151
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Slieker RC, Relton CL, Gaunt TR, Slagboom PE, Heijmans BT. Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception. Epigenetics Chromatin 2018; 11:25. [PMID: 29848354 PMCID: PMC5975493 DOI: 10.1186/s13072-018-0191-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/21/2018] [Indexed: 12/31/2022] Open
Abstract
Background The well-established association of chronological age with changes in DNA methylation is primarily founded on the analysis of large sets of blood samples, while conclusions regarding tissue-specificity are typically based on small number of samples, tissues and CpGs. Here, we systematically investigate the tissue-specific character of age-related DNA methylation changes at the level of the CpG, functional genomic region and nearest gene in a large dataset. Results We assembled a compendium of public data, encompassing genome-wide DNA methylation data (Illumina 450k array) on 8092 samples from 16 different tissues, including 7 tissues with moderate to high sample numbers (Dataset size range 96–1202, Ntotal = 2858). In the 7 tissues (brain, buccal, liver, kidney, subcutaneous fat, monocytes and T-helper cells), we identified 7850 differentially methylated positions that gained (gain-aDMPs; cut-offs: Pbonf ≤ 0.05, effect size ≥ 2%/10 years) and 4,287 that lost DNA methylation with age (loss-aDMPs), 92% of which had not previously been reported for whole blood. The majority of all aDMPs identified occurred in one tissue only (gain-aDMPs: 85.2%; loss-aDMPs: 97.4%), an effect independent of statistical power. This striking tissue-specificity extended to both the functional genomic regions (defined by chromatin state segmentation) and the nearest gene. However, aDMPs did accumulate in regions with the same functional annotation across tissues, namely polycomb-repressed CpG islands for gain-aDMPs and regions marked by active histone modifications for loss-aDMPs. Conclusion Our analysis shows that age-related DNA methylation changes are highly tissue-specific. These results may guide the development of improved tissue-specific markers of chronological and, perhaps, biological age. Electronic supplementary material The online version of this article (10.1186/s13072-018-0191-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roderick C Slieker
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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152
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Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Altmüller J, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Nürnberg P, Marenduzzo D, Rippe K, Papantonis A. HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types. Mol Cell 2018; 70:730-744.e6. [PMID: 29706538 DOI: 10.1016/j.molcel.2018.03.030] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/19/2018] [Accepted: 03/25/2018] [Indexed: 11/30/2022]
Abstract
Processes like cellular senescence are characterized by complex events giving rise to heterogeneous cell populations. However, the early molecular events driving this cascade remain elusive. We hypothesized that senescence entry is triggered by an early disruption of the cells' three-dimensional (3D) genome organization. To test this, we combined Hi-C, single-cell and population transcriptomics, imaging, and in silico modeling of three distinct cells types entering senescence. Genes involved in DNA conformation maintenance are suppressed upon senescence entry across all cell types. We show that nuclear depletion of the abundant HMGB2 protein occurs early on the path to senescence and coincides with the dramatic spatial clustering of CTCF. Knocking down HMGB2 suffices for senescence-induced CTCF clustering and for loop reshuffling, while ectopically expressing HMGB2 rescues these effects. Our data suggest that HMGB2-mediated genomic reorganization constitutes a primer for the ensuing senescent program.
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Affiliation(s)
- Anne Zirkel
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Konstantinos Sofiadis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Jan-Philipp Mallm
- German Cancer Research Center and Bioquant, 69120 Heidelberg, Germany
| | - Chris A Brackley
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Henrike Gothe
- Institute of Molecular Biology, 55128 Mainz, Germany
| | | | - Christian Becker
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Natasa Josipovic
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Lilija Brant
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Julia Franzen
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Mirjam Koker
- Clinic I of Internal Medicine and Center for Integrated Oncology, University Hospital Cologne, 50931 Cologne, Germany
| | - Eduardo G Gusmao
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Interdisciplinary Centre for Clinical Research, RWTH Aachen University Medical School, 52062 Aachen, Germany
| | - Ivan G Costa
- Interdisciplinary Centre for Clinical Research, RWTH Aachen University Medical School, 52062 Aachen, Germany
| | - Roland T Ullrich
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Clinic I of Internal Medicine and Center for Integrated Oncology, University Hospital Cologne, 50931 Cologne, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | | | - Peter Nürnberg
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Karsten Rippe
- German Cancer Research Center and Bioquant, 69120 Heidelberg, Germany
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany.
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153
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Wang C, Wang F, Li Z, Cao Q, Huang L, Chen S. MeCP2-mediated epigenetic regulation in senescent endothelial progenitor cells. Stem Cell Res Ther 2018; 9:87. [PMID: 29615114 PMCID: PMC5883541 DOI: 10.1186/s13287-018-0828-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/25/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cellular aging may be associated with epigenetics. Methyl-CpG-binding protein 2 (MeCP2) and sirtuin 1 (SIRT1) are two important epigenetic factors. Our former work demonstrated that MeCP2 expression increased and SIRT1 expression decreased in senescent endothelial progenitor cells (EPCs). This article aims to reveal the epigenetic regulation caused by MeCP2 in EPCs and discuss its mechanism. METHODS Tube formation assay and cell apoptosis detection were used to evaluate the function of senescent EPCs induced by MeCP2 overexpression. Western blot analysis was used to testify the relative protein expression changed by MeCP2. Bisulfite sequencing methylation assay and chromatin immunoprecipitation assay were used to assess the degree of methylation and the relation of MeCP2 and SIRT1. RESULTS MeCP2 reduced angiogenesis of senescent EPCs, promoted apoptosis, and caused senescent EPC dysfunction through SIRT1 promoter hypermethylation and histone modification. CONCLUSIONS MeCP2 mediated senescent EPC dysfunction through epigenetic regulation.
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Affiliation(s)
- Chunli Wang
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Wang
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Li
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Cao
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liya Huang
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuyan Chen
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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154
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Lenart P, Novak J, Bienertova-Vasku J. PIWI-piRNA pathway: Setting the pace of aging by reducing DNA damage. Mech Ageing Dev 2018; 173:29-38. [PMID: 29580825 DOI: 10.1016/j.mad.2018.03.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/02/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) are powerful drivers of genome evolutionary dynamics but are principally deleterious to the host organism by compromising the integrity and function of the genome. The transposition of TEs may result in mutations and DNA damage. DNA double-strand breaks (DSBs), which may be caused by the transposition, are one of the processes directly linked to aging. TEs may thus be considered to constitute an internal source of aging and the frequency of transposition may, in turn, be considered to affect the pace of aging. The PIWI-piRNA pathway is a widespread strategy used by most animals to effectively suppress transposition. Interestingly, the PIWI-piRNA pathway is expressed predominantly in the animal germline, a more or less continuous immortal lineage set aside after the first few cell divisions of a developing embryo. Recent findings further imply that the PIWI-piRNA pathway and TE suppression constitute an important mechanism regulating aging. This article discusses the proposed role of the PIWI-piRNA pathway in setting the pace of aging as well as the possible mechanisms underlying this process.
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Affiliation(s)
- Peter Lenart
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A18, 625 00, Brno, Czech Republic; Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, Building A29, 625 00, Brno, Czech Republic
| | - Jan Novak
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A18, 625 00, Brno, Czech Republic
| | - Julie Bienertova-Vasku
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A18, 625 00, Brno, Czech Republic; Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, Building A29, 625 00, Brno, Czech Republic.
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155
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Senescent human hematopoietic progenitors show elevated expression of transposable elements and inflammatory genes. Exp Hematol 2018; 62:33-38.e6. [PMID: 29549053 DOI: 10.1016/j.exphem.2018.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/26/2018] [Accepted: 03/04/2018] [Indexed: 12/21/2022]
Abstract
Genomic transposable elements (TEs) constitute the majority of the genome. Expression of TEs is known to activate the double-stranded RNA recognition pathway ("viral mimicry"), leading to the activation of interferon-stimulated genes, inflammation, and immune-mediated cell death. Recently, we showed that the expression of TEs is suppressed along with immune pathways in leukemic stem cells (LSCs) in acute myeloid leukemia, suggesting a potential mechanism for immune escape of LSCs. This indicated that, during oncogenesis, where there is escape from senescence, expression of TEs is suppressed. Senescence is known to activate the interferon response and inflammatory cytokines, known as the senescence-associated secretory phenotype (SASP). We characterized the transcriptome of senescent and active human hematopoietic stem and progenitor cells (HSPCs) in vivo and showed co-occurrence of overexpression of TEs, SASP genes, and gene pathways of inflammation in senescence. The percentage of circulating senescent HSPCs (s-HSPCs) did not increase with age, indicating active clearance. Induction of senescence in human HSPCs in vitro showed increased expression of TE and SASP genes. SASP is known to mediate clearance of senescent cells and active clearance of senescent cells has been shown to increase organismal fitness. We speculate that the expression of TEs in s-HSPCs could contribute to orderly clearance of the cells via activation of immune pathways, warranting further mechanistic studies. This is the first study to characterize the transcriptome of human s-HSPCs in vivo, revealing activated expression of TEs and inflammatory genes.
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156
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Abstract
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.
