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Karetnikov DI, Romanov SE, Baklaushev VP, Laktionov PP. Age Prediction Using DNA Methylation Heterogeneity Metrics. Int J Mol Sci 2024; 25:4967. [PMID: 38732187 PMCID: PMC11084170 DOI: 10.3390/ijms25094967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Dynamic changes in genomic DNA methylation patterns govern the epigenetic developmental programs and accompany the organism's aging. Epigenetic clock (eAge) algorithms utilize DNA methylation to estimate the age and risk factors for diseases as well as analyze the impact of various interventions. High-throughput bisulfite sequencing methods, such as reduced-representation bisulfite sequencing (RRBS) or whole genome bisulfite sequencing (WGBS), provide an opportunity to identify the genomic regions of disordered or heterogeneous DNA methylation, which might be associated with cell-type heterogeneity, DNA methylation erosion, and allele-specific methylation. We systematically evaluated the applicability of five scores assessing the variability of methylation patterns by evaluating within-sample heterogeneity (WSH) to construct human blood epigenetic clock models using RRBS data. The best performance was demonstrated by the model based on a metric designed to assess DNA methylation erosion with an MAE of 3.686 years. We also trained a prediction model that uses the average methylation level over genomic regions. Although this region-based model was relatively more efficient than the WSH-based model, the latter required the analysis of just a few short genomic regions and, therefore, could be a useful tool to design a reduced epigenetic clock that is analyzed by targeted next-generation sequencing.
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Affiliation(s)
- Dmitry I. Karetnikov
- Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Stanislav E. Romanov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vladimir P. Baklaushev
- Federal Center for Brain and Neurotechnologies, Federal Medical and Biological Agency of Russia, 117513 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Medical Nanobiotechnology, Medical and Biological Faculty, Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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2
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Bertucci-Richter EM, Shealy EP, Parrott BB. Epigenetic drift underlies epigenetic clock signals, but displays distinct responses to lifespan interventions, development, and cellular dedifferentiation. Aging (Albany NY) 2024; 16:1002-1020. [PMID: 38285616 PMCID: PMC10866415 DOI: 10.18632/aging.205503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/01/2023] [Indexed: 01/31/2024]
Abstract
Changes in DNA methylation with age are observed across the tree of life. The stereotypical nature of these changes can be modeled to produce epigenetic clocks capable of predicting chronological age with unprecedented accuracy. Despite the predictive ability of epigenetic clocks and their utility as biomarkers in clinical applications, the underlying processes that produce clock signals are not fully resolved, which limits their interpretability. Here, we develop a computational approach to spatially resolve the within read variability or "disorder" in DNA methylation patterns and test if age-associated changes in DNA methylation disorder underlie signals comprising epigenetic clocks. We find that epigenetic clock loci are enriched in regions that both accumulate and lose disorder with age, suggesting a link between DNA methylation disorder and epigenetic clocks. We then develop epigenetic clocks that are based on regional disorder of DNA methylation patterns and compare their performance to other epigenetic clocks by investigating the influences of development, lifespan interventions, and cellular dedifferentiation. We identify common responses as well as critical differences between canonical epigenetic clocks and those based on regional disorder, demonstrating a fundamental decoupling of epigenetic aging processes. Collectively, we identify key linkages between epigenetic disorder and epigenetic clocks and demonstrate the multifaceted nature of epigenetic aging in which stochastic processes occurring at non-random loci produce predictable outcomes.
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Affiliation(s)
- Emily M. Bertucci-Richter
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Ethan P. Shealy
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
| | - Benjamin B. Parrott
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
- Eugene P. Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
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3
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Sands B, Yun SR, Oshima J, Mendenhall AR. Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576748. [PMID: 38328214 PMCID: PMC10849558 DOI: 10.1101/2024.01.22.576748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undefined epigenetic programs act to probabilistically silence individual autosomal alleles, generating unique individuals, even from genetic clones. This sort of random monoallelic expression can explain variation in traits and diseases that differences in genes and environments cannot. Here, we developed the nematode Caenorhabditis elegans to study monoallelic expression in whole tissues, and defined a developmental genetic regulation pathway. We found maternal H3K9 histone methyltransferase (HMT) SET-25/SUV39/G9a works with HPL-2/HP1 and LIN-61/L3MBTL2 to randomly silence alleles in the intestinal progenitor E-cell of 8-cell embryos to cause monoallelic expression. SET-25 was antagonized by another maternal H3K9 HMT, MET-2/SETDB1, which works with LIN-65/ATF7ZIP and ARLE-14/ARL14EP to prevent monoallelic expression. The HMT-catalytic SET domains of both MET-2 and SET-25 were required for regulating monoallelic expression. Our data support a model wherein SET-25 and MET-2 regulate histones during development to generate patterns of somatic monoallelic expression that are persistent but not heritable.
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4
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Mendenhall AR. Mediterranean mechanisms of longevity. Nat Cell Biol 2023; 25:627-628. [PMID: 37127713 DOI: 10.1038/s41556-023-01115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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5
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Zhang J, Burnaevskiy N, Annis J, Han W, Hou D, Ladd P, Lee L, Mendenhall AR, Oshima J, Martin GM. Cell-to-Cell Variation in Gene Expression for Cultured Human Cells Is Controlled in Trans by Diverse Genes: Implications for the Pathobiology of Aging. J Gerontol A Biol Sci Med Sci 2021; 75:2295-2298. [PMID: 31957802 DOI: 10.1093/gerona/glaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell variation in gene expression increases among homologous cells within multiple tissues during aging. We call this phenomenon variegated gene expression (VGE). Long, healthy life requires robust and coordinated gene expression. We posit that nature may have evolved VGE as a bet-hedging mechanism to protect reproductively active populations. The price we may pay is accelerated aging. That hypothesis will require the demonstration that genetic loci are capable of modulating degrees of VGE. While loci controlling VGE in yeast and genes controlling interindividual variation in gene expression in Caenorhabditis elegans have been identified, there has been no compelling evidence for the role of specific genetic loci in modulations of VGE of specific targets in humans. With the assistance of a core facility, we used a customized library of siRNA constructs to screen 1,195 human genes to identify loci contributing to the control of VGE of a gene with relevance to the biology of aging. We identified approximately 50 loci controlling VGE of the prolongevity gene, SIRT1. Because of its partial homology to FOXO3A, a variant of which is enriched in centenarians, our laboratory independently confirmed that the knockdown of FOXF2 greatly diminished VGE of SIRT1 but had little impact upon the VGE of WRN. While the role of these VGE-altering genes on aging in vivo remains to be determined, we hypothesize that some of these genes can be targeted to increase functionality during aging.
