151
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Morris G, Puri BK, Frye RE. The putative role of environmental aluminium in the development of chronic neuropathology in adults and children. How strong is the evidence and what could be the mechanisms involved? Metab Brain Dis 2017; 32:1335-1355. [PMID: 28752219 PMCID: PMC5596046 DOI: 10.1007/s11011-017-0077-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/19/2017] [Indexed: 02/06/2023]
Abstract
The conceptualisation of autistic spectrum disorder and Alzheimer's disease has undergone something of a paradigm shift in recent years and rather than being viewed as single illnesses with a unitary pathogenesis and pathophysiology they are increasingly considered to be heterogeneous syndromes with a complex multifactorial aetiopathogenesis, involving a highly complex and diverse combination of genetic, epigenetic and environmental factors. One such environmental factor implicated as a potential cause in both syndromes is aluminium, as an element or as part of a salt, received, for example, in oral form or as an adjuvant. Such administration has the potential to induce pathology via several routes such as provoking dysfunction and/or activation of glial cells which play an indispensable role in the regulation of central nervous system homeostasis and neurodevelopment. Other routes include the generation of oxidative stress, depletion of reduced glutathione, direct and indirect reductions in mitochondrial performance and integrity, and increasing the production of proinflammatory cytokines in both the brain and peripherally. The mechanisms whereby environmental aluminium could contribute to the development of the highly specific pattern of neuropathology seen in Alzheimer's disease are described. Also detailed are several mechanisms whereby significant quantities of aluminium introduced via immunisation could produce chronic neuropathology in genetically susceptible children. Accordingly, it is recommended that the use of aluminium salts in immunisations should be discontinued and that adults should take steps to minimise their exposure to environmental aluminium.
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Affiliation(s)
- Gerwyn Morris
- Tir Na Nog, Bryn Road seaside 87, Llanelli, Wales, SA15 2LW, UK
| | - Basant K Puri
- Department of Medicine, Imperial College London, Hammersmith Hospital, London, England, W12 0HS, UK.
| | - Richard E Frye
- College of Medicine, Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital Research Institute, Little Rock, AR, 72202, USA
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152
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Siu MT, Weksberg R. Epigenetics of Autism Spectrum Disorder. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:63-90. [PMID: 28523541 DOI: 10.1007/978-3-319-53889-1_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD), one of the most common childhood neurodevelopmental disorders (NDDs), is diagnosed in 1 of every 68 children. ASD is incredibly heterogeneous both clinically and aetiologically. The etiopathogenesis of ASD is known to be complex, including genetic, environmental and epigenetic factors. Normal epigenetic marks modifiable by both genetics and environmental exposures can result in epigenetic alterations that disrupt the regulation of gene expression, negatively impacting biological pathways important for brain development. In this chapter we aim to summarize some of the important literature that supports a role for epigenetics in the underlying molecular mechanism of ASD. We provide evidence from work in genetics, from environmental exposures and finally from more recent studies aimed at directly determining ASD-specific epigenetic patterns, focusing mainly on DNA methylation (DNAm). Finally, we briefly discuss some of the implications of current research on potential epigenetic targets for therapeutics and novel avenues for future work.
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Affiliation(s)
- Michelle T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Department of Paediatrics, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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153
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BECon: a tool for interpreting DNA methylation findings from blood in the context of brain. Transl Psychiatry 2017; 7:e1187. [PMID: 28763057 PMCID: PMC5611738 DOI: 10.1038/tp.2017.171] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/14/2017] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue-specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well-documented. Here, we aimed to provide a resource to the community to aid interpretation of blood-based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450 K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data, we have made available metrics on: the variability of cytosine-phosphate-guanine dinucleotides (CpGs) in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance; https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood-based human DNA methylation results, in the context of brain.