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Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
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157
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Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging. Nat Commun 2018; 9:644. [PMID: 29440637 PMCID: PMC5811577 DOI: 10.1038/s41467-018-03073-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/20/2017] [Indexed: 01/12/2023] Open
Abstract
Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated by cyclical transcriptomic and proteomic activities. Epigenetic factors are also involved in this circadian machinery; however, despite extensive efforts, detection and characterization of circadian cytosine modifications at the nucleotide level have remained elusive. In this study, we report that a large proportion of epigenetically variable cytosines show a circadian pattern in their modification status in mice. Importantly, the cytosines with circadian epigenetic oscillations significantly overlap with the cytosines exhibiting age-related changes in their modification status. Our findings suggest that evolutionary advantageous processes such as circadian rhythmicity can also contribute to an organism’s deterioration. While epigenetic factors have been implicated in the circadian rhythm, the detection of circadian cytosine modifications has remained elusive. Here the authors identify a large number of epigenetically variable cytosines that show circadian oscillations in their modification status in mice.
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158
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Xie W, Kagiampakis I, Pan L, Zhang YW, Murphy L, Tao Y, Kong X, Kang B, Xia L, Carvalho FLF, Sen S, Chiu Yen RW, Zahnow CA, Ahuja N, Baylin SB, Easwaran H. DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk. Cancer Cell 2018; 33:309-321.e5. [PMID: 29438699 PMCID: PMC5813821 DOI: 10.1016/j.ccell.2018.01.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/24/2017] [Accepted: 01/17/2018] [Indexed: 01/08/2023]
Abstract
Overall shared DNA methylation patterns between senescence (Sen) and cancers have led to the model that tumor-promoting epigenetic patterns arise through senescence. We show that transformation-associated methylation changes arise stochastically and independently of programmatic changes during senescence. Promoter hypermethylation events in transformation involve primarily pro-survival and developmental genes, similarly modified in primary tumors. Senescence-associated hypermethylation mainly involves metabolic regulators and appears early in proliferating "near-senescent" cells, which can be immortalized but are refractory to transformation. Importantly, a subset of transformation-associated hypermethylated developmental genes exhibits highest methylation gains at all age-associated cancer risk states across tissue types. These epigenetic changes favoring cell self-renewal and survival, arising during tissue aging, are fundamentally important for stratifying cancer risk and concepts for cancer prevention.
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Affiliation(s)
- Wenbing Xie
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ioannis Kagiampakis
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lixia Pan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yang W Zhang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Lauren Murphy
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yong Tao
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xiangqian Kong
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Byunghak Kang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Limin Xia
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Filipe L F Carvalho
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Subhojit Sen
- UM-DAE Center for Excellence in Basic Sciences (CBS), Mumbai University, Mumbai 400098, India
| | - Ray-Whay Chiu Yen
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Cynthia A Zahnow
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nita Ahuja
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Hariharan Easwaran
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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159
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Jasiulionis MG. Abnormal Epigenetic Regulation of Immune System during Aging. Front Immunol 2018; 9:197. [PMID: 29483913 PMCID: PMC5816044 DOI: 10.3389/fimmu.2018.00197] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to the study of mechanisms controlling the chromatin structure, which has fundamental role in the regulation of gene expression and genome stability. Epigenetic marks, such as DNA methylation and histone modifications, are established during embryonic development and epigenetic profiles are stably inherited during mitosis, ensuring cell differentiation and fate. Under the effect of intrinsic and extrinsic factors, such as metabolic profile, hormones, nutrition, drugs, smoke, and stress, epigenetic marks are actively modulated. In this sense, the lifestyle may affect significantly the epigenome, and as a result, the gene expression profile and cell function. Epigenetic alterations are a hallmark of aging and diseases, such as cancer. Among biological systems compromised with aging is the decline of immune response. Different regulators of immune response have their promoters and enhancers susceptible to the modulation by epigenetic marks, which is fundamental to the differentiation and function of immune cells. Consistent evidence has showed the regulation of innate immune cells, and T and B lymphocytes by epigenetic mechanisms. Therefore, age-dependent alterations in epigenetic marks may result in the decline of immune function and this might contribute to the increased incidence of diseases in old people. In order to maintain health, we need to better understand how to avoid epigenetic alterations related to immune aging. In this review, the contribution of epigenetic mechanisms to the loss of immune function during aging will be discussed, and the promise of new means of disease prevention and management will be pointed.
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Affiliation(s)
- Miriam G Jasiulionis
- Laboratory of Ontogeny and Epigenetics, Pharmacology Department, Universidade Federal de São Paulo, São Paulo, Brazil
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160
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Unnikrishnan A, Hadad N, Masser DR, Jackson J, Freeman WM, Richardson A. Revisiting the genomic hypomethylation hypothesis of aging. Ann N Y Acad Sci 2018; 1418:69-79. [PMID: 29363785 DOI: 10.1111/nyas.13533] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/19/2017] [Accepted: 09/26/2017] [Indexed: 12/26/2022]
Abstract
The genomic hypomethylation hypothesis of aging proposes that an overall decrease in global DNA methylation occurs with age, and it has been argued that the decrease in global DNA methylation could be an important factor in aging, resulting in the relaxation of gene expression regulation and abnormal gene expression. Since it was initially observed that DNA methylation decreased with age in 1974, 16 articles have been published describing the effect of age on global DNA methylation in various tissues from rodents and humans. We critically reviewed the publications on the effect of age on DNA methylation and the expression of the enzymes involved in DNA methylation to evaluate the validity of the hypomethylation hypothesis of aging. On the basis of the current scientific literature, we conclude that a decrease in the global methylation of the genome occurs in most if not all tissues/cells as an animal ages. However, age-related changes in DNA methylation in specific regions or at specific sites in the genome occur even though the global DNA methylation does not change.
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Affiliation(s)
- Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Jordan Jackson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Oklahoma City VA Medical Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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161
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Case Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1069:135-209. [DOI: 10.1007/978-3-319-89354-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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162
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Kim J, Sturgill D, Sebastian R, Khurana S, Tran AD, Edwards GB, Kruswick A, Burkett S, Hosogane EK, Hannon WW, Weyemi U, Bonner WM, Luger K, Oberdoerffer P. Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions. Mol Cell 2017; 69:36-47.e7. [PMID: 29249653 DOI: 10.1016/j.molcel.2017.11.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/05/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Abstract
Recent integrative epigenome analyses highlight the importance of functionally distinct chromatin states for accurate cell function. How these states are established and maintained is a matter of intense investigation. Here, we present evidence for DNA damage as an unexpected means to shape a protective chromatin environment at regions of recurrent replication stress (RS). Upon aberrant fork stalling, DNA damage signaling and concomitant H2AX phosphorylation coordinate the FACT-dependent deposition of macroH2A1.2, a histone variant that promotes DNA repair by homologous recombination (HR). MacroH2A1.2, in turn, facilitates the accumulation of the tumor suppressor and HR effector BRCA1 at replication forks to protect from RS-induced DNA damage. Consequently, replicating primary cells steadily accrue macroH2A1.2 at fragile regions, whereas macroH2A1.2 loss in these cells triggers DNA damage signaling-dependent senescence, a hallmark of RS. Altogether, our findings demonstrate that recurrent DNA damage contributes to the chromatin landscape to ensure the epigenomic integrity of dividing cells.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Simran Khurana
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Garrett B Edwards
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Alex Kruswick
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Eri K Hosogane
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William W Hannon
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Urbain Weyemi
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William M Bonner
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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163
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Tanaka H, Takebayashi SI, Sakamoto A, Igata T, Nakatsu Y, Saitoh N, Hino S, Nakao M. The SETD8/PR-Set7 Methyltransferase Functions as a Barrier to Prevent Senescence-Associated Metabolic Remodeling. Cell Rep 2017; 18:2148-2161. [PMID: 28249161 DOI: 10.1016/j.celrep.2017.02.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/29/2016] [Accepted: 02/06/2017] [Indexed: 01/01/2023] Open
Abstract
Cellular senescence is an irreversible growth arrest that contributes to development, tumor suppression, and age-related conditions. Senescent cells show active metabolism compared with proliferating cells, but the underlying mechanisms remain unclear. Here we show that the SETD8/PR-Set7 methyltransferase, which catalyzes mono-methylation of histone H4 at lysine 20 (H4K20me1), suppresses nucleolar and mitochondrial activities to prevent cellular senescence. SETD8 protein was selectively downregulated in both oncogene-induced and replicative senescence. Inhibition of SETD8 alone was sufficient to trigger senescence. Under these states, the expression of genes encoding ribosomal proteins (RPs) and ribosomal RNAs as well as the cyclin-dependent kinase (CDK) inhibitor p16INK4A was increased, with a corresponding reduction of H4K20me1 at each locus. As a result, the loss of SETD8 concurrently stimulated nucleolar function and retinoblastoma protein-mediated mitochondrial metabolism. In conclusion, our data demonstrate that SETD8 acts as a barrier to prevent cellular senescence through chromatin-mediated regulation of senescence-associated metabolic remodeling.