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Affiliation(s)
- Jiaming Zhang
- Department of Pathology, University of Washington, Seattle
| | | | - James Annis
- Quellos High-throughput Screening Core, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle
| | - Wenyan Han
- Department of Pathology, University of Washington, Seattle
| | - Deyin Hou
- Department of Pathology, University of Washington, Seattle
| | - Paula Ladd
- Department of Pathology, University of Washington, Seattle
| | - Lin Lee
- Department of Pathology, University of Washington, Seattle
| | | | - Junko Oshima
- Department of Pathology, University of Washington, Seattle
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6
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Mendenhall AR, Lithgow GJ, Kim S, Friedman D, Newell-Stamper BL, Johnson TE. Career Retrospective: Tom Johnson-Genetics, Genomics, Stress, Stochastic Variation, and Aging. J Gerontol A Biol Sci Med Sci 2021; 76:e85-e91. [PMID: 33609361 DOI: 10.1093/gerona/glab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington, USA.,University of Washington Nathan Shock Center for Excellence in the Basic Biology of Aging, Department of Laboratory Medicine and Pathology, Seattle, Washington, USA
| | | | - Stuart Kim
- Department of Developmental Biology, Stanford University Medical Center, California, USA
| | - David Friedman
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, USA
| | | | - Thomas E Johnson
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA.,University of Colorado, Institute for Behavioral Genetics, Boulder, Colorado, USA
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Mendenhall AR, Martin GM, Kaeberlein M, Anderson RM. Cell-to-cell variation in gene expression and the aging process. GeroScience 2021; 43:181-196. [PMID: 33595768 PMCID: PMC8050212 DOI: 10.1007/s11357-021-00339-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
There is tremendous variation in biological traits, and much of it is not accounted for by variation in DNA sequence, including human diseases and lifespan. Emerging evidence points to differences in the execution of the genetic program as a key source of variation, be it stochastic variation or programmed variation. Here we discuss variation in gene expression as an intrinsic property and how it could contribute to variation in traits, including the rate of aging. The review is divided into sections describing the historical context and evidence to date for nongenetic variation, the different approaches that may be used to detect nongenetic variation, and recent findings showing that the amount of variation in gene expression can be both genetically programmed and epigenetically controlled. Finally, we present evidence that changes in cell-to-cell variation in gene expression emerge as part of the aging process and may be linked to disease vulnerability as a function of age. These emerging concepts are likely to be important across the spectrum of biomedical research and may well underpin what we understand as biological aging.
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Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA.
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA.
| | - George M Martin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin and Geriatric Research Education and Clinical Center, William S Middleton Memorial Veterans Hospital, Madison, WI, USA.
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8
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Abstract
Recent research suggests that epigenetics, especially DNA methylation, plays a mechanistic role in aging. Epigenetic clocks, which measure changes in a few hundred specific CpG sites, can accurately predict chronological age in a variety of species, including humans. These clocks are currently the bestbiomarkers for predicting mortality in humans. Additionally, several studies have characterized the effects of aging across the methylome in a wide variety of tissues from humans and mice. A small fraction (~2%) of the CpG sites show age-related changes, either hypermethylation or hypomethylation with aging. Evaluation of non-CpG site methylation has only been examined in a few studies, with about ~0.5% of these sites showing achange with age. Therefore, while only a small fraction of cytosines in the genome show changes in DNA methylation with age, this represents 2 to 3 million cytosines in the genome. Importantly, the only study to compare the effect of aging on DNA methylation in male and female mice and humans found that N95% of the age-related changes in DNA methylation in the hippocampus were sexually divergent, i.e., the methylation did not differ between males and females atyoung age but age-related changes occurred in one sex but not the other. The age-related changes in DNA methylation tend to be enriched and under-represented in specific genomic contexts, with some commonalities between tissues and species that require further investigation. The strongest evidence that the age-related changes in DNA methylation play a role in aging comes from studies of anti-aging interventions (e.g., caloric restriction, dwarfism, and rapamycin treatment) in mice. These anti-aging interventions deaccelerate the epigenetic clocks and reverse/prevent 20 to 40% of the age-related changes in DNA methylation. It will be important in the future to demonstrate that at least some of the age-related changes in DNA methylation directly lead to alterations in the transcriptome of cells/tissues that could potentially contribute to aging.
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9
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Song S, Johnson FB. Epigenetic Mechanisms Impacting Aging: A Focus on Histone Levels and Telomeres. Genes (Basel) 2018; 9:genes9040201. [PMID: 29642537 PMCID: PMC5924543 DOI: 10.3390/genes9040201] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/13/2022] Open
Abstract
Aging and age-related diseases pose some of the most significant and difficult challenges to modern society as well as to the scientific and medical communities. Biological aging is a complex, and, under normal circumstances, seemingly irreversible collection of processes that involves numerous underlying mechanisms. Among these, chromatin-based processes have emerged as major regulators of cellular and organismal aging. These include DNA methylation, histone modifications, nucleosome positioning, and telomere regulation, including how these are influenced by environmental factors such as diet. Here we focus on two interconnected categories of chromatin-based mechanisms impacting aging: those involving changes in the levels of histones or in the functions of telomeres.
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Affiliation(s)
- Shufei Song
- Biochemistry and Molecular Biophysics Graduate Group, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Pathology and Laboratory Medicine, and Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, and Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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Vogt G. Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives. J Biosci 2018. [DOI: 10.1007/s12038-018-9741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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Inukai S, Pincus Z, de Lencastre A, Slack FJ. A microRNA feedback loop regulates global microRNA abundance during aging. RNA (NEW YORK, N.Y.) 2018; 24:159-172. [PMID: 29114017 PMCID: PMC5769744 DOI: 10.1261/rna.062190.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/29/2017] [Indexed: 06/07/2023]
Abstract
Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging. Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression. Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span. Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline.
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Affiliation(s)
- Sachi Inukai
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zachary Pincus
- Department of Developmental Biology
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Alexandre de Lencastre
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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12
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Mendenhall A, Crane MM, Tedesco PM, Johnson TE, Brent R. Caenorhabditis elegans Genes Affecting Interindividual Variation in Life-span Biomarker Gene Expression. J Gerontol A Biol Sci Med Sci 2017; 72:1305-1310. [PMID: 28158434 DOI: 10.1093/gerona/glw349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/30/2016] [Indexed: 01/12/2023] Open
Abstract
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior reports showed that the thermosensory neurons and insulin signaling systems controlled the magnitude of the heat shock response, including absolute expression of hsp-16.2. Here, we tested whether these regulatory signals might also influence variation in hsp-16.2 reporter expression. Genetic experiments showed that the action of AFD thermosensory neurons increases interindividual variation in biomarker expression. Further genetic experimentation showed the insulin signaling system acts to decrease interindividual variation in life-span biomarker expression; in other words, insulin signaling canalizes expression of the hsp-16.2-driven life-span biomarker. Our results show that specific signaling systems regulate not only expression level, but also the amount of interindividual expression variation for a life-span biomarker gene. They raise the possibility that manipulation of these systems might offer means to reduce heterogeneity in the aging process.
