101
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Nrf2: Molecular and epigenetic regulation during aging. Ageing Res Rev 2018; 47:31-40. [PMID: 29913211 DOI: 10.1016/j.arr.2018.06.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022]
Abstract
Increase in life-span is commonly related with age-related diseases and with gradual loss of genomic, proteomic and metabolic integrity. Nrf2 (Nuclear factor-erythroid 2-p45 derived factor 2) controls the expression of genes whose products include antioxidant proteins, detoxifying enzymes, drug transporters and numerous cytoprotective proteins. Several experimental approaches have evaluated the potential regulation of the transcription factor Nrf2 to enhance the expression of genes that contend against accumulative oxidative stress and promote healthy aging. Negative regulators of Nrf2 that act preventing it´s binding to DNA-responsive elements, have been identified in young and adult animal models. However, it is not clearly established if Nrf2 decreased activity in several models of aging results from disruption of that regulation. In this review, we present a compilation of evidences showing that changes in the levels or activity of Keap1 (Kelch-like ECH associated protein 1), GSK-3β (glycogen synthase kinase-3), Bach1, p53, Hrd1 (E3 ubiquitin ligase) and miRNAs might impact on Nrf2 activity during elderly. We conclude that understanding Nrf2 regulatory mechanisms is essential to develop a rational strategy to prevent the loss of cellular protection response during aging.
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102
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Shinozaki G, Braun PR, Hing BWQ, Ratanatharathorn A, Klisares MJ, Duncan GN, Jellison SS, Heinzman JT, Nagahama Y, Close L, Sabbagh S, Dlouhy BJ, Howard MA, Kawasaki H, Cho HR. Epigenetics of Delirium and Aging: Potential Role of DNA Methylation Change on Cytokine Genes in Glia and Blood Along With Aging. Front Aging Neurosci 2018; 10:311. [PMID: 30405391 PMCID: PMC6206747 DOI: 10.3389/fnagi.2018.00311] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/14/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Delirium in elderly patients is common and dangerous. Major risk factors include aging and exogenous insults, such as infection or surgery. In animal models, aging enhances pro-inflammatory cytokine release from microglia in response to exogenous insults. The epigenetic mechanism DNA methylation (DNAm) regulates gene expression and changes with age. Older individuals may have methylation changes that influence the increased cytokine upon insult, but the degree to which aging affects DNAm of cytokine genes is not fully understood. Methods: The relationship between DNAm and aging of pro-inflammatory cytokine genes (TNF-alpha, IL1-beta, IL-6) was investigated using methylation array data in two cohorts. Brain and blood samples were collected from a neurosurgery cohort (NSG) of 21 subjects who underwent brain resection. A second cohort, the Grady Trauma Project (GTP), included blood samples from 265 subjects. Results: In the NSG cohort, a significant negative correlation between age and DNAm in brain was found at a CpG in IL-6. With the GTP dataset, significant negative correlations between age and DNAm were seen at most of the CpGs in TNF-alpha. Also, TNF-Alpha expression increases with age. These GTP DNAm correlations were also nominally significant in NSG blood samples. In neuronal negative NSG brain tissue, a similar negative trend was observed. Conclusions: With aging, a decrease in DNAm of cytokines gene CpGs in glia and blood was seen. As this can affect their expression, additional research is needed to fully elucidate the role of DNAm in aging and how it may influence the pathogenesis of delirium.
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Affiliation(s)
- Gen Shinozaki
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Patricia R. Braun
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Benjamin W. Q. Hing
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Andrew Ratanatharathorn
- Department of Epidemiology, School of Public Health, Columbia University Medical Center, Columbia University, New York, NY, United States
| | - Mason J. Klisares
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gabrielle N. Duncan
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Sydney S. Jellison
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Jonathan T. Heinzman
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Yasunori Nagahama
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Liesl Close
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Sayeh Sabbagh
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Brian J. Dlouhy
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Matthew A. Howard
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa, Carver College of Medicine, Iowa City, IA, United States
| | - Hyunkeun R. Cho
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
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103
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Goronzy JJ, Hu B, Kim C, Jadhav RR, Weyand CM. Epigenetics of T cell aging. J Leukoc Biol 2018; 104:691-699. [PMID: 29947427 PMCID: PMC6162101 DOI: 10.1002/jlb.1ri0418-160r] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 02/06/2023] Open
Abstract
T cells are a heterogeneous population of cells that differ in their differentiation stages. Functional states are reflected in the epigenome that confers stability in cellular identity and is therefore important for naïve as well as memory T cell function. In many cellular systems, changes in chromatin structure due to alterations in histone expression, histone modifications and DNA methylation are characteristic of the aging process and cause or at least contribute to cellular dysfunction in senescence. Here, we review the epigenetic changes in T cells that occur with age and discuss them in the context of canonical epigenetic marks in aging model systems as well as recent findings of chromatin accessibility changes in T cell differentiation. Remarkably, transcription factor networks driving T cell differentiation account for many of the age-associated modifications in chromatin structures suggesting that loss of quiescence and activation of differentiation pathways are major components of T cell aging.
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Affiliation(s)
- Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Bin Hu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Chulwoo Kim
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Rohit R. Jadhav
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, United States
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104
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DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
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105
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López-Lluch G, Hernández-Camacho JD, Fernández-Ayala DJM, Navas P. Mitochondrial dysfunction in metabolism and ageing: shared mechanisms and outcomes? Biogerontology 2018; 19:461-480. [PMID: 30143941 DOI: 10.1007/s10522-018-9768-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/21/2018] [Indexed: 12/15/2022]
Abstract
Mitochondria are key in the metabolism of aerobic organisms and in ageing progression and age-related diseases. Mitochondria are essential for obtaining ATP from glucose and fatty acids but also in many other essential functions in cells including aminoacids metabolism, pyridine synthesis, phospholipid modifications and calcium regulation. On the other hand, the activity of mitochondria is also the principal source of reactive oxygen species in cells. Ageing and chronic age-related diseases are associated with the deregulation of cell metabolism and dysfunction of mitochondria. Cell metabolism is controlled by three major nutritional sensors: mTOR, AMPK and Sirtuins. These factors control mitochondrial biogenesis and dynamics by regulating fusion, fission and turnover through mito- and autophagy. A complex interaction between the activity of these nutritional sensors, mitochondrial biogenesis rate and dynamics exists and affect ageing, age-related diseases including metabolic disease. Further, mitochondria maintain a constant communication with nucleus modulating gene expression and modifying epigenetics. In this review we highlight the importance of mitochondria in ageing and the repercussion in the progression of age-related diseases and metabolic disease.
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Affiliation(s)
- Guillermo López-Lluch
- Centro Andaluz de Biología del Desarrollo, CABD-CSIC, CIBERER, Instituto de Salud Carlos III, Universidad Pablo de Olavide, Carretera de Utrera km. 1, 41013, Seville, Spain.
| | - Juan Diego Hernández-Camacho
- Centro Andaluz de Biología del Desarrollo, CABD-CSIC, CIBERER, Instituto de Salud Carlos III, Universidad Pablo de Olavide, Carretera de Utrera km. 1, 41013, Seville, Spain
| | - Daniel J Moreno Fernández-Ayala
- Centro Andaluz de Biología del Desarrollo, CABD-CSIC, CIBERER, Instituto de Salud Carlos III, Universidad Pablo de Olavide, Carretera de Utrera km. 1, 41013, Seville, Spain
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo, CABD-CSIC, CIBERER, Instituto de Salud Carlos III, Universidad Pablo de Olavide, Carretera de Utrera km. 1, 41013, Seville, Spain
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106
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Kochmanski J, Marchlewicz EH, Cavalcante RG, Sartor MA, Dolinoy DC. Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood. Epigenetics 2018; 13:779-792. [PMID: 30079798 PMCID: PMC6224215 DOI: 10.1080/15592294.2018.1507198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/13/2018] [Accepted: 07/25/2018] [Indexed: 01/10/2023] Open
Abstract
DNA methylation at cytosine-phosphate-guanine (CpG) dinucleotides changes as a function of age in humans and animal models, a process that may contribute to chronic disease development. Recent studies have investigated the role of an oxidized form of DNA methylation - 5-hydroxymethylcytosine (5hmC) - in the epigenome, but its contribution to age-related DNA methylation remains unclear. We tested the hypothesis that 5hmC changes with age, but in a direction opposite to 5-methylcytosine (5mC), potentially playing a distinct role in aging. To characterize epigenetic aging, genome-wide 5mC and 5hmC were measured in longitudinal blood samples (2, 4, and 10 months of age) from isogenic mice using two sequencing methods - enhanced reduced representation bisulfite sequencing and hydroxymethylated DNA immunoprecipitation sequencing. Examining the epigenome by age, we identified 28,196 unique differentially methylated CpGs (DMCs) and 8,613 differentially hydroxymethylated regions (DHMRs). Mouse blood showed a general pattern of epigenome-wide hypermethylation and hypo-hydroxymethylation with age. Comparing age-related DMCs and DHMRs, 1,854 annotated genes showed both differential 5mC and 5hmC, including one gene - Nfic - at five CpGs in the same 250 bp chromosomal region. At this region, 5mC and 5hmC levels both decreased with age. Reflecting these age-related epigenetic changes, Nfic RNA expression in blood decreased with age, suggesting that age-related regulation of this gene may be driven by 5hmC, not canonical DNA methylation. Combined, our genome-wide results show age-related differential 5mC and 5hmC, as well as some evidence that changes in 5hmC may drive age-related DNA methylation and gene expression.
