potentially reverse it by causing the clocks to tick backward. Therefore, reprogramming may eventually lead to therapeutic strategies to treat degenerative diseases by altering aging itself, the one condition common to us all.
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Affiliation(s)
| | - Jieun Lee
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| | - Michael D. West
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| | - Ivan Labat
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
| | - Hal Sternberg
- AgeX Therapeutics Inc., Alameda, CA 94501, USA; (J.L.); (M.D.W.); (I.L.); (H.S.)
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26
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Zheng X, Wang Q, Xie Z, Li J. The elevated level of IL-1α in the bone marrow of aged mice leads to MSC senescence partly by down-regulating Bmi-1. Exp Gerontol 2021; 148:111313. [PMID: 33740618 DOI: 10.1016/j.exger.2021.111313] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022]
Abstract
Osteoporosis is becoming increasingly prevalent with individual aging. Recent studies found that bone marrow mesenchymal stem cells (MSCs) undergo senescence along with the progression of age-related osteoporosis, leading to a decreased rate of new bone formation and fracture repair. The underlying mechanism of MSC senescence in the aged bone marrow has not been clarified yet. Here we found that MSCs from aged mice (12-month-old, O-MSCs) exhibited apparent senescent phenotypes compared with those from young controls (2-month-old, Y-MSCs), including lower proliferation rate, impaired self-renewal capacity, increased p16Ink4a expression and shifted differentiation balance to favor adipocytes over osteoblasts. Bmi-1, one of the main factors that regulate stem cell self-renewal, is dramatically decreased in O-MSCs. Knocking-down of Bmi-1 in Y-MSCs lead to cellular senescence, while over-expression of it rejuvenated O-MSCs. We further showed that the level of IL-1α is much higher in the bone marrow fluid of aged mice, which significantly inhibited Bmi-1 expression in MSCs. Our present study indicated that IL-1α, a key component of the senescence-associated secretory phenotype (SASP), is elevated in the aged bone marrow microenvironment, leading to decreased Bmi-1 expression in MSCs and consequently, MSC senescence.
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Affiliation(s)
- Xueling Zheng
- Department of Cell Biology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Qianxing Wang
- Department of Cell Biology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Zhuo Xie
- Department of Cell Biology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Jiao Li
- Department of Cell Biology, Zunyi Medical University, Zunyi 563000, Guizhou, China.
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27
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Qian L, TCW J. Human iPSC-Based Modeling of Central Nerve System Disorders for Drug Discovery. Int J Mol Sci 2021; 22:1203. [PMID: 33530458 PMCID: PMC7865494 DOI: 10.3390/ijms22031203] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
A high-throughput drug screen identifies potentially promising therapeutics for clinical trials. However, limitations that persist in current disease modeling with limited physiological relevancy of human patients skew drug responses, hamper translation of clinical efficacy, and contribute to high clinical attritions. The emergence of induced pluripotent stem cell (iPSC) technology revolutionizes the paradigm of drug discovery. In particular, iPSC-based three-dimensional (3D) tissue engineering that appears as a promising vehicle of in vitro disease modeling provides more sophisticated tissue architectures and micro-environmental cues than a traditional two-dimensional (2D) culture. Here we discuss 3D based organoids/spheroids that construct the advanced modeling with evolved structural complexity, which propels drug discovery by exhibiting more human specific and diverse pathologies that are not perceived in 2D or animal models. We will then focus on various central nerve system (CNS) disease modeling using human iPSCs, leading to uncovering disease pathogenesis that guides the development of therapeutic strategies. Finally, we will address new opportunities of iPSC-assisted drug discovery with multi-disciplinary approaches from bioengineering to Omics technology. Despite technological challenges, iPSC-derived cytoarchitectures through interactions of diverse cell types mimic patients' CNS and serve as a platform for therapeutic development and personalized precision medicine.