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Affiliation(s)
| | | | | | - Thomas E Johnson
- Institute for Behavioral Genetics.,Department of Integrative Physiology.,Biofrontiers Institute, University of Colorado, Boulder
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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13
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Mangold CA, Wronowski B, Du M, Masser DR, Hadad N, Bixler GV, Brucklacher RM, Ford MM, Sonntag WE, Freeman WM. Sexually divergent induction of microglial-associated neuroinflammation with hippocampal aging. J Neuroinflammation 2017; 14:141. [PMID: 28732515 PMCID: PMC5521082 DOI: 10.1186/s12974-017-0920-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 07/13/2017] [Indexed: 01/11/2023] Open
Abstract
Background The necessity of including both males and females in molecular neuroscience research is now well understood. However, there is relatively limited basic biological data on brain sex differences across the lifespan despite the differences in age-related neurological dysfunction and disease between males and females. Methods Whole genome gene expression of young (3 months), adult (12 months), and old (24 months) male and female C57BL6 mice hippocampus was analyzed. Subsequent bioinformatic analyses and confirmations of age-related changes and sex differences in hippocampal gene and protein expression were performed. Results Males and females demonstrate both common expression changes with aging and marked sex differences in the nature and magnitude of the aging responses. Age-related hippocampal induction of neuroinflammatory gene expression was sexually divergent and enriched for microglia-specific genes such as complement pathway components. Sexually divergent C1q protein expression was confirmed by immunoblotting and immunohistochemistry. Similar patterns of cortical sexually divergent gene expression were also evident. Additionally, inter-animal gene expression variability increased with aging in males, but not females. Conclusions These findings demonstrate sexually divergent neuroinflammation with aging that may contribute to sex differences in age-related neurological diseases such as stroke and Alzheimer’s, specifically in the complement system. The increased expression variability in males suggests a loss of fidelity in gene expression regulation with aging. These findings reveal a central role of sex in the transcriptomic response of the hippocampus to aging that warrants further, in depth, investigations. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0920-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colleen A Mangold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, USA
| | - Benjamin Wronowski
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Mei Du
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Dustin R Masser
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Georgina V Bixler
- Genome Sciences Facility, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Robert M Brucklacher
- Genome Sciences Facility, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Matthew M Ford
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon, USA
| | - William E Sonntag
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Reynolds Oklahoma Center on Aging & Nathan Shock Center of Excellence in the Biology of Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA. .,, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.
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14
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Morgan RG, Venturelli M, Gross C, Tarperi C, Schena F, Reggiani C, Naro F, Pedrinolla A, Monaco L, Richardson RS, Donato AJ. Age-Associated ALU Element Instability in White Blood Cells Is Linked to Lower Survival in Elderly Adults: A Preliminary Cohort Study. PLoS One 2017; 12:e0169628. [PMID: 28060910 PMCID: PMC5218400 DOI: 10.1371/journal.pone.0169628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND ALU element instability could contribute to gene function variance in aging, and may partly explain variation in human lifespan. OBJECTIVE To assess the role of ALU element instability in human aging and the potential efficacy of ALU element content as a marker of biological aging and survival. DESIGN Preliminary cohort study. METHODS We measured two high frequency ALU element subfamilies, ALU-J and ALU-Sx, by a single qPCR assay and compared ALU-J/Sx content in white blood cell (WBCs) and skeletal muscle cell (SMCs) biopsies from twenty-three elderly adults with sixteen healthy sex-balanced young adults; all-cause survival rates of elderly adults predicted by ALU-J/Sx content in both tissues; and cardiovascular disease (CVD)- and cancer-specific survival rates of elderly adults predicted by ALU-J/Sx content in both tissues, as planned subgroup analyses. RESULTS We found greater ALU-J/Sx content variance in WBCs from elderly adults than young adults (P < 0.001) with no difference in SMCs (P = 0.94). Elderly adults with low WBC ALU-J/Sx content had worse four-year all-cause and CVD-associated survival than those with high ALU-J/Sx content (both P = 0.03 and hazard ratios (HR) ≥ 3.40), while WBC ALU-J/Sx content had no influence on cancer-associated survival (P = 0.42 and HR = 0.74). SMC ALU-J/Sx content had no influence on all-cause, CVD- or cancer -associated survival (all P ≥ 0.26; HR ≤ 2.07). CONCLUSIONS These initial findings demonstrate that ALU element instability occurs with advanced age in WBCs, but not SMCs, and imparts greater risk of all-cause mortality that is likely driven by an increased risk for CVD and not cancer.
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Affiliation(s)
- R. Garrett Morgan
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
| | - Massimo Venturelli
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cole Gross
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Cantor Tarperi
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Federico Schena
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Fabio Naro
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University, Rome, Italy
| | | | - Lucia Monaco
- Department of Physiology and Pharmacology, Sapienza University of Rome, Italy
| | - Russell S. Richardson
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, United States of America
| | - Anthony J. Donato
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Martin GM. Geroscience: Addressing the mismatch between its exciting research opportunities, its economic imperative and its current funding crisis. Exp Gerontol 2016; 94:46-51. [PMID: 27871822 DOI: 10.1016/j.exger.2016.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022]
Abstract
There is at present a huge disconnect between levels of funding for basic research on fundamental mechanisms of biological aging and, given demographic projections, the anticipated enormous social and economic impacts of a litany of chronic diseases for which aging is by far the major risk factor: One valuable approach, recently instigated by Felipe Sierra & colleagues at the US National Institute on Aging, is the development of a Geroscience Interest Group among virtually all of the NIH institutes. A complementary approach would be to seek major escalations of private funding. The American Federation for Aging Research, the Paul Glenn Foundation and the Ellison Medical Foundation pioneered efforts by the private sector to provide substantial supplements to public sources of funding. It is time for our community to organize efforts towards the enhancements of such crucial contributions, especially in support of the emerging generation of young investigators, many of whom are leaving our ranks to seek alternative employment. To do so, we must provide potential donors with strong economic, humanitarian and scientific rationales. An initial approach to such efforts is briefly outlined in this manuscript as a basis for wider discussions within our community.
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Affiliation(s)
- George M Martin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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16
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Ashapkin VV, Kutueva LI, Vanyushin BF. Aging Epigenetics: Accumulation of Errors or Realization of a Specific Program? BIOCHEMISTRY (MOSCOW) 2016; 80:1406-17. [PMID: 26615432 DOI: 10.1134/s0006297915110024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aging in mammals is known to be accompanied by a progressive loss of methylated cytosines from DNA. This loss is tissue-specific to a certain extent and affects mainly repeated sequences, transposable elements, and intergenic genome parts. Age-dependent DNA hypomethylation is correlated with and perhaps partly caused by a diminished activity of DNA methyltransferases. Along with the global DNA demethylation during aging, hypermethylation of certain genes occurs. On the whole-genome scale, an age-dependent hypermethylation is typical for genes associated with promoter CG islands, whereas hypomethylation mostly affects CG-poor genes, besides the repeated sequences, transposable elements, and intergenic genome parts mentioned above. The methylation levels of certain CG sites display strict correlation to age and thus could be used as a molecular marker to predict biological age of cells, tissues, and organisms. Epigenetic cell reprogramming, such as induced pluripotent stem cell production, leads to complete resetting of their epigenetic age.