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Affiliation(s)
- Hiroshi Tanaka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shin-Ichiro Takebayashi
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Akihisa Sakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Tomoka Igata
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yuko Nakatsu
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Noriko Saitoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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164
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Nacarelli T, Liu P, Zhang R. Epigenetic Basis of Cellular Senescence and Its Implications in Aging. Genes (Basel) 2017; 8:genes8120343. [PMID: 29186801 PMCID: PMC5748661 DOI: 10.3390/genes8120343] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 02/07/2023] Open
Abstract
Cellular senescence is a tumor suppressive response that has become recognized as a major contributor of tissue aging. Senescent cells undergo a stable proliferative arrest that protects against neoplastic transformation, but acquire a secretory phenotype that has long-term deleterious effects. Studies are still unraveling the effector mechanisms that underlie these senescence responses with the goal to identify therapeutic interventions. Such effector mechanisms have been linked to the dramatic remodeling in the epigenetic and chromatin landscape that accompany cellular senescence. We discuss these senescence-associated epigenetic changes and their impact on the senescence phenotypes, notably the proliferative arrest and senescence associated secretory phenotype (SASP). We also explore possible epigenetic targets to suppress the deleterious effects of senescent cells that contribute towards aging.
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165
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Sebastian R, Oberdoerffer P. Transcription-associated events affecting genomic integrity. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160288. [PMID: 28847825 PMCID: PMC5577466 DOI: 10.1098/rstb.2016.0288] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/25/2022] Open
Abstract
Accurate maintenance of genomic as well as epigenomic integrity is critical for proper cell and organ function. Continuous exposure to DNA damage is, thus, often associated with malignant transformation and degenerative diseases. A significant, chronic threat to genome integrity lies in the process of transcription, which can result in the formation of potentially harmful RNA : DNA hybrid structures (R-loops) and has been linked to DNA damage accumulation as well as dynamic chromatin reorganization. In sharp contrast, recent evidence suggests that active transcription, the resulting transcripts as well as R-loop formation can play multi-faceted roles in maintaining and restoring genome integrity. Here, we will discuss the emerging contributions of transcription as both a source of DNA damage and a mediator of DNA repair. We propose that both aspects have significant implications for genome maintenance, and will speculate on possible long-term consequences for the epigenetic integrity of transcribing cells.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
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166
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Karpinski P, Pesz K, Sasiadek MM. Pan-cancer analysis reveals presence of pronounced DNA methylation drift in CpG island methylator phenotype clusters. Epigenomics 2017; 9:1341-1352. [PMID: 28960094 DOI: 10.2217/epi-2017-0070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To provide characteristics of major genomic correlates in CpG island methylator phenotype-high (CIMP-H) subgroups in relation to corresponding non-CIMP-H subgroups by use of phenotypic, DNA methylation and RNAseq data. MATERIALS & METHODS Twenty-three datasets generated by The Cancer Genome Atlas project encompassing over 7200 unique samples were analyzed. We identified 23 CIMP-H clusters by use of unsupervised clustering. RESULTS & CONCLUSION More than 90% of CIMP-H clusters were significantly associated with accelerated epigenetic mitotic clock, demethylation of enhancer sites, backbone and repetitive sequences. Pronounced epigenetic drift observed in majority of CIMP-H subgroups may be related to increased cell division rate, which leads to expansion of DNA methylation errors. This may explain pan-cancer mechanism of establishing CIMP-H in majority of tissue types.
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Affiliation(s)
- Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Karolina Pesz
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
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167
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Lenain C, de Graaf CA, Pagie L, Visser NL, de Haas M, de Vries SS, Peric-Hupkes D, van Steensel B, Peeper DS. Massive reshaping of genome-nuclear lamina interactions during oncogene-induced senescence. Genome Res 2017; 27:1634-1644. [PMID: 28916540 PMCID: PMC5630027 DOI: 10.1101/gr.225763.117] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/21/2017] [Indexed: 01/06/2023]
Abstract
Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reorganization, including the formation of senescence-associated heterochromatic foci (SAHF). The nuclear lamina (NL) is an important contributor to genome organization and has been implicated in cellular senescence and organismal aging. It interacts with multiple regions of the genome called lamina-associated domains (LADs). Some LADs are cell-type specific, whereas others are conserved between cell types and are referred to as constitutive LADs (cLADs). Here, we used DamID to investigate the changes in genome–NL interactions in a model of OIS triggered by the expression of the common BRAFV600E oncogene. We found that OIS cells lose most of their cLADS, suggesting the loss of a specific mechanism that targets cLADs to the NL. In addition, multiple genes relocated to the NL. Unexpectedly, they were not repressed, implying the abrogation of the repressive activity of the NL during OIS. Finally, OIS cells displayed an increased association of telomeres with the NL. Our study reveals that senescent cells acquire a new type of LAD organization and suggests the existence of as yet unknown mechanisms that tether cLADs to the NL and repress gene expression at the NL.
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Affiliation(s)
- Christelle Lenain
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Carolyn A de Graaf
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.,Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ludo Pagie
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marcel de Haas
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sandra S de Vries
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Daniel Peric-Hupkes
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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168
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Epigenetic regulation in cell senescence. J Mol Med (Berl) 2017; 95:1257-1268. [DOI: 10.1007/s00109-017-1581-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022]
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169
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Schlosberg CE, VanderKraats ND, Edwards JR. Modeling complex patterns of differential DNA methylation that associate with gene expression changes. Nucleic Acids Res 2017; 45:5100-5111. [PMID: 28168293 PMCID: PMC5435975 DOI: 10.1093/nar/gkx078] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/26/2017] [Indexed: 12/15/2022] Open
Abstract
Numerous genomic studies are underway to determine which genes are abnormally regulated by DNA methylation in disease. However, we have a poor understanding of how disease-specific methylation changes affect expression. We thus developed an integrative analysis tool, Methylation-based Gene Expression Classification (ME-Class), to explain specific variation in methylation that associates with expression change. This model captures the complexity of methylation changes around a gene promoter. Using 17 whole-genome bisulfite sequencing and RNA-seq datasets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms standard methods using methylation to predict differential gene expression change. To demonstrate its utility, we used ME-Class to analyze 32 datasets from different hematopoietic cell types from the Blueprint Epigenome project. Expression-associated methylation changes were predominantly found when comparing cells from distantly related lineages, implying that changes in the cell's transcriptional program precede associated methylation changes. Training ME-Class on normal-tumor pairs from The Cancer Genome Atlas indicated that cancer-specific expression-associated methylation changes differ from tissue-specific changes. We further show that ME-Class can detect functionally relevant cancer-specific, expression-associated methylation changes that are reversed upon the removal of methylation. ME-Class is thus a powerful tool to identify genes that are dysregulated by DNA methylation in disease.
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Affiliation(s)
- Christopher E Schlosberg
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Nathan D VanderKraats
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - John R Edwards
- Center for Pharmacogenomics, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
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170
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Charting the dynamic epigenome during B-cell development. Semin Cancer Biol 2017; 51:139-148. [PMID: 28851627 DOI: 10.1016/j.semcancer.2017.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The epigenetic landscape undergoes a widespread modulation during embryonic development and cell differentiation. Within the hematopoietic system, B cells are perhaps the cell lineage with a more dynamic DNA methylome during their maturation process, which involves approximately one third of all the CpG sites of the genome. Although each B-cell maturation step displays its own DNA methylation fingerprint, the DNA methylome is more extensively modified in particular maturation transitions. These changes are gradually accumulated in specific chromatin environments as cell differentiation progresses and reflect different features and functional states of B cells. Promoters and enhancers of B-cell transcription factors acquire activation-related epigenetic marks and are sequentially expressed in particular maturation windows. These transcription factors further reconfigure the epigenetic marks and activity state of their target sites to regulate the expression of genes related to B-cell functions. Together with this observation, extensive DNA methylation changes in areas outside gene regulatory elements such as hypomethylation of heterochromatic regions and hypermethylation of CpG-rich regions, also take place in mature B cells, which intriguingly have been described as hallmarks of cancer. This process starts in germinal center B cells, a highly proliferative cell type, and becomes particularly apparent in long-lived cells such as memory and plasma cells. Overall, the characterization of the DNA methylome during B-cell differentiation not only provides insights into the complex epigenetic network of regulatory elements that mediate the maturation process but also suggests that late B cells also passively accumulate epigenetic changes related to cell proliferation and longevity.
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171
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Tumor cell senescence response produces aggressive variants. Cell Death Discov 2017; 3:17049. [PMID: 28845296 PMCID: PMC5563524 DOI: 10.1038/cddiscovery.2017.49] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/09/2017] [Indexed: 01/17/2023] Open
Abstract
Tumors often respond favorably to initial chemotherapy but eventually relapse with drug resistance and increased metastatic potential. Cellular senescence is a major therapeutic outcome of cancer chemotherapy, which leads to tumor stasis or regression through immune clearance of senescent cells. However, senescent tumor cells have been shown to resume proliferation at low frequency. We found that subjecting arrested senescent tumor cells to cytotoxic treatments stimulates the clonogenic proliferation of remaining survivors. The senescence revertants showed a reduced rate of proliferation but increased migration and invasion potential in vitro, and increased tumorigenic potential in vivo. Gene expression profiling showed that the senescence revertants are distinct from both parental and senescent cells. A subset of senescence-activated genes remains active in the revertants. These genes are implicated in regulating cell motility, invasion, and metastasis, which may collectively contribute to the aggressiveness of the revertants. The findings suggest that although therapy-induced senescence has short-term benefits, the response also causes reprogramming of gene expression and activates invasion-related genes that accelerate tumor progression.
