251
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Grover A, Sanjuan-Pla A, Thongjuea S, Carrelha J, Giustacchini A, Gambardella A, Macaulay I, Mancini E, Luis TC, Mead A, Jacobsen SEW, Nerlov C. Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells. Nat Commun 2016; 7:11075. [PMID: 27009448 PMCID: PMC4820843 DOI: 10.1038/ncomms11075] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/17/2016] [Indexed: 02/06/2023] Open
Abstract
Aged haematopoietic stem cells (HSCs) generate more myeloid cells and fewer lymphoid cells compared with young HSCs, contributing to decreased adaptive immunity in aged individuals. However, it is not known how intrinsic changes to HSCs and shifts in the balance between biased HSC subsets each contribute to the altered lineage output. Here, by analysing HSC transcriptomes and HSC function at the single-cell level, we identify increased molecular platelet priming and functional platelet bias as the predominant age-dependent change to HSCs, including a significant increase in a previously unrecognized class of HSCs that exclusively produce platelets. Depletion of HSC platelet programming through loss of the FOG-1 transcription factor is accompanied by increased lymphoid output. Therefore, increased platelet bias may contribute to the age-associated decrease in lymphopoiesis. With age, haematopoietic stem cells (HSCs) produce more myeloid than lymphoid cells, affecting adaptive immunity. By combining HSC single cell transcriptomics with functional studies, Grover et al. find that platelet production is also increased in old murine HSCs and show that the FOG-1 transcription factor contributes to the age-dependent platelet bias.
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Affiliation(s)
- Amit Grover
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Alejandra Sanjuan-Pla
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Supat Thongjuea
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Joana Carrelha
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Haemopoietic Stem Cell Laboratory, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alice Giustacchini
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Haemopoietic Stem Cell Laboratory, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adriana Gambardella
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK.,EMBL Mouse Biology Program, 00015 Monterotondo, Italy
| | - Iain Macaulay
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Haemopoietic Stem Cell Laboratory, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Elena Mancini
- EMBL Mouse Biology Program, 00015 Monterotondo, Italy
| | - Tiago C Luis
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Haemopoietic Stem Cell Laboratory, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam Mead
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Haemopoietic Stem Cell Laboratory, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sten Eirik W Jacobsen
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Haemopoietic Stem Cell Laboratory, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Claus Nerlov
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK.,EMBL Mouse Biology Program, 00015 Monterotondo, Italy
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252
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Tang D, Tao S, Chen Z, Koliesnik IO, Calmes PG, Hoerr V, Han B, Gebert N, Zörnig M, Löffler B, Morita Y, Rudolph KL. Dietary restriction improves repopulation but impairs lymphoid differentiation capacity of hematopoietic stem cells in early aging. J Exp Med 2016; 213:535-53. [PMID: 26951333 PMCID: PMC4821645 DOI: 10.1084/jem.20151100] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 01/26/2016] [Indexed: 12/21/2022] Open
Abstract
Dietary restriction (DR) improves health, delays tissue aging, and elongates survival in flies and worms. However, studies on laboratory mice and nonhuman primates revealed ambiguous effects of DR on lifespan despite improvements in health parameters. In this study, we analyzed consequences of adult-onset DR (24 h to 1 yr) on hematopoietic stem cell (HSC) function. DR ameliorated HSC aging phenotypes, such as the increase in number of HSCs and the skewing toward myeloid-biased HSCs during aging. Furthermore, DR increased HSC quiescence and improved the maintenance of the repopulation capacity of HSCs during aging. In contrast to these beneficial effects, DR strongly impaired HSC differentiation into lymphoid lineages and particularly inhibited the proliferation of lymphoid progenitors, resulting in decreased production of peripheral B lymphocytes and impaired immune function. The study shows that DR-dependent suppression of growth factors and interleukins mediates these divergent effects caused by DR. Supplementation of insulin-like growth factor 1 partially reverted the DR-induced quiescence of HSCs, whereas IL-6/IL-7 substitutions rescued the impairment of B lymphopoiesis exposed to DR. Together, these findings delineate positive and negative effects of long-term DR on HSC functionality involving distinct stress and growth signaling pathways.
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Affiliation(s)
- Duozhuang Tang
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Si Tao
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Zhiyang Chen
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | | | | | - Verena Hoerr
- Institute of Medical Microbiology, Jena University Hospital, 07743 Jena, Germany
| | - Bing Han
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Nadja Gebert
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Martin Zörnig
- Georg Speyer Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt am Main, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, 07743 Jena, Germany
| | - Yohei Morita
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Karl Lenhard Rudolph
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany Faculty of Medicine, Friedrich Schiller University, 07743 Jena, Germany
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253
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Rawji KS, Mishra MK, Michaels NJ, Rivest S, Stys PK, Yong VW. Immunosenescence of microglia and macrophages: impact on the ageing central nervous system. Brain 2016; 139:653-61. [PMID: 26912633 DOI: 10.1093/brain/awv395] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/18/2015] [Indexed: 01/21/2023] Open
Abstract
Ageing of the central nervous system results in a loss of both grey and white matter, leading to cognitive decline. Additional injury to both the grey and white matter is documented in many neurological disorders with ageing, including Alzheimer's disease, traumatic brain and spinal cord injury, stroke, and multiple sclerosis. Accompanying neuronal and glial damage is an inflammatory response consisting of activated macrophages and microglia, innate immune cells demonstrated to be both beneficial and detrimental in neurological repair. This article will propose the following: (i) infiltrating macrophages age differently from central nervous system-intrinsic microglia; (ii) several mechanisms underlie the differential ageing process of these two distinct cell types; and (iii) therapeutic strategies that selectively target these diverse mechanisms may rejuvenate macrophages and microglia for repair in the ageing central nervous system. Most responses of macrophages are diminished with senescence, but activated microglia increase their expression of pro-inflammatory cytokines while diminishing chemotactic and phagocytic activities. The senescence of macrophages and microglia has a negative impact on several neurological diseases, and the mechanisms underlying their age-dependent phenotypic changes vary from extrinsic microenvironmental changes to intrinsic changes in genomic integrity. We discuss the negative effects of age on neurological diseases, examine the response of senescent macrophages and microglia in these conditions, and propose a theoretical framework of therapeutic strategies that target the different mechanisms contributing to the ageing phenotype in these two distinct cell types. Rejuvenation of ageing macrophage/microglia may preserve neurological integrity and promote regeneration in the ageing central nervous system.
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Affiliation(s)
- Khalil S Rawji
- 1 Hotchkiss Brain Institute and the Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Manoj K Mishra
- 1 Hotchkiss Brain Institute and the Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nathan J Michaels
- 1 Hotchkiss Brain Institute and the Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Serge Rivest
- 2 Neuroscience Laboratory, CHU de Québec Research Centre, Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec G1V 4G2, Canada
| | - Peter K Stys
- 1 Hotchkiss Brain Institute and the Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - V Wee Yong
- 1 Hotchkiss Brain Institute and the Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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254
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DNA methylome and transcriptome sequencing in human ovarian granulosa cells links age-related changes in gene expression to gene body methylation and 3'-end GC density. Oncotarget 2016; 6:3627-43. [PMID: 25682867 PMCID: PMC4414142 DOI: 10.18632/oncotarget.2875] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/08/2014] [Indexed: 01/23/2023] Open
Abstract
Diminished ovarian function occurs early and is a primary cause for age-related decline in female fertility; however, its underlying mechanism remains unclear. This study investigated the roles that genome and epigenome structure play in age-related changes in gene expression and ovarian function, using human ovarian granulosa cells as an experimental system. DNA methylomes were compared between two groups of women with distinct age-related differences in ovarian functions, using both Methylated DNA Capture followed by Next Generation Sequencing (MethylCap-seq) and Reduced Representation Bisulfite Sequencing (RRBS); their transcriptomes were investigated using mRNA-seq. Significant, non-random changes in transcriptome and DNA methylome features are observed in human ovarian granulosa cells as women age and their ovarian functions deteriorate. The strongest correlations between methylation and the age-related changes in gene expression are not confined to the promoter region; rather, high densities of hypomethylated CpG-rich regions spanning the gene body are preferentially associated with gene down-regulation. This association is further enhanced where CpG regions are localized near the 3ʹ-end of the gene. Such features characterize several genes crucial in age-related decline in ovarian function, most notably the AMH (Anti-Müllerian Hormone) gene. The genome-wide correlation between the density of hypomethylated intragenic and 3ʹ-end regions and gene expression suggests previously unexplored mechanisms linking epigenome structure to age-related physiology and pathology.