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Affiliation(s)
- V V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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17
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Hadad N, Masser DR, Logan S, Wronowski B, Mangold CA, Clark N, Otalora L, Unnikrishnan A, Ford MM, Giles CB, Wren JD, Richardson A, Sonntag WE, Stanford DR, Freeman W. Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice. Epigenetics Chromatin 2016; 9:30. [PMID: 27413395 PMCID: PMC4942942 DOI: 10.1186/s13072-016-0080-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/06/2016] [Indexed: 02/06/2023] Open
Abstract
Background Changes to the epigenome with aging, and DNA modifications in particular, have been proposed as a central regulator of the aging process, a predictor of mortality, and a contributor to the pathogenesis of age-related diseases. In the central nervous system, control of learning and memory, neurogenesis, and plasticity require changes in cytosine methylation and hydroxymethylation. Although genome-wide decreases in methylation with aging are often reported as scientific dogma, primary research reports describe decreases, increases, or lack of change in methylation and hydroxymethylation and their principle regulators, DNA methyltransferases and ten-eleven translocation dioxygenases in the hippocampus. Furthermore, existing data are limited to only male animals. Results Through examination of the hippocampus in young, adult, and old male and female mice by antibody-based, pyrosequencing, and whole-genome oxidative bisulfite sequencing methods, we provide compelling evidence that contradicts the genomic hypomethylation theory of aging. We also demonstrate that expression of DNA methyltransferases and ten-eleven translocation dioxygenases is not differentially regulated with aging or between the sexes, including the proposed cognitive aging regulator DNMT3a2. Using oxidative bisulfite sequencing that discriminates methylation from hydroxymethylation and by cytosine (CG and non-CG) context, we observe sex differences in average CG methylation and hydroxymethylation of the X chromosome, and small age-related differences in hydroxymethylation of CG island shores and shelves, and methylation of promoter regions. Conclusion These findings clarify a long-standing misconception of the epigenomic response to aging and demonstrate the need for studies of base-specific methylation and hydroxymethylation with aging in both sexes. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0080-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Niran Hadad
- Oklahoma Center for Neuroscience, Oklahoma City, OK USA ; Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Sreemathi Logan
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
| | - Benjamin Wronowski
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Colleen A Mangold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA USA
| | - Nicholas Clark
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Laura Otalora
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA
| | - Matthew M Ford
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR USA
| | - Cory B Giles
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA ; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ; Oklahoma City VA Medical Center, Oklahoma City, OK USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - William E Sonntag
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
| | - Willard Freeman
- Oklahoma Center for Neuroscience, Oklahoma City, OK USA ; Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK 73104 USA ; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA ; Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Hisama FM, Oshima J, Martin GM. How Research on Human Progeroid and Antigeroid Syndromes Can Contribute to the Longevity Dividend Initiative. Cold Spring Harb Perspect Med 2016; 6:a025882. [PMID: 26931459 DOI: 10.1101/cshperspect.a025882] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Although translational applications derived from research on basic mechanisms of aging are likely to enhance health spans and life spans for most of us (the longevity dividend), there will remain subsets of individuals with special vulnerabilities. Medical genetics is a discipline that describes such "private" patterns of aging and can reveal underlying mechanisms, many of which support genomic instability as a major mechanism of aging. We review examples of three classes of informative disorders: "segmental progeroid syndromes" (those that appear to accelerate multiple features of aging), "unimodal progeroid syndromes" (those that impact on a single disorder of aging), and "unimodal antigeroid syndromes," variants that provide enhanced protection against specific disorders of aging; we urge our colleagues to expand our meager research efforts on the latter, including ancillary somatic cell genetic approaches.
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Affiliation(s)
- Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195
| | - Junko Oshima
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195 Department of Medicine, Chiba University, Chiba 260-8670, Japan
| | - George M Martin
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195
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Mendenhall A, Driscoll M, Brent R. Using measures of single-cell physiology and physiological state to understand organismic aging. Aging Cell 2016; 15:4-13. [PMID: 26616110 PMCID: PMC4717262 DOI: 10.1111/acel.12424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2015] [Indexed: 01/13/2023] Open
Abstract
Genetically identical organisms in homogeneous environments have different lifespans and healthspans. These differences are often attributed to stochastic events, such as mutations and 'epimutations', changes in DNA methylation and chromatin that change gene function and expression. But work in the last 10 years has revealed differences in lifespan- and health-related phenotypes that are not caused by lasting changes in DNA or identified by modifications to DNA or chromatin. This work has demonstrated persistent differences in single-cell and whole-organism physiological states operationally defined by values of reporter gene signals in living cells. While some single-cell states, for example, responses to oxygen deprivation, were defined previously, others, such as a generally heightened ability to make proteins, were, revealed by direct experiment only recently, and are not well understood. Here, we review technical progress that promises to greatly increase the number of these measurable single-cell physiological variables and measureable states. We discuss concepts that facilitate use of single-cell measurements to provide insight into physiological states and state transitions. We assert that researchers will use this information to relate cell level physiological readouts to whole-organism outcomes, to stratify aging populations into groups based on different physiologies, to define biomarkers predictive of outcomes, and to shed light on the molecular processes that bring about different individual physiologies. For these reasons, quantitative study of single-cell physiological variables and state transitions should provide a valuable complement to genetic and molecular explanations of how organisms age.
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Affiliation(s)
| | - Monica Driscoll
- Department of Molecular Biology and BiochemistryRutgersThe State University of New JerseyPiscatawayNJUSA
| | - Roger Brent
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleWAUSA
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20
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Vogt G. Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences. J Biosci 2015; 40:159-204. [PMID: 25740150 DOI: 10.1007/s12038-015-9506-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article reviews the production of different phenotypes from the same genotype in the same environment by stochastic cellular events, nonlinear mechanisms during patterning and morphogenesis, and probabilistic self-reinforcing circuitries in the adult life. These aspects of phenotypic variation are summarized under the term 'stochastic developmental variation' (SDV) in the following. In the past, SDV has been viewed primarily as a nuisance, impairing laboratory experiments, pharmaceutical testing, and true-to-type breeding. This article also emphasizes the positive biological effects of SDV and discusses implications for genotype-to-phenotype mapping, biological individuation, ecology, evolution, and applied biology. There is strong evidence from experiments with genetically identical organisms performed in narrowly standardized laboratory set-ups that SDV is a source of phenotypic variation in its own right aside from genetic variation and environmental variation. It is obviously mediated by molecular and higher-order epigenetic mechanisms. Comparison of SDV in animals, plants, fungi, protists, bacteria, archaeans, and viruses suggests that it is a ubiquitous and phylogenetically old phenomenon. In animals, it is usually smallest for morphometric traits and highest for life history traits and behaviour. SDV is thought to contribute to phenotypic diversity in all populations but is particularly relevant for asexually reproducing and genetically impoverished populations, where it generates individuality despite genetic uniformity. In each generation, SDV produces a range of phenotypes around a well-adapted target phenotype, which is interpreted as a bet-hedging strategy to cope with the unpredictability of dynamic environments. At least some manifestations of SDV are heritable, adaptable, selectable, and evolvable, and therefore, SDV may be seen as a hitherto overlooked evolution factor. SDV is also relevant for husbandry, agriculture, and medicine because most pathogens are asexuals that exploit this third source of phenotypic variation to modify infectivity and resistance to antibiotics. Since SDV affects all types of organisms and almost all aspects of life, it urgently requires more intense research and a better integration into biological thinking.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 230, D-69120, Heidelberg, Germany,
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21
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Lakatta EG. So! What's aging? Is cardiovascular aging a disease? J Mol Cell Cardiol 2015; 83:1-13. [PMID: 25870157 PMCID: PMC4532266 DOI: 10.1016/j.yjmcc.2015.04.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 12/21/2022]
Abstract
"Inside every old person is a young person wondering what happened." So, what is aging? Aging is a manifestation of progressive, time-dependent failure of molecular mechanisms that create disorder within a system of DNA and its environment (nuclear, cytosolic, tissue, organ, organism, other organisms, society, terra firma, atmosphere, universe). Continuous signaling, transmitted with different kinetics across each of these environments, confers a "mutual enslavement" that creates ordered functions among the components within the system. Accrual of this molecular disorder over time, i.e. during aging, causes progressive changes in the structure and function of the heart and arteries that are quite similar in humans, non-human primates, rabbits and rats that compromise cardiovascular reserve function, and confer a marked risk for incident cardiovascular disease. Nearly all aspects of signaling within the DNA environment system within the heart and arteries become disordered with advancing age: Signals change, as does sensing of the signals, transmission of signals and responses to signals, impaired cell renewal, changes in the proteome due to alterations in genomic transcription, mRNA translation, and proteostasis. The density of some molecules becomes reduced, and post-translational modifications, e.g. oxidation and nitration phosphorylation, lead to altered misfolding and disordered molecular interactions. The stoichiometry and kinetics of enzymatic and those reactions which underlie crucial cardiac and vascular cell functions and robust reserve mechanisms that remove damaged organelles and proteins deteriorate. The CV cells generate an inflammatory defense in an attempt to limit the molecular disorder. The resultant proinflammatory milieu is not executed by "professional" inflammatory cells (i.e. white blood cells), however, but by activation of renin-angiotensin-aldosterone endothelin signaling cascades that leads to endothelial and vascular smooth muscle and cardiac cells' phenotype shifts, resulting in production of inflammatory cytokines. Progressive molecular disorder within the heart and arteries over time leads to an excessive allostatic load on the CV system, that results in an increase and "overshoot" in the inflammatory defense signaling. This age-associated molecular disorder-induced inflammation that accrues in the heart and arteries does not, itself, cause clinical signs or symptoms of CVD. Clinical signs and symptoms of these CVDs begin to emerge, however, when the age-associated inflammation in the heart and arteries exceeds a threshold. Thus, an emerging school of thought is that accelerated age-associated alterations within the heart and arteries, per se, ought to be considered to be a type of CVD, because the molecular disorder and the inflammatory milieu it creates within the heart and arteries with advancing age are the roots of the pathophysiology of most cardiovascular diseases, e.g. athersclerosis and hypertension. Because many effects of aging on the CV system can be delayed or attenuated by changes in lifestyle, e.g. diet and exercise, or by presently available drugs, e.g. those that suppress Ang II signaling, CV aging is a promising frontier in preventive cardiology that is not only ripe for, but also in dire need of attention! There is an urgency to incorporate the concept of cardiovascular aging as a disease into clinical medicine. But, sadly, the reality of the age-associated molecular disorder within the heart and ateries has, for the most part, been kept outside of mainstream clinical medicine. This article is part of a Special Issue entitled CV Aging.