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172
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Shih CT, Chang YF, Chen YT, Ma CP, Chen HW, Yang CC, Lu JC, Tsai YS, Chen HC, Tan BCM. The PPARγ-SETD8 axis constitutes an epigenetic, p53-independent checkpoint on p21-mediated cellular senescence. Aging Cell 2017; 16:797-813. [PMID: 28514051 PMCID: PMC5506440 DOI: 10.1111/acel.12607] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2017] [Indexed: 01/09/2023] Open
Abstract
Cellular senescence is a permanent proliferative arrest triggered by genome instability or aberrant growth stresses, acting as a protective or even tumor‐suppressive mechanism. While several key aspects of gene regulation have been known to program this cessation of cell growth, the involvement of the epigenetic regulation has just emerged but remains largely unresolved. Using a systems approach that is based on targeted gene profiling, we uncovered known and novel chromatin modifiers with putative link to the senescent state of the cells. Among these, we identified SETD8 as a new target as well as a key regulator of the cellular senescence signaling. Knockdown of SETD8 triggered senescence induction in proliferative culture, irrespectively of the p53 status of the cells; ectopic expression of this epigenetic writer alleviated the extent doxorubicin‐induced cellular senescence. This repressive effect of SETD8 in senescence was mediated by directly maintaining the silencing mark H4K20me1 at the locus of the senescence switch gene p21. Further in support of this regulatory link, depletion of p21 reversed this SETD8‐mediated cellular senescence. Additionally, we found that PPARγ acts upstream and regulates SETD8 expression in proliferating cells. Downregulation of PPARγ coincided with the senescence induction, while its activation inhibited the progression of this process. Viewed together, our findings delineated a new epigenetic pathway through which the PPARγ‐SETD8 axis directly silences p21 expression and consequently impinges on its senescence‐inducing function. This implies that SETD8 may be part of a cell proliferation checkpoint mechanism and has important implications in antitumor therapeutics.
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Affiliation(s)
- Chieh-Tien Shih
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
| | - Yi-Feng Chang
- Molecular Medicine Research Center; Chang Gung University; Tao-Yuan Taiwan
| | - Yi-Tung Chen
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
| | - Chung-Pei Ma
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
| | - Hui-Wen Chen
- Department of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
| | - Chang-Ching Yang
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
- Department of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
| | - Juu-Chin Lu
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
- Department of Physiology and Pharmacology; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
- Division of Endocrinology and Metabolism; Department of Internal Medicine; Chang Gung Memorial Hospital; Linkou, Tao-Yuan Taiwan
| | - Yau-Sheng Tsai
- Institute of Clinical Medicine; National Cheng Kung University; Tainan Taiwan
| | - Hua-Chien Chen
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
- Molecular Medicine Research Center; Chang Gung University; Tao-Yuan Taiwan
- Department of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
| | - Bertrand Chin-Ming Tan
- Graduate Institute of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
- Molecular Medicine Research Center; Chang Gung University; Tao-Yuan Taiwan
- Department of Biomedical Sciences; College of Medicine; Chang Gung University; Kwei-San, Tao-Yuan Taiwan
- Department of Neurosurgery; Lin-Kou Medical Center; Chang Gung Memorial Hospital; Linkou, Tao-Yuan Taiwan
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173
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Delgado-Morales R, Agís-Balboa RC, Esteller M, Berdasco M. Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders. Clin Epigenetics 2017; 9:67. [PMID: 28670349 PMCID: PMC5493012 DOI: 10.1186/s13148-017-0365-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/11/2017] [Indexed: 12/26/2022] Open
Abstract
Ageing is the main risk factor for human neurological disorders. Among the diverse molecular pathways that govern ageing, epigenetics can guide age-associated decline in part by regulating gene expression and also through the modulation of genomic instability and high-order chromatin architecture. Epigenetic mechanisms are involved in the regulation of neural differentiation as well as in functional processes related to memory consolidation, learning or cognition during healthy lifespan. On the other side of the coin, many neurodegenerative diseases are associated with epigenetic dysregulation. The reversible nature of epigenetic factors and, especially, their role as mediators between the genome and the environment make them exciting candidates as therapeutic targets. Rather than providing a broad description of the pathways epigenetically deregulated in human neurological disorders, in this review, we have focused on the potential use of epigenetic enzymes as druggable targets to ameliorate neural decline during normal ageing and especially in neurological disorders. We will firstly discuss recent progress that supports a key role of epigenetic regulation during healthy ageing with an emphasis on the role of epigenetic regulation in adult neurogenesis. Then, we will focus on epigenetic alterations associated with ageing-related human disorders of the central nervous system. We will discuss examples in the context of psychiatric disorders, including schizophrenia and posttraumatic stress disorders, and also dementia or Alzheimer's disease as the most frequent neurodegenerative disease. Finally, methodological limitations and future perspectives are discussed.
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Affiliation(s)
- Raúl Delgado-Morales
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Roberto Carlos Agís-Balboa
- Psychiatric Diseases Research Group, Galicia Sur Health Research Institute, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, CIBERSAM, Vigo, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain
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174
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Jen J, Tang YA, Lu YH, Lin CC, Lai WW, Wang YC. Oct4 transcriptionally regulates the expression of long non-coding RNAs NEAT1 and MALAT1 to promote lung cancer progression. Mol Cancer 2017; 16:104. [PMID: 28615056 PMCID: PMC5471675 DOI: 10.1186/s12943-017-0674-z] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/04/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Oct4, a key stemness transcription factor, is overexpressed in lung cancer. Here, we reveal a novel transcription regulation of long non-coding RNAs (lncRNAs) by Oct4. LncRNAs have emerged as important players in cancer progression. METHODS Oct4 chromatin-immunoprecipitation (ChIP)-sequencing and several lncRNA databases with literature annotation were integrated to identify Oct4-regulated lncRNAs. Luciferase activity, qRT-PCR and ChIP-PCR assays were conducted to examine transcription regulation of lncRNAs by Oct4. Reconstitution experiments of Oct4 and downstream lncRNAs in cell proliferation, migration and invasion assays were performed to confirm the Oct4-lncRNAs signaling axes in promoting lung cancer cell growth and motility. The expression correlations between Oct4 and lncRNAs were investigated in 124 lung cancer patients using qRT-PCR analysis. The clinical significance of Oct4/lncRNAs signaling axes were further evaluated using multivariate Cox regression and Kaplan-Meier analyses. RESULTS We confirmed that seven lncRNAs were upregulated by direct binding of Oct4. Among them, nuclear paraspeckle assembly transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and urothelial carcinoma-associated 1 (UCA1) were validated as Oct4 transcriptional targets through promoter or enhancer activation. We showed that lung cancer cells overexpressing NEAT1 or MALAT1 and the Oct4-silenced cells reconstituted with NEAT1 or MALAT1 promoted cell proliferation, migration and invasion. In addition, knockdown of NEAT1 or MALAT1 abolished Oct4-mediated lung cancer cell growth and motility. These cell-based results suggested that Oct4/NEAT1 or Oct4/MALAT1 axis promoted oncogenesis. Clinically, Oct4/NEAT1/MALAT1 co-overexpression was an independent factor for prediction of poor outcome in 124 lung cancer patients. CONCLUSIONS Our study reveals a novel mechanism by which Oct4 transcriptionally activates NEAT1 via promoter and MALAT1 via enhancer binding to promote cell proliferation and motility, and led to lung tumorigenesis and poor prognosis.
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Affiliation(s)
- Jayu Jen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yen-An Tang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
| | - Ying-Hung Lu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
| | - Che-Chung Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
| | - Wu-Wei Lai
- Division of Thoracic Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701 Taiwan
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175
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Abstract
Cellular senescence is a cell fate characterized by an irreversible cell cycle arrest, but the molecular mechanism underlying this senescence hallmark remains poorly understood. Through an unbiased search for novel senescence regulators in airway basal cells, we discovered that the epigenetic regulator ubiquitin-like with PHD and ring finger domain-containing protein 1 (UHRF1) is critical for regulating cell cycle progression. Upon injury, basal cells in the mouse airway rapidly induce the expression of UHRF1 in order to stimulate stem cell proliferation and tissue repair. Targeted depletion of Uhrf1 specifically in airway basal cells causes a profound defect in cell cycle progression. Consistently, cultured primary human basal cells lacking UHRF1 do not exhibit cell death or differentiation phenotypes but undergo a spontaneous program of senescence. Mechanistically, UHRF1 loss induces G1 cell cycle arrest by abrogating DNA replication factory formation as evidenced by loss of proliferating cell nuclear antigen (PCNA) puncta and an inability to enter the first cell cycle. This proliferation defect is partially mediated by the p15 pathway. Overall, our study provides the first evidence of an indispensable role of UHRF1 in somatic stem cells proliferation during the process of airway regeneration.