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255
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Miyawaki K, Arinobu Y, Iwasaki H, Kohno K, Tsuzuki H, Iino T, Shima T, Kikushige Y, Takenaka K, Miyamoto T, Akashi K. CD41 marks the initial myelo-erythroid lineage specification in adult mouse hematopoiesis: redefinition of murine common myeloid progenitor. Stem Cells 2015; 33:976-87. [PMID: 25446279 DOI: 10.1002/stem.1906] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/30/2014] [Indexed: 12/21/2022]
Abstract
Previous studies have predicted that reciprocal activation of GATA-1 and PU.1 regulates myelo-erythroid versus myelo-lymphoid lineage commitment in early hematopoiesis. Such PU.1-activating myelo-lymphoid progenitors exist within the lymphoid-primed multipotent progenitor (LMPP) population at the primitive Lineage(-) Sca-1(+) c-Kit(+) (LSK) stage. We here show that the counterpart of GATA-1-activating myelo-erythroid progenitor resides also at the LSK stage, expressing CD41 at a high level. Purified CD41(hi) LSK cells showed exceedingly strong and prolonged myelo-erythroid-restricted reconstitution, and primed myelo-erythroid gene expression with a more primitive molecular signature as compared to the original common myeloid progenitor (CMP). The CD41(hi) LSK cells more strongly contributed to emergent and malignant myelopoiesis than LMPPs, and produced the original CMP by downregulating Sca-1 and CD41, suggesting that they are the earliest CMPs. Thus, the hematopoietic developmental map should be revised by integrating the primary branchpoint comprised of the new, isolatable CD41(hi) CMP and the LMPP populations.
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Affiliation(s)
- Kohta Miyawaki
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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256
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A novel strategy for forensic age prediction by DNA methylation and support vector regression model. Sci Rep 2015; 5:17788. [PMID: 26635134 PMCID: PMC4669521 DOI: 10.1038/srep17788] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 11/05/2015] [Indexed: 11/09/2022] Open
Abstract
High deviations resulting from prediction model, gender and population difference have limited age estimation application of DNA methylation markers. Here we identified 2,957 novel age-associated DNA methylation sites (P < 0.01 and R(2) > 0.5) in blood of eight pairs of Chinese Han female monozygotic twins. Among them, nine novel sites (false discovery rate < 0.01), along with three other reported sites, were further validated in 49 unrelated female volunteers with ages of 20-80 years by Sequenom Massarray. A total of 95 CpGs were covered in the PCR products and 11 of them were built the age prediction models. After comparing four different models including, multivariate linear regression, multivariate nonlinear regression, back propagation neural network and support vector regression, SVR was identified as the most robust model with the least mean absolute deviation from real chronological age (2.8 years) and an average accuracy of 4.7 years predicted by only six loci from the 11 loci, as well as an less cross-validated error compared with linear regression model. Our novel strategy provides an accurate measurement that is highly useful in estimating the individual age in forensic practice as well as in tracking the aging process in other related applications.
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257
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258
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Li RQ, Ouyang NY, Ou SB, Ni RM, Mai MQ, Zhang QX, Yang DZ, Wang WJ. Does reducing gamete co-incubation time improve clinical outcomes: a retrospective study. J Assist Reprod Genet 2015; 33:33-8. [PMID: 26631402 DOI: 10.1007/s10815-015-0618-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/12/2015] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The objective of this retrospective study was to determine whether patients undergoing in vitro fertilization (IVF) benefit from reducing the gamete co-incubation time. METHODS Patients (n = 570) were enrolled, including 281 patients in the reduced incubation time group (2-h incubation) and 289 patients in the standard IVF group (18-h incubation). RESULTS The observed outcomes, including the clinical pregnancy rate (CPR), implantation rate (IR), live birth rate (LBR), and miscarriage rate (MR), were similar between the two groups. When the data were divided into two subgroups based on the maternal age (≤30 and >30 years), the rates of top-quality embryos (30.83 vs. 25.89 %; p = 0.028), CPR (66.67 vs. 42.11 %; p = 0.013), and IR (41.90 vs. 31.25 %, p = 0.019) of the 2-h incubation group were significantly higher in the younger subgroup. However, for older patients, only a lower MR (7.59 vs. 20.83 %; p = 0.019) was achieved. Reducing the time of incubation still improved the CPR (OR = 1.993, 95 % CI 1.141-3.480) and MR (OR = 3.173, 95 % CI 1.013-9.936) in the younger and older subgroups, respectively, after it was adjusted for potential confounders. CONCLUSIONS Reducing incubation time improves the clinical results of IVF, although the LBR is not statistically different between the 2- and 18-h incubation time groups. And the specific clinical outcomes of reducing incubation time varied between the >30-year-old and the ≤30-year-old.
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Affiliation(s)
- Rui-Qi Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Neng-Yong Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Song-Bang Ou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Ren-Min Ni
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Mei-Qi Mai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Qing-Xue Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Dong-Zi Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
| | - Wen-Jun Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120. .,Department of Obstetrics and Gynecology, Reproductive Medicine Centre, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China, 510120.
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259
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Epigenetic Control of Haematopoietic Stem Cell Aging and Its Clinical Implications. Stem Cells Int 2015; 2016:5797521. [PMID: 26681950 PMCID: PMC4670691 DOI: 10.1155/2016/5797521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/01/2015] [Indexed: 01/16/2023] Open
Abstract
Aging, chronic inflammation, and environmental insults play an important role in a number of disease processes through alterations of the epigenome. In this review we explore how age-related changes in the epigenetic landscape can affect heterogeneity within the haematopoietic stem cell (HSC) compartment and the deriving clinical implications.
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260
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Hodjat M, Rezvanfar MA, Abdollahi M. A systematic review on the role of environmental toxicants in stem cells aging. Food Chem Toxicol 2015; 86:298-308. [PMID: 26582272 DOI: 10.1016/j.fct.2015.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/19/2022]
Abstract
Stem cells are an important target for environmental toxicants. As they are the main source for replenishing of organs in the body, any changes in their normal function could affect the regenerative potential of organs, leading to the appearance of age-related disease and acceleration of the aging process. Environmental toxicants could exert their adverse effect on stem cell function via multiple cellular and molecular mechanisms, resulting in changes in the stem cell differentiation fate and cell transformation, and reduced self-renewal capacity, as well as induction of stress-induced cellular senescence. The present review focuses on the effect of environmental toxicants on stem cell function associated with the aging process. We categorized environmental toxicants according to their preferred molecular mechanism of action on stem cells, including changes in genomic, epigenomic, and proteomic levels and enhancing oxidative stress. Pesticides, tobacco smoke, radiation and heavy metals are well-studied toxicants that cause stem cell dysfunction via induction of oxidative stress. Transgenerational epigenetic changes are the most important effects of a variety of toxicants on germ cells and embryos that are heritable and could affect health in the next several generations. A better understanding of the underlying mechanisms of toxicant-induced stem cell aging will help us to develop therapeutic intervention strategies against environmental aging. Meanwhile, more efforts are required to find the direct in vivo relationship between adverse effect of environmental toxicants and stem cell aging, leading to organismal aging.
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Affiliation(s)
- Mahshid Hodjat
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center (PSRC), Endocrinology & Metabolism Research Center (EMRC), Toxicology & Poisoning Research Center (TPRC), Tehran University of Medical Sciences (TUMS), Tehran 1417614411, Iran
| | - Mohammad Amin Rezvanfar
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center (PSRC), Endocrinology & Metabolism Research Center (EMRC), Toxicology & Poisoning Research Center (TPRC), Tehran University of Medical Sciences (TUMS), Tehran 1417614411, Iran
| | - Mohammad Abdollahi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center (PSRC), Endocrinology & Metabolism Research Center (EMRC), Toxicology & Poisoning Research Center (TPRC), Tehran University of Medical Sciences (TUMS), Tehran 1417614411, Iran.