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Affiliation(s)
- Edward G Lakatta
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, Biomedical Research Center, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA.
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22
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Day K, Waite LL, Thalacker-Mercer A, West A, Bamman MM, Brooks JD, Myers RM, Absher D. Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol 2015; 14:R102. [PMID: 24034465 PMCID: PMC4053985 DOI: 10.1186/gb-2013-14-9-r102] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/22/2013] [Indexed: 12/30/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that changes with age in human tissues, although the mechanisms and specificity of this process are still poorly understood. We compared CpG methylation changes with age across 283 human blood, brain, kidney, and skeletal muscle samples using methylation arrays to identify tissue-specific age effects. Results We found age-associated CpGs (ageCGs) that are both tissue-specific and common across tissues. Tissue-specific ageCGs are frequently located outside CpG islands with decreased methylation, and common ageCGs show the opposite trend. AgeCGs are significantly associated with poorly expressed genes, but those with decreasing methylation are linked with higher tissue-specific expression levels compared with increasing methylation. Therefore, tissue-specific gene expression may protect against common age-dependent methylation. Distinguished from other tissues, skeletal muscle ageCGs are more associated with expression, enriched near genes related to myofiber contraction, and closer to muscle-specific CTCF binding sites. Kidney-specific ageCGs are more increasingly methylated compared to other tissues as measured by affiliation with kidney-specific expressed genes. Underlying chromatin features also mark common and tissue-specific age effects reflective of poised and active chromatin states, respectively. In contrast with decreasingly methylated ageCGs, increasingly methylated ageCGs are also generally further from CTCF binding sites and enriched within lamina associated domains. Conclusions Our data identified common and tissue-specific DNA methylation changes with age that are reflective of CpG landscape and suggests both common and unique alterations within human tissues. Our findings also indicate that a simple epigenetic drift model is insufficient to explain all age-related changes in DNA methylation.
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Kishi S, Bayliss PE, Hanai JI. A prospective epigenetic paradigm between cellular senescence and epithelial-mesenchymal transition in organismal development and aging. Transl Res 2015; 165:241-9. [PMID: 24924348 DOI: 10.1016/j.trsl.2014.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/09/2014] [Accepted: 05/14/2014] [Indexed: 12/17/2022]
Abstract
Epigenetic states can govern the plasticity of a genome to be adaptive to environments where many stress stimuli and insults compromise the homeostatic system with age. Although certain elastic power may autonomously reset, reprogram, rejuvenate, or reverse the organismal aging process, enforced genetic manipulations could at least reset and reprogram epigenetic states beyond phenotypic plasticity and elasticity in cells, which can be further manipulated into organisms. The question, however, remains how we can rejuvenate intrinsic resources and infrastructures in a noninvasive manner, particularly in a whole complex aging organism. Given inevitable increase of cancer with age, presumably any failure of resetting, reprogramming, or even rejuvenation could be a prominent causative factor of malignancy. Accompanied by progressive deteriorations of physiological functions in organisms with advancing age, aging-associated cancer risk may essentially arise from unforeseen complications in cellular senescence. At the cellular level, epithelial-mesenchymal plasticity (dynamic and reversible transitions between epithelial and mesenchymal phenotypic states) is enabled by underlying shifts in epigenetic regulation. Thus, the epithelial-mesenchymal transition (EMT) and its reversal (mesenchymal-epithelial transition [MET]) function as a key of cellular transdifferentiation programs. On the one hand, the EMT-MET process was initially appreciated in developmental biology, but is now attracting increasing attention in oncogenesis and senescence, because the process is involved in the malignant progression vs regression of cancer. On the other hand, senescence is often considered the antithesis of early development, but yet between these 2 phenomena, there may be common factors and governing mechanisms such as the EMT-MET program, to steer toward rejuvenation of the biological aging system, thereby precisely controlling or avoiding cancer through epigenetic interventions.
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Affiliation(s)
- Shuji Kishi
- Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, Florida.
| | - Peter E Bayliss
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jun-Ichi Hanai
- Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts; Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Mass
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24
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Kishi S. Using zebrafish models to explore genetic and epigenetic impacts on evolutionary developmental origins of aging. Transl Res 2014; 163:123-35. [PMID: 24239812 PMCID: PMC3969878 DOI: 10.1016/j.trsl.2013.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/20/2013] [Accepted: 10/21/2013] [Indexed: 01/10/2023]
Abstract
Can we reset, reprogram, rejuvenate, or reverse the organismal aging process? Certain genetic manipulations could at least reset and reprogram epigenetic dynamics beyond phenotypic plasticity and elasticity in cells, which can be manipulated further into organisms. However, in a whole complex aging organism, how can we rejuvenate intrinsic resources and infrastructures in an intact and noninvasive manner? The incidence of diseases increases exponentially with age, accompanied by progressive deteriorations of physiological functions in organisms. Aging-associated diseases are sporadic but essentially inevitable complications arising from senescence. Senescence is often considered the antithesis of early development, but yet there may be factors and mechanisms in common between these 2 phenomena to rejuvenate over the dynamic process of aging. The association between early development and late-onset disease with advancing age is thought to come from a consequence of developmental plasticity, the phenomenon by which one genotype can give rise to a range of physiologically and/or morphologically adaptive states based on diverse epigenotypes in response to intrinsic or extrinsic environmental cues and genetic perturbations. We hypothesized that the future aging process can be predictive based on adaptivity during the early developmental period. Modulating the thresholds and windows of plasticity and its robustness by molecular genetic and chemical epigenetic approaches, we have successfully conducted experiments to isolate zebrafish mutants expressing apparently altered senescence phenotypes during their embryonic and/or larval stages ("embryonic/larval senescence"). Subsequently, at least some of these mutant animals were found to show a shortened life span, whereas others would be expected to live longer into adulthood. We anticipate that previously uncharacterized developmental genes may mediate the aging process and play a pivotal role in senescence. On the other hand, unexpected senescence-related genes might also be involved in the early developmental process and its regulation. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes, genotypes, and epigenotypes that can be linked to the senescence phenotype, which facilitates searching for the evolutionary and developmental origins of aging in vertebrates.