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176
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Dillinger S, Straub T, Németh A. Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation. PLoS One 2017; 12:e0178821. [PMID: 28575119 PMCID: PMC5456395 DOI: 10.1371/journal.pone.0178821] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/21/2017] [Indexed: 01/10/2023] Open
Abstract
Mammalian chromosomes are organized in structural and functional domains of 0.1–10 Mb, which are characterized by high self-association frequencies in the nuclear space and different contact probabilities with nuclear sub-compartments. They exhibit distinct chromatin modification patterns, gene expression levels and replication timing. Recently, nucleolus-associated chromosomal domains (NADs) have been discovered, yet their precise genomic organization and dynamics are still largely unknown. Here, we use nucleolus genomics and single-cell experiments to address these questions in human embryonic fibroblasts during replicative senescence. Genome-wide mapping reveals 1,646 NADs in proliferating cells, which cover about 38% of the annotated human genome. They are mainly heterochromatic and correlate with late replicating loci. Using Hi-C data analysis, we show that interactions of NADs dominate interphase chromosome contacts in the 10–50 Mb distance range. Interestingly, only minute changes in nucleolar association are observed upon senescence. These spatial rearrangements in subdomains smaller than 100 kb are accompanied with local transcriptional changes. In contrast, large centromeric and pericentromeric satellite repeat clusters extensively dissociate from nucleoli in senescent cells. Accordingly, H3K9me3-marked heterochromatin gets remodelled at the perinucleolar space as revealed by immunofluorescence analyses. Collectively, this study identifies connections between the nucleolus, 3D genome structure, and cellular aging at the level of interphase chromosome organization.
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Affiliation(s)
- Stefan Dillinger
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
| | - Tobias Straub
- Biomedical Center, Bioinformatics, Ludwig-Maximilians-University, Munich, Germany
| | - Attila Németh
- Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany
- * E-mail: ,
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177
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Salmonowicz H, Passos JF. Detecting senescence: a new method for an old pigment. Aging Cell 2017; 16:432-434. [PMID: 28185406 PMCID: PMC5418201 DOI: 10.1111/acel.12580] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2017] [Indexed: 01/23/2023] Open
Abstract
Cellular senescence is a state of irreversible cell cycle arrest induced by different types of cellular stresses. The field of senescence has made significant advances in the understanding of many of the mechanisms governing this phenomenon; however, a universal biomarker that unambiguously distinguishes senescent from proliferating cells has not been found. In this issue of Aging Cell, Evangelou and colleagues developed a sensitive method for identification of senescent cells in different types of biological material based on the detection of lipofuscin using an analogue of Sudan Black B (SBB) histochemical dye coupled with biotin, which they named GL13. The authors propose that this method is more sensitive and versatile than using SBB alone. Lipofuscin, a nondegradable oxidation product of lipids, proteins and metals, is found in senescent cells. Detection of lipofuscin using GL13 staining may be a more feasible method than others currently used for identification of senescent cells both in cell culture and tissues.
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Affiliation(s)
- Hanna Salmonowicz
- Institute for Cell and Molecular Biosciences & Newcastle University Institute for Ageing; Newcastle upon Tyne NE4 5PL UK
| | - João F. Passos
- Institute for Cell and Molecular Biosciences & Newcastle University Institute for Ageing; Newcastle upon Tyne NE4 5PL UK
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178
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McCulloch K, Litherland GJ, Rai TS. Cellular senescence in osteoarthritis pathology. Aging Cell 2017; 16:210-218. [PMID: 28124466 PMCID: PMC5334539 DOI: 10.1111/acel.12562] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2016] [Indexed: 12/19/2022] Open
Abstract
Cellular senescence is a state of stable proliferation arrest of cells. The senescence pathway has many beneficial effects and is seen to be activated in damaged/stressed cells, as well as during embryonic development and wound healing. However, the persistence and accumulation of senescent cells in various tissues can also impair function and have been implicated in the pathogenesis of many age‐related diseases. Osteoarthritis (OA), a severely debilitating chronic condition characterized by progressive tissue remodeling and loss of joint function, is the most prevalent disease of the synovial joints, and increasing age is the primary OA risk factor. The profile of inflammatory and catabolic mediators present during the pathogenesis of OA is strikingly similar to the secretory profile observed in ‘classical’ senescent cells. During OA, chondrocytes (the sole cell type present within articular cartilage) exhibit increased levels of various senescence markers, such as senescence‐associated beta‐galactosidase (SAβGal) activity, telomere attrition, and accumulation of p16ink4a. This suggests the hypothesis that senescence of cells within joint tissues may play a pathological role in the causation of OA. In this review, we discuss the mechanisms by which senescent cells may predispose synovial joints to the development and/or progression of OA, as well as touching upon various epigenetic alterations associated with both OA and senescence.
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Affiliation(s)
- Kendal McCulloch
- Institute of Biomedical and Environmental Health Research; University of the West of Scotland; Paisley PA1 2BE UK
| | - Gary J. Litherland
- Institute of Biomedical and Environmental Health Research; University of the West of Scotland; Paisley PA1 2BE UK
| | - Taranjit Singh Rai
- Institute of Biomedical and Environmental Health Research; University of the West of Scotland; Paisley PA1 2BE UK
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179
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Veitia RA, Govindaraju DR, Bottani S, Birchler JA. Aging: Somatic Mutations, Epigenetic Drift and Gene Dosage Imbalance. Trends Cell Biol 2017; 27:299-310. [DOI: 10.1016/j.tcb.2016.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
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180
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Barriers to Infection of Human Cells by Feline Leukemia Virus: Insights into Resistance to Zoonosis. J Virol 2017; 91:JVI.02119-16. [PMID: 28031367 PMCID: PMC5309941 DOI: 10.1128/jvi.02119-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/20/2016] [Indexed: 12/16/2022] Open
Abstract
The human genome displays a rich fossil record of past gammaretrovirus infections, yet no current epidemic is evident, despite environmental exposure to viruses that infect human cells in vitro. Feline leukemia viruses (FeLVs) rank high on this list, but neither domestic nor workplace exposure has been associated with detectable serological responses. Nonspecific inactivation of gammaretroviruses by serum factors appears insufficient to explain these observations. To investigate further, we explored the susceptibilities of primary and established human cell lines to FeLV-B, the most likely zoonotic variant. Fully permissive infection was common in cancer-derived cell lines but was also a feature of nontransformed keratinocytes and lung fibroblasts. Cells of hematopoietic origin were generally less permissive and formed discrete groups on the basis of high or low intracellular protein expression and virion release. Potent repression was observed in primary human blood mononuclear cells and a subset of leukemia cell lines. However, the early steps of reverse transcription and integration appear to be unimpaired in nonpermissive cells. FeLV-B was subject to G→A hypermutation with a predominant APOBEC3G signature in partially permissive cells but was not mutated in permissive cells or in nonpermissive cells that block secondary viral spread. Distinct cellular barriers that protect primary human blood cells are likely to be important in protection against zoonotic infection with FeLV. IMPORTANCE Domestic exposure to gammaretroviruses such as feline leukemia viruses (FeLVs) occurs worldwide, but the basis of human resistance to infection remains incompletely understood. The potential threat is evident from the human genome sequence, which reveals many past epidemics of gammaretrovirus infection, and from recent cross-species jumps of gammaretroviruses from rodents to primates and marsupials. This study examined resistance to infection at the cellular level with the most prevalent human cell-tropic FeLV variant, FeLV-B. We found that blood cells are uniquely resistant to infection with FeLV-B due to the activity of cellular enzymes that mutate the viral genome. A second block, which appears to suppress viral gene expression after the viral genome has integrated into the host cell genome, was identified. Since cells derived from other normal human cell types are fully supportive of FeLV replication, innate resistance of blood cells could be critical in protecting against cross-species infection.
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181
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Franzen J, Zirkel A, Blake J, Rath B, Benes V, Papantonis A, Wagner W. Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells. Aging Cell 2017; 16:183-191. [PMID: 27785870 PMCID: PMC5242294 DOI: 10.1111/acel.12544] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2016] [Indexed: 01/01/2023] Open
Abstract
Replicative senescence has a major impact on function and integrity of cell preparations. This process is reflected by continuous DNA methylation (DNAm) changes at specific CpG dinucleotides in the course of in vitro culture, and such modifications can be used to estimate the state of cellular senescence for quality control of cell preparations. Still, it is unclear how senescence‐associated DNAm changes are regulated and whether they occur simultaneously across a cell population. In this study, we analyzed global DNAm profiles of human mesenchymal stem cells (MSCs) and human umbilical vein endothelial cells (HUVECs) to demonstrate that senescence‐associated DNAm changes are overall similar in these different cell types. Subsequently, an Epigenetic‐Senescence‐Signature, based on six CpGs, was either analyzed by pyrosequencing or by bar‐coded bisulfite amplicon sequencing. There was a good correlation between predicted and real passage numbers in bulk populations of MSCs (R2 = 0.67) and HUVECs (R2 = 0.97). However, when we analyzed the Epigenetic‐Senescence‐Signature in subclones of MSCs, the predictions revealed high variation and they were not related to the adipogenic or osteogenic differentiation potential of the subclones. Notably, in clonally derived subpopulations, the DNAm levels of neighboring CpGs differed extensively, indicating that these genomic regions are not synchronously modified during senescence. Taken together, senescence‐associated DNAm changes occur in a highly reproducible manner, but they are not synchronously co‐regulated. They rather appear to be acquired stochastically—potentially evoked by other epigenetic modifications.
