201
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Bhatia-Dey N, Kanherkar RR, Stair SE, Makarev EO, Csoka AB. Cellular Senescence as the Causal Nexus of Aging. Front Genet 2016; 7:13. [PMID: 26904101 PMCID: PMC4751276 DOI: 10.3389/fgene.2016.00013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 01/26/2016] [Indexed: 12/15/2022] Open
Abstract
In this paper we present cellular senescence as the ultimate driver of the aging process, as a "causal nexus" that bridges microscopic subcellular damage with the phenotypic, macroscopic effect of aging. It is important to understand how the various types of subcellular damage correlated with the aging process lead to the larger, visible effects of anatomical aging. While it has always been assumed that subcellular damage (cause) results in macroscopic aging (effect), the bridging link between the two has been hard to define. Here, we propose that this bridge, which we term the "causal nexus", is in fact cellular senescence. The subcellular damage itself does not directly cause the visible signs of aging, but rather, as the damage accumulates and reaches a critical mass, cells cease to proliferate and acquire the deleterious "senescence-associated secretory phenotype" (SASP) which then leads to the macroscopic consequences of tissue breakdown to create the physiologically aged phenotype. Thus senescence is a precondition for anatomical aging, and this explains why aging is a gradual process that remains largely invisible during most of its progression. The subcellular damage includes shortening of telomeres, damage to mitochondria, aneuploidy, and DNA double-strand breaks triggered by various genetic, epigenetic, and environmental factors. Damage pathways acting in isolation or in concert converge at the causal nexus of cellular senescence. In each species some types of damage can be more causative than in others and operate at a variable pace; for example, telomere erosion appears to be a primary cause in human cells, whereas activation of tumor suppressor genes is more causative in rodents. Such species-specific mechanisms indicate that despite different initial causes, most of aging is traced to a single convergent causal nexus: senescence. The exception is in some invertebrate species that escape senescence, and in non-dividing cells such as neurons, where senescence still occurs, but results in the SASP rather than loss of proliferation plus SASP. Aging currently remains an inevitable endpoint for most biological organisms, but the field of cellular senescence is primed for a renaissance and as our understanding of aging is refined, strategies capable of decelerating the aging process will emerge.
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Affiliation(s)
- Naina Bhatia-Dey
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
| | - Riya R Kanherkar
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
| | | | - Evgeny O Makarev
- Vision Genomics, LLCWashington, DC, USA; InSilico Medicine, Emerging Technology Center, Johns Hopkins UniversityBaltimore, MD, USA
| | - Antonei B Csoka
- Epigenetics Laboratory, Department of Anatomy, Howard UniversityWashington, DC, USA; InSilico Medicine, Emerging Technology Center, Johns Hopkins UniversityBaltimore, MD, USA
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202
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DNA, the central molecule of aging. Mutat Res 2016; 786:1-7. [PMID: 26871429 DOI: 10.1016/j.mrfmmm.2016.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 02/07/2023]
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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203
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Loaiza N, Demaria M. Cellular senescence and tumor promotion: Is aging the key? Biochim Biophys Acta Rev Cancer 2016; 1865:155-67. [PMID: 26845683 DOI: 10.1016/j.bbcan.2016.01.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 01/07/2023]
Abstract
The senescence response is a potent tumor suppressor mechanism characterized by an irreversible growth arrest in response to potentially oncogenic signals to prevent the proliferation of damaged cells. Late in life, some of the features of senescent cells seem to mediate the development of age-related pathologies, including cancer. In the present review, we present a summary of the current knowledge regarding the causes, effector pathways and cellular features of senescence. We also discuss how the senescence response, initially a tumor suppressor mechanism, turns into a tumor promoter apparently as a consequence of aging. We argue that three age-related phenomena--senescence-associated secretory phenotype (SASP) dysregulation, decline in the immune system function and genomic instability--could contribute, independently or synergistically, to deteriorate the efficacy of the senescence response in stopping cancer. As a consequence, senescent cells could be considered premalignant cells, and targeting senescent cells could be a preventive and therapeutic strategy against cancer.
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Affiliation(s)
- Natalia Loaiza
- University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Marco Demaria
- University Medical Center Groningen (UMCG), Groningen, The Netherlands; European Research Institute for the Biology of Aging (ERIBA), Groningen, The Netherlands.
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204
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Criscione SW, De Cecco M, Siranosian B, Zhang Y, Kreiling JA, Sedivy JM, Neretti N. Reorganization of chromosome architecture in replicative cellular senescence. SCIENCE ADVANCES 2016; 2:e1500882. [PMID: 26989773 PMCID: PMC4788486 DOI: 10.1126/sciadv.1500882] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/02/2015] [Indexed: 05/02/2023]
Abstract
Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.
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Affiliation(s)
- Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Benjamin Siranosian
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Yue Zhang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Jill A. Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - John M. Sedivy
- 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
- Corresponding author. E-mail:
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205
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Walters HE, Deneka-Hannemann S, Cox LS. Reversal of phenotypes of cellular senescence by pan-mTOR inhibition. Aging (Albany NY) 2016; 8:231-44. [PMID: 26851731 PMCID: PMC4789579 DOI: 10.18632/aging.100872] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellular senescence, a state of essentially irreversible proliferation arrest, serves as a potent tumour suppressor mechanism. However, accumulation of senescent cells with chronological age is likely to contribute to loss of tissue and organ function and organismal aging. A crucial biochemical modulator of aging is mTOR; here, we have addressed the question of whether acute mTORC inhibition in near-senescent cells can modify phenotypes of senescence. We show that acute short term treatment of human skin fibroblasts with low dose ATP mimetic pan-mTORC inhibitor AZD8055 leads to reversal of many phenotypes that develop as cells near replicative senescence, including reduction in cell size and granularity, loss of SA-β-gal staining and reacquisition of fibroblastic spindle morphology. AZD8055 treatment also induced rearrangement of the actin cytoskeleton, providing a possible mechanism of action for the observed rejuvenation. Importantly, short-term drug exposure had no detrimental effects on cell proliferation control across the life-course of the fibroblasts. Our findings suggest that combined inhibition of both mTORC1 and mTORC2 may provide a promising strategy to reverse the development of senescence-associated features in near-senescent cells.
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Affiliation(s)
- Hannah E Walters
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Sylwia Deneka-Hannemann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Current address: Oxford BioMedica Plc, Oxford, OX4 6LT, United Kingdom
| | - Lynne S Cox
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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206
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Wagner W, Fernandez-Rebollo E, Frobel J. DNA-methylation changes in replicative senescence and aging: two sides of the same coin? Epigenomics 2016; 8:1-3. [DOI: 10.2217/epi.15.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
| | - Eduardo Fernandez-Rebollo
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
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207
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Vandiver AR, Idrizi A, Rizzardi L, Feinberg AP, Hansen KD. DNA methylation is stable during replication and cell cycle arrest. Sci Rep 2015; 5:17911. [PMID: 26648411 PMCID: PMC4673417 DOI: 10.1038/srep17911] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/09/2015] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is an epigenetic modification with important functions in development. Large-scale loss of DNA methylation is a hallmark of cancer. Recent work has identified large genomic blocks of hypomethylation associated with cancer, EBV transformation and replicative senescence, all of which change the proportion of actively proliferating cells within the population measured. We asked if replication or cell-cycle arrest affects the global levels of methylation or leads to hypomethylated blocks as observed in other settings. We used fluorescence activated cell sorting to isolate primary dermal fibroblasts in G0, G1 and G2 based on DNA content and Ki67 staining. We additionally examined G0 cells arrested by contact inhibition for one week to determine the effects of extended arrest. We analyzed genome wide DNA methylation from sorted cells using whole genome bisulfite sequencing. This analysis demonstrated no global changes or large-scale hypomethylated blocks in any of the examined cell cycle phases, indicating that global levels of methylation are stable with replication and arrest.