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Affiliation(s)
- Lu Qian
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Ronald Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia TCW
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Ronald Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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28
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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: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Jensen ET, Langefeld CD, Zimmerman KD, Howard TD, Dellon ES. Epigenetic methylation in Eosinophilic Esophagitis: Molecular ageing and novel biomarkers for treatment response. Clin Exp Allergy 2020; 50:1372-1380. [PMID: 32986922 DOI: 10.1111/cea.13748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/09/2020] [Accepted: 09/20/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND Treatment failure in eosinophilic esophagitis (EoE) is common. We hypothesize that DNA methylation differs between patients by treatment response to topical steroids (oral viscous budesonide), thus offering the potential to inform targeting therapies. OBJECTIVE We sought to identify differentially methylated sites and affiliated genes in pre-treatment oesophageal cells between responders and non-responders and test for accelerated epigenetic ageing in oesophageal cells of EoE patients. METHODS DNA was extracted from prospectively collected and biobanked oesophageal biopsies from 36 Caucasian treatment naïve EoE patients at diagnosis. Methylation assays were completed using the Infinium HumanMethylation450 BeadChip. Normalized β values for each CpG site were tested (t test) for differential methylation. Further, 353 CpG probes were used to estimate epigenetic age for each patient and a linear regression model tested whether chronologic age and epigenetic age differed. Epigenetic age results were confirmed in an independent cohort of healthy controls. RESULTS Eighteen CpG sites were differentially methylated by treatment response (P < .00001). The mean epigenetic age and chronological age were 56.1 ± 11.1 and 36.7 ± 12.3 years, a mean age difference of 19.3 ± 5.2 years (P < .0001); accelerated ageing was not observed in the oesophageal cells of healthy controls. CONCLUSIONS AND CLINICAL RELEVANCE EoE patients that respond versus do not respond to treatment have differences in their methylation profile, including enrichment of genes in pathways consistent with cellular injury and repair due to environmental stress and cell adhesion and barrier integrity. EoE also appears to accelerate cellular ageing. Whether treatment can arrest or reverse accelerated epigenetic ageing and the implications for long-term disease progression is important areas for future research.
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Affiliation(s)
- Elizabeth T Jensen
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Internal Medicine, Section on Gastroenterology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kip D Zimmerman
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Evan S Dellon
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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30
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Jung YD, Park SK, Kang D, Hwang S, Kang MH, Hong SW, Moon JH, Shin JS, Jin DH, You D, Lee JY, Park YY, Hwang JJ, Kim CS, Suh N. Epigenetic regulation of miR-29a/miR-30c/DNMT3A axis controls SOD2 and mitochondrial oxidative stress in human mesenchymal stem cells. Redox Biol 2020; 37:101716. [PMID: 32961441 PMCID: PMC7509080 DOI: 10.1016/j.redox.2020.101716] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
The use of human mesenchymal stem cells (hMSCs) in clinical applications requires large-scale cell expansion prior to administration. However, the prolonged culture of hMSCs results in cellular senescence, impairing their proliferation and therapeutic potentials. To understand the role of microRNAs (miRNAs) in regulating cellular senescence in hMSCs, we globally depleted miRNAs by silencing the DiGeorge syndrome critical region 8 (DGCR8) gene, an essential component of miRNA biogenesis. DGCR8 knockdown hMSCs exhibited severe proliferation defects and senescence-associated alterations, including increased levels of reactive oxygen species (ROS). Transcriptomic analysis revealed that the antioxidant gene superoxide dismutase 2 (SOD2) was significantly downregulated in DGCR8 knockdown hMSCs. Moreover, we found that DGCR8 silencing in hMSCs resulted in hypermethylation in CpG islands upstream of SOD2. 5-aza-2'-deoxycytidine treatment restored SOD2 expression and ROS levels. We also found that these effects were dependent on the epigenetic regulator DNA methyltransferase 3 alpha (DNMT3A). Using computational and experimental approaches, we demonstrated that DNMT3A expression was regulated by miR-29a-3p and miR-30c-5p. Overexpression of miR-29a-3p and/or miR-30c-5p reduced ROS levels in DGCR8 knockdown hMSCs and rescued proliferation defects, mitochondrial dysfunction, and premature senescence. Our findings provide novel insights into hMSCs senescence regulation by the miR-29a-3p/miR-30c-5p/DNMT3A/SOD2 axis.
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Affiliation(s)
- Yi-Deun Jung
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea; Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Seul-Ki Park
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea; Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Dayeon Kang
- Department of Pharmaceutical Engineering, College of Medical Sciences, Soon Chun Hyang University, Asan, 31538, Republic of Korea
| | - Supyong Hwang
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Myoung-Hee Kang
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Seung-Woo Hong
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Jai-Hee Moon
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Jae-Sik Shin
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Dong-Hoon Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Dalsan You
- Department of Urology, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Joo-Yong Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Yun-Yong Park
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Jung Jin Hwang
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Choung Soo Kim
- Department of Urology, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Nayoung Suh
- Department of Pharmaceutical Engineering, College of Medical Sciences, Soon Chun Hyang University, Asan, 31538, Republic of Korea.