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Affiliation(s)
- Shuji Kishi
- Department of Metabolism & Aging, The Scripps Research Institute, Scripps Florida, Jupiter, Fla.
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25
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Lin SC, Karoly ED, Taatjes DJ. The human ΔNp53 isoform triggers metabolic and gene expression changes that activate mTOR and alter mitochondrial function. Aging Cell 2013; 12:863-72. [PMID: 23734707 DOI: 10.1111/acel.12108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2013] [Indexed: 12/20/2022] Open
Abstract
A naturally occurring p53 isoform that lacks 39 residues at the N-terminus (denoted ΔNp53), when expressed with wild-type p53 (WTp53), forms mixed ΔNp53:WTp53 tetramers and causes accelerated aging in mice. Cellular alterations specific to ΔNp53:WTp53 have been difficult to assess because ΔNp53 and WTp53 coexpression results in tetramer heterogeneity, including formation of contaminating WTp53 tetramers. Based on the p53 tetramer structure, we expressed ΔNp53 and WTp53 as a single transcript that maintained tetramer architecture, ensuring a 2:2 ΔNp53:WTp53 stoichiometry. As expected, ΔNp53:WTp53 tetramers were stable and transcriptionally active in vitro and in cells, largely mimicking the function of WTp53 tetramers. Microarray analyses, however, revealed about 80 genes whose expression was altered twofold or more in ΔNp53:WTp53 cells. Moreover, global metabolomic profiling quantitated hundreds of biochemicals across different experiments (WTp53, ΔNp53:WTp53, plus controls). When evaluated collectively, these data suggested altered mTOR signaling and mitochondrial function-each canonical regulators of longevity-in cells expressing ΔNp53:WTp53 vs. WTp53. Increased levels of free amino acids, increased expression of IRS-1, and decreased expression of INPP5D/SHIP-1 suggested activated mTOR signaling in ΔNp53:WTp53 cells; this was confirmed upon comparative analyses of several mTOR pathway intermediates. We also observed changes in mitochondrial function in ΔNp53:WTp53 cells, which correlated with increased MARS2 expression and increased levels of carnitine, acetyl CoA, ATP, and Krebs cycle intermediates. Finally, increased levels of succinate and 2-hydroxyglutarate indicate potential epigenetic means to propagate ΔNp53:WTp53-induced gene expression changes to cell progeny. This may be especially important for aging, as biological effects manifest over time.
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Affiliation(s)
- Shih-Chieh Lin
- Department of Chemistry and Biochemistry; University of Colorado; Boulder; CO 80303; USA
| | | | - Dylan J. Taatjes
- Department of Chemistry and Biochemistry; University of Colorado; Boulder; CO 80303; USA
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26
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Sasaki T, Kishi S. Molecular and chemical genetic approaches to developmental origins of aging and disease in zebrafish. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1362-70. [PMID: 23660559 DOI: 10.1016/j.bbadis.2013.04.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 12/13/2022]
Abstract
The incidence of diseases increases rapidly with age, accompanied by progressive deteriorations of physiological functions in organisms. Aging-associated diseases are sporadic but mostly inevitable complications arising from senescence. Senescence is often considered the antithesis of early development, but yet there may be factors and mechanisms in common between these two phenomena over the dynamic process of aging. The association between early development and late-onset disease with advancing age is thought to come from a consequence of developmental plasticity, the phenomenon by which one genotype can give rise to a range of physiologically and/or morphologically adaptive states in response to different environmental or genetic perturbations. On the one hand, we hypothesized that the future aging process can be predictive based on adaptivity during the early developmental period. Modulating the thresholds of adaptive plasticity by chemical genetic approaches, we have been investigating whether any relationship exists between the regulatory mechanisms that function in early development and in senescence using the zebrafish (Danio rerio), a small freshwater fish and a useful model animal for genetic studies. We have successfully conducted experiments to isolate zebrafish mutants expressing apparently altered senescence phenotypes during embryogenesis ("embryonic senescence"), subsequently showing shortened lifespan in adulthoods. We anticipate that previously uncharacterized developmental genes may mediate the aging process and play a pivotal role in senescence. On the other hand, unexpected senescence-related genes might also be involved in the early developmental process and regulation. The ease of manipulation using the zebrafish system allows us to conduct an exhaustive exploration of novel genes and small molecular compounds that can be linked to the senescence phenotype, and thereby facilitates searching for the evolutionary and developmental origins of aging in vertebrates. This article is part of a Special Issue entitled: Animal Models of Disease.
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Affiliation(s)
- Tomoyuki Sasaki
- Department of Metabolism & Aging, The Scripps Research Institute, USA
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27
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Hypothalamic programming of systemic ageing involving IKK-β, NF-κB and GnRH. Nature 2013; 497:211-6. [PMID: 23636330 PMCID: PMC3756938 DOI: 10.1038/nature12143] [Citation(s) in RCA: 609] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 04/02/2013] [Indexed: 01/02/2023]
Abstract
Ageing is a result of gradual and overall functional deteriorations across the body; however, it is unknown whether an individual tissue primarily works to mediate the ageing progress and control lifespan. Here we show that the hypothalamus is important for the development of whole-body ageing in mice, and that the underlying basis involves hypothalamic immunity mediated by IκB kinase-β (IKK-β), nuclear factor κB (NF-κB) and related microglia-neuron immune crosstalk. Several interventional models were developed showing that ageing retardation and lifespan extension are achieved in mice by preventing ageing-related hypothalamic or brain IKK-β and NF-κB activation. Mechanistic studies further revealed that IKK-β and NF-κB inhibit gonadotropin-releasing hormone (GnRH) to mediate ageing-related hypothalamic GnRH decline, and GnRH treatment amends ageing-impaired neurogenesis and decelerates ageing. In conclusion, the hypothalamus has a programmatic role in ageing development via immune-neuroendocrine integration, and immune inhibition or GnRH restoration in the hypothalamus/brain represent two potential strategies for optimizing lifespan and combating ageing-related health problems.