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Affiliation(s)
- Amy R Vandiver
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Lindsay Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine.,Department of Medicine, Johns Hopkins University School of Medicine
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
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208
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Cannuyer J, Van Tongelen A, Loriot A, De Smet C. A gene expression signature identifying transient DNMT1 depletion as a causal factor of cancer-germline gene activation in melanoma. Clin Epigenetics 2015; 7:114. [PMID: 26504497 PMCID: PMC4620642 DOI: 10.1186/s13148-015-0147-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
Background Many human tumors show aberrant activation of a group of germline-specific genes, termed cancer-germline (CG) genes, several of which appear to exert oncogenic functions. Although activation of CG genes in tumors has been linked to promoter DNA demethylation, the mechanisms underlying this epigenetic alteration remain unclear. Two main processes have been proposed: awaking of a gametogenic program directing demethylation of target DNA sequences via specific regulators, or general deficiency of DNA methylation activities resulting from mis-targeting or down-regulation of the DNMT1 methyltransferase. Results By the analysis of transcriptomic data, we searched to identify gene expression changes associated with CG gene activation in melanoma cells. We found no evidence linking CG gene activation with differential expression of gametogenic regulators. Instead, CG gene activation correlated with decreased expression of a set of mitosis/division-related genes (ICCG genes). Interestingly, a similar gene expression signature was previously associated with depletion of DNMT1. Consistently, analysis of a large set of melanoma tissues revealed that DNMT1 expression levels were often lower in samples showing activation of multiple CG genes. Moreover, by using immortalized melanocytes and fibroblasts carrying an inducible anti-DNMT1 small hairpin RNA (shRNA), we demonstrate that transient depletion of DNMT1 can lead to long-term activation of CG genes and repression of ICCG genes at the same time. For one of the ICCG genes (CDCA7L), we found that its down-regulation in melanoma cells was associated with deposition of repressive chromatin marks, including H3K27me3. Conclusions Together, our observations point towards transient DNMT1 depletion as a causal factor of CG gene activation in vivo in melanoma. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0147-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Cannuyer
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Aurélie Van Tongelen
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Axelle Loriot
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Charles De Smet
- Group of Genetics and Epigenetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
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209
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Lowe R, Overhoff MG, Ramagopalan SV, Garbe JC, Koh J, Stampfer MR, Beach DH, Rakyan VK, Bishop CL. The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans. Genome Biol 2015; 16:194. [PMID: 26381124 PMCID: PMC4574115 DOI: 10.1186/s13059-015-0748-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/10/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. Here, we perform methylome analysis of actively dividing and deeply senescent normal human epithelial cells. RESULTS We identify senescence-associated differentially methylated positions (senDMPs) from multiple experiments using cells from one donor. We find that human senDMP epigenetic signatures are positively and significantly correlated with both cancer and ageing-associated methylation dynamics. We also identify germline genetic variants, including those associated with the p16INK4A locus, which are associated with the presence of in vivo senDMP signatures. Importantly, we also demonstrate that a single senDMP signature can be effectively reversed in a newly-developed protocol of transient senescence reversal. CONCLUSIONS The senDMP signature has significant potential for understanding some of the key (epi)genetic etiological factors that may lead to cancer and age-related diseases in humans.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Marita G Overhoff
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Sreeram V Ramagopalan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - James C Garbe
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James Koh
- Division of Surgical Sciences, Department of Surgery, Duke University Medical School, Durham, NC, 27710, USA
| | - Martha R Stampfer
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David H Beach
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
| | - Cleo L Bishop
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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210
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Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol 2015; 16:593-610. [PMID: 26373265 DOI: 10.1038/nrm4048] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ageing is affected by both genetic and non-genetic factors. Here, we review the chromatin-based epigenetic changes that occur during ageing, the role of chromatin modifiers in modulating lifespan and the importance of epigenetic signatures as biomarkers of ageing. We also discuss how epigenome remodelling by environmental stimuli affects several aspects of transcription and genomic stability, with important consequences for longevity, and outline epigenetic differences between the 'mortal soma' and the 'immortal germ line'. Finally, we discuss the inheritance of characteristics of ageing and potential chromatin-based strategies to delay or reverse hallmarks of ageing or age-related diseases.
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211
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Miousse IR, Currie R, Datta K, Ellinger-Ziegelbauer H, French JE, Harrill AH, Koturbash I, Lawton M, Mann D, Meehan RR, Moggs JG, O'Lone R, Rasoulpour RJ, Pera RAR, Thompson K. Importance of investigating epigenetic alterations for industry and regulators: An appraisal of current efforts by the Health and Environmental Sciences Institute. Toxicology 2015; 335:11-9. [PMID: 26134581 DOI: 10.1016/j.tox.2015.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/15/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022]
Abstract
Recent technological advances have led to rapid progress in the characterization of epigenetic modifications that control gene expression in a generally heritable way, and are likely involved in defining cellular phenotypes, developmental stages and disease status from one generation to the next. On November 18, 2013, the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) held a symposium entitled "Advances in Assessing Adverse Epigenetic Effects of Drugs and Chemicals" in Washington, D.C. The goal of the symposium was to identify gaps in knowledge and highlight promising areas of progress that represent opportunities to utilize epigenomic profiling for risk assessment of drugs and chemicals. Epigenomic profiling has the potential to provide mechanistic information in toxicological safety assessments; this is especially relevant for the evaluation of carcinogenic or teratogenic potential and also for drugs that directly target epigenetic modifiers, like DNA methyltransferases or histone modifying enzymes. Furthermore, it can serve as an endpoint or marker for hazard characterization in chemical safety assessment. The assessment of epigenetic effects may also be approached with new model systems that could directly assess transgenerational effects or potentially sensitive stem cell populations. These would enhance the range of safety assessment tools for evaluating xenobiotics that perturb the epigenome. Here we provide a brief synopsis of the symposium, update findings since that time and then highlight potential directions for future collaborative efforts to incorporate epigenetic profiling into risk assessment.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Richard Currie
- Syngenta Jealotts Hill International Research Centre, Bracknell, Berkshire, UK
| | | | - Heidrun Ellinger-Ziegelbauer
- Toxicology, Bayer Pharma AG, Wuppertal, Germany; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - John E French
- National Institute for Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | - Alison H Harrill
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Derek Mann
- Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - Jonathan G Moggs
- Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland; Member of the Innovative Medicines Initiative (IMI) BioMARkers & molecular tumor classification for non-genotoxic CARcinogenesis (MARCAR) consortium www.imi-marcar.eu
| | - Raegan O'Lone
- ILSI Health and Environmental Sciences Institute, Washington, D.C., USA
| | - Reza J Rasoulpour
- Toxicology Environmental Research and Consulting, The Dow Chemical Company, Midland, MI, USA
| | | | - Karol Thompson
- Division of Applied Regulatory Science, OCP, CDER, US FDA, Silver Spring, MD, USA
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212
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Abstract
The second International Symposium on the Genetics of Aging and Life History was held at the campus of Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea, from May 14 to 16, 2014. Many leading scientists in the field of aging research from all over the world contributed to the symposium by attending and presenting their recent work and thoughts. The aim of the symposium was to stimulate international collaborations and interactions among scientists who work on the biology of aging. In the symposium, the most recent and exciting work on aging research was presented, covering a wide range of topics, including the genetics of aging, age-associated diseases, and cellular senescence. The work was conducted in various organisms, includingC. elegans, mice, plants, and humans. Topics covered in the symposium stimulated discussion of novel directions for future research on aging. The meeting ended with a commitment for the third International Symposium on the Genetics of Aging and Life History, which will be held in 2016.