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31
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Zhou X, Hong Y, Zhang H, Li X. Mesenchymal Stem Cell Senescence and Rejuvenation: Current Status and Challenges. Front Cell Dev Biol 2020; 8:364. [PMID: 32582691 PMCID: PMC7283395 DOI: 10.3389/fcell.2020.00364] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Over the past decades, mesenchymal stem cell (MSC)-based therapy has been intensively investigated and shown promising results in the treatment of various diseases due to their easy isolation, multiple lineage differentiation potential and immunomodulatory effects. To date, hundreds of phase I and II clinical trials using MSCs have been completed and many are ongoing. Accumulating evidence has shown that transplanted allogeneic MSCs lose their beneficial effects due to immunorejection. Nevertheless, the function of autologous MSCs is adversely affected by age, a process termed senescence, thus limiting their therapeutic potential. Despite great advances in knowledge, the potential mechanisms underlying MSC senescence are not entirely clear. Understanding the molecular mechanisms that contribute to MSC senescence is crucial when exploring novel strategies to rejuvenate senescent MSCs. In this review, we aim to provide an overview of the biological features of senescent MSCs and the recent progress made regarding the underlying mechanisms including epigenetic changes, autophagy, mitochondrial dysfunction and telomere shortening. We also summarize the current approaches to rejuvenate senescent MSCs including gene modification and pretreatment strategies. Collectively, rejuvenation of senescent MSCs is a promising strategy to enhance the efficacy of autologous MSC-based therapy, especially in elderly patients.
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Affiliation(s)
- Xueke Zhou
- Department of Emergency Medicine, Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Yimei Hong
- Department of Emergency Medicine, Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hao Zhang
- School of Pharmacy, Bengbu Medical College, Bengbu, China
| | - Xin Li
- Department of Emergency Medicine, Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
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32
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Raj K, Horvath S. Current perspectives on the cellular and molecular features of epigenetic ageing. Exp Biol Med (Maywood) 2020; 245:1532-1542. [PMID: 32276545 DOI: 10.1177/1535370220918329] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IMPACT STATEMENT The field of epigenetic ageing is relatively new, and the speed of its expansion presents a challenge in keeping abreast with new discoveries and their implications. Several reviews have already addressed the great number of pathologies, health conditions, life-style, and external stressors that are associated with changes to the rate of epigenetic ageing. While these associations highlight and affirm the ability of epigenetic clock to capture biologically meaningful changes associated with age, they do not inform us about the underlying mechanisms. In this very early period since the development of the clock, there have been rather limited experimental research that are aimed at uncovering the mechanism. Hence, the perspective that we proffer is derived from available but nevertheless limited lines of evidence that together provide a seemingly coherent narrative that can be tested. This, we believe would be helpful towards uncovering the workings of the epigenetic clock.
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Affiliation(s)
- Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA and Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, CA 90095, USA
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33
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Lowe R, Danson AF, Rakyan VK, Yildizoglu S, Saldmann F, Viltard M, Friedlander G, Faulkes CG. DNA methylation clocks as a predictor for ageing and age estimation in naked mole-rats, Heterocephalus glaber. Aging (Albany NY) 2020; 12:4394-4406. [PMID: 32126024 PMCID: PMC7093186 DOI: 10.18632/aging.102892] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/25/2020] [Indexed: 01/07/2023]
Abstract
The naked mole-rat, Heterocephalus glaber (NMR), the longest-lived rodent, is of significance and interest in the study of biomarkers for ageing. Recent breakthroughs in this field have revealed ‘epigenetic clocks’ that are based on the temporal accumulation of DNA methylation at specific genomic sites. Here, we validate the hypothesis of an epigenetic clock in NMRs based on changes in methylation of targeted CpG sites. We initially analysed 51 CpGs in NMR livers spanning an age range of 39-1,144 weeks and found 23 to be significantly associated with age (p<0.05). We then built a predictor of age using these sites. To test the accuracy of this model, we analysed an additional set of liver samples, and were successfully able to predict their age with a root mean squared error of 166 weeks. We also profiled skin samples with the same age range, finding a striking correlation between their predicted age versus their actual age (R=0.93), but which was lower when compared to the liver, suggesting that skin ages slower than the liver in NMRs. Our model will enable the prediction of age in wild-caught and captive NMRs of unknown age, and will be invaluable for further mechanistic studies of mammalian ageing.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Amy F Danson
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Centre for Genomic Health, Queen Mary University of London, London, UK
| | - Selin Yildizoglu