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Affiliation(s)
- Joseph Kochmanski
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth H. Marchlewicz
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Raymond G. Cavalcante
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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107
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Harper EI, Sheedy EF, Stack MS. With Great Age Comes Great Metastatic Ability: Ovarian Cancer and the Appeal of the Aging Peritoneal Microenvironment. Cancers (Basel) 2018; 10:E230. [PMID: 29996539 PMCID: PMC6070816 DOI: 10.3390/cancers10070230] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/22/2022] Open
Abstract
Age is one of the biggest risk factors for ovarian cancer. Older women have higher rates of diagnosis and death associated with the disease. In mouse models, it was shown that aged mice had greater tumor burden than their younger counterparts when intraperitoneally injected with ovarian tumor cells. While very few papers have been published looking at the direct link between ovarian cancer metastasis and age, there is a wealth of information on how age affects metastatic microenvironments. Mesothelial cells, the peritoneal extracellular matrix (ECM), fibroblasts, adipocytes and immune cells all exhibit distinct changes with age. The aged peritoneum hosts a higher number of senescent cells than its younger counterpart, in both the mesothelium and the stroma. These senescent cells promote an inflammatory profile and overexpress Matrix Metalloproteinases (MMPs), which remodel the ECM. The aged ECM is also modified by dysregulated collagen and laminin synthesis, increases in age-related crosslinking and increasing ovarian cancer invasion into the matrix. These changes contribute to a vastly different microenvironment in young and aged models for circulating ovarian cancer cells, creating a more welcoming “soil”.
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Affiliation(s)
- Elizabeth I Harper
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46617, USA.
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA.
- Integrated Biomedical Sciences Program, University of Notre Dame, South Bend, IN 46617, USA.
| | - Emma F Sheedy
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA.
- Department of Mathematics, University of Notre Dame, South Bend, IN 46617, USA.
| | - M Sharon Stack
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46617, USA.
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46617, USA.
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108
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109
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Jung SE, Shin KJ, Lee HY. DNA methylation-based age prediction from various tissues and body fluids. BMB Rep 2018; 50:546-553. [PMID: 28946940 PMCID: PMC5720467 DOI: 10.5483/bmbrep.2017.50.11.175] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Indexed: 12/13/2022] Open
Abstract
Aging is a natural and gradual process in human life. It is influenced by heredity, environment, lifestyle, and disease. DNA methylation varies with age, and the ability to predict the age of donor using DNA from evidence materials at a crime scene is of considerable value in forensic investigations. Recently, many studies have reported age prediction models based on DNA methylation from various tissues and body fluids. Those models seem to be very promising because of their high prediction accuracies. In this review, the changes of age-associated DNA methylation and the age prediction models for various tissues and body fluids were examined, and then the applicability of the DNA methylation-based age prediction method to the forensic investigations was discussed. This will improve the understandings about DNA methylation markers and their potential to be used as biomarkers in the forensic field, as well as the clinical field.
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Affiliation(s)
- Sang-Eun Jung
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
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110
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Flunkert J, Maierhofer A, Dittrich M, Müller T, Horvath S, Nanda I, Haaf T. Genetic and epigenetic changes in clonal descendants of irradiated human fibroblasts. Exp Cell Res 2018; 370:322-332. [PMID: 29964050 DOI: 10.1016/j.yexcr.2018.06.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for variation in radiation sensitivity, all experiments were performed with two different fibroblast strains. After a single X-ray dose of 2 Gy more than half of the irradiated clones exhibited radiation-induced genome instability (RIGI). Irradiated clones displayed an increased rate of loss of chromosome Y (LOY) and copy number variations (CNVs), compared to controls. CNV breakpoints clustered in specific chromosome regions, in particular 3p14.2 and 7q11.21, coinciding with common fragile sites. CNVs affecting the FHIT gene in FRA3B were observed in independent unstable clones and may drive RIGI. Bisulfite pyrosequencing of control clones and the respective primary culture revealed global hypomethylation of ALU, LINE-1, and alpha-satellite repeats as well as rDNA hypermethylation during in vitro ageing. Irradiated clones showed further reduced ALU and alpha-satellite methylation and increased rDNA methylation, compared to controls. Methylation arrays identified several hundred differentially methylated genes and several enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic (LOY and CNVs) and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis. We did not observe epigenetic differences between stable and unstable irradiated clones. The fact that the DNA methylation (DNAm) age of clones derived from the same primary culture varied greatly suggests that DNAm age of a single cell (represented by a clone) can be quite different from the DNAm age of a tissue. We propose that DNAm age reflects the emergent property of a large number of individual cells whose respective DNAm ages can be highly variable.
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Affiliation(s)
- Julia Flunkert
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.
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111
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Freire-Aradas A, Phillips C, Girón-Santamaría L, Mosquera-Miguel A, Gómez-Tato A, Casares de Cal MÁ, Álvarez-Dios J, Lareu MV. Tracking age-correlated DNA methylation markers in the young. Forensic Sci Int Genet 2018; 36:50-59. [PMID: 29933125 DOI: 10.1016/j.fsigen.2018.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 01/03/2023]
Abstract
DNA methylation is the most extensively studied epigenetic signature, with a large number of studies reporting age-correlated CpG sites in overlapping genes. However, most of these studies lack sample coverage of individuals under 18 years old and therefore little is known about the progression of DNA methylation patterns in children and adolescents. In the present study we aimed to select candidate age-correlated DNA methylation markers based on public datasets from Illumina BeadChip arrays and previous publications, then to explore the resulting markers in 209 blood samples from donors aged between 2 to 18 years old using the EpiTYPER® DNA methylation analysis system. Results from our analyses identified six genes highly correlated with age in the young, in particular the gene KCNAB3, which indicates its potential as a highly informative and specific age biomarker for childhood and adolescence. We outline a preliminary age prediction model based on quantile regression that uses data from the six CpG sites most strongly correlated with age ranges extended to include children and adolescents.
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Affiliation(s)
- Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Lorena Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Ana Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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112
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Stoccoro A, Coppedè F. Role of epigenetics in Alzheimer's disease pathogenesis. Neurodegener Dis Manag 2018; 8:181-193. [PMID: 29888987 DOI: 10.2217/nmt-2018-0004] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Advances in molecular biology technologies have allowed uncovering the role of epigenetic regulation in several complex diseases, such as cancer and neurodegenerative disorders. Although the role of epigenetic mechanisms in Alzheimer's disease is still little understood, recent findings clearly show that such mechanisms are dysregulated during disease progression, already in its early stages. However, it is not clear if the observed epigenetic changes represent a cause or a consequence of the disease. Promising results are emerging from studies performed in peripheral blood DNA that could provide early biomarkers of the pathology. Moreover, given the dynamic nature of the epigenetic marks, intense research is carried out to investigate the therapeutic efficacy of compounds exerting epigenetic properties.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research & New Technologies in Medicine & Surgery, Section of Medical Genetics, University of Pisa, Via Roma 55, 56126 Pisa, Italy.,Department of Medical Biotechnologies, Doctoral School in Genetics, Oncology & Clinical Medicine, University of Siena, Siena, Italy
| | - Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Section of Medical Genetics, University of Pisa, Via Roma 55, 56126 Pisa, Italy
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113
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Lu S, Niu Z, Chen Y, Tu Q, Zhang Y, Chen W, Tong W, Zhang Z. Repetitive Element DNA Methylation is Associated with Menopausal Age. Aging Dis 2018; 9:435-443. [PMID: 29896431 PMCID: PMC5988598 DOI: 10.14336/ad.2017.0810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/10/2017] [Indexed: 12/21/2022] Open
Abstract
To investigate associations between the age of menopause and the DNA methylation levels of two repetitive elements, Alu and LINE-1, we performed plasma DNA extraction on 161 subjects and serum cell-free DNA extraction on 120 subjects. We grouped women by menopausal age as follows: ≤ 48 years (earlier menopause), ≥ 52 years (later menopause), and 48-52 years (control). The DNA methylation levels of Alu and LINE-1 were measured by MethyLight PCR. The results showed that the DNA methylation levels of both Alu and LINE-1 were inversely correlated with menopausal age in the plasma DNA cohort (r = 0.079, P < 0.001 for Alu; r = 0.045, P = 0.007 for LINE-1) as well as in the serum DNA cohort (r = 0.087, P = 0.001 for Alu; r = 0.041, P = 0.026 for LINE-1). Alu methylation levels in both the plasma and serum DNA cohorts and LINE-1 methylation levels in the plasma cohort were remarkably higher in the earlier menopause group than in the later menopause and control groups (P < 0.01 and P < 0.05, respectively). In the serum DNA cohort, the LINE-1 methylation levels in the later menopause group were significantly lower than that in the earlier menopause group and control group (P < 0.05). Therefore, methylation levels of Alu and LINE-1 were significantly associated with menopausal age. Women with earlier menopause showed hypermethylation in both repetitive elements, while women with later menopause showed hypomethylation. These findings suggest that altered DNA methylation in leukocytes and serum cell-free DNA may represent a biomarker of menopausal age.
