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      Is Open Access

      The transcriptional landscape of age in human peripheral blood

      research-article
      1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , NABEC/UKBEC Consortium, 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 2 , 3 , 2 , 28 , 29 , 2 , 3 , 30 , 1 , 30 , 1 , 30 , 1 , 1 , 1 , 1 , 1 , 1 , 10 , 31 , 10 , 32 , 33 , 31 , 34 , 32 , 33 , 35 , 36 , 35 , 37 , 35 , 36 , 37 , 38 , 35 , 36 , 35 , 36 , 39 , 5 , 40 , 41 , 5 , 42 , 4 , 4 , 43 , 44 , 45 , 20 , 20 , 20 , 20 , 12 , 46 , 47 , 48 , 49 , 50 , 51 , 51 , 52 , 53 , 10 , 17 , 18 , 17 , 18 , 54 , 55 , 18 , 9 , 56 , 57 , 58 , 58 , 57 , 7 , 58 , 59 , 60 , 60 , 61 , 62 , 62 , 63 , 64 , 65 , 19 , 63 , 19 , 11 , 66 , 15 , 15 , 15 , 67 , 68 , 69 , 70 , 71 , 56 , 72 , 20 , 19 , 57 , 49 , 50 , 12 , 17 , 18 , 73 , 49 , 50 , 15 , 11 , 16 , 13 , 14 , 74 , 10 , 46 , 75 , 76 , 5 , a , 1 , b , 2 , 3
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          Abstract

          Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts.

          Abstract

          Ageing increases the risk of many diseases. Here the authors compare blood cell transcriptomes of over 14,000 individuals and identify a set of about 1,500 genes that are differently expressed with age, shedding light on transcriptional programs linked to the ageing process and age-associated diseases.

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          Most cited references52

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          The role of mitochondria in aging.

          Over the last decade, accumulating evidence has suggested a causative link between mitochondrial dysfunction and major phenotypes associated with aging. Somatic mitochondrial DNA (mtDNA) mutations and respiratory chain dysfunction accompany normal aging, but the first direct experimental evidence that increased mtDNA mutation levels contribute to progeroid phenotypes came from the mtDNA mutator mouse. Recent evidence suggests that increases in aging-associated mtDNA mutations are not caused by damage accumulation, but rather are due to clonal expansion of mtDNA replication errors that occur during development. Here we discuss the caveats of the traditional mitochondrial free radical theory of aging and highlight other possible mechanisms, including insulin/IGF-1 signaling (IIS) and the target of rapamycin pathways, that underlie the central role of mitochondria in the aging process.
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            • Abstract: found
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            Decline in skeletal muscle mitochondrial function with aging in humans.

            Cumulative mtDNA damage occurs in aging animals, and mtDNA mutations are reported to accelerate aging in mice. We determined whether aging results in increased DNA oxidative damage and reduced mtDNA abundance and mitochondrial function in skeletal muscle of human subjects. Studies performed in 146 healthy men and women aged 18-89 yr demonstrated that mtDNA and mRNA abundance and mitochondrial ATP production all declined with advancing age. Abundance of mtDNA was positively related to mitochondrial ATP production rate, which in turn, was closely associated with aerobic capacity and glucose tolerance. The content of several mitochondrial proteins was reduced in older muscles, whereas the level of the oxidative DNA lesion, 8-oxo-deoxyguanosine, was increased, supporting the oxidative damage theory of aging. These results demonstrate that age-related muscle mitochondrial dysfunction is related to reduced mtDNA and muscle functional changes that are common in the elderly.
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              • Abstract: found
              • Article: not found

              Meta-analysis of age-related gene expression profiles identifies common signatures of aging.