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Frédéric Saldmann
- Fondation pour la Recherche en Physiologie, Brussels, Belgium.,Service de Physiologie et Explorations Fonctionnelles, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Melanie Viltard
- Fondation pour la Recherche en Physiologie, Brussels, Belgium
| | - Gérard Friedlander
- Service de Physiologie et Explorations Fonctionnelles, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes, Faculté de Médecine, Paris, France.,INSERM UMR_S1151 CNRS UMR8253 Institut Necker-Enfants Malades (INEM), Paris, France
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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34
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Neri S, Borzì RM. Molecular Mechanisms Contributing to Mesenchymal Stromal Cell Aging. Biomolecules 2020; 10:E340. [PMID: 32098040 PMCID: PMC7072652 DOI: 10.3390/biom10020340] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are a reservoir for tissue homeostasis and repair that age during organismal aging. Beside the fundamental in vivo role of MSCs, they have also emerged in the last years as extremely promising therapeutic agents for a wide variety of clinical conditions. MSC use frequently requires in vitro expansion, thus exposing cells to replicative senescence. Aging of MSCs (both in vivo and in vitro) can affect not only their replicative potential, but also their properties, like immunomodulation and secretory profile, thus possibly compromising their therapeutic effect. It is therefore of critical importance to unveil the underlying mechanisms of MSC senescence and to define shared methods to assess MSC aging status. The present review will focus on current scientific knowledge about MSC aging mechanisms, control and effects, including possible anti-aging treatments.
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Affiliation(s)
- Simona Neri
- IRCCS Istituto Ortopedico Rizzoli, Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, 40136 Bologna, Italy;
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35
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Paluvai H, Di Giorgio E, Brancolini C. The Histone Code of Senescence. Cells 2020; 9:cells9020466. [PMID: 32085582 PMCID: PMC7072776 DOI: 10.3390/cells9020466] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Senescence is the end point of a complex cellular response that proceeds through a set of highly regulated steps. Initially, the permanent cell-cycle arrest that characterizes senescence is a pro-survival response to irreparable DNA damage. The maintenance of this prolonged condition requires the adaptation of the cells to an unfavorable, demanding and stressful microenvironment. This adaptation is orchestrated through a deep epigenetic resetting. A first wave of epigenetic changes builds a dam on irreparable DNA damage and sustains the pro-survival response and the cell-cycle arrest. Later on, a second wave of epigenetic modifications allows the genomic reorganization to sustain the transcription of pro-inflammatory genes. The balanced epigenetic dynamism of senescent cells influences physiological processes, such as differentiation, embryogenesis and aging, while its alteration leads to cancer, neurodegeneration and premature aging. Here we provide an overview of the most relevant histone modifications, which characterize senescence, aging and the activation of a prolonged DNA damage response.
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36
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Martínez-Cué C, Rueda N. Cellular Senescence in Neurodegenerative Diseases. Front Cell Neurosci 2020; 14:16. [PMID: 32116562 PMCID: PMC7026683 DOI: 10.3389/fncel.2020.00016] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a homeostatic biological process characterized by a permanent state of cell cycle arrest that can contribute to the decline of the regenerative potential and function of tissues. The increased presence of senescent cells in different neurodegenerative diseases suggests the contribution of senescence in the pathophysiology of these disorders. Although several factors can induce senescence, DNA damage, oxidative stress, neuroinflammation, and altered proteostasis have been shown to play a role in its onset. Oxidative stress contributes to accelerated aging and cognitive dysfunction stages affecting neurogenesis, neuronal differentiation, connectivity, and survival. During later life stages, it is implicated in the progression of cognitive decline, synapse loss, and neuronal degeneration. Also, neuroinflammation exacerbates oxidative stress, synaptic dysfunction, and neuronal death through the harmful effects of pro-inflammatory cytokines on cell proliferation and maturation. Both oxidative stress and neuroinflammation can induce DNA damage and alterations in DNA repair that, in turn, can exacerbate them. Another important feature associated with senescence is altered proteostasis. Because of the disruption in the function and balance of the proteome, senescence can modify the proper synthesis, folding, quality control, and degradation rate of proteins producing, in some diseases, misfolded proteins or aggregation of abnormal proteins. There is an extensive body of literature that associates cellular senescence with several neurodegenerative disorders including Alzheimer’s disease (AD), Down syndrome (DS), and Parkinson’s disease (PD). This review summarizes the evidence of the shared neuropathological events in these neurodegenerative diseases and the implication of cellular senescence in their onset or aggravation. Understanding the role that cellular senescence plays in them could help to develop new therapeutic strategies.