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Affiliation(s)
- Sha Lu
- 1Department of Obstetrics and Gynecology, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China.,2Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Zheng Niu
- 1Department of Obstetrics and Gynecology, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Yueming Chen
- 3Laboratory of Gene Diagnosis, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Qiaofeng Tu
- 3Laboratory of Gene Diagnosis, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Yue Zhang
- 2Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Wenli Chen
- 4Department of Obstetrics and Gynecology, the Second People's Hospital of Tonglu, Hangzhou, China
| | - Wenjuan Tong
- 3Laboratory of Gene Diagnosis, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China
| | - Zhifen Zhang
- 1Department of Obstetrics and Gynecology, the Affiliated Hangzhou People's Hospital of Nanjing Medical University, Hangzhou, China.,2Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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114
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Epigenetic Modifications of the α-Synuclein Gene and Relative Protein Content Are Affected by Ageing and Physical Exercise in Blood from Healthy Subjects. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:3740345. [PMID: 29849887 PMCID: PMC5924988 DOI: 10.1155/2018/3740345] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/15/2018] [Indexed: 12/20/2022]
Abstract
Epigenetic regulation may contribute to the beneficial effects of physical activity against age-related neurodegeneration. For example, epigenetic alterations of the gene encoding for α-synuclein (SNCA) have been widely explored in both brain and peripheral tissues of Parkinson's disease samples. However, no data are currently available about the effects of physical exercise on SNCA epigenetic regulation in ageing healthy subjects. The present paper explored whether, in healthy individuals, age and physical activity are related to blood intron1-SNCA (SNCAI1) methylation, as well as further parameters linked to such epigenetic modification (total, oligomeric α-synuclein and DNA methyltransferase concentrations in the blood). Here, the SNCAI1 methylation status increased with ageing, and consistent with this result, low α-synuclein levels were found in the blood. The direct relationship between SNCAI1 methylation and α-synuclein levels was observed in samples characterized by blood α-synuclein concentrations of 76.3 ng/mg protein or lower (confidence interval (CI) = 95%). In this selected population, higher physical activity reduced the total and oligomeric α-synuclein levels. Taken together, our data shed light on ageing- and physical exercise-induced changes on the SNCA methylation status and protein levels of α-synuclein.
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Ray D, Yung R. Immune senescence, epigenetics and autoimmunity. Clin Immunol 2018; 196:59-63. [PMID: 29654845 DOI: 10.1016/j.clim.2018.04.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022]
Abstract
Aging of the immune system in humans and animals is characterized by a decline in both adaptive and innate immune responses. Paradoxically, aging is also associated with a state of chronic inflammation ("inflammaging") and an increased likelihood of developing autoimmune diseases. Epigenetic changes in non-dividing and dividing cells, including immune cells, due to environmental factors contribute to the inflammation and autoimmunity that characterize both the state and diseases of aging. Here, we review the epigenetic mechanisms involved in the development of immune senescence and autoimmunity in old age.
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Affiliation(s)
- Donna Ray
- Division of Rheumatology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Raymond Yung
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, United States.
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116
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Promoter methylation status of the TIMP2 and ADAMTS4 genes and patellar tendinopathy. J Sci Med Sport 2018; 21:378-382. [DOI: 10.1016/j.jsams.2017.08.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/03/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022]
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117
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Bürkle A. In memoriam Olivier Toussaint – Stress-induced premature senescence and the role of DNA damage. Mech Ageing Dev 2018. [DOI: 10.1016/j.mad.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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118
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Najar RA, Wani NA, Bhat JA, Dar NJ, Rahat B, Gupta AP, Kaur J, Kaur J, Hamid A. Modulation of dietary folate with age confers selective hepatocellular epigenetic imprints through DNA methylation. J Nutr Biochem 2018; 53:121-132. [PMID: 29220669 DOI: 10.1016/j.jnutbio.2017.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/15/2017] [Accepted: 10/16/2017] [Indexed: 02/03/2023]
Abstract
The present study has been designed to determine the effect of folate modulation (deficiency/supplementation) with aging on the promoter methylation of tumor suppressor and proto-oncogenes to understand the underlying mechanism of epigenetic alterations. Folate deficiency was induced for 3 and 5 months in weanling, young and adult groups, and after 3 months of folate deficiency, they were repleted with physiological folate (2 mg/kg diet) and folate oversupplementation (8 mg/kg diet) for another 2 months. The methylation facet in the present study revealed that the combined effect of folate deficiency and aging decreased the methylation index. Folate deficiency with age resulted in the up-regulation of proto-oncogenes (C-MYC and C-JUN) and cell cycle regulator gene Cyclin E as a result of promoter hypomethylation. However, in case of tumor suppressor genes (p53, p15ink4b and p16ink4a), the expression levels were found to be decreased at transcriptional level due to promoter hypermethylation. Upon repletion with physiological folate and folate oversupplementation, we found down-regulation of proto-oncogenes and up-regulation of tumor suppressor genes as a result of promoter hypermethylation and hypomethylation, respectively. Deregulation of these important genes due to folate deficiency may contribute toward the pathogenesis at cellular level.
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Affiliation(s)
- Rauf Ahmad Najar
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Nissar Ahmad Wani
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Javeed Ahmad Bhat
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Nawab John Dar
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Beenish Rahat
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ajai Prakash Gupta
- Quality Control and Quality Assurance Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Jaspreet Kaur
- University Institute of Engineering and Technology, Panjab University, Chandigarh 160016, India
| | - Jyotdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Abid Hamid
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India.
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Kuzmina NS, Lapteva NS, Rusinova GG, Azizova TV, Vyazovskaya NS, Rubanovich AV. Gene hypermethylation in blood leukocytes in humans long term after radiation exposure - Validation set. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:935-942. [PMID: 29253833 DOI: 10.1016/j.envpol.2017.12.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED Hypermethylation of СpG islands in the promoter regions of several genes with basic protective function in blood leukocytes of individuals exposed to ionizing radiation long time ago (2-46 years), and differential effects of age and radiation exposure on hypermethylation was reported in our previous work. To validate these results, epigenetic modifications were assessed in an independent series of 49 nuclear industry workers from the "Mayak" facility (67-84 years old at sampling) with documented individual accumulated doses from the prolonged external γ-radiation exposure (95.9-409.5 cGy, end of work with radiation:0.3-39 years ago), and in 50 non-exposed persons matched by age. In addition to the genes analyzed before (RASSF1A, p16/INK4A, p14/ARF, GSTP1), four additional loci were analyzed: TP53, ATM, SOD3, ESR1. The frequency of individuals displaying promoter methylation of at least one of the 8 genes (71.4%) was significantly higher in exposed group as compared to the control group (40%), p = .002, OR = 3.75. A significantly elevated frequency of individuals with hypermethylated СpG islands in GSTP1, TP53, SOD3 promoters was revealed among exposed subjects as compared to the control group (p = .012, OR = 8.41; p = .041, OR = 4.02 and p = .009, OR = 3.42, respectively). A similar trend (p = .12, OR = 3.06) was observed for the p16/INK4A gene. As a whole, p16/INK4A and GSTP1 promoter hypermethylation in irradiated subjects from both previously and currently analyzed groups was pronounced. Thus, the direction of the effects was fully confirmed, suggesting the result reproducibility. No statistically significant correlation between promoter methylation and individual radiation dose was found. Further studies are required to create an array of blood epigenetic markers of radiation exposure associating with premature aging and age-related diseases and to accurately evaluate radiation-added effect across the range of doses. SYNTHESIS The results of studies of epigenetic changes in two independent samples of irradiated subjects indicated the significance of radiation factor in the induction of hypermethylation of CpG islands in gene promoters that is revealed in blood cells years and decades after exposure.
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Affiliation(s)
- Nina S Kuzmina
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
| | - Nellya Sh Lapteva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
| | | | | | | | - Alexander V Rubanovich
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
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Masser DR, Hadad N, Porter H, Stout MB, Unnikrishnan A, Stanford DR, Freeman WM. Analysis of DNA modifications in aging research. GeroScience 2018; 40:11-29. [PMID: 29327208 PMCID: PMC5832665 DOI: 10.1007/s11357-018-0005-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging. With recent methodological advances, such as whole genome bisulfite sequencing (WGBS), bisulfite oligonucleotide capture sequencing (BOCS), and bisulfite amplicon sequencing (BSAS), cytosine modifications can now be readily analyzed with base-specific, absolute quantitation at both cytosine-guanine dinucleotide (CG) and non-CG sites throughout the genome or within specific regions of interest by next-generation sequencing. Additional advances, such as oxidative bisulfite conversion to differentiate methylation from hydroxymethylation and analysis of limited input/single-cells, have great promise for continuing to expand epigenomic capabilities. This review provides a background on DNA modifications, the current state-of-the-art for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.
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Affiliation(s)
- Dustin R Masser
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for 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
| | - Hunter Porter
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for 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
| | - Michael B Stout
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Nathan Shock Center for 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.
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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121
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DNA methylation is not involved in dietary restriction induced lifespan extension in adult Drosophila. Genet Res (Camb) 2018; 100:e1. [PMID: 29386085 DOI: 10.1017/s0016672317000064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dietary restriction (DR) is widely regarded as a viable intervention to extend lifespan and healthspan in diverse organisms. The precise molecular regulatory mechanisms are largely unknown. Epigenetic modifications are not stable upon DR and also keep changing with age. Here, we employed whole genome bisulfite sequencing to determine the DNA methylation changes upon DR in adult Drosophila. Our results indicate that although a low level of DNA methylation exists in the adult Drosophila genome, there is no significant difference in DNA methylation levels upon DR when compared to unrestricted flies. This suggests that other epigenetic components such as histone modifications might be altered by DR.
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122
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Ravaioli F, Bacalini MG, Franceschi C, Garagnani P. Age-Related Epigenetic Derangement upon Reprogramming and Differentiation of Cells from the Elderly. Genes (Basel) 2018; 9:genes9010039. [PMID: 29337900 PMCID: PMC5793190 DOI: 10.3390/genes9010039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023] Open
Abstract
Aging is a complex multi-layered phenomenon. The study of aging in humans is based on the use of biological material from hard-to-gather tissues and highly specific cohorts. The introduction of cell reprogramming techniques posed promising features for medical practice and basic research. Recently, a growing number of studies have been describing the generation of induced pluripotent stem cells (iPSCs) from old or centenarian biologic material. Nonetheless, Reprogramming techniques determine a profound remodelling on cell epigenetic architecture whose extent is still largely debated. Given that cell epigenetic profile changes with age, the study of cell-fate manipulation approaches on cells deriving from old donors or centenarians may provide new insights not only on regenerative features and physiology of these cells, but also on reprogramming-associated and age-related epigenetic derangement.