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261
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Murakami S, Motohashi H. Roles of Nrf2 in cell proliferation and differentiation. Free Radic Biol Med 2015; 88:168-178. [PMID: 26119783 DOI: 10.1016/j.freeradbiomed.2015.06.030] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 02/07/2023]
Abstract
The Keap1-Nrf2 system plays pivotal roles in defense mechanisms by regulating cellular redox homeostasis. Nrf2 is an inducible transcription factor that activates a battery of genes encoding antioxidant proteins and phase II enzymes in response to oxidative stress and electrophilic xenobiotics. The activity of Nrf2 is regulated by Keap1, which promotes the ubiquitination and subsequent degradation of Nrf2 under normal conditions and releases the inhibited Nrf2 activity upon exposure to the stresses. Though an impressive contribution of the Keap1-Nrf2 system to the protection from exogenous and endogenous electrophilic insults has been well established, a line of evidence has suggested that the Keap1-Nrf2 system has various novel functions, particularly in cell proliferation and differentiation. Because the proliferation and differentiation of diverse cell types are often influenced and modulated by the cellular redox balance, Nrf2 has been considered to control these cellular processes by regulating the cellular levels of reactive oxygen species (ROS). In addition, analyses of the genome-wide distribution of Nrf2 have identified new sets of Nrf2 target genes whose products are involved in cell proliferation and differentiation but not necessarily in the regulation of oxidative stress. Considering the most characteristic features of Nrf2 as an inducible transcription factor, a newly emerged concept proposes that the Keap1-Nrf2 system translates environmental stresses into regulatory network signals in cell fate determination. In this review, we introduce the contribution of Nrf2 to lineage-specific differentiation, maintenance and differentiation of stem cells, and proliferation of normal and cancer cells, and we discuss how the response to fluctuating environments modulates cell behavior through the Keap1-Nrf2 system.
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Affiliation(s)
- Shohei Murakami
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
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262
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Yun MH. Changes in Regenerative Capacity through Lifespan. Int J Mol Sci 2015; 16:25392-432. [PMID: 26512653 PMCID: PMC4632807 DOI: 10.3390/ijms161025392] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/30/2015] [Accepted: 09/30/2015] [Indexed: 12/14/2022] Open
Abstract
Most organisms experience changes in regenerative abilities through their lifespan. During aging, numerous tissues exhibit a progressive decline in homeostasis and regeneration that results in tissue degeneration, malfunction and pathology. The mechanisms responsible for this decay are both cell intrinsic, such as cellular senescence, as well as cell-extrinsic, such as changes in the regenerative environment. Understanding how these mechanisms impact on regenerative processes is essential to devise therapeutic approaches to improve tissue regeneration and extend healthspan. This review offers an overview of how regenerative abilities change through lifespan in various organisms, the factors that underlie such changes and the avenues for therapeutic intervention. It focuses on established models of mammalian regeneration as well as on models in which regenerative abilities do not decline with age, as these can deliver valuable insights for our understanding of the interplay between regeneration and aging.
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Affiliation(s)
- Maximina H Yun
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
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263
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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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264
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Reactive Oxygen Species in Mesenchymal Stem Cell Aging: Implication to Lung Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:486263. [PMID: 26273422 PMCID: PMC4529978 DOI: 10.1155/2015/486263] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 04/15/2015] [Accepted: 05/01/2015] [Indexed: 12/13/2022]
Abstract
MSCs have become an emerging cell source with their immune modulation, high proliferation rate, and differentiation potential; indeed, they have been challenged in clinical trials. Recently, it has shown that ROS play a dual role as both deleterious and beneficial species depending on their concentration in MSCs. Various environmental stresses-induced excessive production of ROS triggers cellular senescence and abnormal differentiation on MSCs. Moreover, MSCs have been suggested to participate in the treatment of ALI/ARDS and COPD as a major cause of high morbidity and mortality. Therapeutic mechanisms of MSCs in the treatment of ARDS/COPD were focused on cell engraftment and paracrine action. However, ROS-mediated therapeutic mechanisms of MSCs still remain largely unknown. Here, we review the key factors associated with cell cycle and chromatin remodeling to accelerate or delay the MSC aging process. In addition, the enhanced ROS production and its associated pathophysiological pathways will be discussed along with the MSC senescence process. Furthermore, the present review highlights how the excessive amount of ROS-mediated oxidative stress might interfere with homeostasis of lungs and residual lung cells in the pathogenesis of ALI/ARDS and COPD.
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265
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Montgomery RR, Shaw AC. Paradoxical changes in innate immunity in aging: recent progress and new directions. J Leukoc Biol 2015; 98:937-43. [PMID: 26188078 DOI: 10.1189/jlb.5mr0315-104r] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/23/2015] [Indexed: 12/29/2022] Open
Abstract
Immunosenescence, describing alterations, including decline of immune responses with age, is comprised of inappropriate elevations, decreases, and dysregulated immune responses, leading to more severe consequences of bacterial and viral infections and reduced responses to vaccination. In adaptive immunity, these changes include increased proportions of antigen-experienced B and T cells at the cost of naïve cell populations. Innate immune changes in aging are complex in spanning multiple cell types, activation states, and tissue context. Innate immune responses are dampened in aging, yet there is also a paradoxical increase in certain signaling pathways and cytokine levels. Here, we review recent progress and highlight novel directions for expected advances that can lead the aging field to a new era of discovery that will embrace the complexity of aging in human populations.
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Affiliation(s)
- Ruth R Montgomery
- Sections of *Rheumatology and Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Albert C Shaw
- Sections of *Rheumatology and Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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266
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Cappellini MD, Motta I. Anemia in Clinical Practice-Definition and Classification: Does Hemoglobin Change With Aging? Semin Hematol 2015; 52:261-9. [PMID: 26404438 DOI: 10.1053/j.seminhematol.2015.07.006] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Anemia is a global public health problem affecting both developing and developed countries at all ages. According to the World Health Organization (WHO), anemia is defined as hemoglobin (Hb) levels <12.0 g/dL in women and <13.0 g/dL in men. However, normal Hb distribution varies not only with sex but also with ethnicity and physiological status. New lower limits of normal Hb values have been proposed, according to ethnicity, gender, and age. Anemia is often multifactorial and is not an independent phenomenon. For the classification and diagnosis the hematologic parameters, the underlying pathological mechanism and patient history should be taken into account. The aging of population, especially in Western countries, causes an increase of anemia in elderly people. In this population, anemia, recently defined by levels of Hb <12 g/dL in both sexes, is mostly of mild degree (10-12 g/dL). Understanding the pathophysiology of anemia in this population is important because it contributes to morbidity and mortality. In one third of the patients, anemia is due to nutritional deficiency, including iron, folate, or vitamin B12 deficiency; moreover, anemia of chronic disease accounts for about another third of the cases. However, in one third of patients anemia cannot be explained by an underlying disease or by a specific pathological process, and for this reason it is defined "unexplained anemia". Unexplained anemia might be due to the progressive resistance of bone marrow erythroid progenitors to erythropoietin, and a chronic subclinical pro-inflammatory state.
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Affiliation(s)
- M Domenica Cappellini
- Department of Medicine, IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy.
| | - Irene Motta
- Department of Medicine, IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
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267
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Wang C, Oshima M, Sashida G, Tomioka T, Hasegawa N, Mochizuki-Kashio M, Nakajima-Takagi Y, Kusunoki Y, Kyoizumi S, Imai K, Nakachi K, Iwama A. Non-Lethal Ionizing Radiation Promotes Aging-Like Phenotypic Changes of Human Hematopoietic Stem and Progenitor Cells in Humanized Mice. PLoS One 2015; 10:e0132041. [PMID: 26161905 PMCID: PMC4498777 DOI: 10.1371/journal.pone.0132041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022] Open
Abstract
Precise understanding of radiation effects is critical to develop new modalities for the prevention and treatment of radiation-induced damage. We previously reported that non-lethal doses of X-ray irradiation induce DNA damage in human hematopoietic stem and progenitor cells (HSPCs) reconstituted in NOD/Shi-scid IL2rγnull (NOG) immunodeficient mice and severely compromise their repopulating capacity. In this study, we analyzed in detail the functional changes in human HSPCs in NOG mice following non-lethal radiation. We transplanted cord blood CD34+ HSPCs into NOG mice. At 12 weeks post-transplantation, the recipients were irradiated with 0, 0.5, or 1.0 Gy. At 2 weeks post-irradiation, human CD34+ HSPCs recovered from the primary recipient mice were transplanted into secondary recipients. CD34+ HSPCs from irradiated mice showed severely impaired reconstitution capacity in the secondary recipient mice. Of interest, non-lethal radiation compromised contribution of HSPCs to the peripheral blood cells, particularly to CD19+ B lymphocytes, which resulted in myeloid-biased repopulation. Co-culture of limiting numbers of CD34+ HSPCs with stromal cells revealed that the frequency of B cell-producing CD34+ HSPCs at 2 weeks post-irradiation was reduced more than 10-fold. Furthermore, the key B-cell regulator genes such as IL-7R and EBF1 were downregulated in HSPCs upon 0.5 Gy irradiation. Given that compromised repopulating capacity and myeloid-biased differentiation are representative phenotypes of aged HSCs, our findings indicate that non-lethal ionizing radiation is one of the critical external stresses that promote aging of human HSPCs in the bone marrow niche.