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Affiliation(s)
- Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Spain
| | - Noemí Rueda
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Spain
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37
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Schmeer C, Kretz A, Wengerodt D, Stojiljkovic M, Witte OW. Dissecting Aging and Senescence-Current Concepts and Open Lessons. Cells 2019; 8:cells8111446. [PMID: 31731770 PMCID: PMC6912776 DOI: 10.3390/cells8111446] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 01/10/2023] Open
Abstract
In contrast to the programmed nature of development, it is still a matter of debate whether aging is an adaptive and regulated process, or merely a consequence arising from a stochastic accumulation of harmful events that culminate in a global state of reduced fitness, risk for disease acquisition, and death. Similarly unanswered are the questions of whether aging is reversible and can be turned into rejuvenation as well as how aging is distinguishable from and influenced by cellular senescence. With the discovery of beneficial aspects of cellular senescence and evidence of senescence being not limited to replicative cellular states, a redefinition of our comprehension of aging and senescence appears scientifically overdue. Here, we provide a factor-based comparison of current knowledge on aging and senescence, which we converge on four suggested concepts, thereby implementing the newly emerging cellular and molecular aspects of geroconversion and amitosenescence, and the signatures of a genetic state termed genosenium. We also address the possibility of an aging-associated secretory phenotype in analogy to the well-characterized senescence-associated secretory phenotype and delineate the impact of epigenetic regulation in aging and senescence. Future advances will elucidate the biological and molecular fingerprints intrinsic to either process.
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Affiliation(s)
- Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
- Correspondence:
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
| | - Milan Stojiljkovic
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
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Sturm G, Cardenas A, Bind MA, Horvath S, Wang S, Wang Y, Hägg S, Hirano M, Picard M. Human aging DNA methylation signatures are conserved but accelerated in cultured fibroblasts. Epigenetics 2019; 14:961-976. [PMID: 31156022 DOI: 10.1080/15592294.2019.1626651] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aging is associated with progressive and site-specific changes in DNA methylation (DNAm). These global changes are captured by DNAm clocks that accurately predict chronological age in humans but relatively little is known about how clocks perform in vitro. Here we culture primary human fibroblasts across the cellular lifespan (~6 months) and use four different DNAm clocks to show that age-related DNAm signatures are conserved and accelerated in vitro. The Skin & Blood clock shows the best linear correlation with chronological time (r = 0.90), including during replicative senescence. Although similar in nature, the rate of epigenetic aging is approximately 62x times faster in cultured cells than in the human body. Consistent with in vivo data, cells aged under hyperglycemic conditions exhibit an approximately three years elevation in baseline DNAm age. Moreover, candidate gene-based analyses further corroborate the conserved but accelerated biological aging process in cultured fibroblasts. Fibroblasts mirror the established DNAm topology of the age-related ELOVL2 gene in human blood and the rapid hypermethylation of its promoter cg16867657, which correlates with a linear decrease in ELOVL2 mRNA levels across the lifespan. Using generalized additive modeling on twelve timepoints across the lifespan, we also show how single CpGs exhibit loci-specific, linear and nonlinear trajectories that reach rates up to -47% (hypomethylation) to +23% (hypermethylation) per month. Together, these high-temporal resolution global, gene-specific, and single CpG data highlight the conserved and accelerated nature of epigenetic aging in cultured fibroblasts, which may constitute a system to evaluate age-modifying interventions across the lifespan.
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Affiliation(s)
- Gabriel Sturm
- a Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center , New York , NY , USA
| | - Andres Cardenas
- b Division of Environmental Health Sciences, University of California, Berkeley, School of Public Health , Berkeley , CA , USA
| | - Marie-Abèle Bind
- c Department of Statistics, Harvard University , Cambridge , MA , USA
| | - Steve Horvath
- d Human Genetics, David Geffen School of Medicine, University of California Los Angeles , Los Angeles , CA , USA
| | - Shuang Wang
- e Department of Biostatistics, Mailman School of Public Health, Columbia University Medical Center , New York , NY , USA
| | - Yunzhang Wang
- f Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , Stockholm , Sweden
| | - Sara Hägg
- f Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , Stockholm , Sweden
| | - Michio Hirano
- g Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center , New York , NY , USA
| | - Martin Picard
- a Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center , New York , NY , USA.,g Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center , New York , NY , USA.,h Columbia Aging Center, Columbia University Mailman School of Public Health , New York , NY , USA
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