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Affiliation(s)
- Francesco Ravaioli
- Department of Specialty, Diagnostic and Experimental Medicine (DIMES), Via San Giacomo 12, 40126 Bologna, Italy.
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Via G. Petroni 26, 40126 Bologna, Italy.
| | - Maria G Bacalini
- IRCCS Institute of Neurological Sciences, Via Altura 1-8, 40139 Bologna, Italy.
| | - Claudio Franceschi
- IRCCS Institute of Neurological Sciences, Via Altura 1-8, 40139 Bologna, Italy.
| | - Paolo Garagnani
- Department of Specialty, Diagnostic and Experimental Medicine (DIMES), Via San Giacomo 12, 40126 Bologna, Italy.
- CIG, Interdepartmental Center 'L. Galvani', Alma Mater Studiorum, Via G. Petroni 26, 40126 Bologna, Italy.
- Karolinska Institute, Clinical Chemistry, Department of Laboratory Medicine (LABMED), H5, Huddinge University Hospital, 14186 Stockholm, Sweden.
- CNR Institute of Molecular Genetics, Unit of Bologna, 40136 Bologna, Italy.
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy.
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123
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Jones MJ, Moore SR, Kobor MS. Principles and Challenges of Applying Epigenetic Epidemiology to Psychology. Annu Rev Psychol 2018; 69:459-485. [DOI: 10.1146/annurev-psych-122414-033653] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Meaghan J. Jones
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Sarah R. Moore
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
- Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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124
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de Brito Alves JL, Costa-Silva JH. Maternal protein malnutrition induced-hypertension: New evidence about the autonomic and respiratory dysfunctions and epigenetic mechanisms. Clin Exp Pharmacol Physiol 2017; 45:422-429. [PMID: 29164748 DOI: 10.1111/1440-1681.12892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022]
Abstract
Maternal protein malnutrition during the critical stages of development (pregnancy, lactation and first infancy) can lead to adult hypertension. Studies have shown that renal and cardiovascular dysfunctions can be associated to the development of hypertension in humans and rats exposed to maternal protein malnutrition. The etiology of hypertension, however, includes a complex network involved in central and peripheral blood pressure control. Recently, the hyperactivity of the sympathetic nervous system in protein-restricted rats has been reported. Studies have shown that protein malnutrition during pregnancy and/or lactation alters blood pressure control through mechanisms that include central sympathetic-respiratory dysfunctions and epigenetic modifications, which may contribute to adult hypertension. Thus, this review will discuss the historical context, new evidences of neurogenic disruption in respiratory-sympathetic activities and possible epigenetic mechanisms involved in maternal protein malnutrition induced- hypertension.
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Affiliation(s)
- José Luiz de Brito Alves
- Department of Nutrition, Health Sciences Center, Federal University of Paraíba, UFPB, João Pessoa, Brazil
| | - João Henrique Costa-Silva
- Department of Physical Education and Sport Sciences, Federal University of Pernambuco, UFPE, Vitória de Santo Antão-PE, Brazil
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125
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Blossom SJ, Gilbert KM. Epigenetic underpinnings of developmental immunotoxicity and autoimmune disease. CURRENT OPINION IN TOXICOLOGY 2017; 10:23-30. [PMID: 30613805 DOI: 10.1016/j.cotox.2017.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The concordance rate for developing autoimmune disease in identical twins is around 50% demonstrating that gene and environmental interactions contribute to disease etiology. The environmental contribution to autoimmune disease is a wide-ranging concept including exposure to immunotoxic environmental chemicals. Because the immune system is immature during development suggests that adult-onset autoimmunity may originate when the immune system is particularly sensitive. Among the pollutants most closely associated with inflammation and/or autoimmunity include Bisphenol-A, mercury, TCDD, and trichloroethylene. These toxicants have been shown to impart epigenetic changes (e.g., DNA methylation) that may alter immune function and promote autoreactivity. Here we review these autoimmune-promoting toxicants and their relation to immune cell epigenetics both in terms of adult and developmental exposure.
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Affiliation(s)
- Sarah J Blossom
- University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
| | - Kathleen M Gilbert
- University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
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126
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Masser DR, Hadad N, Porter HL, Mangold CA, Unnikrishnan A, Ford MM, Giles CB, Georgescu C, Dozmorov MG, Wren JD, Richardson A, Stanford DR, Freeman WM. Sexually divergent DNA methylation patterns with hippocampal aging. Aging Cell 2017; 16:1342-1352. [PMID: 28948711 PMCID: PMC5676057 DOI: 10.1111/acel.12681] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2017] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is a central regulator of genome function, and altered methylation patterns are indicative of biological aging and mortality. Age‐related cellular, biochemical, and molecular changes in the hippocampus lead to cognitive impairments and greater vulnerability to neurodegenerative disease that varies between the sexes. The role of hippocampal epigenomic changes with aging in these processes is unknown as no genome‐wide analyses of age‐related methylation changes have considered the factor of sex in a controlled animal model. High‐depth, genome‐wide bisulfite sequencing of young (3 month) and old (24 month) male and female mouse hippocampus revealed that while total genomic methylation amounts did not change with aging, specific sites in CG and non‐CG (CH) contexts demonstrated age‐related increases or decreases in methylation that were predominantly sexually divergent. Differential methylation with age for both CG and CH sites was enriched in intergenic and intronic regions and under‐represented in promoters, CG islands, and specific enhancer regions in both sexes, suggesting that certain genomic elements are especially labile with aging, even if the exact genomic loci altered are predominantly sex‐specific. Lifelong sex differences in autosomal methylation at CG and CH sites were also observed. The lack of genome‐wide hypomethylation, sexually divergent aging response, and autosomal sex differences at CG sites was confirmed in human data. These data reveal sex as a previously unappreciated central factor of hippocampal epigenomic changes with aging. In total, these data demonstrate an intricate regulation of DNA methylation with aging by sex, cytosine context, genomic location, and methylation level.
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Affiliation(s)
- Dustin R. Masser
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Oklahoma Center for Neuroscience University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Hunter L. Porter
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Oklahoma Center for Neuroscience University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Colleen A. Mangold
- Department of Biochemistry and Molecular Biology Pennsylvania State University University Park PA USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Department of Geriatric Medicine University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Matthew M. Ford
- Division of Neuroscience Oregon National Primate Research Center Beaverton OR USA
| | - Cory B. Giles
- Arthritis & Clinical Immunology Program Oklahoma Medical Research Foundation Oklahoma OK USA
| | - Constantin Georgescu
- Arthritis & Clinical Immunology Program Oklahoma Medical Research Foundation Oklahoma OK USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics Virginia Commonwealth University School of Medicine Richmond VA USA
| | - Jonathan D. Wren
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Arthritis & Clinical Immunology Program Oklahoma Medical Research Foundation Oklahoma OK USA
- Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center Oklahoma OK USA
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Department of Geriatric Medicine University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma City VA Medical Center Oklahoma OK USA
| | - David R. Stanford
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
| | - Willard M. Freeman
- Reynolds Oklahoma Center on Aging Oklahoma OK USA
- Department of Physiology University of Oklahoma Health Sciences Center Oklahoma OK USA
- Oklahoma Nathan Shock Center for Aging Oklahoma OK USA
- Oklahoma Center for Neuroscience University of Oklahoma Health Sciences Center Oklahoma OK USA
- Department of Geriatric Medicine University of Oklahoma Health Sciences Center Oklahoma OK USA
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127
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Song MA, Brasky TM, Weng DY, McElroy JP, Marian C, Higgins MJ, Ambrosone C, Spear SL, Llanos AA, Kallakury BVS, Freudenheim JL, Shields PG. Landscape of genome-wide age-related DNA methylation in breast tissue. Oncotarget 2017; 8:114648-114662. [PMID: 29383109 PMCID: PMC5777721 DOI: 10.18632/oncotarget.22754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 11/06/2017] [Indexed: 12/15/2022] Open
Abstract
Despite known age-related DNA methylation (aDNAm) changes in breast tumors, little is known about aDNAm in normal breast tissues. Breast tissues from a cross-sectional study of 121 cancer-free women, were assayed for genome-wide DNA methylation. mRNA expression was assayed by microarray technology. Analysis of covariance was used to identify aDNAm’s. Altered methylation was correlated with expression of the corresponding gene and with DNA methyltransferase protein DNMT3A, assayed by immunohistochemistry. Publically-available TCGA-BRCA data were used for replication. 1,214 aDNAm’s were identified; 97% with increased methylation, and all on autosomes. Sites with increased methylation were predominantly in CpG lslands and non-enhancers. aDNAm’s with decreased methylation were generally located in intergenic regions, non-CpG Islands, and enhancers. Of the aDNAm’s identified, 650 are known to be involved in cancer, including ESR1 and beta-estradiol responsive genes. Expression of DNMT3A was positively associated with age. Two aDNAm’s showed borderline significant associations with DNMT3A expression; KRR1 (OR 6.57, 95% CI: 2.51–17.23) and DHRS12 (OR 6.08, 95% CI: 2.33–15.86). A subset of aDNAm’s co-localized within vulnerable regions for somatic mutations in cancers including breast cancer. Expression of C19orf48 was inversely and significantly correlated with its methylation level. In the TCGA dataset, 84% and 64% of the previously identified aDNAm’s were correlated with age in both normal-adjacent and tumor breast tissues, with differential associations by histological subtype. Given the similarity of findings in the breast tissues of healthy women and breast tumors, aDNAm’s may be one pathway for increased breast cancer risk with age.