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213
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Lin Q, Wagner W. Epigenetic Aging Signatures Are Coherently Modified in Cancer. PLoS Genet 2015; 11:e1005334. [PMID: 26110659 PMCID: PMC4482318 DOI: 10.1371/journal.pgen.1005334] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/03/2015] [Indexed: 12/31/2022] Open
Abstract
Aging is associated with highly reproducible DNA methylation (DNAm) changes, which may contribute to higher prevalence of malignant diseases in the elderly. In this study, we analyzed epigenetic aging signatures in 5,621 DNAm profiles of 25 cancer types from The Cancer Genome Atlas (TCGA). Overall, age-associated DNAm patterns hardly reflect chronological age of cancer patients, but they are coherently modified in a non-stochastic manner, particularly at CpGs that become hypermethylated upon aging in non-malignant tissues. This coordinated regulation in epigenetic aging signatures can therefore be used for aberrant epigenetic age-predictions, which facilitate disease stratification. For example, in acute myeloid leukemia (AML) higher epigenetic age-predictions are associated with increased incidence of mutations in RUNX1, WT1, and IDH2, whereas mutations in TET2, TP53, and PML-PARA translocation are more frequent in younger age-predictions. Furthermore, epigenetic aging signatures correlate with overall survival in several types of cancer (such as lower grade glioma, glioblastoma multiforme, esophageal carcinoma, chromophobe renal cell carcinoma, cutaneous melanoma, lung squamous cell carcinoma, and neuroendocrine neoplasms). In conclusion, age-associated DNAm patterns in cancer are not related to chronological age of the patient, but they are coordinately regulated, particularly at CpGs that become hypermethylated in normal aging. Furthermore, the apparent epigenetic age-predictions correlate with clinical parameters and overall survival in several types of cancer, indicating that regulation of DNAm patterns in age-associated CpGs is relevant for cancer development. Our genome harbors epigenetic marks, such as DNA methylation (DNAm) at cytosine residues, which govern cellular differentiation. Some epigenetic modifications accumulate throughout life in a highly reproducible manner–they may contribute to the aging process and facilitate reliable age-predictions. So far, little is known how these “epigenetic aging signatures” are modified in cancer tissue and whether or not they are accelerated as compared to normal tissue. In this study, we systematically analyzed age-associated DNAm patterns in many types of cancer. In contrast to non-malignant tissue the epigenetic aging signatures hardly reflect chronological age of cancer patients. This may at least partially be attributed to the fact that cancer is a clonal disease capturing only the epigenetic make-up of the tumor-initiating cell. Notably, the aberrant DNAm patterns are not randomly distributed but reveal co-regulation at regions that become methylated upon aging in non-malignant tissue. Furthermore, we demonstrate that deviations of epigenetic age-predictions correlate with clinical parameters. In fact, they are clearly associated with overall survival in many types of cancer. These findings are particularly important, as they indicate relevance of age-associated DNA methylation patterns for malignant transformation, cancer development and prognosis.
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Affiliation(s)
- Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- * E-mail:
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214
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Swanson EC, Rapkin LM, Bazett-Jones DP, Lawrence JB. Unfolding the story of chromatin organization in senescent cells. Nucleus 2015; 6:254-60. [PMID: 26107557 DOI: 10.1080/19491034.2015.1057670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Cell senescence, the permanent withdrawal of a cell from the cell cycle, is characterized by dramatic, cytological scale changes to DNA condensation throughout the genome. While prior emphasis has been placed on increases in heterochromatin, such as the formation of compact Senescent Associated Heterochromatin Foci (SAHF) structures, our recent findings showed that SAHF formation is preceded by the unravelling of constitutive heterochromatin into visibly extended structures, which we have termed Senescent Associated Distension of Satellites or SADS. Interestingly, neither of these marked changes in DNA condensation appear to be mediated by changes in canonical, heterochromatin-associated histone modifications. Rather, several observations suggest that these events may be facilitated by changes in LaminB1 levels and/or other factors that control higher-order chromatin architecture. Here, we review what is known about senescence-associated chromatin reorganization and present preliminary results using high-resolution microscopy techniques to show that each peri/centromeric satellite in senescent cells is comprised of several condensed domains connected by thin fibrils of satellite DNA. We then discuss the potential importance of these striking changes in chromatin condensation for cell senescence, and also as a model to provide a needed window into the higher-order packaging of the genome.
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Affiliation(s)
- Eric C Swanson
- a Department of Cell and Developmental Biology ; University of Massachusetts Medical School ; Worcester , MA USA
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215
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Weidner CI, Wagner W. The epigenetic tracks of aging. Biol Chem 2015; 395:1307-14. [PMID: 25205717 DOI: 10.1515/hsz-2014-0180] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/18/2014] [Indexed: 11/15/2022]
Abstract
Abstract Aging is associated with the deterioration of biological functions, which is either caused by accumulation of random defects or mediated by a controlled process. This article provides an overview of age-associated epigenetic alterations in the histone code, DNA-methylation (DNAm) pattern, and chromatin structure. In particular, age-related DNAm changes are highly reproducible at specific sites in the genome. The DNAm level at few CpGs facilitates estimation of chronological age and there is evidence that such predictions are indicative for biological age. Overall, aging appears to be associated with a tightly regulated epigenetic process, but the underlying mechanism remains to be elucidated.
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216
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Whole-genome fingerprint of the DNA methylome during human B cell differentiation. Nat Genet 2015; 47:746-56. [PMID: 26053498 DOI: 10.1038/ng.3291] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/03/2015] [Indexed: 02/06/2023]
Abstract
We analyzed the DNA methylome of ten subpopulations spanning the entire B cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays. We observed that non-CpG methylation disappeared upon B cell commitment, whereas CpG methylation changed extensively during B cell maturation, showing an accumulative pattern and affecting around 30% of all measured CpG sites. Early differentiation stages mainly displayed enhancer demethylation, which was associated with upregulation of key B cell transcription factors and affected multiple genes involved in B cell biology. Late differentiation stages, in contrast, showed extensive demethylation of heterochromatin and methylation gain at Polycomb-repressed areas, and genes with apparent functional impact in B cells were not affected. This signature, which has previously been linked to aging and cancer, was particularly widespread in mature cells with an extended lifespan. Comparing B cell neoplasms with their normal counterparts, we determined that they frequently acquire methylation changes in regions already undergoing dynamic methylation during normal B cell differentiation.
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217
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Abstract
Aging is characterized by a decrease in genome integrity, impaired organ maintenance, and an increased risk of cancer, which coincide with clonal dominance of expanded mutant stem and progenitor cell populations in aging tissues, such as the intestinal epithelium, the hematopoietic system, and the male germline. Here we discuss possible explanations for age-associated increases in the initiation and/or progression of mutant stem/progenitor clones and highlight the roles of stem cell quiescence, replication-associated DNA damage, telomere shortening, epigenetic alterations, and metabolic challenges as determinants of stem cell mutations and clonal dominance in aging.