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Affiliation(s)
- Changshan Wang
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
- College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Motohiko Oshima
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
| | - Goro Sashida
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto City 860–0811, Japan
| | - Takahisa Tomioka
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
| | - Nagisa Hasegawa
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
- Department of Hematology, Chiba University Hospital, Chiba 260–8670, Japan
| | - Makiko Mochizuki-Kashio
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
| | - Yaeko Nakajima-Takagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
| | - Yoichiro Kusunoki
- Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima 732–0815, Japan
| | - Seishi Kyoizumi
- Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima 732–0815, Japan
| | - Kazue Imai
- Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima 732–0815, Japan
| | - Kei Nakachi
- Department of Radiobiology/Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima 732–0815, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260–8670, Japan
- * E-mail:
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268
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Loiseau C, Ali A, Itzykson R. New therapeutic approaches in myelodysplastic syndromes: Hypomethylating agents and lenalidomide. Exp Hematol 2015; 43:661-72. [PMID: 26123365 DOI: 10.1016/j.exphem.2015.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 01/17/2023]
Abstract
Recent advances in the treatment of myelodysplastic syndromes have come from the use of the hypomethylating agents decitabine and azacitidine as well as the immunomodulatory drug lenalidomide. Their clinical benefit has been demonstrated by randomized phase III clinical trials, mostly in high-risk and del(5q) myelodysplastic syndromes, respectively. Neither drug, however, appears to eradicate myelodysplastic stem cells, and thus they currently do not represent curative options. Here, we review data from both clinical and translational research on those drugs to identify their molecular and cellular mechanisms of action and to delineate paths for improved treatment allocation and further therapeutic advances in myelodysplastic syndromes.
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Affiliation(s)
- Clémence Loiseau
- Department of Hematology, Saint-Louis Hospital, Assistance Publique, Hopitaux de Paris, Paris Diderot University, Paris, France
| | - Ashfaq Ali
- Institut National de la Santé et de la Recherche Médicale, Saint-Louis Institute, Paris, France
| | - Raphael Itzykson
- Department of Hematology, Saint-Louis Hospital, Assistance Publique, Hopitaux de Paris, Paris Diderot University, Paris, France; Institut National de la Santé et de la Recherche Médicale, Saint-Louis Institute, Paris, France.
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269
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Wakeling LA, Ions LJ, Escolme SM, Cockell SJ, Su T, Dey M, Hampton EV, Jenkins G, Wainwright LJ, McKay JA, Ford D. SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing. Hum Genomics 2015; 9:14. [PMID: 26104761 PMCID: PMC4480908 DOI: 10.1186/s40246-015-0036-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/16/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND SIRT1 is likely to play a role in the extension in healthspan induced by dietary restriction. Actions of SIRT1 are pleiotropic, and effects on healthspan may include effects on DNA methylation. Polycomb group protein target genes (PCGTs) are suppressed by epigenetic mechanisms in stem cells, partly through the actions of the polycomb repressive complexes (PRCs), and have been shown previously to correspond with loci particularly susceptible to age-related changes in DNA methylation. We hypothesised that SIRT1 would affect DNA methylation particularly at PCGTs. To map the sites in the genome where SIRT1 affects DNA methylation, we altered SIRT1 expression in human intestinal (Caco-2) and vascular endothelial (HuVEC) cells by transient transfection with an expression construct or with siRNA. DNA was enriched for the methylated fraction then sequenced (HuVEC) or hybridised to a human promoter microarray (Caco-2). RESULTS The profile of genes where SIRT1 manipulation affected DNA methylation was enriched for PCGTs in both cell lines, thus supporting our hypothesis. SIRT1 knockdown affected the mRNA for none of seven PRC components nor for DNMT1 or DNMT3b. We thus find no evidence that SIRT1 affects DNA methylation at PCGTs by affecting the expression of these gene transcripts. EZH2, a component of PRC2 that can affect DNA methylation through association with DNA methyltransferases (DNMTs), did not co-immunoprecipitate with SIRT1, and SIRT1 knockdown did not affect the expression of EZH2 protein. Thus, it is unlikely that the effects of SIRT1 on DNA methylation at PCGTs are mediated through direct intermolecular association with EZH2 or through effects in its expression. CONCLUSIONS SIRT1 affects DNA methylation across the genome, but particularly at PCGTs. Although the mechanism through which SIRT1 has these effects is yet to be uncovered, this action is likely to contribute to extended healthspan, for example under conditions of dietary restriction.
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Affiliation(s)
- Luisa A Wakeling
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Laura J Ions
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Suzanne M Escolme
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Simon J Cockell
- Faculty of Medical Sciences, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Tianhong Su
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Madhurima Dey
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Emily V Hampton
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Gail Jenkins
- Unilever R&D, Colworth Discover, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Linda J Wainwright
- Unilever R&D, Colworth Discover, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Jill A McKay
- Institute of Health and Society, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
| | - Dianne Ford
- Institute for Cell and Molecular Biosciences, Human Nutrition Research Centre, Newcastle University Medical School, Newcastle upon Tyne, NE2 4HH, UK.
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270
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Koyuncu S, Irmak D, Saez I, Vilchez D. Defining the General Principles of Stem Cell Aging: Lessons from Organismal Models. CURRENT STEM CELL REPORTS 2015. [DOI: 10.1007/s40778-015-0017-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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271
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Graffmann N, Brands J, Görgens A, Vitoriano da Conceição Castro S, Santourlidis S, Reckert A, Michele I, Ritz-Timme S, Fischer JC, Adjaye J, Kögler G, Giebel B, Uhrberg M. Age-Related Increase of EED Expression in Early Hematopoietic Progenitor Cells is Associated with Global Increase of the Histone Modification H3K27me3. Stem Cells Dev 2015; 24:2018-31. [PMID: 25961873 DOI: 10.1089/scd.2014.0435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human hematopoietic stem and progenitor cells (HSPCs) from umbilical cord blood exhibit higher differentiation potential and repopulation capacity compared to adult HSPCs. The molecular basis for these functional differences is currently unknown. Upon screening for epigenetic effector genes being differentially expressed in neonatal and adult HSPC subpopulations, the Polycomb Repressive Complex 2 (PRC2) member EED was identified. Even though EED is expressed at comparable amounts in neonatal and adult multipotent HSPCs, early adult lineage committed progenitors of the lymphomyeloid (LM) and erythromyeloid lineages expressed higher EED amounts than neonatal HPCs. We demonstrate that EED overexpression directly leads to higher H3K27me3 levels, a repressive histone modification that is mediated by the PRC2 complex. Quantitative analysis of H3K27me3 levels by FPLC-based ELISA revealed elevated levels in primary blood cells from adults. Besides quantitative changes, gene ontology analysis of the genome-wide H3K27me3 distribution revealed qualitative changes in adult HSPCs with elevated levels in genes associated with nonhematopoietic development pathways. In contrast, H3K4me3 which labels active chromatin was enriched on hematopoietic genes. In vitro differentiation of EED-transfected neonatal HSPCs revealed aberrant expression of the myelopoietic marker CD14, suggesting that EED affects the lymphoid versus myeloid decision processes within the lymphomyeloid lineage. This is in line with LM progenitors having the most pronounced differences in EED expression. Highlighting the dynamic roles of epigenetic modifications in human hematopoiesis, the present data demonstrate shifts in the PRC2-associated histone modification H3K27me3 from birth to adulthood.
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Affiliation(s)
- Nina Graffmann
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany .,2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Jens Brands
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - André Görgens
- 3 Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Symone Vitoriano da Conceição Castro
- 3 Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen , Essen, Germany .,4 CAPES Foundation, Ministry of Education of Brazil , Brasília, Brazil
| | - Simeon Santourlidis
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Alexandra Reckert
- 5 Institute of Forensic Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Inga Michele
- 5 Institute of Forensic Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Stefanie Ritz-Timme
- 5 Institute of Forensic Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Johannes C Fischer
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - James Adjaye
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Gesine Kögler
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Bernd Giebel
- 3 Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Markus Uhrberg
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
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272
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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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273
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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274
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Sarkozy C, Salles G, Falandry C. The Biology of Aging and Lymphoma: a Complex Interplay. Curr Oncol Rep 2015; 17:32. [DOI: 10.1007/s11912-015-0457-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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275
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Jung M, Jin SG, Zhang X, Xiong W, Gogoshin G, Rodin AS, Pfeifer GP. Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. Nucleic Acids Res 2015; 43:e100. [PMID: 25977295 PMCID: PMC4551908 DOI: 10.1093/nar/gkv473] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/29/2015] [Indexed: 12/28/2022] Open
Abstract
Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.