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Affiliation(s)
- Min-Ae Song
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.,College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Theodore M Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Joseph P McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA.,Center for Biostatistics and Department of Bioinformatics, The Ohio State University, Columbus, OH, USA
| | - Catalin Marian
- Biochemistry and Pharmacology Department, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Scott L Spear
- Department of Plastic Surgery, Georgetown University, Washington, DC, USA
| | - Adana A Llanos
- Department of Epidemiology, Rutgers School of Public Health and Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
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128
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Ferrosenescence: The iron age of neurodegeneration? Mech Ageing Dev 2017; 174:63-75. [PMID: 29180225 DOI: 10.1016/j.mad.2017.11.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 12/15/2022]
Abstract
Aging has been associated with iron retention in many cell types, including the neurons, promoting neurodegeneration by ferroptosis. Excess intracellular iron accelerates aging by damaging the DNA and blocking genomic repair systems, a process we define as ferrosenescence. Novel neuroimaging and proteomic techniques have pinpointed indicators of both iron retention and ferrosenescence, allowing for their early correction, potentially bringing prevention of neurodegenerative disorders within reach. In this review, we take a closer look at the early markers of iron dyshomeostasis in neurodegenerative disorders, focusing on preventive strategies based on nutritional and microbiome manipulations.
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129
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Valentini E, Zampieri M, Malavolta M, Bacalini MG, Calabrese R, Guastafierro T, Reale A, Franceschi C, Hervonen A, Koller B, Bernhardt J, Slagboom PE, Toussaint O, Sikora E, Gonos ES, Breusing N, Grune T, Jansen E, Dollé MET, Moreno-Villanueva M, Sindlinger T, Bürkle A, Ciccarone F, Caiafa P. Analysis of the machinery and intermediates of the 5hmC-mediated DNA demethylation pathway in aging on samples from the MARK-AGE Study. Aging (Albany NY) 2017; 8:1896-1922. [PMID: 27587280 PMCID: PMC5076444 DOI: 10.18632/aging.101022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022]
Abstract
Gradual changes in the DNA methylation landscape occur throughout aging virtually in all human tissues. A widespread reduction of 5-methylcytosine (5mC), associated with highly reproducible site-specific hypermethylation, characterizes the genome in aging. Therefore, an equilibrium seems to exist between general and directional deregulating events concerning DNA methylation controllers, which may underpin the age-related epigenetic changes. In this context, 5mC-hydroxylases (TET enzymes) are new potential players. In fact, TETs catalyze the stepwise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), driving the DNA demethylation process based on thymine DNA glycosylase (TDG)-mediated DNA repair pathway. The present paper reports the expression of DNA hydroxymethylation components, the levels of 5hmC and of its derivatives in peripheral blood mononuclear cells of age-stratified donors recruited in several European countries in the context of the EU Project 'MARK-AGE'. The results provide evidence for an age-related decline of TET1, TET3 and TDG gene expression along with a decrease of 5hmC and an accumulation of 5caC. These associations were independent of confounding variables, including recruitment center, gender and leukocyte composition. The observed impairment of 5hmC-mediated DNA demethylation pathway in blood cells may lead to aberrant transcriptional programs in the elderly.
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Affiliation(s)
- Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Marco Malavolta
- National Institute of Health and Science on Aging (INRCA), Nutrition and Ageing Centre, Scientific and Technological Research Area, 60100 Ancona, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40126, Italy.,CIG-Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Tiziana Guastafierro
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Anna Reale
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40126, Italy.,CIG-Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Antti Hervonen
- The School of Medicine, The University of Tampere, 33014 Tampere, Finland
| | - Bernhard Koller
- Department for Internal Medicine, University Teaching Hospital Hall in Tirol, Tirol, Austria
| | | | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Olivier Toussaint
- University of Namur, Research Unit on Cellular Biology, Namur B-5000, Belgium
| | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Nicolle Breusing
- Institute of Nutritional Medicine (180c), University of Hohenheim, 70599 Stuttgart, Gemany
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - Eugène Jansen
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - María Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thilo Sindlinger
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Fabio Ciccarone
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy.,Shared senior authorship
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.,Shared senior authorship
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130
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Park M, Min B, Jeon K, Cho S, Park JS, Kim J, Jeon J, Song J, Kim S, Jeong S, Seo H, Kang YK. Age-associated chromatin relaxation is enhanced in Huntington's disease mice. Aging (Albany NY) 2017; 9:803-822. [PMID: 28288000 PMCID: PMC5391233 DOI: 10.18632/aging.101193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/26/2017] [Indexed: 12/13/2022]
Abstract
Expansion of polyglutamine stretch in the huntingtin (HTT) protein is a major cause of Huntington's disease (HD). The polyglutamine part in HTT interacts with various proteins implicated in epigenetic regulation of genes, suggesting that mutant HTT may disturb the integrity of the epigenetic system. Here, we used a PCRseq-based method to examine expression profile of 395 exonic segments from 260 “epi-driver” genes in splenic T lymphocytes from aged HD mice. We identified 67 exonic segments differentially expressed between young and aged HD mice, most of them upregulated in the aged. Polycomb-repressive complex (PRC)-regulated genes (PRGs) were markedly upregulated in aged HD mice, consistent with downregulation of PRC genes. Epi-driver gene categories of lysine-methylation, lysine-demethylation, arginine-methylation, and PRG showed differential age-associated changes between HD and control. Analyzing the pattern of change in epi-driver gene expressions hinted at an enhanced shift in HD chromatin to a more accessible state with age, which was experimentally demonstrated by DNase-I-hypersensitivity sequencing showing increased chromatin accessibility in HD cells compared to control. We suggest the global change can potentially relieve chromatin-induced repression of many genes, and the unintended expressions of some detrimental proteins could alter T cell function to a greater degree in aged HD mice.
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Affiliation(s)
- Myungsun Park
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Byungkuk Min
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea.,Department of Functional Genomics, University of Science and Technology (UST), Yuseong-gu, Daejeon, 305-350, South Korea
| | - Sunwha Cho
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea.,Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea
| | - Jisun Kim
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do, 15588, South Korea
| | - Jeha Jeon
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do, 15588, South Korea
| | - Jinhoi Song
- Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea
| | - Seokho Kim
- Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea
| | - Sangkyun Jeong
- Mibyeong Research Center, Korea Institute of Oriental Medicine (KIOM), Yuseong-gu, Daejeon, 305-811, South Korea
| | - Hyemyung Seo
- Department of Molecular and Life Sciences, Hanyang University, Sangnok-gu, Ansan, Gyeonggi-do, 15588, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, KRIBB, Yuseong-gu, Daejeon, 305-806, South Korea.,Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, South Korea.,Department of Functional Genomics, University of Science and Technology (UST), Yuseong-gu, Daejeon, 305-350, South Korea
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131
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Boström AE, Ciuculete DM, Attwood M, Krattinger R, Nikontovic L, Titova OE, Kullak-Ublick GA, Mwinyi J, Schiöth HB. A MIR4646 associated methylation locus is hypomethylated in adolescent depression. J Affect Disord 2017; 220:117-128. [PMID: 28618313 DOI: 10.1016/j.jad.2017.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/04/2017] [Accepted: 05/06/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Studies of epigenetics and transcriptional activity in adolescents may provide knowledge about possible preventive strategies of depression. METHODS We present a methylome-wide association study (MWAS) and cohort validation analysis of depression in adolescents, in two separate cohorts: discovery (n=93) and validation data set 1 (n=78). The genome-wide methylation pattern was measured from whole blood using the Illumina 450K array. A second validation cohort, validation data set 2, consists of post-mortem brain biopsies from depressed adults (n=58). We performed a MWAS by robust multiple linear regressions of methylation to a modified risk-score assessment of depression. Methylation levels of candidate CpG sites were correlated with expression levels of the associated gene in an independent cohort of 11 healthy volunteers. RESULTS The methylation state of two CpG sites reliably predicted ratings of depression in adolescents (cg13227623 and cg04102384) (p<10E-06). Cohort validation analysis confirmed cg04102384 - located in the promoter region of microRNA 4646 (MIR4646) - to be hypomethylated in both validation data set 1 and validation data set 2 (p<0.05). Cg04102384 was inversely correlated to expression levels of MIR4646-3p in healthy controls (p<0.05). LIMITATIONS MIR4646 was not differentially expressed in a subset of samples with adolescent depression measured by qRT-PCR measurements. CONCLUSION We identify a specific MIR4646 associated epigenetic risk site to be associated with depression in adolescents. Cg04102384 putatively regulates gene expression of MIR4646-3p. Target gene prediction and gene set overrepresentation analysis revealed involvement of this miRNA in fatty acid elongation, a process related to omega-3 fatty acids, previously associated with depression.