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Affiliation(s)
- Peter D Adams
- University of Glasgow and Beatson Institute for Cancer Research, Glasgow G61 1BD, UK
| | - Heinrich Jasper
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400, USA
| | - K Lenhard Rudolph
- Leibniz Institute for Age Research - Fritz Lipmann Institute e.V. (FLI), Beutenbergstr. 11, 07745 Jena, Germany.
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218
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Saade E, Pirozhkova I, Aimbetov R, Lipinski M, Ogryzko V. Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis). Aging Cell 2015; 14:322-33. [PMID: 25720734 PMCID: PMC4406661 DOI: 10.1111/acel.12332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 12/22/2022] Open
Abstract
The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed.
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Affiliation(s)
- Evelyne Saade
- Faculty of Public Health Lebanese University LU Beirut Lebanon
| | - Iryna Pirozhkova
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Rakhan Aimbetov
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Marc Lipinski
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Vasily Ogryzko
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
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219
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Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol 2015; 16:80. [PMID: 25886480 PMCID: PMC4423110 DOI: 10.1186/s13059-015-0644-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/23/2015] [Indexed: 01/09/2023] Open
Abstract
Background Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging and/or chronic sun exposure in humans. Results We compare epidermis and dermis of both sun-protected and sun-exposed skin derived from younger subjects (under 35 years old) and older subjects (over 60 years old), using the Infinium HumanMethylation450 array and whole genome bisulfite sequencing. We observe large blocks of the genome that are hypomethylated in older, sun-exposed epidermal samples, with the degree of hypomethylation associated with clinical measures of photo-aging. We replicate these findings using whole genome bisulfite sequencing, comparing epidermis from an additional set of younger and older subjects. These blocks largely overlap known hypomethylated blocks in colon cancer and we observe that these same regions are similarly hypomethylated in squamous cell carcinoma samples. Conclusions These data implicate large scale epigenomic change in mediating the effects of environmental damage with photo-aging. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0644-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amy R Vandiver
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Rafael A Irizarry
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA. .,Dana-Farber Cancer Institute, CLSB 11007, 450 Brookline Ave, Boston, MA, 02215, USA.
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA. .,Department of Biostatistics and Institute for Genetic Medicine, Johns Hopkins University School of Medicine, 615N. Wolfe St, E3527, Baltimore, MD, 21205, USA.
| | - Luis A Garza
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Arni Runarsson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Xin Li
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Anna L Chien
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Timothy S Wang
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Sherry G Leung
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Sewon Kang
- Department of Dermatology, Johns Hopkins University School of Medicine, CRB II Room 204, 1550 Orleans Street, Baltimore, MD, 21287, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Rangos 570, 855N. Wolfe St, Baltimore, MD, 21205, USA. .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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220
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Controlled induction of DNA double-strand breaks in the mouse liver induces features of tissue ageing. Nat Commun 2015; 6:6790. [PMID: 25858675 PMCID: PMC4394211 DOI: 10.1038/ncomms7790] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/27/2015] [Indexed: 01/07/2023] Open
Abstract
DNA damage has been implicated in ageing, but direct evidence for a causal relationship is lacking, owing to the difficulty of inducing defined DNA lesions in cells and tissues without simultaneously damaging other biomolecules and cellular structures. Here we directly test whether highly toxic DNA double-strand breaks (DSBs) alone can drive an ageing phenotype using an adenovirus-based system based on tetracycline-controlled expression of the SacI restriction enzyme. We deliver the adenovirus to mice and compare molecular and cellular end points in the liver with normally aged animals. Treated, 3-month-old mice display many, but not all signs of normal liver ageing as early as 1 month after treatment, including ageing pathologies, markers of senescence, fused mitochondria and alterations in gene expression profiles. These results, showing that DSBs alone can cause distinct ageing phenotypes in mouse liver, provide new insights in the role of DNA damage as a driver of tissue ageing. Accumulation of DNA damage is a hallmark of cellular ageing but cause and effect are unclear. Here White et al. induce clean DNA double-strand breaks in the liver of mice using a modified restriction enzyme and demonstrate that DNA damage alone is sufficient to recapitulate some aspects of tissue ageing.
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221
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In vitro evidence for senescent multinucleated melanocytes as a source for tumor-initiating cells. Cell Death Dis 2015; 6:e1711. [PMID: 25837487 PMCID: PMC4650540 DOI: 10.1038/cddis.2015.71] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 01/12/2023]
Abstract
Oncogenic signaling in melanocytes results in oncogene-induced senescence (OIS), a stable cell-cycle arrest frequently characterized by a bi- or multinuclear phenotype that is considered as a barrier to cancer progression. However, the long-sustained conviction that senescence is a truly irreversible process has recently been challenged. Still, it is not known whether cells driven into OIS can progress to cancer and thereby pose a potential threat. Here, we show that prolonged expression of the melanoma oncogene N-RAS61K in pigment cells overcomes OIS by triggering the emergence of tumor-initiating mononucleated stem-like cells from senescent cells. This progeny is dedifferentiated, highly proliferative, anoikis-resistant and induces fast growing, metastatic tumors. Our data describe that differentiated cells, which are driven into senescence by an oncogene, use this senescence state as trigger for tumor transformation, giving rise to highly aggressive tumor-initiating cells. These observations provide the first experimental in vitro evidence for the evasion of OIS on the cellular level and ensuing transformation.
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222
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Burton DGA, Faragher RGA. Cellular senescence: from growth arrest to immunogenic conversion. AGE (DORDRECHT, NETHERLANDS) 2015; 37:27. [PMID: 25787341 PMCID: PMC4365077 DOI: 10.1007/s11357-015-9764-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/27/2015] [Indexed: 05/23/2023]
Abstract
Cellular senescence was first reported in human fibroblasts as a state of stable in vitro growth arrest following extended culture. Since that initial observation, a variety of other phenotypic characteristics have been shown to co-associate with irreversible cell cycle exit in senescent fibroblasts. These include (1) a pro-inflammatory secretory response, (2) the up-regulation of immune ligands, (3) altered responses to apoptotic stimuli and (4) promiscuous gene expression (stochastic activation of genes possibly as a result of chromatin remodeling). Many features associated with senescent fibroblasts appear to promote conversion to an immunogenic phenotype that facilitates self-elimination by the immune system. Pro-inflammatory cytokines can attract and activate immune cells, the presentation of membrane bound immune ligands allows for specific recognition and promiscuous gene expression may function to generate an array of tissue restricted proteins that could subsequently be processed into peptides for presentation via MHC molecules. However, the phenotypes of senescent cells from different tissues and species are often assumed to be broadly similar to those seen in senescent human fibroblasts, but the data show a more complex picture in which the growth arrest mechanism, tissue of origin and species can all radically modulate this basic pattern. Furthermore, well-established triggers of cell senescence are often associated with a DNA damage response (DDR), but this may not be a universal feature of senescent cells. As such, we discuss the role of DNA damage in regulating an immunogenic response in senescent cells, in addition to discussing less established "atypical" senescent states that may occur independent of DNA damage.