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BYRNE JAMESA. NUCLEAR REPROGRAMMING AND THE CURRENT CHALLENGES IN ADVANCING PERSONALIZED PLURIPOTENT STEM CELL-BASED THERAPIES. ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1568558612300028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Talens RP, Christensen K, Putter H, Willemsen G, Christiansen L, Kremer D, Suchiman HED, Slagboom PE, Boomsma DI, Heijmans BT. Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs. Aging Cell 2012; 11:694-703. [PMID: 22621408 PMCID: PMC3399918 DOI: 10.1111/j.1474-9726.2012.00835.x] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The accumulation of epigenetic changes was proposed to contribute to the age-related increase in the risk of most common diseases. In this study on 230 monozygotic twin pairs (MZ pairs), aged 18–89 years, we investigated the occurrence of epigenetic changes over the adult lifespan. Using mass spectrometry, we investigated variation in global (LINE1) DNA methylation and in DNA methylation at INS, KCNQ1OT1, IGF2, GNASAS, ABCA1, LEP, and CRH, candidate loci for common diseases. Except for KCNQ1OT1, interindividual variation in locus-specific DNA methylation was larger in old individuals than in young individuals, ranging from 1.2-fold larger at ABCA1 (P = 0.010) to 1.6-fold larger at INS (P = 3.7 × 10−07). Similarly, there was more within-MZ-pair discordance in old as compared with young MZ pairs, except for GNASAS, ranging from an 8% increase in discordance each decade at CRH (P = 8.9 × 10−06) to a 16% increase each decade at LEP (P = 2.0 × 10−08). Still, old MZ pairs with strikingly similar DNA methylation were also observed at these loci. After 10-year follow-up in elderly twins, the variation in DNA methylation showed a similar pattern of change as observed cross-sectionally. The age-related increase in methylation variation was generally attributable to unique environmental factors, except for CRH, for which familial factors may play a more important role. In conclusion, sustained epigenetic differences arise from early adulthood to old age and contribute to an increasing discordance of MZ twins during aging.
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Affiliation(s)
- Rudolf P. Talens
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kaare Christensen
- The Danish Aging Research Center and The Danish Twin Registry, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Hein Putter
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Lene Christiansen
- The Danish Aging Research Center and The Danish Twin Registry, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Dennis Kremer
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - H. Eka D. Suchiman
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P. Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Bastiaan T. Heijmans
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
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Martin GM. Stochastic modulations of the pace and patterns of ageing: impacts on quasi-stochastic distributions of multiple geriatric pathologies. Mech Ageing Dev 2012; 133:107-11. [PMID: 21963385 PMCID: PMC3403812 DOI: 10.1016/j.mad.2011.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 11/22/2022]
Abstract
All phenotypes result from interactions between Nature, Nurture and Chance. The constitutional genome is clearly the dominant factor in explaining the striking differences in the pace and patterns of ageing among species. We are now in a position to reveal salient features underlying these differential modulations, which are likely to be dominated by regulatory domains. By contrast, I shall argue that stochastic events are the major players underlying the surprisingly large intra-specific variations in lifespan and healthspan. I shall review well established as well as more speculative categories of chance events--somatic mutations, protein synthesis error catastrophe and variegations of gene expression (epigenetic drift), with special emphasis upon the latter. I shall argue that stochastic drifts in variegated gene expression are the major contributors to intra-specific differences in the pace and patterns of ageing within members of the same species. They may be responsible for the quasi-stochastic distributions of major types of geriatric pathologies, including the "big three" of Alzheimer's disease, atherosclerosis and, via the induction of hyperplasias, cancer. They may be responsible for altered stoichiometries of heteromultimeric mitochondrial complexes, potentially leading to such disorders as sarcopenia, nonischemic cardiomyopathy and Parkinson's disease.
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Affiliation(s)
- George M Martin
- Department of Pathology, University of Washington, Seattle, WA 98195-7470, USA.
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Rando TA, Chang HY. Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock. Cell 2012; 148:46-57. [PMID: 22265401 DOI: 10.1016/j.cell.2012.01.003] [Citation(s) in RCA: 344] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Indexed: 12/30/2022]
Abstract
The underlying cause of aging remains one of the central mysteries of biology. Recent studies in several different systems suggest that not only may the rate of aging be modified by environmental and genetic factors, but also that the aging clock can be reversed, restoring characteristics of youthfulness to aged cells and tissues. This Review focuses on the emerging biology of rejuvenation through the lens of epigenetic reprogramming. By defining youthfulness and senescence as epigenetic states, a framework for asking new questions about the aging process emerges.
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Affiliation(s)
- Thomas A Rando
- The Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Davey Smith G. Epigenetics for the masses: more than Audrey Hepburn and yellow mice? Int J Epidemiol 2012. [DOI: 10.1093/ije/dys030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Martin GM. Commentary: a gerontological perspective on Klaus Gärtner's discovery that phenotypic variability of mammals is driven by stochastic events. Int J Epidemiol 2012; 41:354-6. [PMID: 22266058 DOI: 10.1093/ije/dyr224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
In this contribution to the series of reflective essays celebrating the 25th anniversary of The FASEB Journal, our task is to assess the growth of research on the biology of aging during this period and to suggest where we might be heading during the next 25 yr. A review of the literature suggests a healthy acceleration of progress during the past decade, perhaps largely due to progress on the genetics of longevity of model organisms. Progress on the genetics of health span in these model organisms has lagged, however. Research on the genetic basis of the remarkable interspecific variations in life span has only recently begun to be seriously addressed. The spectacular advances in genomics should greatly accelerate progress. Research on environmental effects on life span and health span needs to be accelerated. Stochastic variations in gene expression in aging have only recently been addressed. These can lead to random departures from homeostasis during aging.-Martin, G. M. The biology of aging: 1985-2010 and beyond.
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Affiliation(s)
- George M Martin
- Departments of Pathology and Genome Sciences, University of Washington, Seattle, Washington, 98195-7470, USA.
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Smith GD. Epidemiology, epigenetics and the 'Gloomy Prospect': embracing randomness in population health research and practice. Int J Epidemiol 2011; 40:537-62. [PMID: 21807641 DOI: 10.1093/ije/dyr117] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Epidemiologists aim to identify modifiable causes of disease, this often being a prerequisite for the application of epidemiological findings in public health programmes, health service planning and clinical medicine. Despite successes in identifying causes, it is often claimed that there are missing additional causes for even reasonably well-understood conditions such as lung cancer and coronary heart disease. Several lines of evidence suggest that largely chance events, from the biographical down to the sub-cellular, contribute an important stochastic element to disease risk that is not epidemiologically tractable at the individual level. Epigenetic influences provide a fashionable contemporary explanation for such seemingly random processes. Chance events-such as a particular lifelong smoker living unharmed to 100 years-are averaged out at the group level. As a consequence population-level differences (for example, secular trends or differences between administrative areas) can be entirely explicable by causal factors that appear to account for only a small proportion of individual-level risk. In public health terms, a modifiable cause of the large majority of cases of a disease may have been identified, with a wild goose chase continuing in an attempt to discipline the random nature of the world with respect to which particular individuals will succumb. The quest for personalized medicine is a contemporary manifestation of this dream. An evolutionary explanation of why randomness exists in the development of organisms has long been articulated, in terms of offering a survival advantage in changing environments. Further, the basic notion that what is near-random at one level may be almost entirely predictable at a higher level is an emergent property of many systems, from particle physics to the social sciences. These considerations suggest that epidemiological approaches will remain fruitful as we enter the decade of the epigenome.
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Affiliation(s)
- George Davey Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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Kishi S. The search for evolutionary developmental origins of aging in zebrafish: A novel intersection of developmental and senescence biology in the zebrafish model system. ACTA ACUST UNITED AC 2011; 93:229-48. [DOI: 10.1002/bdrc.20217] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Klauke K, de Haan G. Polycomb group proteins in hematopoietic stem cell aging and malignancies. Int J Hematol 2011; 94:11-23. [PMID: 21523335 DOI: 10.1007/s12185-011-0857-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/06/2011] [Indexed: 12/31/2022]
Abstract
Protection of the transcriptional "stemness" network is important to maintain a healthy hematopoietic stem cells (HSCs) compartment during the lifetime of the organism. Recent evidence shows that fundamental changes in the epigenetic status of HSCs might be one of the driving forces behind many age-related HSC changes and might pave the way for HSC malignant transformation and subsequent leukemia development, the incidence of which increases exponentially with age. Polycomb group (PcG) proteins are key epigenetic regulators of HSC cellular fate decisions and are often found to be misregulated in human hematopoietic malignancies. In this review, we speculate that PcG proteins balance HSC aging against the risk of developing cancer, since a disturbance in PcG genes and proteins affects several important cellular processes such as cell fate decisions, senescence, apoptosis, and DNA damage repair.