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Affiliation(s)
- Adrian E Boström
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden..
| | - Diana-Maria Ciuculete
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Misty Attwood
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Regina Krattinger
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Switzerland
| | - Lamia Nikontovic
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Olga E Titova
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Gerd A Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Switzerland
| | - Jessica Mwinyi
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Division of Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
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132
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Tidwell TR, Søreide K, Hagland HR. Aging, Metabolism, and Cancer Development: from Peto's Paradox to the Warburg Effect. Aging Dis 2017; 8:662-676. [PMID: 28966808 PMCID: PMC5614328 DOI: 10.14336/ad.2017.0713] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Medical advances made over the last century have increased our lifespan, but age-related diseases are a fundamental health burden worldwide. Aging is therefore a major risk factor for cardiovascular disease, cancer, diabetes, obesity, and neurodegenerative diseases, all increasing in prevalence. However, huge inter-individual variations in aging and disease risk exist, which cannot be explained by chronological age, but rather physiological age decline initiated even at young age due to lifestyle. At the heart of this lies the metabolic system and how this is regulated in each individual. Metabolic turnover of food to energy leads to accumulation of co-factors, byproducts, and certain proteins, which all influence gene expression through epigenetic regulation. How these epigenetic markers accumulate over time is now being investigated as the possible link between aging and many diseases, such as cancer. The relationship between metabolism and cancer was described as early as the late 1950s by Dr. Otto Warburg, before the identification of DNA and much earlier than our knowledge of epigenetics. However, when the stepwise gene mutation theory of cancer was presented, Warburg's theories garnered little attention. Only in the last decade, with epigenetic discoveries, have Warburg's data on the metabolic shift in cancers been brought back to life. The stepwise gene mutation theory fails to explain why large animals with more cells, do not have a greater cancer incidence than humans, known as Peto's paradox. The resurgence of research into the Warburg effect has given us insight to what may explain Peto's paradox. In this review, we discuss these connections and how age-related changes in metabolism are tightly linked to cancer development, which is further affected by lifestyle choices modulating the risk of aging and cancer through epigenetic control.
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Affiliation(s)
- Tia R. Tidwell
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hanne R. Hagland
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
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133
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Goel N, Karir P, Garg VK. Role of DNA methylation in human age prediction. Mech Ageing Dev 2017; 166:33-41. [DOI: 10.1016/j.mad.2017.08.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/24/2017] [Accepted: 08/20/2017] [Indexed: 12/19/2022]
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134
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Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data. Genetics 2017; 207:1547-1560. [PMID: 28855307 DOI: 10.1534/genetics.117.300217] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/23/2017] [Indexed: 02/01/2023] Open
Abstract
The evolutionary theories of mutation accumulation (MA) and disposable soma (DS) provide possible explanations for the existence of human aging. To better understand the relative importance of these theories, we devised a test to identify MA- and DS-consistent sites across the genome using familial DNA methylation data. Two key characteristics of DNA methylation allowed us to do so. First, DNA methylation exhibits distinct and widespread changes with age, with numerous age-differentially-methylated sites observed across the genome. Second, many sites show heritable DNA methylation patterns within families. We extended heritability predictions of MA and DS to DNA methylation, predicting that MA-consistent age-differentially-methylated sites will show increasing heritability with age, while DS-consistent sites will show the opposite. Variance components models were used to test for changing heritability of methylation with age at 48,601 age-differentially-methylated sites across the genome in 610 individuals from 176 families. Of these, 102 sites showed significant MA-consistent increases in heritability with age, while 2266 showed significant DS-consistent decreases in heritability. These results suggest that both MA and DS play a role in explaining aging and aging-related changes, and that while the majority of DNA methylation changes observed in aging are consistent with epigenetic drift, targeted changes exist and may mediate effects of aging-related genes.
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135
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Davis EG, Humphreys KL, McEwen LM, Sacchet MD, Camacho MC, MacIsaac JL, Lin DTS, Kobor MS, Gotlib IH. Accelerated DNA methylation age in adolescent girls: associations with elevated diurnal cortisol and reduced hippocampal volume. Transl Psychiatry 2017; 7:e1223. [PMID: 28850111 PMCID: PMC5611751 DOI: 10.1038/tp.2017.188] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/06/2017] [Accepted: 07/04/2017] [Indexed: 12/21/2022] Open
Abstract
Numerous studies have linked exposure to stress to adverse health outcomes through the effects of cortisol, a product of the stress response system, on cellular aging processes. Accelerated DNA methylation age is a promising epigenetic marker associated with stress and disease risk that may constitute a link from stress response to changes in neural structures. Specifically, elevated glucocorticoid signaling likely contributes to accelerating DNA methylation age, which may signify a maladaptive stress-related cascade that leads to hippocampal atrophy. We examined the relations among diurnal cortisol levels, DNA methylation age and hippocampal volume in a longitudinal study of 46 adolescent girls. We computed area under the curve from two daily cortisol collection periods, and calculated DNA methylation age using previously established methods based on a set of CpG sites associated with chronological age. We computed a residual score by partialling out chronological age; higher discrepancies reflect relatively accelerated DNA methylation age. We assessed hippocampal volume via T1-weighted images and automated volumetric segmentation. We found that greater diurnal cortisol production was associated with accelerated DNA methylation age, which in turn was associated with reduced left hippocampal volume. Finally, accelerated DNA methylation age significantly mediated the association between diurnal cortisol and left hippocampal volume. Thus, accelerated DNA methylation age may be an epigenetic marker linking hypothalamic-pituitary-adrenal axis dysregulation with neural structure. If these findings are replicated, the current study provides a method for advancing our understanding of mechanisms by which glucocorticoid signaling is associated with cellular aging and brain development.
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Affiliation(s)
- E G Davis
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - K L Humphreys
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - L M McEwen
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - M D Sacchet
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - M C Camacho
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - J L MacIsaac
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - D T S Lin
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - M S Kobor
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - I H Gotlib
- Department of Psychology, Stanford University, Stanford, CA, USA
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136
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Theophanides T, Anastassopoulou J. The effects of metal ion contaminants on the double stranded DNA helix and diseases. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2017; 52:1030-1040. [PMID: 28758877 DOI: 10.1080/10934529.2017.1328950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mineral metal ions are essential for the maintenance of the reactions that regulate homeostasis and the functions of our body. It is known that the regulation of the neurodegenerative system depends directly on life metal ions, such as Na, K, Mg, Ca, Fe, Mo, Cu, Co, Zn, Cr, Mn, while the toxic metals Cd, Pb, Hg, etc disturb homeostasis, leading to diseases. Particularly significant is the effect of toxic metals on the double stranded forms of DNA and conformations. It was found that the toxic metal ions by reacting specifically with the nucleic bases and electrostatically with the negatively phosphate groups of the DNA backbone cause changes in the structure of the DNA double helix, leading to breaks of single or double strands. Accumulation of these defects affects the protecting systems of the body and induces mutations, eventually leading to serious diseases. There are many metal ions, such as Cr, Al, Cd, Cu, Ni, which by binding directly to DNA molecule or by developing oxidative stress increase the instability of DNA, promoting epigenetic changes that lead to DNA damage. Toxic metal ions induce indirect DNA damage and influence the gene stability by inactivating encoding proteins or by changing the redox potential and the signaling of metalloenzymes.
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Affiliation(s)
- T Theophanides
- a National Technical University of Athens, Chemical Engineering Department, Radiation Chemistry & Biospectroscopy , Zografou Campus, Zografou , Athens , Greece
| | - J Anastassopoulou
- b International Anticancer Research Institute , Kapandritiou-Kalamou Road, Kapandriti , Attiki , Greece
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137
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Identification, replication and characterization of epigenetic remodelling in the aging genome: a cross population analysis. Sci Rep 2017; 7:8183. [PMID: 28811542 PMCID: PMC5557932 DOI: 10.1038/s41598-017-08346-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/09/2017] [Indexed: 01/27/2023] Open
Abstract
Aging is a complex biological process regulated by multiple cellular pathways and molecular mechanisms including epigenetics. Using genome-wide DNA methylation data measured in a large collection of Scottish old individuals, we performed discovery association analysis to identify age-methylated CpGs and replicated them in two independent Danish cohorts. The double-replicated CpGs were characterized by distribution over gene regions and location in relation to CpG islands. The replicated CpGs were further characterized by involvement in biological pathways to study their functional implications in aging. We identified 67,604 age-associated CpG sites reaching genome-wide significance of FWER <0.05, 86% demethylated with increasing age. Double-replication resulted in 5,168 CpGs (39% age-methylated and 61% age-demethylated) which were characterized by high concentration of age-methylated CpGs at 1stExon and TSS200 and a dominant pattern of age-demethylated CpGs at other gene regions, and by overwhelming age-related methylation in CpG islands and demethylation at shore/shelf and open sea. The differential distribution patterns over gene regions for methylated and demethylated CpGs both relate to reduced gene activity during aging. Pathway analysis showed that age-dependent methylations were especially involved in cellular signalling activities while demethylations particularly linked to functions of the extracellular matrix, all implicated in the aging process and age-related disease risk.
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138
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Abstract
During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death. Exactly when and how this decline occurs is unknown. Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline. These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging. We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging. Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases.
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Affiliation(s)
- Lauren N Booth
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA.