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154
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Reilly J, Gallagher L, Chen JL, Leader G, Shen S. Bio-collections in autism research. Mol Autism 2017; 8:34. [PMID: 28702161 PMCID: PMC5504648 DOI: 10.1186/s13229-017-0154-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with diverse clinical manifestations and symptoms. In the last 10 years, there have been significant advances in understanding the genetic basis for ASD, critically supported through the establishment of ASD bio-collections and application in research. Here, we summarise a selection of major ASD bio-collections and their associated findings. Collectively, these include mapping ASD candidate genes, assessing the nature and frequency of gene mutations and their association with ASD clinical subgroups, insights into related molecular pathways such as the synapses, chromatin remodelling, transcription and ASD-related brain regions. We also briefly review emerging studies on the use of induced pluripotent stem cells (iPSCs) to potentially model ASD in culture. These provide deeper insight into ASD progression during development and could generate human cell models for drug screening. Finally, we provide perspectives concerning the utilities of ASD bio-collections and limitations, and highlight considerations in setting up a new bio-collection for ASD research.
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Affiliation(s)
- Jamie Reilly
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | - Louise Gallagher
- Trinity Translational Medicine Institute and Department of Psychiatry, Trinity Centre for Health Sciences, St. James Hospital Street, Dublin 8, Ireland
| | - June L Chen
- Department of Special Education, Faculty of Education, East China Normal University, Shanghai, 200062 China
| | - Geraldine Leader
- Irish Centre for Autism and Neurodevelopmental Research (ICAN), Department of Psychology, National University of Ireland Galway, University Road, Galway, Ireland
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
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155
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Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Brandon NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR. Altered expression of histamine signaling genes in autism spectrum disorder. Transl Psychiatry 2017; 7:e1126. [PMID: 28485729 PMCID: PMC5534955 DOI: 10.1038/tp.2017.87] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 12/18/2022] Open
Abstract
The histaminergic system (HS) has a critical role in cognition, sleep and other behaviors. Although not well studied in autism spectrum disorder (ASD), the HS is implicated in many neurological disorders, some of which share comorbidity with ASD, including Tourette syndrome (TS). Preliminary studies suggest that antagonism of histamine receptors 1-3 reduces symptoms and specific behaviors in ASD patients and relevant animal models. In addition, the HS mediates neuroinflammation, which may be heightened in ASD. Together, this suggests that the HS may also be altered in ASD. Using RNA sequencing (RNA-seq), we investigated genome-wide expression, as well as a focused gene set analysis of key HS genes (HDC, HNMT, HRH1, HRH2, HRH3 and HRH4) in postmortem dorsolateral prefrontal cortex (DLPFC) initially in 13 subjects with ASD and 39 matched controls. At the genome level, eight transcripts were differentially expressed (false discovery rate <0.05), six of which were small nucleolar RNAs (snoRNAs). There was no significant diagnosis effect on any of the individual HS genes but expression of the gene set of HNMT, HRH1, HRH2 and HRH3 was significantly altered. Curated HS gene sets were also significantly differentially expressed. Differential expression analysis of these gene sets in an independent RNA-seq ASD data set from DLPFC of 47 additional subjects confirmed these findings. Understanding the physiological relevance of an altered HS may suggest new therapeutic options for the treatment of ASD.