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Affiliation(s)
- D. G. A. Burton
- Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - R. G. A. Faragher
- School of Pharmacy & Biomolecular Science, University of Brighton, Huxley Building, Brighton, UK
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223
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Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W. Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. Clin Epigenetics 2015; 7:19. [PMID: 25763115 PMCID: PMC4356053 DOI: 10.1186/s13148-015-0057-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/10/2015] [Indexed: 02/08/2023] Open
Abstract
Background Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown - it may involve stochastic DNAm drift due to imperfect maintenance of epigenetic marks or it is directly regulated at specific sites in the genome. Results In this study, we analyzed the reorganization of nuclear architecture and DNAm changes during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). We demonstrate that telomeres shorten and shift towards the nuclear center at later passages. In addition, DNAm profiles, either analyzed by MethylCap-seq or by 450k IlluminaBeadChip technology, revealed consistent senescence-associated hypermethylation in regions associated with H3K27me3, H3K4me3, and H3K4me1 histone marks, whereas hypomethylation was associated with chromatin containing H3K9me3 and lamina-associated domains (LADs). DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages. Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes. Conclusions Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence. These results indicate that tightly regulated epigenetic modifications during long-term culture contribute to changes in nuclear organization and gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0057-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonja Hänzelmann
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Eduardo G Gusmao
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Carmen M Koch
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
| | - Sebastian Hummel
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Sylvia Joussen
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - George Reid
- Institute for Molecular Biology, Mainz, Germany
| | - Ivan G Costa
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
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224
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Kirschner K, Samarajiwa SA, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet 2015; 11:e1005053. [PMID: 25790137 PMCID: PMC4366240 DOI: 10.1371/journal.pgen.1005053] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023] Open
Abstract
The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.
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Affiliation(s)
- Kristina Kirschner
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Shamith A. Samarajiwa
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Jonathan M. Cairns
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Pedro A. Pérez-Mancera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Camino Bermejo-Rodriguez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Tamir Chandra
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Masako Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Scott K. Lyons
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Andy G. Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and Technology, Tottori University, Yonago, Japan
| | - Simon Tavaré
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
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225
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Weiner-Gorzel K, Dempsey E, Milewska M, McGoldrick A, Toh V, Walsh A, Lindsay S, Gubbins L, Cannon A, Sharpe D, O'Sullivan J, Murphy M, Madden SF, Kell M, McCann A, Furlong F. Overexpression of the microRNA miR-433 promotes resistance to paclitaxel through the induction of cellular senescence in ovarian cancer cells. Cancer Med 2015; 4:745-58. [PMID: 25684390 PMCID: PMC4430267 DOI: 10.1002/cam4.409] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 12/18/2022] Open
Abstract
Annually, ovarian cancer (OC) affects 240,000 women worldwide and is the most lethal gynecological malignancy. High-grade serous OC (HGSOC) is the most common and aggressive OC subtype, characterized by widespread genome changes and chromosomal instability and is consequently poorly responsive to chemotherapy treatment. The objective of this study was to investigate the role of the microRNA miR-433 in the cellular response of OC cells to paclitaxel treatment. We show that stable miR-433 expression in A2780 OC cells results in the induction of cellular senescence demonstrated by morphological changes, downregulation of phosphorylated retinoblastoma (p-Rb), and an increase in β-galactosidase activity. Furthermore, in silico analysis identified four possible miR-433 target genes associated with cellular senescence: cyclin-dependent kinase 6 (CDK6), MAPK14, E2F3, and CDKN2A. Mechanistically, we demonstrate that downregulation of p-Rb is attributable to a miR-433-dependent downregulation of CDK6, establishing it as a novel miR-433 associated gene. Interestingly, we show that high miR-433 expressing cells release miR-433 into the growth media via exosomes which in turn can induce a senescence bystander effect. Furthermore, in relation to a chemotherapeutic response, quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that only PEO1 and PEO4 OC cells with the highest miR-433 expression survive paclitaxel treatment. Our data highlight how the aberrant expression of miR-433 can adversely affect intracellular signaling to mediate chemoresistance in OC cells by driving cellular senescence.
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Affiliation(s)
- Karolina Weiner-Gorzel
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Eugene Dempsey
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | | | - Aloysius McGoldrick
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Valerie Toh
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Aoibheann Walsh
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Sinead Lindsay
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Luke Gubbins
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Aoife Cannon
- Molecular Department of Surgery, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital, Dublin 8, Ireland
| | - Daniel Sharpe
- School of Pharmacy, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Jacintha O'Sullivan
- Molecular Department of Surgery, Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James's Hospital, Dublin 8, Ireland
| | - Madeline Murphy
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Stephen F Madden
- Molecular Therapeutics for Cancer Ireland, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Malcolm Kell
- Department of Surgery, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Amanda McCann
- UCD School of Medicine and Medical Science (SMMS), UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Fiona Furlong
- School of Pharmacy, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom
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226
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Abstract
Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. This review by Iwafuchi-Doi and Zaret focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatin-binding properties, and facilitators and impediments to chromatin binding. A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in “closed” chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as “pioneer factors” to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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227
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Nestor CE, Ottaviano R, Reinhardt D, Cruickshanks HA, Mjoseng HK, McPherson RC, Lentini A, Thomson JP, Dunican DS, Pennings S, Anderton SM, Benson M, Meehan RR. Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems. Genome Biol 2015; 16:11. [PMID: 25648825 PMCID: PMC4334405 DOI: 10.1186/s13059-014-0576-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022] Open
Abstract
Background The DNA methylation profiles of mammalian cell lines differ from those of the primary tissues from which they were derived, exhibiting increasing divergence from the in vivo methylation profile with extended time in culture. Few studies have directly examined the initial epigenetic and transcriptional consequences of adaptation of primary mammalian cells to culture, and the potential mechanisms through which this epigenetic dysregulation occurs is unknown. Results We demonstrate that adaptation of mouse embryonic fibroblasts to cell culture results in a rapid reprogramming of epigenetic and transcriptional states. We observed global 5-hydroxymethylcytosine (5hmC) erasure within three days of culture initiation. Loss of genic 5hmC was independent of global 5-methylcytosine (5mC) levels and could be partially rescued by addition of vitamin C. Significantly, 5hmC loss was not linked to concomitant changes in transcription. Discrete promoter-specific gains of 5mC were also observed within seven days of culture initiation. Against this background of global 5hmC loss we identified a handful of developmentally important genes that maintained their 5hmC profile in culture, including the imprinted loci Gnas and H19. Similar outcomes were identified in the adaption of CD4+ T cells to culture. Conclusions We report a dramatic and novel consequence of adaptation of mammalian cells to culture in which global loss of 5hmC occurs, suggesting rapid concomitant loss of methylcytosine dioxygenase activity. The observed epigenetic and transcriptional re-programming occurs much earlier than previously assumed, and has significant implications for the use of cell lines as faithful mimics of in vivo epigenetic and physiological processes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0576-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colm E Nestor
- Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Raffaele Ottaviano
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Diana Reinhardt
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Hazel A Cruickshanks
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Heidi K Mjoseng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Rhoanne C McPherson
- MRC Centre for Inflammation Research, Centre for Multiple Sclerosis Research and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH16 4TJ, UK.
| | - Antonio Lentini
- Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden.
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
| | - Stephen M Anderton
- MRC Centre for Inflammation Research, Centre for Multiple Sclerosis Research and Centre for Immunity Infection and Evolution, University of Edinburgh, Edinburgh, EH16 4TJ, UK.
| | - Mikael Benson
- Centre for Individualised Medicine, Faculty of Health Sciences, Linköping University, Linköping, 581 83, Sweden.