              Numerous microarray studies of aging have been conducted, yet given the noisy nature of gene expression changes with age, elucidating the transcriptional features of aging and how these relate to physiological, biochemical and pathological changes remains a critical problem. We performed a meta-analysis of age-related gene expression profiles using 27 datasets from mice, rats and humans. Our results reveal several common signatures of aging, including 56 genes consistently overexpressed with age, the most significant of which was APOD, and 17 genes underexpressed with age. We characterized the biological processes associated with these signatures and found that age-related gene expression changes most notably involve an overexpression of inflammation and immune response genes and of genes associated with the lysosome. An underexpression of collagen genes and of genes associated with energy metabolism, particularly mitochondrial genes, as well as alterations in the expression of genes related to apoptosis, cell cycle and cellular senescence biomarkers, were also observed. By employing a new method that emphasizes sensitivity, our work further reveals previously unknown transcriptional changes with age in many genes, processes and functions. We suggest these molecular signatures reflect a combination of degenerative processes but also transcriptional responses to the process of aging. Overall, our results help to understand how transcriptional changes relate to the process of aging and could serve as targets for future studies. http://genomics.senescence.info/uarrays/signatures.html. Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                22 October 2015
                2015
                : 6
                : 8570
                Affiliations
                [1 ]Department of Internal Medicine, Erasmus Medical Centre Rotterdam , Rotterdam 3000CA, The Netherlands
                [2 ]The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study , Framingham, Massachusetts 01702, USA
                [3 ]Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute , Bethesda, Maryland 20817, USA
                [4 ]Epidemiology and Public Health, University of Exeter Medical School , Exeter EX4 1DB, UK
                [5 ]Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Greifswald 17493, Germany
                [6 ]The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity & Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai , One Gustave L. Levy Place, New York 10029, USA
                [7 ]Department of Human Genetics, School of Medicine, Emory University , Atlanta, Georgia 30301, USA
                [8 ]Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland , St Lucia, Brisbane, Queensland 4000, Australia
                [9 ]The Institute for Molecular Bioscience, University of Queensland , Brisbane, Queensland 4000, Australia
                [10 ]Estonian Genome Center, University of Tartu , Tartu 0794, Estonia
                [11 ]Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory , Bar Harbor, Maine 04609, USA
                [12 ]Department of Genetics, University Medical Center Groningen, University of Groningen , Groningen 9700RB, The Netherlands
                [13 ]Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health , Neuherberg 85764, Germany
                [14 ]Institute of Human Genetics, Technical University Munich , Munich 85540, Germany
                [15 ]Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney , Sydney, New South Wales 2006, Australia
                [16 ]Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health , Phoenix, Arizona 85001, USA
                [17 ]Institute for Molecular Medicine Finland FIMM, University of Helsinki , Helsinki 00131, Finland
                [18 ]Department of Chronic Disease Prevention, National Institute for Health and Welfare , Helsinki 00131, Finland
                [19 ]Department of Molecular Epidemiology, Leiden University Medical Center , Leiden 2300RC, The Netherlands
                [20 ]Department of Genetics, Texas Biomedical Research Institute , San Antonio, Texas 78201, USA
                [21 ]Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Sciences , Center at Houston, Texas 77001, USA
                [22 ]Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston , Houston, Texas 77001, USA
                [23 ]Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine , Winston-Salem, North Carolina 27101, USA
                [24 ]Computational Medicine Core, Center for Lung Biology, University of Washington , Seattle, Washington 98101, USA
                [25 ]Section of Genetic Medicine, Institute for Genomics and Systems Biology, University of Chicago , Chicago, Illinois 60290, USA
                [26 ]Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02108, USA
                [27 ]Center of Human Development and Aging, New Jersey Medical School , Newark 07101, USA
                [28 ]General Internal Medicine Section, Boston University , Boston, Massachusetts 02108, USA
                [29 ]The Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health , Bethesda, Maryland 20817, USA
                [30 ]Department of Epidemiology, Erasmus Medical Center , Rotterdam 3000CA, The Netherlands
                [31 ]Molecular Pathology, Institute of Biomedicine, University of Tartu , Tartu 0794, Estonia
                [32 ]Department of Cardiovascular Sciences, University of Leicester , Leicester LE1, UK
                [33 ]National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital , Leicester LE1, UK
                [34 ]Institute of Molecular and Cell Biology, Estonian Genome Center, University of Tartu , Tartu 0794, Estonia
                [35 ]Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health , Neuherberg 85764, Germany
                [36 ]Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health , Neuherberg 85764, Germany
                [37 ]Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf , Düsseldorf 40593, Germany
                [38 ]Division of Endocrinology and Diabetology, University Hospital Düsseldorf, Heinrich Heine University , Düsseldorf 40593, Germany
                [39 ]Hannover Unified Biobank, Hannover Medical School , Hannover 30519, Germany