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Affiliation(s)
- Karin Klauke
- Department of Cell Biology, Section of Stem Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,European Research Institute on the Biology of Ageing (ERIBA), Groningen, The Netherlands
| | - Gerald de Haan
- Department of Cell Biology, Section of Stem Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,European Research Institute on the Biology of Ageing (ERIBA), Groningen, The Netherlands.
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Hjelmeland LM. Dark matters in AMD genetics: epigenetics and stochasticity. Invest Ophthalmol Vis Sci 2011; 52:1622-31. [PMID: 21429863 DOI: 10.1167/iovs.10-6765] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Leonard M Hjelmeland
- Department of Ophthalmology and Vision Science, School of Medicine, University of California, Davis, California, USA.
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Thornburg KL, Shannon J, Thuillier P, Turker MS. In utero life and epigenetic predisposition for disease. ADVANCES IN GENETICS 2010; 71:57-78. [PMID: 20933126 DOI: 10.1016/b978-0-12-380864-6.00003-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Regulatory regions of the human genome can be modified through epigenetic processes during prenatal life to make an individual more likely to suffer chronic diseases when they reach adulthood. The modification of chromatin and DNA contributes to a larger well-documented process known as "programming" whereby stressors in the womb give rise to adult onset diseases, including cancer. It is now well known that death from ischemic heart disease is related to birth weight; the lower the birth weight, the higher the risk of death from cardiovascular disease as well as type 2 diabetes and osteoporosis. Recent epidemiological data link rapid growth in the womb to metabolic disease and obesity and also to breast and lung cancers. There is increasing evidence that "marked" regions of DNA can become "unmarked" under the influence of dietary nutrients. This gives hope for reversing propensities for cancers and other diseases that were acquired in the womb. For several cancers, the size and shape of the placenta are associated with a person's cardiovascular and cancer risks as are maternal body mass index and height. The features of placental growth and nutrient transport properties that lead to adult disease have been little studied. In conclusion, several cancers have their origins in the womb, including lung and breast cancer. More research is needed to determine the epigenetic processes that underlie the programming of these diseases.
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Affiliation(s)
- Kent L Thornburg
- Department of Medicine, Division of Cardiovascular Medicine, Oregon Health & Science University, Portland, Oregon, USA
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Tchkonia T, Morbeck DE, Von Zglinicki T, Van Deursen J, Lustgarten J, Scrable H, Khosla S, Jensen MD, Kirkland JL. Fat tissue, aging, and cellular senescence. Aging Cell 2010; 9:667-84. [PMID: 20701600 PMCID: PMC2941545 DOI: 10.1111/j.1474-9726.2010.00608.x] [Citation(s) in RCA: 740] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fat tissue, frequently the largest organ in humans, is at the nexus of mechanisms involved in longevity and age-related metabolic dysfunction. Fat distribution and function change dramatically throughout life. Obesity is associated with accelerated onset of diseases common in old age, while fat ablation and certain mutations affecting fat increase life span. Fat cells turn over throughout the life span. Fat cell progenitors, preadipocytes, are abundant, closely related to macrophages, and dysdifferentiate in old age, switching into a pro-inflammatory, tissue-remodeling, senescent-like state. Other mesenchymal progenitors also can acquire a pro-inflammatory, adipocyte-like phenotype with aging. We propose a hypothetical model in which cellular stress and preadipocyte overutilization with aging induce cellular senescence, leading to impaired adipogenesis, failure to sequester lipotoxic fatty acids, inflammatory cytokine and chemokine generation, and innate and adaptive immune response activation. These pro-inflammatory processes may amplify each other and have systemic consequences. This model is consistent with recent concepts about cellular senescence as a stress-responsive, adaptive phenotype that develops through multiple stages, including major metabolic and secretory readjustments, which can spread from cell to cell and can occur at any point during life. Senescence could be an alternative cell fate that develops in response to injury or metabolic dysfunction and might occur in nondividing as well as dividing cells. Consistent with this, a senescent-like state can develop in preadipocytes and fat cells from young obese individuals. Senescent, pro-inflammatory cells in fat could have profound clinical consequences because of the large size of the fat organ and its central metabolic role.
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Affiliation(s)
- Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
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Pincus Z, Slack FJ. Developmental biomarkers of aging in Caenorhabditis elegans. Dev Dyn 2010; 239:1306-14. [PMID: 20151474 DOI: 10.1002/dvdy.22224] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The developmental process of the nematode Caenorhabditis elegans is famously invariant; however, these animals have surprisingly variable lifespans, even in extremely homogenous environments. Inter-individual differences in muscle-function decline, accumulation of lipofuscin in the gut, internal growth of food bacteria, and ability to mobilize heat-shock responses all appear to be predictive of a nematode's remaining lifespan; whether these are causal, or mere correlates of individual decline and death, has yet to be determined. Moreover, few "upstream" causes of inter-individual variability have been identified. It may be the case that variability in lifespan is entirely due to stochastic damage accumulation; alternately, perhaps such variability has a developmental origin and/or genes involved in developmental canalization also act to buffer phenotypic heterogeneity later in life. We review these two hypotheses with an eye toward whether they can be experimentally differentiated.
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Affiliation(s)
- Zachary Pincus
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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Vogt G. Suitability of the clonal marbled crayfish for biogerontological research: a review and perspective, with remarks on some further crustaceans. Biogerontology 2010; 11:643-69. [PMID: 20582627 DOI: 10.1007/s10522-010-9291-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 06/11/2010] [Indexed: 12/20/2022]
Abstract
This article examines the suitability of the parthenogenetic marbled crayfish for research on ageing and longevity. The marbled crayfish is an emerging laboratory model for development, epigenetics and toxicology that produces up to 400 genetically identical siblings per batch. It is easily cultured, has an adult size of 4-9 cm, a generation time of 6-7 months and a life span of 2-3 years. Experimental data and biological peculiarities like isogenicity, direct development, indeterminate growth, high regeneration capacity and negligible senescence suggest that the marbled crayfish is particularly suitable to investigate the dependency of ageing and longevity from non-genetic factors such as stochastic developmental variation, allocation of metabolic resources, damage and repair, caloric restriction and social stress. It is also well applicable to examine alterations of the epigenetic code with increasing age and to identify mechanisms that keep stem cells active until old age. As a representative of the sparsely investigated crustaceans and of animals with indeterminate growth and extended brood care the marbled crayfish may even contribute to evolutionary theories of ageing and longevity. Some relatives are recommended as substitutes for investigation of topics, for which the marbled crayfish is less suitable like genetics of ageing and achievement of life spans of decades under conditions of low food and low temperature. Research on ageing in the marbled crayfish and its relatives is of practical relevance for crustacean fisheries and aquaculture and may offer starting points for the development of novel anti-ageing interventions in humans.
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Affiliation(s)
- Günter Vogt
- Department of Zoology, University of Heidelberg, Germany.
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