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139
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Owczarz M, Budzinska M, Domaszewska-Szostek A, Borkowska J, Polosak J, Gewartowska M, Slusarczyk P, Puzianowska-Kuznicka M. miR-34a and miR-9 are overexpressed and SIRT genes are downregulated in peripheral blood mononuclear cells of aging humans. Exp Biol Med (Maywood) 2017; 242:1453-1461. [PMID: 28699360 PMCID: PMC5544174 DOI: 10.1177/1535370217720884] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/17/2017] [Indexed: 12/23/2022] Open
Abstract
Increased expression of sirtuins lowers the risk of age-related diseases, while their role in the regulation of longevity is not firmly established. Since aging is associated with immunosenescence, we tested whether sirtuin expression was modified in peripheral blood mononuclear cells (PBMC) in an age-related manner and whether this might result from altered expression of the selected miRNAs. The expression of seven SIRT genes and of SIRT1 mRNA-interacting miR-9, miR-34a, miR-132, and miR-199a-5p was evaluated by real-time PCR in PBMC originating from young (Y, n = 57, mean age 27 ± 4.3 years), elderly (E, n = 52, 65 ± 3.4 years), and long-lived (L, n = 56, 94 ± 3.5 years) individuals. Older age was associated with a decreased expression of the majority of the SIRT genes. Most severely affected were median expressions of SIRT1 ( P = 0.000001 for the whole studied group, Y vs. E: P < 0.000001, Y vs. L: P < 0.000001), and of SIRT3 ( P = 0.000001, Y vs. E: P = 0.000004, Y vs. L: P = 0.000028). Older age was also associated with the increased median expression of miR-34a ( P = 0.000001, Y vs. E: P = 0.001, Y vs. L: P = 0.000004) and of miR-9 ( P = 0.05, Y vs. L: P = 0.054). In functional studies, miR-9 interacted with the 3'UTR of SIRT1 mRNA. The SIRT1 mRNA level negatively correlated with the expression of miR-34a ( r = -0.234, P = 0.003). In conclusion, age-related decrease of SIRT1 expression in PBMC might in part result from overexpression of miR-34a and miR-9. In addition, the sustained expression of the SIRT genes in PBMC is not a prerequisite to longevity in humans but might be one of the reasons for the immune system dysfunction in the elderly. Impact statement High expression of sirtuins, particularly SIRT1, lowers the risk of age-related diseases and probably slows down the rate of aging; therefore, their sustained expression should be one of the features of longevity. However, in this work we show that in peripheral blood mononuclear cells (PBMC) of long-lived individuals, expression of majority of the SIRT genes is significantly lower than in cells of young study subjects. In long-lived individuals, downregulation of SIRT1 coexists with upregulation of SIRT1 mRNA-interacting miR-34a and miR-9, indicating the role of epigenetic drift in age-dependent deregulation of SIRT1 expression. Such constellation of SIRT1, miR-34a, and miR-9 expression in PBMC of successfully aging long-lived individuals indicates that, at least in these individuals, it is not a risk factor for morbidity and mortality. It might however affect the function of the immune system and, therefore, aging individuals can profit from interventions increasing the level of SIRT1.
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Affiliation(s)
- Magdalena Owczarz
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland
| | - Monika Budzinska
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland
| | | | - Joanna Borkowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre PAS, 02-106 Warsaw, Poland
| | - Jacek Polosak
- Department of Human Epigenetics, Mossakowski Medical Research Centre PAS, 02-106 Warsaw, Poland
| | - Magdalena Gewartowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre PAS, 02-106 Warsaw, Poland
| | - Przemyslaw Slusarczyk
- PolSenior Project, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Monika Puzianowska-Kuznicka
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland
- Department of Human Epigenetics, Mossakowski Medical Research Centre PAS, 02-106 Warsaw, Poland
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140
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miRNA-34b is directly involved in the aging of macrophages. Aging Clin Exp Res 2017; 29:599-607. [PMID: 27538833 DOI: 10.1007/s40520-016-0611-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) are a class of short noncoding RNA that play important regulatory roles in living organisms. These RNA molecules are implicated in the development and progression of malignant diseases such as cancer and are closely associated with cell aging. Findings demonstrating that microRNA is associated with aging in macrophages have nevertheless rarely been reported. AIMS This study's objective was to investigate if miRNA-34 is linked to aging process of macrophages. METHODS We built a cell aging model in mouse RAW264.7 macrophages using D-galactose and determined the expression levels of miRNA-34a, miRNA-34b, and miRNA-34c in aging and normal macrophages by fluorescence quantitative polymerase chain reaction (q-PCR). We predicted a target gene of miRNA-34 using biological information techniques and constructed the recombinant plasmid pGL3-E2f3 for the putative target gene E2f3. RESULTS The expression level of miRNA-34b was 5.23 times higher in aging macrophages than in normal macrophages. The luciferase activity decreased by nearly 50 % in cells transfected with miRNA-34b mimics, while no significant decrease in luciferase activity was noted in cells transfected with the miRNA-34b inhibitor or unrelated sequences. DISCUSSION Our findings provide the groundwork for further research into the molecular mechanisms whereby miRNA-34b regulates the aging of macrophages. CONCLUSIONS miRNA-34b is associated with the aging of RAW264.7 macrophages, and E2f3 is a target gene of miRNA-34b.
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141
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Shiels PG, McGuinness D, Eriksson M, Kooman JP, Stenvinkel P. The role of epigenetics in renal ageing. Nat Rev Nephrol 2017. [PMID: 28626222 DOI: 10.1038/nrneph.2017.78] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An ability to separate natural ageing processes from processes specific to morbidities is required to understand the heterogeneity of age-related organ dysfunction. Mechanistic insight into how epigenetic factors regulate ageing throughout the life course, linked to a decline in renal function with ageing, is already proving to be of value in the analyses of clinical and epidemiological cohorts. Noncoding RNAs provide epigenetic regulatory circuits within the kidney, which reciprocally interact with DNA methylation processes, histone modification and chromatin. These interactions have been demonstrated to reflect the biological age and function of renal allografts. Epigenetic factors control gene expression and activity in response to environmental perturbations. They also have roles in highly conserved signalling pathways that modulate ageing, including the mTOR and insulin/insulin-like growth factor signalling pathways, and regulation of sirtuin activity. Nutrition, the gut microbiota, inflammation and environmental factors, including psychosocial and lifestyle stresses, provide potential mechanistic links between the epigenetic landscape of ageing and renal dysfunction. Approaches to modify the renal epigenome via nutritional intervention, targeting the methylome or targeting chromatin seem eminently feasible, although caution is merited owing to the potential for intergenerational and transgenerational effects.
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Affiliation(s)
- Paul G Shiels
- Section of Epigenetics, Institute of Cancer Sciences, Wolfson Wohl Translational Research Centre, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Dagmara McGuinness
- Section of Epigenetics, Institute of Cancer Sciences, Wolfson Wohl Translational Research Centre, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Maria Eriksson
- Department of Biosciences and Nutrition (BioNut), H2, Eriksson, Novum 141, 83 Huddinge, Sweden
| | - Jeroen P Kooman
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastrich, Netherlands
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Huddinge, Karolinska Institutet, SE-14157 Stockholm, Sweden
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142
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Golson ML, Kaestner KH. Epigenetics in formation, function, and failure of the endocrine pancreas. Mol Metab 2017; 6:1066-1076. [PMID: 28951829 PMCID: PMC5605720 DOI: 10.1016/j.molmet.2017.05.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 01/17/2023] Open
Abstract
Background Epigenetics, in the broadest sense, governs all aspects of the life of any multicellular organism, as it controls how differentiated cells arrive at their unique phenotype during development and differentiation, despite having a uniform (with some exceptions such as T-cells and germ cells) genetic make-up. The endocrine pancreas is no exception. Transcriptional regulators and epigenetic modifiers shape the differentiation of the five major endocrine cell types from their common precursor in the fetal pancreatic bud. Beyond their role in cell differentiation, interactions of the organism with the environment are also often encoded into permanent or semi-permanent epigenetic marks and affect cellular behavior and organismal health. Epigenetics is defined as any heritable – at least through one mitotic cell division – change in phenotype or trait that is not the result of a change in genomic DNA sequence, and it forms the basis that mediates the environmental impact on diabetes susceptibility and islet function. Scope of review We will summarize the impact of epigenetic regulation on islet cell development, maturation, function, and pathophysiology. We will briefly recapitulate the major epigenetic marks and their relationship to gene activity, and outline novel strategies to employ targeted epigenetic modifications as a tool to improve islet cell function. Major conclusions The improved understanding of the epigenetic underpinnings of islet cell differentiation, function and breakdown, as well as the development of innovative tools for their manipulation, is key to islet cell biology and the discovery of novel approaches to therapies for islet cell failure.
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Affiliation(s)
- Maria L Golson
- University of Pennsylvania, Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA, USA
| | - Klaus H Kaestner
- University of Pennsylvania, Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA, USA
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143
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Santiago JA, Bottero V, Potashkin JA. Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology. Front Aging Neurosci 2017; 9:166. [PMID: 28611656 PMCID: PMC5446999 DOI: 10.3389/fnagi.2017.00166] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer’s (AD), Parkinson’s (PD) and Huntington’s diseases (HD). We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.
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Affiliation(s)
- Jose A Santiago
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and ScienceNorth Chicago, IL, United States
| | - Virginie Bottero
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and ScienceNorth Chicago, IL, United States
| | - Judith A Potashkin
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and ScienceNorth Chicago, IL, United States
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144
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Alivand MR, Soheili ZS, Pornour M, Solali S, Sabouni F. Novel Epigenetic Controlling of Hypoxia Pathway Related to Overexpression and Promoter Hypomethylation of TET1 and TET2 in RPE Cells. J Cell Biochem 2017; 118:3193-3204. [PMID: 28252217 DOI: 10.1002/jcb.25965] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 02/28/2017] [Indexed: 12/19/2022]
Abstract
CpG methylation of DNA takes part in a specific epigenetic memory that plays crucial roles in the differentiation and abnormality of the cells. The methylation pattern aberration of genomes is affected in three ways, namely DNA methyltransferase (DNMT), ten-eleven translocation (TET), and methyl-binding domain (MBD) proteins. Of these, TET enzymes have recently been demonstrated to be master modifier enzymes in the DNA methylation process. Additionally, recent studies emphasize that not only epigenetic phenomena play a role in controlling hypoxia pathway, but the hypoxia condition also triggers hypomethylation of genomes that may help with the expression of hypoxia pathway genes. In this study, we suggested that TET1 and TET2 could play a role in the demethylation of genomes under chemical hypoxia conditions. Herein, the evaluating methylation status and mRNA expression of mentioned genes were utilized through real-time PCR and methylation-specific PCR (MSP), respectively. Our results showed that TET1 and TET2 genes were overexpressed (P < 0.05) under chemical hypoxia conditions in Retinal Pigment Epithelial (RPE) cells, whereas the promoter methylation status of them were hypomethylated in the same condition. Therefore, chemical hypoxia not only causes overexpression of TET1 and TET2 but also could gradually do promoter demethylation of same genes. This is the first study to show the relationship between epigenetics and the expression of mentioned genes related to hypoxia pathways. Furthermore, it seems that these associations in RPE cells are subjected to chemical hypoxia as a mechanism that could play a crucial role in methylation pattern changes of hypoxia-related diseases such as cancer and ischemia. J. Cell. Biochem. 118: 3193-3204, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra-Soheila Soheili
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Saeed Solali
- Department of Hematology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Sabouni
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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145
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Petkovich DA, Podolskiy DI, Lobanov AV, Lee SG, Miller RA, Gladyshev VN. Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions. Cell Metab 2017; 25:954-960.e6. [PMID: 28380383 PMCID: PMC5578459 DOI: 10.1016/j.cmet.2017.03.016] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/09/2017] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Abstract
The DNA methylation levels of certain CpG sites are thought to reflect the pace of human aging. Here, we developed a robust predictor of mouse biological age based on 90 CpG sites derived from partial blood DNA methylation profiles. The resulting clock correctly determines the age of mouse cohorts, detects the longevity effects of calorie restriction and gene knockouts, and reports rejuvenation of fibroblast-derived iPSCs. The data show that mammalian DNA methylomes are characterized by CpG sites that may represent the organism's biological age. They are scattered across the genome, they are distinct in human and mouse, and their methylation gradually changes with age. The clock derived from these sites represents a biomarker of aging and can be used to determine the biological age of organisms and evaluate interventions that alter the rate of aging.