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Affiliation(s)
- Julia Franzen
- Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University Medical School; 52074 Aachen Germany
| | - Anne Zirkel
- Center for Molecular Medicine (CMMC); University of Cologne; 50931 Cologne Germany
| | - Jonathon Blake
- Genomics Core Facility; European Molecular Biology Laboratory (EMBL); 69117 Heidelberg Germany
| | - Björn Rath
- Department for Orthopedics; RWTH Aachen University Medical School; 52074 Aachen Germany
| | - Vladimir Benes
- Genomics Core Facility; European Molecular Biology Laboratory (EMBL); 69117 Heidelberg Germany
| | - Argyris Papantonis
- Center for Molecular Medicine (CMMC); University of Cologne; 50931 Cologne Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University Medical School; 52074 Aachen Germany
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182
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Epigenetics in Alzheimer's Disease: Perspective of DNA Methylation. Mol Neurobiol 2017; 55:1026-1044. [PMID: 28092081 DOI: 10.1007/s12035-016-0357-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
Research over the years has shown that causes of Alzheimer's disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus. In this review, we summarized and reviewed the involvement of different epigenetic mechanisms especially the DNA methylation in Alzheimer's disease (AD), late-onset Alzheimer's disease (LOAD), familial Alzheimer's disease (FAD), and autosomal dominant Alzheimer's disease (ADAD). Down to the minutest of details, we tried to discuss the methylation patterns like mitochondrial DNA methylation and ribosomal DNA (rDNA) methylation. Additionally, we mentioned some therapeutic approaches related to epigenetics, which could provide a potential cure for AD. Moreover, we reviewed some recent studies that validate DNA methylation as a potential biomarker and its role in AD. We hope that this review will provide new insights into the understanding of AD pathogenesis from the epigenetic perspective especially from the perspective of DNA methylation.
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183
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Taschner-Mandl S, Schwarz M, Blaha J, Kauer M, Kromp F, Frank N, Rifatbegovic F, Weiss T, Ladenstein R, Hohenegger M, Ambros IM, Ambros PF. Metronomic topotecan impedes tumor growth of MYCN-amplified neuroblastoma cells in vitro and in vivo by therapy induced senescence. Oncotarget 2016; 7:3571-86. [PMID: 26657295 PMCID: PMC4823128 DOI: 10.18632/oncotarget.6527] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022] Open
Abstract
Poor prognosis and frequent relapses are major challenges for patients with high-risk neuroblastoma (NB), especially when tumors show MYCN amplification. High-dose chemotherapy triggers apoptosis, necrosis and senescence, a cellular stress response leading to permanent proliferative arrest and a typical senescence-associated secretome (SASP). SASP components reinforce growth-arrest and act immune-stimulatory, while others are tumor-promoting. We evaluated whether metronomic, i.e. long-term, repetitive low-dose, drug treatment induces senescence in vitro and in vivo. And importantly, by using the secretome as a discriminator for beneficial versus adverse effects of senescence, drugs with a tumor-inhibiting SASP were identified. We demonstrate that metronomic application of chemotherapeutic drugs induces therapy-induced senescence, characterized by cell cycle arrest, p21WAF/CIP1 up-regulation and DNA double-strand breaks selectively in MYCN-amplified NB. Low-dose topotecan (TPT) was identified as an inducer of a favorable SASP while lacking NFKB1/p50 activation. In contrast, Bromo-deoxy-uridine induced senescent NB-cells secret a tumor-promoting SASP in a NFKB1/p50-dependent manner. Importantly, TPT-treated senescent tumor cells act growth-inhibitory in a dose-dependent manner on non-senescent tumor cells and MYCN expression is significantly reduced in vitro and in vivo. Furthermore, in a mouse xenotransplant-model for MYCN-amplified NB metronomic TPT leads to senescence selectively in tumor cells, complete or partial remission, prolonged survival and a favorable SASP. This new mode-of-action of metronomic TPT treatment, i.e. promoting a tumor-inhibiting type of senescence in MYCN-amplified tumors, is clinically relevant as metronomic regimens are increasingly implemented in therapy protocols of various cancer entities and are considered as a feasible maintenance treatment option with moderate adverse event profiles.
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Affiliation(s)
| | | | - Johanna Blaha
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | | | - Florian Kromp
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | - Nelli Frank
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | | | - Tamara Weiss
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | - Ruth Ladenstein
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Martin Hohenegger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Inge M Ambros
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria
| | - Peter F Ambros
- CCRI, Chlidren's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
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184
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Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems. Cell Rep 2016; 17:2101-2111. [PMID: 27851971 PMCID: PMC5889099 DOI: 10.1016/j.celrep.2016.10.054] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 01/15/2023] Open
Abstract
DNA methylation and the localization and post-translational modification of nucleosomes are interdependent factors that contribute to the generation of distinct phenotypes from genetically identical cells. With 112 whole-genome bisulfite sequencing datasets from the BLUEPRINT Epigenome Project, we analyzed the global development of DNA methylation patterns during lineage commitment and maturation of a range of immune system effector cells and the cancers that arise from them. We show clear trends in methylation patterns that are distinct in the innate and adaptive arms of the human immune system, both globally and in relation to consistently positioned nucleosomes. Most notable are a progressive loss of methylation in developing lymphocytes and the consistent occurrence of non-CG methylation in specific cell types. Cancer samples from the two lineages are further polarized, suggesting the involvement of distinct lineage-specific epigenetic mechanisms. We anticipate broad utility for this resource as a basis for further comparative epigenetic analyses.
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Affiliation(s)
- Ronald P Schuyler
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Angelika Merkel
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Emanuele Raineri
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Lucia Altucci
- Dipartimento di Biochimica Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, Napoli 80138, Italy
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Farzin Pourfarzad
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands; Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH Cambridge, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - José I Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.
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185
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Abstract
There is a dynamic interplay between metabolic processes and gene regulation via the remodeling of chromatin. Most chromatin-modifying enzymes use cofactors, which are products of metabolic processes. This article explores the biosynthetic pathways of the cofactors nicotinamide adenine dinucleotide (NAD), acetyl coenzyme A (acetyl-CoA), S-adenosyl methionine (SAM), α-ketoglutarate, and flavin adenine dinucleotide (FAD), and their role in metabolically regulating chromatin processes. A more detailed look at the interaction between chromatin and the metabolic processes of circadian rhythms and aging is described as a paradigm for this emerging interdisciplinary field.
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Affiliation(s)
- Shelley L Berger
- Department of Cell & Developmental Biology, Department of Biology, and Department of Genetics, Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6508
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-4049
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186
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Abstract
Cancers induced by gene mutation, deletion, and genome instability might be related to aging. With similar pathways of aging but distinct functions, senescence at the cellular level is an irreversible arrest of cell cycle. Senescence has long been believed as a barrier to restrict tumor expansion. However, more and more evidence has been shown that senescence inducers regulate epithelial-mesenchymal transition, stem cell self-renewal, inflammatory response, crosstalk with the oncogenic bypass signaling, and conversion of oncogene to tumor suppressor. Here we will discuss the most recent findings of the oncogenic aspects of senescence which crosstalk with multiple pathways in cancer progression.
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Affiliation(s)
- Qing Yang
- a Department of Biology , School of Science and Technology, Nazarbayev University , Astana , Kazakhstan
| | - Yingqiu Xie
- a Department of Biology , School of Science and Technology, Nazarbayev University , Astana , Kazakhstan
| | - Lixia Miao
- b College of Basic Medicine, Wuhan University , Wuhan , China
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187
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Klein HU, Bennett DA, De Jager PL. The epigenome in Alzheimer's disease: current state and approaches for a new path to gene discovery and understanding disease mechanism. Acta Neuropathol 2016; 132:503-14. [PMID: 27573688 DOI: 10.1007/s00401-016-1612-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/14/2016] [Accepted: 08/24/2016] [Indexed: 02/07/2023]
Abstract
The advent of new technologies and analytic approaches is beginning to provide an unprecedented look at features of the human genome that affect RNA expression. These "epigenomic" features are found in a number of different forms: they include DNA methylation, covalent modifications of histone proteins and non-coding RNAs. Some of these features have now been implicated in Alzheimer's disease (AD). Here, we focus on recent studies that have identified robust observations relating to DNA methylation and chromatin in human brain tissue; these findings will ground the next generation of studies and provide a model for the design of such studies. Stemming from observations that compounds with histone deacetylase activity may be beneficial in AD, epigenome-wide studies in cortical samples from large numbers of human subjects have now shown that AD-associated epigenomic changes are reproducible, are not driven by genetic risk factors, and are widespread at specific locations in the genome. A fundamental question of whether such changes are causal remains to be demonstrated, but it is already clear that well-powered investigations of the human epigenome in the target organ of a neurodegenerative disease are feasible, are implicating new areas of the genome in the disease, and will be an important tool for future studies. We are now at an inflection point: as genome-wide association studies of genetic variants come to an end, a new generation of studies exploring the epigenome will provide an important new layer of information with which to enrich our understanding of AD pathogenesis and to possibly guide development of new therapeutic targets.