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
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228
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Chandra T, Ewels PA, Schoenfelder S, Furlan-Magaril M, Wingett SW, Kirschner K, Thuret JY, Andrews S, Fraser P, Reik W. Global reorganization of the nuclear landscape in senescent cells. Cell Rep 2015; 10:471-83. [PMID: 25640177 PMCID: PMC4542308 DOI: 10.1016/j.celrep.2014.12.055] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/13/2014] [Accepted: 12/22/2014] [Indexed: 02/03/2023] Open
Abstract
Cellular senescence has been implicated in tumor suppression, development, and aging and is accompanied by large-scale chromatin rearrangements, forming senescence-associated heterochromatic foci (SAHF). However, how the chromatin is reorganized during SAHF formation is poorly understood. Furthermore, heterochromatin formation in senescence appears to contrast with loss of heterochromatin in Hutchinson-Gilford progeria. We mapped architectural changes in genome organization in cellular senescence using Hi-C. Unexpectedly, we find a dramatic sequence- and lamin-dependent loss of local interactions in heterochromatin. This change in local connectivity resolves the paradox of opposing chromatin changes in senescence and progeria. In addition, we observe a senescence-specific spatial clustering of heterochromatic regions, suggesting a unique second step required for SAHF formation. Comparison of embryonic stem cells (ESCs), somatic cells, and senescent cells shows a unidirectional loss in local chromatin connectivity, suggesting that senescence is an endpoint of the continuous nuclear remodelling process during differentiation.
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Affiliation(s)
- Tamir Chandra
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.
| | | | | | | | | | - Kristina Kirschner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Jean-Yves Thuret
- CEA, iBiTec-S, SBIGeM/CNRS FRE3377 I2BC/Université Paris-Sud, Gif-sur-Yvette 91191, France
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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229
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Sugawara H, Bundo M, Asai T, Sunaga F, Ueda J, Ishigooka J, Kasai K, Kato T, Iwamoto K. Effects of quetiapine on DNA methylation in neuroblastoma cells. Prog Neuropsychopharmacol Biol Psychiatry 2015; 56:117-21. [PMID: 25194461 DOI: 10.1016/j.pnpbp.2014.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 02/05/2023]
Abstract
Epigenetic regulation may be involved in the pathophysiology of mental disorders, such as schizophrenia and bipolar disorder, and in the pharmacological action of drugs. Characterizing the epigenetic effects of drugs is an important step to optimal treatment. We performed comprehensive and gene-specific DNA methylation analyses of quetiapine using human neuroblastoma cells. Human neuroblastoma cells were cultured with quetiapine for 8 days, and DNA methylation analysis was performed using Infinium HumanMethylation27 BeadChip. A total of 1173 genes showed altered DNA methylation. Altered DNA methylation predominantly occurred as hypomethylation within the CpG island compared to DNA isolated from non-treated cells. Gene ontology analysis revealed that these genes were related to the cellular process of intracellular protein binding. There was no common effect of quetiapine with three mood stabilizers (lithium, valproate, and carbamazepine). However, common DNA methylation changes in eight genes, including ADRA1A, which encodes adrenoceptor alpha 1A, were found with quetiapine and lithium treatments. Finally, bisulfite-sequencing analysis revealed that quetiapine decreased the DNA methylation level of the promoter region of SLC6A4, where hypermethylation with bipolar disorder and hypomethylation with mood stabilizers have been reported.
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Affiliation(s)
- Hiroko Sugawara
- Department of Psychiatry, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Miki Bundo
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tatsuro Asai
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Fumiko Sunaga
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Junko Ueda
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Jun Ishigooka
- Department of Psychiatry, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuya Iwamoto
- Department of Molecular Psychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
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230
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Beishline K, Azizkhan-Clifford J. Sp1 and the 'hallmarks of cancer'. FEBS J 2015; 282:224-58. [PMID: 25393971 DOI: 10.1111/febs.13148] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 09/26/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
Abstract
For many years, transcription factor Sp1 was viewed as a basal transcription factor and relegated to a role in the regulation of so-called housekeeping genes. Identification of Sp1's role in recruiting the general transcription machinery in the absence of a TATA box increased its importance in gene regulation, particularly in light of recent estimates that the majority of mammalian genes lack a TATA box. In this review, we briefly consider the history of Sp1, the founding member of the Sp family of transcription factors. We review the evidence suggesting that Sp1 is highly regulated by post-translational modifications that positively and negatively affect the activity of Sp1 on a wide array of genes. Sp1 is over-expressed in many cancers and is associated with poor prognosis. Targeting Sp1 in cancer treatment has been suggested; however, our review of the literature on the role of Sp1 in the regulation of genes that contribute to the 'hallmarks of cancer' illustrates the extreme complexity of Sp1 functions. Sp1 both activates and suppresses the expression of a number of essential oncogenes and tumor suppressors, as well as genes involved in essential cellular functions, including proliferation, differentiation, the DNA damage response, apoptosis, senescence and angiogenesis. Sp1 is also implicated in inflammation and genomic instability, as well as epigenetic silencing. Given the apparently opposing effects of Sp1, a more complete understanding of the function of Sp1 in cancer is required to validate its potential as a therapeutic target.
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Affiliation(s)
- Kate Beishline
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
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231
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Rai TS, Cole JJ, Nelson DM, Dikovskaya D, Faller WJ, Vizioli MG, Hewitt RN, Anannya O, McBryan T, Manoharan I, van Tuyn J, Morrice N, Pchelintsev NA, Ivanov A, Brock C, Drotar ME, Nixon C, Clark W, Sansom OJ, Anderson KI, King A, Blyth K, Adams PD. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes Dev 2014; 28:2712-25. [PMID: 25512559 PMCID: PMC4265675 DOI: 10.1101/gad.247528.114] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 11/04/2014] [Indexed: 01/06/2023]
Abstract
Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression.
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Affiliation(s)
- Taranjit Singh Rai
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom; Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, United Kingdom
| | - John J Cole
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - David M Nelson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Dina Dikovskaya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - William J Faller
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Maria Grazia Vizioli
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Rachael N Hewitt
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Orchi Anannya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Tony McBryan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Indrani Manoharan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - John van Tuyn
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Nicholas Morrice
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Nikolay A Pchelintsev
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Andre Ivanov
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Claire Brock
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Mark E Drotar
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Colin Nixon
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - William Clark
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Owen J Sansom
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Kurt I Anderson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Ayala King
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Karen Blyth
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Peter D Adams
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom;
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232
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Oberdoerffer P. Stop relaxing: How DNA damage-induced chromatin compaction may affect epigenetic integrity and disease. Mol Cell Oncol 2014; 2:e970952. [PMID: 27308388 PMCID: PMC4905243 DOI: 10.4161/23723548.2014.970952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 09/12/2014] [Accepted: 09/13/2014] [Indexed: 11/25/2022]
Abstract
DNA damage is widely recognized for its potential to impair epigenetic integrity. Epigenetic defects are closely associated with a variety of diseases. We have recently uncovered DNA double-strand break-induced chromatin condensation as a critical modulator of repair outcome. Here, we discuss the possible implications for cell functions beyond repair.