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Affiliation(s)
- C Wright
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,AstraZeneca Postdoc Program, Innovative Medicines and Early Development, Waltham, MA, USA
| | - J H Shin
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - A Rajpurohit
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - A Deep-Soboslay
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - L Collado-Torres
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - N J Brandon
- AstraZeneca Neuroscience, Innovative Medicines and Early Development, Waltham, MA, USA
| | - T M Hyde
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - J E Kleinman
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - A E Jaffe
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - A J Cross
- AstraZeneca Neuroscience, Innovative Medicines and Early Development, Waltham, MA, USA
| | - D R Weinberger
- Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA,The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Lieber Institute for Brain Development, Clinical Sciences, Johns Hopkins School of Medicine, Johns Hopkins Medical Campus, 855 North Wolfe Street, Suite 300, 3rd Floor, Baltimore, MD 21205, USA. E-mail:
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156
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Rivollier F, Chaumette B, Bendjemaa N, Chayet M, Millet B, Jaafari N, Barhdadi A, Lemieux Perreault LP, Provost S, Dubé MP, Gaillard R, Krebs MO, Kebir O. Methylomic changes in individuals with psychosis, prenatally exposed to endocrine disrupting compounds: Lessons from diethylstilbestrol. PLoS One 2017; 12:e0174783. [PMID: 28406917 PMCID: PMC5390994 DOI: 10.1371/journal.pone.0174783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/15/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In the Western world, between 1940 and 1970, more than 2 million people were exposed in utero to diethylstilbestrol (DES). In exposed individuals, and in their descendants, adverse outcomes have been linked to such exposure, including cancers, genital malformations, and less consistently, psychiatric disorders. We aimed to explore whether prenatal DES exposure would be associated with DNA methylation changes, and whether these epigenetic modifications would be associated with increased risk of psychosis. METHODS From 247 individuals born from mothers exposed to DES, we selected 69 siblings from 30 families. In each family, at least one sibling was exposed in utero to DES. We performed a methylome-wide association study using HumanMethylation450 DNA Analysis BeadChip® in peripheral blood. We analyzed methylation changes at individual CpGs or regions in exposed (n = 37) versus unexposed individuals (n = 32). We also compared exposed individuals with (n = 7) and without psychosis (n = 30). RESULTS There were more individuals with schizophrenia in the DES-exposed group. We found no significant differences between exposed and unexposed individuals with respect to differentially methylated CpGs or regions. The largest difference was in a region near the promoter of an ADAMTS proteoglycanase gene (ADAMTS9). Compared to exposed individuals without psychosis, exposed individuals with psychosis had differential methylation in the region encompassing the gene encoding the zinc finger protein 57 (ZFP57). CONCLUSIONS In utero exposure to DES was not associated with methylation changes at specific CpG or regions. In exposed individuals, however, psychosis was associated with specific methylomic modifications that could impact neurodevelopment and neuroplasticity.
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Affiliation(s)
- Fabrice Rivollier
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Boris Chaumette
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Narjes Bendjemaa
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Mélanie Chayet
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Bruno Millet
- Department of Adults Psychiatry, ICM-A-IHU, UPMC UMR S 975, Inserm U 1127, CNRS UMR 7225, GH Pitié-Salpêtrière, Paris, France
| | - Nematollah Jaafari
- Unité de Recherche Clinique en Psychiatrie Pierre Deniker, Centre Hospitalier Henri Laborit, INSERM CIC-P 1402, INSERM U 1084 Laboratoire Expérimental et Clinique en Neurosciences, Univ Poitiers, CHU Poitiers, Groupement De Recherche CNRS 3557, Poitiers, France
| | - Amina Barhdadi
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | | | - Sylvie Provost
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - Marie-Pierre Dubé
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - Raphaël Gaillard
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Marie-Odile Krebs
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Oussama Kebir
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
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157
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Lyall K, Croen L, Daniels J, Fallin MD, Ladd-Acosta C, Lee BK, Park BY, Snyder NW, Schendel D, Volk H, Windham GC, Newschaffer C. The Changing Epidemiology of Autism Spectrum Disorders. Annu Rev Public Health 2017; 38:81-102. [PMID: 28068486 PMCID: PMC6566093 DOI: 10.1146/annurev-publhealth-031816-044318] [Citation(s) in RCA: 550] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with lifelong impacts. Genetic and environmental factors contribute to ASD etiology, which remains incompletely understood. Research on ASD epidemiology has made significant advances in the past decade. Current prevalence is estimated to be at least 1.5% in developed countries, with recent increases primarily among those without comorbid intellectual disability. Genetic studies have identified a number of rare de novo mutations and gained footing in the areas of polygenic risk, epigenetics, and gene-by-environment interaction. Epidemiologic investigations focused on nongenetic factors have established advanced parental age and preterm birth as ASD risk factors, indicated that prenatal exposure to air pollution and short interpregnancy interval are potential risk factors, and suggested the need for further exploration of certain prenatal nutrients, metabolic conditions, and exposure to endocrine-disrupting chemicals. We discuss future challenges and goals for ASD epidemiology as well as public health implications.
