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      Epigenetics of Delirium and Aging: Potential Role of DNA Methylation Change on Cytokine Genes in Glia and Blood Along With Aging

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          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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          Most cited references33

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          Delirium in older persons.

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            Epigenetic Mechanisms of Longevity and Aging.

            Aging is an inevitable outcome of life, characterized by progressive decline in tissue and organ function and increased risk of mortality. Accumulating evidence links aging to genetic and epigenetic alterations. Given the reversible nature of epigenetic mechanisms, these pathways provide promising avenues for therapeutics against age-related decline and disease. In this review, we provide a comprehensive overview of epigenetic studies from invertebrate organisms, vertebrate models, tissues, and in vitro systems. We establish links between common operative aging pathways and hallmark chromatin signatures that can be used to identify "druggable" targets to counter human aging and age-related disease.
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              Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

              Summary: The minfi package is widely used for analyzing Illumina DNA methylation array data. Here we describe modifications to the minfi package required to support the HumanMethylationEPIC (‘EPIC’) array from Illumina. We discuss methods for the joint analysis and normalization of data from the HumanMethylation450 (‘450k’) and EPIC platforms. We introduce the single-sample Noob (ssNoob) method, a normalization procedure suitable for incremental preprocessing of individual methylation arrays and conclude that this method should be used when integrating data from multiple generations of Infinium methylation arrays. We show how to use reference 450k datasets to estimate cell type composition of samples on EPIC arrays. The cumulative effect of these updates is to ensure that minfi provides the tools to best integrate existing and forthcoming Illumina methylation array data. Availability and Implementation: The minfi package version 1.19.12 or higher is available for all platforms from the Bioconductor project. Contact: khansen@jhsph.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                Journal
                Front Aging Neurosci
                Front Aging Neurosci
                Front. Aging Neurosci.
                Frontiers in Aging Neuroscience
                Frontiers Media S.A.
                1663-4365
                23 October 2018
                2018
                : 10
                : 311
                Affiliations
                [1] 1Department of Psychiatry, Carver College of Medicine, University of Iowa , Iowa City, IA, United States
                [2] 2Department of Psychiatry and Behavioral Sciences, Johns Hopkins University , Baltimore, MD, United States
                [3] 3Department of Epidemiology, School of Public Health, Columbia University Medical Center, Columbia University , New York, NY, United States
                [4] 4Department of Neurosurgery, University of Iowa, Carver College of Medicine , Iowa City, IA, United States
                [5] 5Department of Biostatistics, College of Public Health, University of Iowa , Iowa City, IA, United States
                Author notes

                Edited by: Ashok Kumar, University of Florida, United States

                Reviewed by: Aida Karachi, University of Florida, United States; Alexander V. Favorov, Johns Hopkins University, United States

                *Correspondence: Gen Shinozaki gen-shinozaki@ 123456uiowa.edu
                Article
                10.3389/fnagi.2018.00311
                6206747
                30405391
                ae92428f-6bd5-4403-aeaf-6f2709888a21
                Copyright © 2018 Shinozaki, Braun, Hing, Ratanatharathorn, Klisares, Duncan, Jellison, Heinzman, Nagahama, Close, Sabbagh, Dlouhy, Howard, Kawasaki and Cho.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 18 July 2018
                : 14 September 2018
                Page count
                Figures: 4, Tables: 2, Equations: 0, References: 51, Pages: 10, Words: 7947
                Categories
                Neuroscience
                Original Research

                Neurosciences
                delirium,epigenetics,dna methylation,cytokine,tnf-alpha,aging
                Neurosciences
                delirium, epigenetics, dna methylation, cytokine, tnf-alpha, aging

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