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Affiliation(s)
- Marc Jung
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Seung-Gi Jin
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaoying Zhang
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Wenying Xiong
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Grigoriy Gogoshin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Andrei S Rodin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gerd P Pfeifer
- Department of Cancer Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA Department of Diabetes and Metabolic Diseases Research, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
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276
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Goodell MA, Nguyen H, Shroyer N. Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments. Nat Rev Mol Cell Biol 2015; 16:299-309. [PMID: 25907613 PMCID: PMC5317203 DOI: 10.1038/nrm3980] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Somatic stem cells replenish many tissues throughout life to repair damage and to maintain tissue homeostasis. Stem cell function is frequently described as following a hierarchical model in which a single master cell undergoes self-renewal and differentiation into multiple cell types and is responsible for most regenerative activity. However, recent data from studies on blood, skin and intestinal epithelium all point to the concomitant action of multiple types of stem cells with distinct everyday roles. Under stress conditions such as acute injury, the surprising developmental flexibility of these stem cells enables them to adapt to diverse roles and to acquire different regeneration capabilities. This paradigm shift raises many new questions about the developmental origins, inter-relationships and molecular regulation of these multiple stem cell types.
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Affiliation(s)
- Margaret A Goodell
- Stem Cells and Regenerative Medicine Center and Departments of Pediatrics, Molecular and Cellular Biology, and Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Hoang Nguyen
- Stem Cells and Regenerative Medicine Center and Departments of Pediatrics, Molecular and Cellular Biology, and Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Noah Shroyer
- Stem Cells and Regenerative Medicine Center and Departments of Pediatrics, Molecular and Cellular Biology, and Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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277
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Göttgens B. Regulatory network control of blood stem cells. Blood 2015; 125:2614-20. [PMID: 25762179 DOI: 10.1182/blood-2014-08-570226] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/06/2014] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are characterized by their ability to execute a wide range of cell fate choices, including self-renewal, quiescence, and differentiation into the many different mature blood lineages. Cell fate decision making in HSCs, as indeed in other cell types, is driven by the interplay of external stimuli and intracellular regulatory programs. Given the pivotal nature of HSC decision making for both normal and aberrant hematopoiesis, substantial research efforts have been invested over the last few decades into deciphering some of the underlying mechanisms. Central to the intracellular decision making processes are transcription factor proteins and their interactions within gene regulatory networks. More than 50 transcription factors have been shown to affect the functionality of HSCs. However, much remains to be learned about the way in which individual factors are connected within wider regulatory networks, and how the topology of HSC regulatory networks might affect HSC function. Nevertheless, important progress has been made in recent years, and new emerging technologies suggest that the pace of progress is likely to accelerate. This review will introduce key concepts, provide an integrated view of selected recent studies, and conclude with an outlook on possible future directions for this field.
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Affiliation(s)
- Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust & Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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278
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McCarty G, Loeb DM. Hypoxia-sensitive epigenetic regulation of an antisense-oriented lncRNA controls WT1 expression in myeloid leukemia cells. PLoS One 2015; 10:e0119837. [PMID: 25794157 PMCID: PMC4368825 DOI: 10.1371/journal.pone.0119837] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/19/2015] [Indexed: 01/09/2023] Open
Abstract
WT1 is a transcription factor expressed in hematopoietic stem cells and in most cases of myeloid leukemia. We investigated the roles of hypoxia and epigenetics in the regulation of WT1 expression in myeloid leukemia cells. WT1 expression correlates with hypomethylation of the CpG island in Intron 1, and pharmacologic demethylation of this CpG island induces WT1 mRNA expression. Hypoxia causes decreases in DNMT expression and activity and increased expression and activity of TET2 and TET3, resulting in demethylation of this CpG island and expression of WT1 mRNA. Demethylation of the CpG island, either from pharmacologic treatment or induction of hypoxia, results in transcription of an antisense-oriented lncRNA, and inhibiting lncRNA expression with shRNA blocks WT1 mRNA expression. These results reveal a novel model of hypoxia-mediated epigenetic gene regulation. In addition, this is the first report that TET2 and TET3, increasingly recognized as important epigenetic regulators of gene expression in stem cells and in cancer cells, can be regulated by hypoxia, providing a solid mechanistic link between hypoxia and epigenetic regulation of gene expression with important implications for the role of hypoxia in stem cell function.
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MESH Headings
- Base Sequence
- Cell Line, Tumor
- CpG Islands
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases/genetics
- Dioxygenases/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation, Leukemic
- Genetic Loci
- Humans
- Hypoxia/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Introns
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Molecular Sequence Data
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Antisense/genetics
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- WT1 Proteins/chemistry
- WT1 Proteins/genetics
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Affiliation(s)
- Gregory McCarty
- Department of Oncology, Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States of America
| | - David M. Loeb
- Department of Oncology, Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States of America
- * E-mail:
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279
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Cheng Y, Xie N, Jin P, Wang T. DNA methylation and hydroxymethylation in stem cells. Cell Biochem Funct 2015; 33:161-73. [PMID: 25776144 DOI: 10.1002/cbf.3101] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 02/17/2015] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
Abstract
In mammals, DNA methylation and hydroxymethylation are specific epigenetic mechanisms that can contribute to the regulation of gene expression and cellular functions. DNA methylation is important for the function of embryonic stem cells and adult stem cells (such as haematopoietic stem cells, neural stem cells and germline stem cells), and changes in DNA methylation patterns are essential for successful nuclear reprogramming. In the past several years, the rediscovery of hydroxymethylation and the TET enzymes expanded our insights tremendously and uncovered more dynamic aspects of cytosine methylation regulation. Here, we review the current knowledge and highlight the most recent advances in DNA methylation and hydroxymethylation in embryonic stem cells, induced pluripotent stem cells and several well-studied adult stems cells. Our current understanding of stem cell epigenetics and new advances in the field will undoubtedly stimulate further clinical applications of regenerative medicine in the future.
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Affiliation(s)
- Ying Cheng
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Nina Xie
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Tao Wang
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, CA, USA
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280
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Carrió E, Suelves M. DNA methylation dynamics in muscle development and disease. Front Aging Neurosci 2015; 7:19. [PMID: 25798107 PMCID: PMC4350440 DOI: 10.3389/fnagi.2015.00019] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/15/2015] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts revealing a more dynamic regulation than originally thought, since active DNA methylation and demethylation occur during cellular differentiation and tissue specification. Satellite cells are the primary stem cells in adult skeletal muscle and are responsible for postnatal muscle growth, hypertrophy, and muscle regeneration. This review outlines the published data regarding DNA methylation changes along the skeletal muscle program, in both physiological and pathological conditions, to better understand the epigenetic mechanisms that control myogenesis.
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Affiliation(s)
- Elvira Carrió
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Sciences Research Institute Germans Trias I Pujol (IGTP) Badalona, Spain
| | - Mònica Suelves
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Sciences Research Institute Germans Trias I Pujol (IGTP) Badalona, Spain
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281
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Ebina W, Rossi DJ. Transcription factor-mediated reprogramming toward hematopoietic stem cells. EMBO J 2015; 34:694-709. [PMID: 25712209 DOI: 10.15252/embj.201490804] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
De novo generation of human hematopoietic stem cells (HSCs) from renewable cell types has been a long sought-after but elusive goal in regenerative medicine. Paralleling efforts to guide pluripotent stem cell differentiation by manipulating developmental cues, substantial progress has been made recently toward HSC generation via combinatorial transcription factor (TF)-mediated fate conversion, a paradigm established by Yamanaka's induction of pluripotency in somatic cells by mere four TFs. This review will integrate the recently reported strategies to directly convert a variety of starting cell types toward HSCs in the context of hematopoietic transcriptional regulation and discuss how these findings could be further developed toward the ultimate generation of therapeutic human HSCs.
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Affiliation(s)
- Wataru Ebina
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Harvard Stem Cell Institute, Cambridge, MA, USA
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282
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Zampieri M, Ciccarone F, Calabrese R, Franceschi C, Bürkle A, Caiafa P. Reconfiguration of DNA methylation in aging. Mech Ageing Dev 2015; 151:60-70. [PMID: 25708826 DOI: 10.1016/j.mad.2015.02.002] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 12/12/2022]
Abstract
A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.
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Affiliation(s)
- Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental Pathology, Alma Mater Studiorum, University of Bologna, Bologna 40126, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.