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Affiliation(s)
- Daniel A Petkovich
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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146
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The epigenetic landscape of age-related diseases: the geroscience perspective. Biogerontology 2017; 18:549-559. [PMID: 28352958 PMCID: PMC5514215 DOI: 10.1007/s10522-017-9695-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/14/2017] [Indexed: 12/11/2022]
Abstract
In this review, we summarize current knowledge regarding the epigenetics of age-related diseases, focusing on those studies that have described DNA methylation landscape in cardio-vascular diseases, musculoskeletal function and frailty. We stress the importance of adopting the conceptual framework of “geroscience”, which starts from the observation that advanced age is the major risk factor for several of these pathologies and aims at identifying the mechanistic links between aging and age-related diseases. DNA methylation undergoes a profound remodeling during aging, which includes global hypomethylation of the genome, hypermethylation at specific loci and an increase in inter-individual variation and in stochastic changes of DNA methylation values. These epigenetic modifications can be an important contributor to the development of age-related diseases, but our understanding on the complex relationship between the epigenetic signatures of aging and age-related disease is still poor. The most relevant results in this field come from the use of the so called “epigenetics clocks” in cohorts of subjects affected by age-related diseases. We report these studies in final section of this review.
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147
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Hahn O, Grönke S, Stubbs TM, Ficz G, Hendrich O, Krueger F, Andrews S, Zhang Q, Wakelam MJ, Beyer A, Reik W, Partridge L. Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. Genome Biol 2017; 18:56. [PMID: 28351387 PMCID: PMC5370449 DOI: 10.1186/s13059-017-1187-1] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/02/2017] [Indexed: 12/11/2022] Open
Abstract
Background Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by which DR interacts with the aging process to improve health in old age are poorly understood. DNA methylation could play an important role in mediating the effects of DR because it is sensitive to the effects of nutrition and can affect gene expression memory over time. Results Here, we profile genome-wide changes in DNA methylation, gene expression and lipidomics in response to DR and aging in female mouse liver. DR is generally strongly protective against age-related changes in DNA methylation. During aging with DR, DNA methylation becomes targeted to gene bodies and is associated with reduced gene expression, particularly of genes involved in lipid metabolism. The lipid profile of the livers of DR mice is correspondingly shifted towards lowered triglyceride content and shorter chain length of triglyceride-associated fatty acids, and these effects become more pronounced with age. Conclusions Our results indicate that DR remodels genome-wide patterns of DNA methylation so that age-related changes are profoundly delayed, while changes at loci involved in lipid metabolism affect gene expression and the resulting lipid profile. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1187-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oliver Hahn
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.,Cellular Networks and Systems Biology, CECAD, University of Cologne, Joseph-Stelzmann-Str. 26, Cologne, 50931, Germany
| | - Sebastian Grönke
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Thomas M Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Oliver Hendrich
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Qifeng Zhang
- Inositide Lab, The Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Andreas Beyer
- Cellular Networks and Systems Biology, CECAD, University of Cologne, Joseph-Stelzmann-Str. 26, Cologne, 50931, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50931, Germany.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany. .,Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, WC1E 6BT, UK.
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148
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Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol 2017; 18:57. [PMID: 28351423 PMCID: PMC5371228 DOI: 10.1186/s13059-017-1186-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans. RESULTS We first examined whether mice and humans experience similar patterns of change in the methylome with age. We found moderate conservation of CpG sites for which methylation is altered with age, with both species showing an increase in methylome disorder during aging. Based on this analysis, we formulated an epigenetic-aging model in mice using the liver methylomes of 107 mice from 0.2 to 26.0 months old. To examine whether epigenetic aging signatures are slowed by longevity-promoting interventions, we analyzed 28 additional methylomes from mice subjected to lifespan-extending conditions, including Prop1df/df dwarfism, calorie restriction or dietary rapamycin. We found that mice treated with these lifespan-extending interventions were significantly younger in epigenetic age than their untreated, wild-type age-matched controls. CONCLUSIONS This study shows that lifespan-extending conditions can slow molecular changes associated with an epigenetic clock in mice livers.
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Affiliation(s)
- Tina Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brian Tsui
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Neil A Robertson
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Andrew M Gross
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael Ku Yu
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Holly M Brown-Borg
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Peter D Adams
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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149
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Dozmorov MG, Coit P, Maksimowicz-McKinnon K, Sawalha AH. Age-associated DNA methylation changes in naive CD4 + T cells suggest an evolving autoimmune epigenotype in aging T cells. Epigenomics 2017; 9:429-445. [PMID: 28322571 DOI: 10.2217/epi-2016-0143] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM We sought to define age-associated DNA methylation changes in naive CD4+ T cells. MATERIALS & METHODS Naive CD4+ T cells were collected from 74 healthy individuals (age 19-66 years), and age-related DNA methylation changes were characterized. RESULTS We identified 11,431 age-associated CpG sites, 57% of which were hypermethylated with age. Hypermethylated sites were enriched in CpG islands and repressive transcription factor binding sites, while hypomethylated sites showed T cell specific enrichment in active enhancers marked by H3K27ac and H3K4me1. Our data emphasize cancer-related DNA methylation changes with age, and also reveal age-associated hypomethylation in immune-related pathways, such as T cell receptor signaling, FCγR-mediated phagocytosis, apoptosis and the mammalian target of rapamycin signaling pathway. The MAPK signaling pathway was hypermethylated with age, consistent with a defective MAPK signaling in aging T cells. CONCLUSION Age-associated DNA methylation changes may alter regulatory mechanisms and signaling pathways that predispose to autoimmunity.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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150
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Wang D, Huang JH, Zeng QH, Gu C, Ding S, Lu JY, Chen J, Yang SB. Increased 5-hydroxymethylcytosine and Ten-eleven Translocation Protein Expression in Ultraviolet B-irradiated HaCaT Cells. Chin Med J (Engl) 2017; 130:594-599. [PMID: 28229992 PMCID: PMC5339934 DOI: 10.4103/0366-6999.200539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine (5mC) is catalyzed to 5- hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) family proteins. Recent studies have revealed that aberrant TETs expression or 5hmC level may play important roles in the occurrence and development of various pathological and physiological processes including cancer and aging. This study aimed to explore the relation between aberrant DNA hydroxymethylation with skin photoaging and to investigate the levels of TETs, 5mC, and 5hmC expression 24 h after 40 mJ/cm2 and 80 mJ/cm2 doses of ultraviolet B (UVB) irradiation to HaCaT cells. Methods: To explore whether aberrant DNA hydroxymethylation is also related to skin photoaging, 40 mJ/cm2 and 80 mJ/cm2 doses of UVB were chosen to treat keratinocytes (HaCaT cells). After 24 h of UVB irradiation, 5mC and 5hmC levels were determined by immunohistochemistry (IHC) and immunofluorescence (IF), and at the same time, the expression levels of matrix metalloproteinase 1 (MMP-1) and TETs were assessed by reverse transcription-polymerase chain reaction or Western blot analysis. Results: After 40 mJ/cm2 and 80 mJ/cm2 doses of UVB exposure, both IHC and IF results showed that 5hmC levels increased significantly, while the 5mC levels did not exhibit significant changes in HaCaT cells, compared with HaCat cells without UVB exposure. Moreover, compared with HaCat cells without UVB exposure, the levels of TET1, TET2, and TET3 mRNA and protein expression were significantly upregulated (mRNA: P = 0.0022 and 0.0043 for TET1; all P < 0.0001 for TET2; all P = 0.0006 for TET3; protein: P = 0.0012 and 0.0006 for TET1; all P = 0.0022 for TET2; and all P = 0.0002 for TET3), and the levels of MMP-1 mRNA expression increased dose dependently in 40 mJ/cm2 and 80 mJ/cm2 UVB-irradiated groups. Conclusion: UVB radiation could cause increased 5hmC and TET expression, which might become a novel biomarker in UVB-related skin aging.
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Affiliation(s)
- Dan Wang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jin-Hua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Qing-Hai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Can Gu
- Department of Community Nursing, Xiangya School of Nursing, Central South University, Changsha, Hunan 410013, China
| | - Shu Ding
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jian-Yun Lu
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Sheng-Bo Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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