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Affiliation(s)
- Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression. National Cancer Institute; NIH ; Bethesda, MD USA
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233
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Wagner W, Weidner CI, Lin Q. Do age-associated DNA methylation changes increase the risk of malignant transformation? Bioessays 2014; 37:20-4. [DOI: 10.1002/bies.201400063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
| | - Carola I. Weidner
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
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234
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Lund K, Cole JJ, VanderKraats ND, McBryan T, Pchelintsev NA, Clark W, Copland M, Edwards JR, Adams PD. DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. Genome Biol 2014; 15:406. [PMID: 25315154 PMCID: PMC4165364 DOI: 10.1186/s13059-014-0406-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/09/2014] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are neoplastic disorders of hematopoietic stem cells. DNA methyltransferase inhibitors, 5-azacytidine and 5-aza-2'-deoxycytidine (decitabine), benefit some MDS/AML patients. However, the role of DNA methyltransferase inhibitor-induced DNA hypomethylation in regulation of gene expression in AML is unclear. RESULTS We compared the effects of 5-azacytidine on DNA methylation and gene expression using whole-genome single-nucleotide bisulfite-sequencing and RNA-sequencing in OCI-AML3 cells. For data analysis, we used an approach recently developed for discovery of differential patterns of DNA methylation associated with changes in gene expression, that is tailored to single-nucleotide bisulfite-sequencing data (Washington University Interpolated Methylation Signatures). Using this approach, we find that a subset of genes upregulated by 5-azacytidine are characterized by 5-azacytidine-induced signature methylation loss flanking the transcription start site. Many of these genes show increased methylation and decreased expression in OCI-AML3 cells compared to normal hematopoietic stem and progenitor cells. Moreover, these genes are preferentially upregulated by decitabine in human primary AML blasts, and control cell proliferation, death, and development. CONCLUSIONS Our approach identifies a set of genes whose methylation and silencing in AML is reversed by DNA methyltransferase inhibitors. These genes are good candidates for direct regulation by DNA methyltransferase inhibitors, and their reactivation by DNA methyltransferase inhibitors may contribute to therapeutic activity.
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Affiliation(s)
- Kirstin Lund
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- />Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
- />Paul O’Gorman Leukemia Research Centre, Glasgow, G12 0ZD UK
| | - John J Cole
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- />Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Nathan D VanderKraats
- />Center for Pharmacogenomics, Washington University School of Medicine, St Louis, MO 63110 USA
| | - Tony McBryan
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- />Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Nikolay A Pchelintsev
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- />Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - William Clark
- />Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Mhairi Copland
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- />Paul O’Gorman Leukemia Research Centre, Glasgow, G12 0ZD UK
| | - John R Edwards
- />Center for Pharmacogenomics, Washington University School of Medicine, St Louis, MO 63110 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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235
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Zane L, Sharma V, Misteli T. Common features of chromatin in aging and cancer: cause or coincidence? Trends Cell Biol 2014; 24:686-94. [PMID: 25103681 DOI: 10.1016/j.tcb.2014.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 02/06/2023]
Abstract
Age is a major risk factor for cancer. Alterations in DNA methylation, histone modifications, chromatin structure, and epigenetic regulatory mechanisms are prominent hallmarks of both the aging process and cancer. Intriguingly--or possibly coincidentally--several chromatin features are common between aging and cancer. Here we ask whether, and if so how, aging-associated chromatin modifications contribute to tumor susceptibility and tumorigenesis.
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Affiliation(s)
- Linda Zane
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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236
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Physiological and pathological consequences of cellular senescence. Cell Mol Life Sci 2014; 71:4373-86. [PMID: 25080110 PMCID: PMC4207941 DOI: 10.1007/s00018-014-1691-3] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/11/2022]
Abstract
Cellular senescence, a permanent state of cell cycle arrest accompanied by a complex phenotype, is an essential mechanism that limits tumorigenesis and tissue damage. In physiological conditions, senescent cells can be removed by the immune system, facilitating tumor suppression and wound healing. However, as we age, senescent cells accumulate in tissues, either because an aging immune system fails to remove them, the rate of senescent cell formation is elevated, or both. If senescent cells persist in tissues, they have the potential to paradoxically promote pathological conditions. Cellular senescence is associated with an enhanced pro-survival phenotype, which most likely promotes persistence of senescent cells in vivo. This phenotype may have evolved to favor facilitation of a short-term wound healing, followed by the elimination of senescent cells by the immune system. In this review, we provide a perspective on the triggers, mechanisms and physiological as well as pathological consequences of senescent cells.
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237
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Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias. Neoplasia 2014; 16:606-15. [PMID: 25065939 PMCID: PMC4198827 DOI: 10.1016/j.neo.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
We have previously described gene expression changes during spontaneous immortalization of T-cells, thereby identifying cellular processes important for cell growth crisis escape and unlimited proliferation. Here, we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre-crisis and post-crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with preferential increased methylation close to transcription start sites (TSSs), islands, and shore regions. Methylation and gene expression alterations did not correlate for the majority of genes, but for the fraction that correlated, gain of methylation close to TSS was associated with decreased gene expression. Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype positive. These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion, and cell signaling processes. The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis.
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238
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Kaneda A, Matsusaka K, Sakai E, Funata S. DNA methylation accumulation and its predetermination of future cancer phenotypes. J Biochem 2014; 156:63-72. [PMID: 24962701 DOI: 10.1093/jb/mvu038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aberant DNA methylation is a common epigenomic alteration in carcinogenesis. Comprehensive analyses of DNA methylation have stratified gastrointestinal cancer into several subgroups according to specific DNA methylation accumulation. In gastric cancer, Helicobacter pylori infection is a cause of methylation accumulation in apparently normal mucosa. Epstein-Barr virus infection is another methylation inducer that causes more genome-wide methylation, resulting in the formation of unique epigenotype with extensive methylation. In colorectal carcinogenesis, accumulation of high levels of methylation in combination with BRAF mutation is characteristic of the serrated pathway, but not of the adenoma-carcinoma sequence through conventional adenoma. In a de novo pathway, laterally spreading tumours generate intermediate- and low-methylation epigenotypes, accompanied by different genetic features and different macroscopic morphologies. These methylation epigenotypes, with specific genomic aberrations, are mostly completed by the adenoma stage, and additional molecular aberration, such as TP53 mutation, is suggested to lead to cancer development with the corresponding epigenotype. Accumulation of DNA methylation and formation of the epigenotype is suggested to occur during the early stages of carcinogenesis and predetermines the future cancer type.
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Affiliation(s)
- Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, JapanDepartment of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, JapanDepartment of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Eiji Sakai
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, JapanDepartment of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Sayaka Funata
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, JapanDepartment of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; and Department of Gastroenterology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
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239
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Chromatin maintenance and dynamics in senescence: a spotlight on SAHF formation and the epigenome of senescent cells. Chromosoma 2014; 123:423-36. [PMID: 24861957 DOI: 10.1007/s00412-014-0469-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 01/28/2023]
Abstract
Senescence is a stable proliferation arrest characterized by profound changes in cellular morphology and metabolism as well as by extensive chromatin reorganization in the nucleus. One particular hallmark of chromatin changes during senescence is the formation of punctate DNA foci in DAPI-stained senescent cells that have been called senescence-associated heterochromatin foci (SAHF). While many advances have been made concerning our understanding of the effectors of senescence, how chromatin is reorganized and maintained in senescent cells has remained largely elusive. Because chromatin structure is inherently dynamic, senescent cells face the challenge of developing chromatin maintenance mechanisms in the absence of DNA replication in order to maintain the senescent phenotype. Here, we summarize and review recent findings shedding light on SAHF composition and formation via spatial repositioning of chromatin, with a specific focus on the role of lamin B1 for this process. In addition, we discuss the physiological implication of SAHF formation, the role of histone variants, and histone chaperones during senescence and also elaborate on the more general changes observed in the epigenome of the senescent cells.