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283
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Yuan T, Jiao Y, de Jong S, Ophoff RA, Beck S, Teschendorff AE. An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet 2015; 11:e1004996. [PMID: 25692570 PMCID: PMC4334892 DOI: 10.1371/journal.pgen.1004996] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/10/2015] [Indexed: 12/21/2022] Open
Abstract
Recent studies have demonstrated that the DNA methylome changes with age. This epigenetic drift may have deep implications for cellular differentiation and disease development. However, it remains unclear how much of this drift is functional or caused by underlying changes in cell subtype composition. Moreover, no study has yet comprehensively explored epigenetic drift at different genomic length scales and in relation to regulatory elements. Here we conduct an in-depth analysis of epigenetic drift in blood tissue. We demonstrate that most of the age-associated drift is independent of the increase in the granulocyte to lymphocyte ratio that accompanies aging and that enrichment of age-hypermethylated CpG islands increases upon adjustment for cellular composition. We further find that drift has only a minimal impact on in-cis gene expression, acting primarily to stabilize pre-existing baseline expression levels. By studying epigenetic drift at different genomic length scales, we demonstrate the existence of mega-base scale age-associated hypomethylated blocks, covering approximately 14% of the human genome, and which exhibit preferential hypomethylation in age-matched cancer tissue. Importantly, we demonstrate the feasibility of integrating Illumina 450k DNA methylation with ENCODE data to identify transcription factors with key roles in cellular development and aging. Specifically, we identify REST and regulatory factors of the histone methyltransferase MLL complex, whose function may be disrupted in aging. In summary, most of the epigenetic drift seen in blood is independent of changes in blood cell type composition, and exhibits patterns at different genomic length scales reminiscent of those seen in cancer. Integration of Illumina 450k with appropriate ENCODE data may represent a fruitful approach to identify transcription factors with key roles in aging and disease. Two well-known features of aging are the gradual decline of the body’s ability to regenerate tissues, as well as an increased incidence of diseases like cancer and Alzheimers. One of the most recent exciting findings which may underlie the aging process is a gradual modification of DNA, called epigenetic drift, which is effected by the covalent addition and removal of methyl groups, which in turn can deregulate the activity of nearby genes. However, this study presents the most convincing evidence to date that epigenetic drift acts to stabilize the activity levels of nearby genes. This study shows that instead, epigenetic drift may act primarly to disrupt DNA binding patterns of proteins which regulate the activity of many genes, and moreover identifies specific regulatory proteins with key roles in cancer and Alzheimers. The study also performs the most comprehensive analysis of epigenetic drift at different spatial scales, demonstrating that epigenetic drift on the largest length scales is highly reminiscent of those seen in cancer. In summary, this work substantially supports the view that epigenetic drift may contribute to the age-associated increased risk of diseases like cancer and Alzheimers, by disrupting master regulators of genomewide gene activity.
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Affiliation(s)
- Tian Yuan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
| | - Yinming Jiao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
| | - Simone de Jong
- Center for Neurobehavioral Genetics, Los Angeles, California, USA
| | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Los Angeles, California, USA
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Andrew E. Teschendorff
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai, China
- Statistical Genomics Group, UCL Cancer Institute, University College London, London, United Kingdom
- * E-mail: (AET), (AET)
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284
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The histone demethylase Jarid1b is required for hematopoietic stem cell self-renewal in mice. Blood 2015; 125:2075-8. [PMID: 25655602 DOI: 10.1182/blood-2014-08-596734] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Jarid1b/KDM5b is a histone demethylase that regulates self-renewal and differentiation in stem cells and cancer; however, its function in hematopoiesis is unclear. Here, we find that Jarid1b is highly expressed in primitive hematopoietic compartments and is overexpressed in acute myeloid leukemias. Constitutive genetic deletion of Jarid1b did not impact steady-state hematopoiesis. In contrast, acute deletion of Jarid1b from bone marrow increased peripheral blood T cells and, following secondary transplantation, resulted in loss of bone marrow reconstitution. Our results reveal that deletion of Jarid1b compromises hematopoietic stem cell (HSC) self-renewal capacity and suggest that Jarid1b is a positive regulator of HSC potential.
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285
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Ido Y, Duranton A, Lan F, Weikel KA, Breton L, Ruderman NB. Resveratrol prevents oxidative stress-induced senescence and proliferative dysfunction by activating the AMPK-FOXO3 cascade in cultured primary human keratinocytes. PLoS One 2015; 10:e0115341. [PMID: 25647160 PMCID: PMC4315597 DOI: 10.1371/journal.pone.0115341] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/21/2014] [Indexed: 01/27/2023] Open
Abstract
The aging process is perceived as resulting from a combination of intrinsic factors such as changes in intracellular signaling and extrinsic factors, most notably environmental stressors. In skin, the relationship between intrinsic changes and keratinocyte function is not clearly understood. Previously, we found that increasing the activity of AMP-activated protein kinase (AMPK) suppressed senescence in hydrogen peroxide (H2O2)-treated human primary keratinocytes, a model of oxidative stress-induced cellular aging. Using this model in the present study, we observed that resveratrol, an agent that increases the activities of both AMPK and sirtuins, ameliorated two age-associated phenotypes: cellular senescence and proliferative dysfunction. In addition, we found that treatment of keratinocytes with Ex527, a specific inhibitor of sirtuin 1 (SIRT1), attenuated the ability of resveratrol to suppress senescence. In keeping with the latter observation, we noted that compared to non-senescent keratinocytes, senescent cells lacked SIRT1. In addition to these effects on H2O2-induced senescence, resveratrol also prevented the H2O2-induced decrease in proliferation (as indicated by 3H-thymidine incorporation) in the presence of insulin. This effect was abrogated by inhibition of AMPK but not SIRT1. Compared to endothelium, we found that human keratinocytes expressed relatively high levels of Forkhead box O3 (FOXO3), a downstream target of both AMPK and SIRT1. Treatment of keratinocytes with resveratrol transactivated FOXO3 and increased the expression of its target genes including catalase. Resveratrol’s effects on both senescence and proliferation disappeared when FOXO3 was knocked down. Finally, we performed an exploratory study which showed that skin from humans over 50 years old had lower AMPK activity than skin from individuals under age 20. Collectively, these findings suggest that the effects of resveratrol on keratinocyte senescence and proliferation are regulated by the AMPK-FOXO3 pathway and in some situations, but not all, by SIRT1.
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Affiliation(s)
- Yasuo Ido
- Diabetes and Metabolism Unit, Boston University Medical Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| | | | - Fan Lan
- Endocrinology, Second Affiliated Hospital Chongqing Medical University, Chongqing, China
| | - Karen A. Weikel
- Diabetes and Metabolism Unit, Boston University Medical Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Lionel Breton
- L’OREAL Research and Innovation, Aulnay sous bois, France
| | - Neil B. Ruderman
- Diabetes and Metabolism Unit, Boston University Medical Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
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286
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Abstract
In this Opinion article, we summarize how changes in DNA methylation occur during aging in mammals and discuss examples of how such events may contribute to the aging process. We explore mechanisms that could facilitate DNA methylation changes in a site-specific manner and highlight a model in which region-specific DNA hypermethylation during aging is facilitated in a competitive manner by destabilization of the Polycomb repressive complex.
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287
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Lotem J, Levanon D, Negreanu V, Bauer O, Hantisteanu S, Dicken J, Groner Y. Runx3 at the interface of immunity, inflammation and cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:131-43. [PMID: 25641675 DOI: 10.1016/j.bbcan.2015.01.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 02/06/2023]
Abstract
Inactivation of tumor suppressor genes (TSG) in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago claims arose that the RUNX3 member of the RUNX transcription factor family is a major TSG inactivated in gastric cancer, a postulate extended later to other cancers. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. Here we critically re-appraise this paradigm in light of recent high-throughput, quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models. Collectively, these studies unequivocally demonstrate that RUNX3 is not a bona fide cell-autonomous TSG. Accordingly, RUNX3 is not recognized as a TSG and is not included among the 2000 cancer genes listed in the "Cancer Gene Census" or "Network for Cancer Genes" repositories. In contrast, RUNX3 does play important functions in immunity and inflammation and may thereby indirectly influence epithelial tumor development.