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Affiliation(s)
- Hans-Ulrich Klein
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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188
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Criscione SW, Teo YV, Neretti N. The Chromatin Landscape of Cellular Senescence. Trends Genet 2016; 32:751-761. [PMID: 27692431 DOI: 10.1016/j.tig.2016.09.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/20/2022]
Abstract
Cellular senescence, an irreversible growth arrest triggered by a variety of stressors, plays important roles in normal physiology and tumor suppression, but accumulation of senescent cells with age contributes to the functional decline of tissues. Senescent cells undergo dramatic alterations to their chromatin landscape that affect genome accessibility and their transcriptional program. These include the loss of DNA-nuclear lamina interactions, the distension of centromeres, and changes in chromatin composition that can lead to the activation of retrotransposons. Here we discuss these findings, as well as recent advances in microscopy and genomics that have revealed the importance of the higher-order spatial organization of the genome in defining and maintaining the senescent state.
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Affiliation(s)
- Steven W Criscione
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Yee Voan Teo
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.
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189
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Abstract
Aging is an inevitable outcome of life, characterized by progressive decline in tissue and organ function and increased risk of mortality. Accumulating evidence links aging to genetic and epigenetic alterations. Given the reversible nature of epigenetic mechanisms, these pathways provide promising avenues for therapeutics against age-related decline and disease. In this review, we provide a comprehensive overview of epigenetic studies from invertebrate organisms, vertebrate models, tissues, and in vitro systems. We establish links between common operative aging pathways and hallmark chromatin signatures that can be used to identify "druggable" targets to counter human aging and age-related disease.
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Affiliation(s)
- Payel Sen
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Parisha P Shah
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Raffaella Nativio
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA
| | - Shelley L Berger
- Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19130, USA.
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190
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Parry AJ, Narita M. Old cells, new tricks: chromatin structure in senescence. Mamm Genome 2016; 27:320-31. [PMID: 27021489 PMCID: PMC4935760 DOI: 10.1007/s00335-016-9628-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/16/2016] [Indexed: 12/20/2022]
Abstract
Cellular senescence is a stable form of cell cycle arrest with roles in many pathophysiological processes including development, tissue repair, cancer, and aging. Senescence does not represent a single entity but rather a heterogeneous phenotype that depends on the trigger and cell type of origin. Such heterogeneous features include alterations to chromatin structure and epigenetic states. New technologies are beginning to unravel the distinct mechanisms regulating chromatin structure during senescence. Here, we describe the multiple levels of chromatin organization associated with senescence: global and focal, linear, and higher order.
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Affiliation(s)
- Aled John Parry
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE UK
| | - Masashi Narita
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE UK
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191
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Nelson DM, Jaber-Hijazi F, Cole JJ, Robertson NA, Pawlikowski JS, Norris KT, Criscione SW, Pchelintsev NA, Piscitello D, Stong N, Rai TS, McBryan T, Otte GL, Nixon C, Clark W, Riethman H, Wu H, Schotta G, Garcia BA, Neretti N, Baird DM, Berger SL, Adams PD. Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biol 2016; 17:158. [PMID: 27457071 PMCID: PMC4960804 DOI: 10.1186/s13059-016-1017-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although H4K20me3 abundance increases during cellular senescence, a stable proliferation arrest and tumor suppressor process, triggered by diverse molecular cues, including activated oncogenes. Here, we investigate the function of H4K20me3 in senescence and tumor suppression. RESULTS Using immunofluorescence and ChIP-seq we determine the distribution of H4K20me3 in proliferating and senescent human cells. Altered H4K20me3 in senescence is coupled to H4K16ac and DNA methylation changes in senescence. In senescent cells, H4K20me3 is especially enriched at DNA sequences contained within specialized domains of senescence-associated heterochromatin foci (SAHF), as well as specific families of non-genic and genic repeats. Altered H4K20me3 does not correlate strongly with changes in gene expression between proliferating and senescent cells; however, in senescent cells, but not proliferating cells, H4K20me3 enrichment at gene bodies correlates inversely with gene expression, reflecting de novo accumulation of H4K20me3 at repressed genes in senescent cells, including at genes also repressed in proliferating cells. Although elevated SUV420H2 upregulates H4K20me3, this does not accelerate senescence of primary human cells. However, elevated SUV420H2/H4K20me3 reinforces oncogene-induced senescence-associated proliferation arrest and slows tumorigenesis in vivo. CONCLUSIONS These results corroborate a role for chromatin in underpinning the senescence phenotype but do not support a major role for H4K20me3 in initiation of senescence. Rather, we speculate that H4K20me3 plays a role in heterochromatinization and stabilization of the epigenome and genome of pre-malignant, oncogene-expressing senescent cells, thereby suppressing epigenetic and genetic instability and contributing to long-term senescence-mediated tumor suppression.
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Affiliation(s)
- David M. Nelson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Farah Jaber-Hijazi
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - John J. Cole
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Neil A. Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Jeffrey S. Pawlikowski
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Kevin T. Norris
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903 USA
| | - Nikolay A. Pchelintsev
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Desiree Piscitello
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | | | - Taranjit Singh Rai
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, PA1 2BE UK
| | - Tony McBryan
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Gabriel L. Otte
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Colin Nixon
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - William Clark
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | | | - Hong Wu
- Fox Chase Cancer Center, Philadelphia, PA 19111 USA
| | - Gunnar Schotta
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried, Germany
| | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903 USA
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Shelley L. Berger
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Peter D. Adams
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
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192
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Wang Y, Xu Q, Sack L, Kang C, Elledge SJ. A gain-of-function senescence bypass screen identifies the homeobox transcription factor DLX2 as a regulator of ATM-p53 signaling. Genes Dev 2016; 30:293-306. [PMID: 26833729 PMCID: PMC4743059 DOI: 10.1101/gad.271445.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Wang et al. performed a two-stage, gain-of function screen to select for the genes whose enhanced expression can bypass replicative senescence. Among the new genes that they identified, DLX2 reduces the protein components of the TTI1/TTI2/TEL2 complex, a key complex required for the proper folding and stabilization of ATM and other members of the PIKK family kinase, leading to reduced ATM–p53 signaling and senescence bypass. Senescence stimuli activate multiple tumor suppressor pathways to initiate cycle arrest and a differentiation program characteristic of senescent cells. We performed a two-stage, gain-of-function screen to select for the genes whose enhanced expression can bypass replicative senescence. We uncovered multiple genes known to be involved in p53 and Rb regulation and ATM regulation, two components of the CST (CTC1–STN1–TEN1) complex involved in preventing telomere erosion, and genes such as REST and FOXO4 that have been implicated in aging. Among the new genes now implicated in senescence, we identified DLX2, a homeobox transcription factor that has been shown to be required for tumor growth and metastasis and is associated with poor cancer prognosis. Growth analysis showed that DLX2 expression led to increased cellular replicative life span. Our data suggest that DLX2 expression reduces the protein components of the TTI1/TTI2/TEL2 complex, a key complex required for the proper folding and stabilization of ATM and other members of the PIKK (phosphatidylinositol 3-kinase-related kinase) family kinase, leading to reduced ATM–p53 signaling and senescence bypass. We also found that the overexpression of DLX2 exhibited a mutually exclusive relationship with p53 alterations in cancer patients. Our functional screen identified novel players that may promote tumorigenesis by regulating the ATM–p53 pathway and senescence.
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Affiliation(s)
- Yifan Wang
- Department of Genetics, Harvard University Medical School, Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA
| | - Qikai Xu
- Department of Genetics, Harvard University Medical School, Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA
| | - Laura Sack
- Department of Genetics, Harvard University Medical School, Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA
| | - Chanhee Kang
- Department of Genetics, Harvard University Medical School, Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA
| | - Stephen J Elledge
- Department of Genetics, Harvard University Medical School, Howard Hughes Medical Institute, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA
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193
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194
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Prime SS, Cirillo N, Hassona Y, Lambert DW, Paterson IC, Mellone M, Thomas GJ, James ENL, Parkinson EK. Fibroblast activation and senescence in oral cancer. J Oral Pathol Med 2016; 46:82-88. [PMID: 27237745 DOI: 10.1111/jop.12456] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2016] [Indexed: 12/13/2022]
Abstract
There is now compelling evidence that the tumour stroma plays an important role in the pathogenesis of cancers of epithelial origin. The pre-eminent cell type of the stroma is carcinoma-associated fibroblasts. These cells demonstrate remarkable heterogeneity with activation and senescence being common stress responses. In this review, we summarise the part that these cells play in cancer, particularly oral cancer, and present evidence to show that activation and senescence reflect a unified programme of fibroblast differentiation. We report advances concerning the senescent fibroblast metabolome, mechanisms of gene regulation in these cells and ways in which epithelial cell adhesion is dysregulated by the fibroblast secretome. We suggest that the identification of fibroblast stress responses may be a valuable diagnostic tool in the determination of tumour behaviour and patient outcome. Further, the fact that stromal fibroblasts are a genetically stable diploid cell population suggests that they may be ideal therapeutic targets and early work in this context is encouraging.