                [40 ]Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, University Medicine Greifswald , Greifswald 17489, Germany
                [41 ]Institute for Community Medicine, University Medicine Greifswald , Greifswald 17489, Germany
                [42 ]Unit of Periodontology, Department of Restorative Dentistry, Periodontology and Endodontology, University Medicine Greifswald , Greifswald 17489, Germany
                [43 ]Genetics of Complex Traits, University of Exeter Medical School, University of Exeter , Exeter EX2 5DW, UK
                [44 ]Geriatric Unit, Azienda Sanitaria di Firenze , Florence 50123, Italy
                [45 ]Centre for Genetic Origins of Health and Disease, The University of Western Australia, and Faculty of Health Sciences, Curtin University , Perth, Western Australia 9011, Australia
                [46 ]Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge 02138, USA
                [47 ]Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , Boston, Massachusetts 02108, USA
                [48 ]Partners Center for Personalized Genetic Medicine , Boston, Massachusetts 02108, USA
                [49 ]The Queensland Brain Institute, University of Queensland , Brisbane, Queensland 4000, Australia
                [50 ]University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital , Brisbane, Queensland 4000, Australia
                [51 ]Department of Epidemiology, University of Michigan , Ann Arbor, Michigan 48103, USA
                [52 ]Department of Biosciences, University of Helsinki , Helsinki 00100, Finland
                [53 ]Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare , Helsinki 00100, Finland
                [54 ]Wellcome Trust Sanger Institute , Hinxton, Cambridge CB4, UK
                [55 ]Department of Public Health, Hjelt Institute, University of Helsinki , Helsinki 00100, Finland
                [56 ]QIMR Berghofer Medical Research Institute , Brisbane, Queensland 4000, Australia
                [57 ]Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine , Atlanta, Georgia 30301, USA
                [58 ]Max-Planck Institute of Psychiatry , Munich 80331, Germany
                [59 ]Department of Internal Medicine, Wake Forest School of Medicine , Winston-Salem, North Carolina 27101, USA
                [60 ]Department of Epidemiology, University of Washington , Seattle, Washington 98101, USA
                [61 ]Cardiovascular Health Research Unit, Department of Medicine, University of Washington , Seattle, Washington 98101, USA
                [62 ]Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, California 90501, USA
                [63 ]Department of Medical Statistics, Leiden University Medical Center , Leiden 2300RC, The Netherlands
                [64 ]Department of Rheumatology, Leiden University Medical Center , Leiden 2300RC, The Netherlands
                [65 ]Department of Clinical Epidemiology, Leiden University Medical Center , Leiden 2300RC, The Netherlands
                [66 ]Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02138, USA
                [67 ]Cardiovascular Health Research Unit, Department of Medicine, University of Washington , Seattle, Washington 98195, USA
                [68 ]Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington , Seattle, Washington 98195, USA
                [69 ]Cardiovascular Health Research Unit, Department of Health Services, University of Washington , Seattle, Washington 98195, USA
                [70 ]Group Health Research Institute, Group Health Cooperative , Seattle, Washington 98195, USA
                [71 ]Department of Pathology, University of Vermont College of Medicine , Colchester, Vermont 98195, USA
                [72 ]Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic , Rochester, Minnesota 55901, USA
                [73 ]Computational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu , Oulu 90570, Finland
                [74 ]Clinical Research Branch, National Institute on Aging , Baltimore, Maryland 21218, USA
                [75 ]Division of Endocrinology, Children's Hospital Boston , Boston, Massachusetts 02108, USA
                [76 ]Department of Genetics, Harvard Medical School , Boston, Massachusetts 02108, USA
                [77 ]Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health , Bethesda, Maryland 20817, USA.
                [78 ]Reta Lila Weston Institute and Department of Molecular Neuroscience, UCL Institute of Neurology , Queen Square, London WC1N 3BG, UK.
                [79 ]Department of Medical and Molecular Genetics, King's College London, Guy's Hospital , London SE1 9RT, UK.
                [80 ]Research Resources Branch, National Institute on Aging, National Institutes of Health, Bethesda , Maryland 20817, USA.
                [81 ]Department of Neuroscience, Karolinska Institutet , Stockholm 10044, Sweden.
                [82 ]Department of Neuropathology, MRC Sudden Death Brain Bank Project, University of Edinburgh , Edinburgh EH13, UK.
                [83 ]Lymphocyte Cell Biology Unit, Laboratory of Immunology, National Institute on Aging, National Institutes of Health , Baltimore, Maryland 20817, USA.
                [84 ]Department of Genetics, King Faisal Specialist Hospital and Research Centre 11564, Saudi Arabia.
                [85 ]Brain Resource Center, Johns Hopkins University , Baltimore, Maryland 20817, USA.
                [86 ]ITGR Biomarker Discovery Group, Genentech , South San Francisco, California 94101, USA.
                [87 ]NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland Medical School , Baltimore, Maryland 2117, USA.
                Author notes
                [*]

                These authors contributed equally to this work.

                [†]

                These authors jointly supervised the work.

                [‡]

                A full list of consortium members appears below.

                Article
                ncomms9570
                10.1038/ncomms9570
                4639797
                26490707
                5e35d9ca-e9fb-455f-aa3b-2542ccb77bcf
                Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 16 January 2015
                : 07 September 2015
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