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Affiliation(s)
- Joseph Lotem
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ditsa Levanon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Omri Bauer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Hantisteanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Dicken
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoram Groner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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288
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Huh SJ, Clement K, Jee D, Merlini A, Choudhury S, Maruyama R, Yoo R, Chytil A, Boyle P, Ran FA, Moses HL, Barcellos-Hoff MH, Jackson-Grusby L, Meissner A, Polyak K. Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells. Stem Cell Reports 2015; 4:297-311. [PMID: 25619437 PMCID: PMC4325231 DOI: 10.1016/j.stemcr.2014.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 12/16/2014] [Accepted: 12/16/2014] [Indexed: 12/13/2022] Open
Abstract
Postnatal mammary gland development and differentiation occur during puberty and pregnancy. To explore the role of DNA methylation in these processes, we determined the genome-wide DNA methylation and gene expression profiles of CD24(+)CD61(+)CD29(hi), CD24(+)CD61(+)CD29(lo), and CD24(+)CD61(-)CD29(lo) cell populations that were previously associated with distinct biological properties at different ages and reproductive stages. We found that pregnancy had the most significant effects on CD24(+)CD61(+)CD29(hi) and CD24(+)CD61(+)CD29(lo) cells, inducing distinct epigenetic states that were maintained through life. Integrated analysis of gene expression, DNA methylation, and histone modification profiles revealed cell-type- and reproductive-stage-specific changes. We identified p27 and TGFβ signaling as key regulators of CD24(+)CD61(+)CD29(lo) cell proliferation, based on their expression patterns and results from mammary gland explant cultures. Our results suggest that relatively minor changes in DNA methylation occur during luminal differentiation compared with the effects of pregnancy on CD24(+)CD61(+)CD29(hi) and CD24(+)CD61(+)CD29(lo) cells.
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Affiliation(s)
- Sung Jin Huh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - David Jee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alessandra Merlini
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Unit of Immunology and General Pathology, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Sibgat Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Reo Maruyama
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ronnie Yoo
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Anna Chytil
- Department of Cancer Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Patrick Boyle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fei Ann Ran
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Harold L Moses
- Department of Cancer Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mary Helen Barcellos-Hoff
- Departments of Radiation Oncology and Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Laurie Jackson-Grusby
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
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289
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Abstract
The aging phenotype is the result of a complex interaction between genetic, epigenetic and environmental factors, and it is among the most complex phenotypes studied to date. Evidence suggests that epigenetic factors, including DNA methylation, histone modifications and microRNA expression, may affect the aging process and may be one of the central mechanisms by which aging predisposes to many age-related diseases. The total number of altered methylation sites increases with increasing age, such that they could serve as a biomarker for chronological age. This chapter summarizes the mechanisms by which these epigenetic factors contribute to aging and how they may affect the complex physiology of aging, lifespan and age-associated diseases.
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Affiliation(s)
- Dan Ben-Avraham
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, 10461, Bronx, NY, USA,
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290
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Abstract
Stem cells persist in replenishing functional mature cells throughout life by self-renewal and multilineage differentiation. Hematopoietic stem cells (HSCs) are among the best-characterized and understood stem cells, and they are responsible for the life-long production of all lineages of blood cells. HSCs are a heterogeneous population containing lymphoid-biased, myeloid-biased, and balanced subsets. HSCs undergo age-associated phenotypic and functional changes, and the composition of the HSC pool alters with aging. HSCs and their lineage-biased subfractions can be identified and analyzed by flow cytometry based on cell surface makers. Fluorescence-activated cell sorting (FACS) enables the isolation and purification of HSCs that greatly facilitates the mechanistic study of HSCs and their aging process at both cellular and molecular levels. The mouse model has been extensively used in HSC aging study. Bone marrow cells are isolated from young and old mice and stained with fluorescence-conjugated antibodies specific for differentiated and stem cells. HSCs are selected based on the negative expression of lineage markers and positive selection for several sets of stem cell markers. Lineage-biased HSCs can be further distinguished by the level of SLAM/CD150 expression and the extent of Hoechst efflux.
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Affiliation(s)
- Yi Liu
- Division of Hematology/Bone Marrow Transplantation, Department of Internal Medicine, Markey Cancer Center, University of Kentucky, 800 Rose Street, Lexington, KY, 40536, USA
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291
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Wahlestedt M, Pronk CJ, Bryder D. Concise review: hematopoietic stem cell aging and the prospects for rejuvenation. Stem Cells Transl Med 2014; 4:186-94. [PMID: 25548388 DOI: 10.5966/sctm.2014-0132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Because of the continuous increases in lifetime expectancy, the incidence of age-related diseases will, unless counteracted, represent an increasing problem at both the individual and socioeconomic levels. Studies on the processes of blood cell formation have revealed several shortcomings as a consequence of chronological age. They include a reduced ability to mount adaptive immune responses and a blood cell composition skewed toward myeloid cells, with the latter coinciding with a dramatically increased incidence of myelogenous diseases, including cancer. Conversely, the dominant forms of acute leukemia affecting children associate with the lymphoid lineages. A growing body of evidence has suggested that aging of various organs and cellular systems, including the hematopoietic system, associates with a functional demise of tissue-resident stem cell populations. Mechanistically, DNA damage and/or altered transcriptional landscapes appear to be major drivers of the hematopoietic stem cell aging state, with recent data proposing that stem cell aging phenotypes are characterized by at least some degree of reversibility. These findings suggest the possibility of rejuvenating, or at least dampening, stem cell aging phenotypes in the elderly for therapeutic benefit.
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Affiliation(s)
- Martin Wahlestedt
- Immunology Section, Institution for Experimental Medical Science, Lund University, Lund, Sweden; Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
| | - Cornelis Jan Pronk
- Immunology Section, Institution for Experimental Medical Science, Lund University, Lund, Sweden; Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
| | - David Bryder
- Immunology Section, Institution for Experimental Medical Science, Lund University, Lund, Sweden; Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
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292
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Sun D, Luo M, Jeong M, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Göttgens B, Darlington GJ, Li W, Goodell MA. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell 2014; 14:673-88. [PMID: 24792119 DOI: 10.1016/j.stem.2014.03.002] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 12/16/2013] [Accepted: 03/05/2014] [Indexed: 12/15/2022]
Abstract
To investigate the cell-intrinsic aging mechanisms that erode the function of somatic stem cells during aging, we have conducted a comprehensive integrated genomic analysis of young and aged cells. We profiled the transcriptome, DNA methylome, and histone modifications of young and old murine hematopoietic stem cells (HSCs). Transcriptome analysis indicated reduced TGF-β signaling and perturbation of genes involved in HSC proliferation and differentiation. Aged HSCs exhibited broader H3K4me3 peaks across HSC identity and self-renewal genes and showed increased DNA methylation at transcription factor binding sites associated with differentiation-promoting genes combined with a reduction at genes associated with HSC maintenance. Altogether, these changes reinforce HSC self-renewal and diminish differentiation, paralleling phenotypic HSC aging behavior. Ribosomal biogenesis emerged as a particular target of aging with increased transcription of ribosomal protein and RNA genes and hypomethylation of rRNA genes. This data set will serve as a reference for future epigenomic analysis of stem cell aging.
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Affiliation(s)
- Deqiang Sun
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Min Luo
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Benjamin Rodriguez
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zheng Xia
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Hannah
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge University, Hills Road, CB2 0XY Cambridge, UK
| | - Hui Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thuc Le
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and the Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and the Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christoph Bock
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02142, USA
| | | | - Berthold Göttgens
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge University, Hills Road, CB2 0XY Cambridge, UK
| | | | - Wei Li
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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293
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Abstract
Aging is associated with impairments in hematopoietic stem cell (HSC) function and an increased risk of leukemogenesis. In this issue of Cell Stem Cell, Sun et al. (2014) use highly purified HSCs along with an integrated genomic approach to evaluate aging-associated alterations in the epigenome and transcriptome of HSCs.
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Affiliation(s)
- Stefan Tümpel
- Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena, Germany
| | - K Lenhard Rudolph
- Leibniz Institute for Age Research, Fritz Lipmann Institute, D-07745 Jena, Germany.
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294
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Wahlestedt M, Ameur A, Moraghebi R, Norddahl GL, Sten G, Woods NB, Bryder D. Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects. Stem Cells 2014; 32:1173-82. [PMID: 24446123 DOI: 10.1002/stem.1630] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/27/2013] [Indexed: 01/19/2023]
Abstract
It has become increasingly clear that several age-associated pathologies associate with mutations in the mitochondrial genome. Experimental modeling of such events has revealed that acquisition of mitochondrial DNA (mtDNA) damage can impair respiratory function and, as a consequence, can lead to widespread decline in cellular function. This includes premature aging syndromes. By taking advantage of a mutator mouse model with an error-prone mtDNA polymerase, we here investigated the impact of an established mtDNA mutational load with regards to the generation, maintenance, and differentiation of induced pluripotent stem (iPS) cells. We demonstrate that somatic cells with a heavy mtDNA mutation burden were amenable for reprogramming into iPS cells. However, mutator iPS cells displayed delayed proliferation kinetics and harbored extensive differentiation defects. While mutator iPS cells had normal ATP levels and glycolytic activity, the induction of differentiation coincided with drastic decreases in ATP production and a hyperactive glycolysis. These data demonstrate the differential requirements of mitochondrial integrity for pluripotent stem cell self-renewal versus differentiation and highlight the relevance of assessing the mitochondrial genome when aiming to generate iPS cells with robust differentiation potential.