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Affiliation(s)
- S S Prime
- Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - N Cirillo
- Melbourne Dental School and Oral Health CRC, University of Melbourne, Carlton, VIC, Australia
| | - Y Hassona
- Department of Dentistry, University of Jordan, Amman, Jordan
| | - D W Lambert
- Integrated Biosciences, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - I C Paterson
- Department of Oral Biology and Biomedical Sciences and Oral Cancer Research and Co-ordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - M Mellone
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - G J Thomas
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - E N L James
- Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - E K Parkinson
- Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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195
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ROS, Cell Senescence, and Novel Molecular Mechanisms in Aging and Age-Related Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:3565127. [PMID: 27247702 PMCID: PMC4877482 DOI: 10.1155/2016/3565127] [Citation(s) in RCA: 598] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/02/2016] [Accepted: 04/06/2016] [Indexed: 12/15/2022]
Abstract
The aging process worsens the human body functions at multiple levels, thus causing its gradual decrease to resist stress, damage, and disease. Besides changes in gene expression and metabolic control, the aging rate has been associated with the production of high levels of Reactive Oxygen Species (ROS) and/or Reactive Nitrosative Species (RNS). Specific increases of ROS level have been demonstrated as potentially critical for induction and maintenance of cell senescence process. Causal connection between ROS, aging, age-related pathologies, and cell senescence is studied intensely. Senescent cells have been proposed as a target for interventions to delay the aging and its related diseases or to improve the diseases treatment. Therapeutic interventions towards senescent cells might allow restoring the health and curing the diseases that share basal processes, rather than curing each disease in separate and symptomatic way. Here, we review observations on ROS ability of inducing cell senescence through novel mechanisms that underpin aging processes. Particular emphasis is addressed to the novel mechanisms of ROS involvement in epigenetic regulation of cell senescence and aging, with the aim to individuate specific pathways, which might promote healthy lifespan and improve aging.
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196
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Lenart P, Krejci L. Reprint of "DNA, the central molecule of aging". Mutat Res 2016; 788:25-31. [PMID: 27133220 DOI: 10.1016/j.mrfmmm.2016.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/16/2016] [Accepted: 01/30/2016] [Indexed: 01/05/2023]
Abstract
Understanding the molecular mechanism of aging could have enormous medical implications. Despite a century of research, however, there is no universally accepted theory regarding the molecular basis of aging. On the other hand, there is plentiful evidence suggesting that DNA constitutes the central molecule in this process. Here, we review the roles of chromatin structure, DNA damage, and shortening of telomeres in aging and propose a hypothesis for how their interplay leads to aging phenotypes.
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Affiliation(s)
- Peter Lenart
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
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197
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Acevedo M, Vernier M, Mignacca L, Lessard F, Huot G, Moiseeva O, Bourdeau V, Ferbeyre G. A CDK4/6-Dependent Epigenetic Mechanism Protects Cancer Cells from PML-induced Senescence. Cancer Res 2016; 76:3252-64. [PMID: 27206849 DOI: 10.1158/0008-5472.can-15-2347] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/10/2016] [Indexed: 12/17/2022]
Abstract
Promyelocytic leukemia (PML) plays a tumor suppressive role by inducing cellular senescence in response to oncogenic stress. However, tumor cell lines fail to engage in complete senescence upon PML activation. In this study, we investigated the mechanisms underlying resistance to PML-induced senescence. Here, we report that activation of the cyclin-dependent kinases CDK4 and CDK6 are essential and sufficient to impair senescence induced by PML expression. Disrupting CDK function by RNA interference or pharmacological inhibition restored senescence in tumor cells and diminished their tumorigenic potential in mouse xenograft models. Complete senescence correlated with an increase in autophagy, repression of E2F target genes, and an gene expression signature of blocked DNA methylation. Accordingly, treatment of tumor cells with inhibitors of DNA methylation reversed resistance to PML-induced senescence. Further, CDK inhibition with palbociclib promoted autophagy-dependent degradation of the DNA methyltransferase DNMT1. Lastly, we found that CDK4 interacted with and phosphorylated DNMT1 in vitro, suggesting that CDK activity is required for its stabilization. Taken together, our findings highlight a potentially valuable feature of CDK4/6 inhibitors as epigenetic modulators to facilitate activation of senescence programs in tumor cells. Cancer Res; 76(11); 3252-64. ©2016 AACR.
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Affiliation(s)
- Mariana Acevedo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Mathieu Vernier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Lian Mignacca
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Frédéric Lessard
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Geneviève Huot
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Olga Moiseeva
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Véronique Bourdeau
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada.
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada.
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198
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Truong TP, Sakata-Yanagimoto M, Yamada M, Nagae G, Enami T, Nakamoto-Matsubara R, Aburatani H, Chiba S. Age-Dependent Decrease of DNA Hydroxymethylation in Human T Cells. J Clin Exp Hematop 2016; 55:1-6. [PMID: 26105999 DOI: 10.3960/jslrt.55.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Hydroxymethylcytosine (hmC) is a natural nucleobase, which is converted from methylcytosine (mC) by tet methylcytosine dioxygenase (TET) family (TET1-3) enzymes. Decrease of genomic hmC is postulated to confer a risk for myeloid-lineage as well as T-cell neoplasms, based on the fact that loss-of-function mutations in the TET2 gene were frequently identified in these diseases. The relationship between hmC and aging remains to be elucidated. Here, we demonstrated that hmC content decreased with age in the peripheral blood T cells of 53 human volunteers. We further identified that the mRNA expression levels of TET1 and TET3 decreased with age, while those of TET2 were not influenced by age. The genomic hmC content was correlated with the mRNA expression level of TET3, but not those of TET1 and TET2. Our study suggests the presence of new epigenetic regulatory mechanisms in aging T cells.
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Affiliation(s)
- Thien Phu Truong
- Department of Hematology, Graduate School of Comprehensive Human Science, University of Tsukuba
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199
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Wang Y, Zhang J, Xiao X, Liu H, Wang F, Li S, Wen Y, Wei Y, Su J, Zhang Y, Zhang Y. The identification of age-associated cancer markers by an integrative analysis of dynamic DNA methylation changes. Sci Rep 2016; 6:22722. [PMID: 26949191 PMCID: PMC4779991 DOI: 10.1038/srep22722] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 02/18/2016] [Indexed: 12/29/2022] Open
Abstract
As one of the most widely studied epigenetic modifications, DNA methylation has an important influence on human traits and cancers. Dynamic variations in DNA methylation have been reported in malignant neoplasm and aging; however, the mechanisms remain poorly understood. By constructing an age-associated and cancer-related weighted network (ACWN) based on the correlation of the methylation level and the protein-protein interaction, we found that DNA methylation changes associated with age were closely related to the occurrence of cancer. Additional analysis of 102 module genes mined from the ACWN revealed discrimination based on two main patterns. One pattern involved methylation levels that increased with aging and were higher in cancer patients compared with normal controls (HH pattern). The other pattern involved methylation levels that decreased with aging and were lower in cancer compared with normal (LL pattern). Upon incorporation with gene expression levels, 25 genes were filtered based on negative regulation by DNA methylation. These genes were regarded as potential cancer risk markers that were influenced by age in the process of carcinogenesis. Our results will facilitate further studies regarding the impact of the epigenetic effects of aging on diseases and will aid in the development of tailored cancer preventive strategies.
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Affiliation(s)
- Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jingyu Zhang
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xingjun Xiao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin 150086, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Song Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yanhua Wen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jianzhong Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yunming Zhang
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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200
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Perrigue PM, Najbauer J, Barciszewski J. Histone demethylase JMJD3 at the intersection of cellular senescence and cancer. Biochim Biophys Acta Rev Cancer 2016; 1865:237-44. [PMID: 26957416 DOI: 10.1016/j.bbcan.2016.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/13/2016] [Accepted: 03/04/2016] [Indexed: 01/08/2023]
Abstract
Cellular senescence is defined by an irreversible growth arrest and is an important biological mechanism for suppression of tumor formation. Although deletion/mutation to DNA sequences is one mechanism by which cancer cells can escape senescence, little is known about the epigenetic factors contributing to this process. Histone modifications and chromatin remodeling related to the function of a histone demethylase, jumonji domain-containing protein 3 (JMJD3; also known as KDM6B), play an important role in development, tissue regeneration, stem cells, inflammation, and cellular senescence and aging. The role of JMJD3 in cancer is poorly understood and its function may be at the intersection of many pathways promoted in a dysfunctional manner such as activation of the senescence-associated secretory phenotype (SASP) observed in aging.
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Affiliation(s)
- Patrick M Perrigue
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Joseph Najbauer
- Department of Immunology and Biotechnology, University of Pécs Medical School, Pécs, Hungary.
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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