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240
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Schellenberg A, Joussen S, Moser K, Hampe N, Hersch N, Hemeda H, Schnitker J, Denecke B, Lin Q, Pallua N, Zenke M, Merkel R, Hoffmann B, Wagner W. Matrix elasticity, replicative senescence and DNA methylation patterns of mesenchymal stem cells. Biomaterials 2014; 35:6351-8. [PMID: 24824582 DOI: 10.1016/j.biomaterials.2014.04.079] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/22/2014] [Indexed: 12/28/2022]
Abstract
Matrix elasticity guides differentiation of mesenchymal stem cells (MSCs) but it is unclear if these effects are only transient - while the cells reside on the substrate - or if they reflect persistent lineage commitment. In this study, MSCs were continuously culture-expanded in parallel either on tissue culture plastic (TCP) or on polydimethylsiloxane (PDMS) gels of different elasticity to compare impact on replicative senescence, in vitro differentiation, gene expression, and DNA methylation (DNAm) profiles. The maximal number of cumulative population doublings was not affected by matrix elasticity. Differentiation towards adipogenic and osteogenic lineage was increased on soft and rigid biomaterials, respectively - but this propensity was no more evident if cells were transferred to TCP. Global gene expression profiles and DNAm profiles revealed relatively few differences in MSCs cultured on soft or rigid matrices. Furthermore, only moderate DNAm changes were observed upon culture on very soft hydrogels of human platelet lysate. Our results support the notion that matrix elasticity influences cellular behavior while the cells reside on the substrate, but it does not have major impact on cell-intrinsic lineage determination, replicative senescence or DNAm patterns.
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Affiliation(s)
- Anne Schellenberg
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany
| | - Kristin Moser
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany; Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Nico Hampe
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Nils Hersch
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany
| | - Jan Schnitker
- Institute of Complex Systems, ICS-8: Bioelectronics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Bernd Denecke
- Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany; Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Norbert Pallua
- Department of Plastic and Reconstructive Surgery, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Rudolf Merkel
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Bernd Hoffmann
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany.
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241
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Matsusaka K, Funata S, Fukayama M, Kaneda A. DNA methylation in gastric cancer, related to Helicobacter pylori and Epstein-Barr virus. World J Gastroenterol 2014; 20:3916-3926. [PMID: 24744581 PMCID: PMC3983447 DOI: 10.3748/wjg.v20.i14.3916] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/08/2014] [Accepted: 02/17/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer is a leading cause of cancer death worldwide, and significant effort has been focused on clarifying the pathology of gastric cancer. In particular, the development of genome-wide analysis tools has enabled the detection of genetic and epigenetic alterations in gastric cancer; for example, aberrant DNA methylation in gene promoter regions is thought to play a crucial role in gastric carcinogenesis. The etiological viewpoint is also essential for the study of gastric cancers, and two distinct pathogens, Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV), are known to participate in gastric carcinogenesis. Chronic inflammation of the gastric epithelium due to H. pylori infection induces aberrant polyclonal methylation that may lead to an increased risk of gastric cancer. In addition, EBV infection is known to cause extensive methylation, and EBV-positive gastric cancers display a high methylation epigenotype, in which aberrant methylation extends to not only Polycomb repressive complex (PRC)-target genes in embryonic stem cells but also non-PRC-target genes. Here, we review aberrant DNA methylation in gastric cancer and the association between methylation and infection with H. pylori and EBV.
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242
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Abstract
A conserved organizational feature of eukaryotic nuclei is the peripheral heterochromatin compartment, which provides a protected area for epigenetically silent genes and gene-poor DNA. In metazoan cells this compartment is associated with the nuclear lamina, the protein meshwork at the inner edge of the nucleus. Heterochromatin-nuclear lamina interactions promote epigenetic gene silencing, which may drive many normal and diseased biological processes. We recently obtained evidence that a previously unstudied human protein, PRR14, participates in the tethering of heterochromatin to the inner nuclear periphery. PRR14 associates with the nuclear lamina and attaches to heterochromatin through its binding partner, heterochromatin protein 1 (HP1). After disassembly early in mitosis, PRR14 reassembles in two steps, first binding to anaphase chromosomes through HP1, followed by association with the nuclear lamina in telophase. PRR14 may thereby play a role in specifying HP1-bound heterochromatin for reattachment to the nuclear lamina at mitotic exit. Here we review the relevant literature, summarize our initial work, and provide additional comments and findings.
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Affiliation(s)
- Andrey Poleshko
- Fox Chase Cancer Center; Institute for Cancer Research; Philadelphia, PA USA
| | - Richard A Katz
- Fox Chase Cancer Center; Institute for Cancer Research; Philadelphia, PA USA
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243
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Jayasena AS, Secco D, Bernath-Levin K, Berkowitz O, Whelan J, Mylne JS. Next generation sequencing and de novo transcriptomics to study gene evolution. PLANT METHODS 2014; 10:34. [PMID: 25364374 PMCID: PMC4216380 DOI: 10.1186/1746-4811-10-34] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/08/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Studying gene evolution in non-model species by PCR-based approaches is limited to highly conserved genes. The plummeting cost of next generation sequencing enables the application of de novo transcriptomics to any species. RESULTS Here we describe how to apply de novo transcriptomics to pursue the evolution of a single gene of interest. We follow a rapidly evolving seed protein that encodes small, stable peptides. We use software that needs limited bioinformatics background and assemble four de novo seed transcriptomes. To demonstrate the quality of the assemblies, we confirm the predicted genes at the peptide level on one species which has over ten copies of our gene of interest. We explain strategies that favour assembly of low abundance genes, what assembly parameters help capture the maximum number of transcripts, how to develop a suite of control genes to test assembly quality and we compare several sequence depths to optimise cost and data volume. CONCLUSIONS De novo transcriptomics is an effective approach for studying gene evolution in species for which genome support is lacking.
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Affiliation(s)
- Achala S Jayasena
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - David Secco
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - Kalia Bernath-Levin
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - Oliver Berkowitz
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
- />The University of Western Australia, School of Plant Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - James Whelan
- />La Trobe University, Department of Botany, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Melbourne, Bundoora Victoria 3086 Australia
| | - Joshua S Mylne
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
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244
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Crowe EP, Nacarelli T, Bitto A, Lerner C, Sell C, Torres C. Detecting senescence: methods and approaches. Methods Mol Biol 2014; 1170:425-45. [PMID: 24906328 DOI: 10.1007/978-1-4939-0888-2_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The detection of senescent cells has become an important area of research in the aging field. Due to the complexity of the senescence program and the lack of a unique signature for senescence, the detection of these cells remains problematic. This is especially true for in vivo detection in aged or diseased tissue samples. This chapter outlines approaches for the detection of senescent cells based upon methods established for mesenchymal cells in culture. A stepwise approach to the detection of senescent cells using multiple techniques is provided.
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Affiliation(s)
- Elizabeth P Crowe
- Department of Pathology, Drexel University College of Medicine, 245 N. 15th Street, MS 435, Philadelphia, PA, 19102, USA
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