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Affiliation(s)
- Martin Wahlestedt
- Medical Faculty, Institution for Experimental Medical Science, Immunology Section, Lund Stem Cell Center, Lund University, Lund, Sweden
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295
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Chun KT, Li B, Dobrota E, Tate C, Lee JH, Khan S, Haneline L, HogenEsch H, Skalnik DG. The epigenetic regulator CXXC finger protein 1 is essential for murine hematopoiesis. PLoS One 2014; 9:e113745. [PMID: 25470594 PMCID: PMC4254612 DOI: 10.1371/journal.pone.0113745] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/30/2014] [Indexed: 11/18/2022] Open
Abstract
CXXC finger protein 1 (Cfp1), encoded by the Cxxc1 gene, binds to DNA sequences containing an unmethylated CpG dinucleotide and is an epigenetic regulator of both cytosine and histone methylation. Cxxc1-null mouse embryos fail to gastrulate, and Cxxc1-null embryonic stem cells are viable but cannot differentiate, suggesting that Cfp1 is required for chromatin remodeling associated with stem cell differentiation and embryogenesis. Mice homozygous for a conditional Cxxc1 deletion allele and carrying the inducible Mx1-Cre transgene were generated to assess Cfp1 function in adult animals. Induction of Cre expression in adult animals led to Cfp1 depletion in hematopoietic cells, a failure of hematopoiesis with a nearly complete loss of lineage-committed progenitors and mature cells, elevated levels of apoptosis, and death within two weeks. A similar pathology resulted following transplantation of conditional Cxxc1 bone marrow cells into wild type recipients, demonstrating this phenotype is intrinsic to Cfp1 function within bone marrow cells. Remarkably, the Lin- Sca-1+ c-Kit+ population of cells in the bone marrow, which is enriched for hematopoietic stem cells and multi-potential progenitor cells, persists and expands in the absence of Cfp1 during this time frame. Thus, Cfp1 is necessary for hematopoietic stem and multi-potential progenitor cell function and for the developmental potential of differentiating hematopoietic cells.
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Affiliation(s)
- Kristin T Chun
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Biology Department, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, Indiana, United States of America
| | - Binghui Li
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Erika Dobrota
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Courtney Tate
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jeong-Heon Lee
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Shehnaz Khan
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Laura Haneline
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Departments of Microbiology & Immunology and Cellular & Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Harm HogenEsch
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, United States of America
| | - David G Skalnik
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Biology Department, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, Indiana, United States of America
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296
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Liyanage VRB, Jarmasz JS, Murugeshan N, Del Bigio MR, Rastegar M, Davie JR. DNA modifications: function and applications in normal and disease States. BIOLOGY 2014; 3:670-723. [PMID: 25340699 PMCID: PMC4280507 DOI: 10.3390/biology3040670] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone, and non-histone chromosomal proteins, which establish a complex regulatory network that controls genome function. Methylation of DNA at the fifth position of cytosine in CpG dinucleotides (5-methylcytosine, 5mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5hmC), which is a product of the ten-eleven translocation (TET) proteins converting 5mC to 5hmC. In this review, we will highlight current studies on the role of 5mC and 5hmC in regulating gene expression (using some aspects of brain development as examples). Further the roles of these modifications in detection of pathological states (type 2 diabetes, Rett syndrome, fetal alcohol spectrum disorders and teratogen exposure) will be discussed.
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Affiliation(s)
- Vichithra R B Liyanage
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Jessica S Jarmasz
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Nanditha Murugeshan
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Marc R Del Bigio
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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297
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Abstract
Aging is marked by changes that affect organs and resident stem cell function. Shorting of telomeres, DNA damage, oxidative stress, deregulation of genes and proteins, impaired cell-cell communication, and an altered systemic environment cause the eventual demise of cells. At the same time, reparative activities also decline. It is intriguing to correlate aging with the decline of regenerative abilities. Animal models with strong regenerative capabilities imply that aging processes might not be affecting regeneration. In this review, we selectively present age-dependent changes in stem/progenitor cells that are vital for tissue homeostasis and repair. In addition, the aging effect on regeneration following injury in organs such as lung, skeletal muscle, heart, nervous system, cochlear hair, lens, and liver are discussed. These tissues are also known for diseases such as heart attack, stroke, cognitive impairment, cataract, and hearing loss that occur mostly during aging in humans. Conclusively, vertebrate regeneration declines with age with the loss of stem/progenitor cell function. Future studies on improving the function of stem cells, along with studies in fish and amphibians where regeneration does not decline with age, will undoubtedly provide insights into both processes.
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Affiliation(s)
- Konstantinos Sousounis
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio, USA
| | - Joelle A Baddour
- Department of Chemical and Materials Engineering and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio, USA
| | - Panagiotis A Tsonis
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton, Dayton, Ohio, USA.
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298
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Stem cell aging: mechanisms, regulators and therapeutic opportunities. Nat Med 2014; 20:870-80. [PMID: 25100532 DOI: 10.1038/nm.3651] [Citation(s) in RCA: 479] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/09/2014] [Indexed: 12/14/2022]
Abstract
Aging tissues experience a progressive decline in homeostatic and regenerative capacities, which has been attributed to degenerative changes in tissue-specific stem cells, stem cell niches and systemic cues that regulate stem cell activity. Understanding the molecular pathways involved in this age-dependent deterioration of stem cell function will be critical for developing new therapies for diseases of aging that target the specific causes of age-related functional decline. Here we explore key molecular pathways that are commonly perturbed as tissues and stem cells age and degenerate. We further consider experimental evidence both supporting and refuting the notion that modulation of these pathways per se can reverse aging phenotypes. Finally, we ask whether stem cell aging establishes an epigenetic 'memory' that is indelibly written or one that can be reset.
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299
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Mangialardi G, Spinetti G, Reni C, Madeddu P. Reactive oxygen species adversely impacts bone marrow microenvironment in diabetes. Antioxid Redox Signal 2014; 21:1620-33. [PMID: 25089632 PMCID: PMC4175424 DOI: 10.1089/ars.2014.5944] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
UNLABELLED Significance: Patients with diabetes mellitus suffer an excess of cardiovascular complications and recover worse from them as compared with their nondiabetic peers. It is well known that microangiopathy is the cause of renal damage, blindness, and heart attacks in patients with diabetes. This review highlights molecular deficits in stem cells and a supporting microenvironment, which can be traced back to oxidative stress and ultimately reduce stem cells therapeutic potential in diabetic patients. RECENT ADVANCES New research has shown that increased oxidative stress contributes to inducing microangiopathy in bone marrow (BM), the tissue contained inside the bones and the main source of stem cells. These precious cells not only replace old blood cells but also exert an important reparative function after acute injuries and heart attacks. CRITICAL ISSUES The starvation of BM as a consequence of microangiopathy can lead to a less efficient healing in diabetic patients with ischemic complications. Furthermore, stem cells from a patient's BM are the most used in regenerative medicine trials to mend hearts damaged by heart attacks. FUTURE DIRECTIONS A deeper understanding of redox signaling in BM stem cells will lead to new modalities for preserving local and systemic homeostasis and to more effective treatments of diabetic cardiovascular complications.
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Affiliation(s)
- Giuseppe Mangialardi
- 1 Regenerative Medicine Section, Bristol Heart Institute, School of Clinical Sciences, University of Bristol , Bristol, United Kingdom
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300
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Abstract
Growth hormone receptor (Ghr) signaling is important in a wide variety of cellular processes including aging; however, the role of Ghr signaling in hematopoietic stem cell (HSC) biology remains unexplored. Within the hematopoietic system, Ghr is expressed in a highly HSC-specific manner and is significantly upregulated during aging. Exposure of young and old HSCs to recombinant growth hormone ex vivo led to diminished short-term reconstitution and restored B-cell output from old HSCs. Hematopoietic-specific genetic deletion of Ghr neither impacted steady-state hematopoiesis nor serial transplantation potential. Repeat challenge with 5-fluorouracil showed that Ghr was dispensable for HSC activation and homeostatic recovery in vivo and, after challenge, Ghr-deficient HSCs functioned normally through serial transplantation. Although exogenous Gh induces age-dependent HSC effects, these results indicate that Ghr signaling appears largely dispensable for HSC function and aging.
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