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Affiliation(s)
- Kristen Lyall
- A.J. Drexel Autism Institute, Philadelphia, Pennsylvania 19104;
| | - Lisa Croen
- Kaiser Permanente Division of Research, Oakland, California 94612
| | - Julie Daniels
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, North Carolina 27599
| | - M Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Brian K Lee
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, Philadelphia, Pennsylvania 19104
- Department of Medical Epidemiology and Biostatistics and Department of Public Health Sciences, Karolinska Institute, SE 171-77 Stockholm, Sweden
| | - Bo Y Park
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | | | - Diana Schendel
- Department of Economics and Business, National Centre for Register-Based Research, Aarhus University, DK-8210 Aarhus, Denmark
- Department of Public Health, Section for Epidemiology, Aarhus University, DK-8000 Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Heather Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Gayle C Windham
- California Department of Public Health, Division of Environmental and Occupational Disease Control, Richmond, California 94805
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158
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Long HY, Feng L, Kang J, Luo ZH, Xiao WB, Long LL, Yan XX, Zhou L, Xiao B. Blood DNA methylation pattern is altered in mesial temporal lobe epilepsy. Sci Rep 2017; 7:43810. [PMID: 28276448 PMCID: PMC5343463 DOI: 10.1038/srep43810] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
Mesial temporal lobe epilepsy (MTLE) is a common epileptic disorder; little is known whether it is associated with peripheral epigenetic changes. Here we compared blood whole genomic DNA methylation pattern in MTLE patients (n = 30) relative to controls (n = 30) with the Human Methylation 450 K BeadChip assay, and explored genes and pathways that were differentially methylated using bioinformatics profiling. The MTLE and control groups showed significantly different (P < 1.03e-07) DNA methylation at 216 sites, with 164 sites involved hyper- and 52 sites hypo- methylation. Two hyper- and 32 hypo-methylated sites were associated with promoters, while 87 hyper- and 43 hypo-methylated sites corresponded to coding regions. The differentially methylated genes were largely related to pathways predicted to participate in anion binding, oxidoreductant activity, growth regulation, skeletal development and drug metabolism, with the most distinct ones included SLC34A2, CLCN6, CLCA4, CYP3A43, CYP3A4 and CYP2C9. Among the MTLE patients, panels of genes also appeared to be differentially methylated relative to disease duration, resistance to anti-epileptics and MRI alterations of hippocampal sclerosis. The peripheral epigenetic changes observed in MTLE could be involved in certain disease-related modulations and warrant further translational investigations.
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Affiliation(s)
- Hong-Yu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jin Kang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhao-Hui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wen-Biao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li-Li Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University School of Basic Medicine, Changsha, Hunan 410013, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Changsha, Hunan 410008, China
| | - Luo Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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159
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Ellis SE, Gupta S, Moes A, West AB, Arking DE. Exaggerated CpH methylation in the autism-affected brain. Mol Autism 2017; 8:6. [PMID: 28316770 PMCID: PMC5351204 DOI: 10.1186/s13229-017-0119-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/09/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The etiology of autism, a complex, heritable, neurodevelopmental disorder, remains largely unexplained. Given the unexplained risk and recent evidence supporting a role for epigenetic mechanisms in the development of autism, we explored the role of CpG and CpH (H = A, C, or T) methylation within the autism-affected cortical brain tissue. METHODS Reduced representation bisulfite sequencing (RRBS) was completed, and analysis was carried out in 63 post-mortem cortical brain samples (Brodmann area 19) from 29 autism-affected and 34 control individuals. Analyses to identify single sites that were differentially methylated and to identify any global methylation alterations at either CpG or CpH sites throughout the genome were carried out. RESULTS We report that while no individual site or region of methylation was significantly associated with autism after multi-test correction, methylated CpH dinucleotides were markedly enriched in autism-affected brains (~2-fold enrichment at p < 0.05 cutoff, p = 0.002). CONCLUSIONS These results further implicate epigenetic alterations in pathobiological mechanisms that underlie autism.
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Affiliation(s)
- Shannon E. Ellis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Simone Gupta
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Anna Moes
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Andrew B. West
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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160
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Kronfol MM, Dozmorov MG, Huang R, Slattum PW, McClay JL. The role of epigenomics in personalized medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017; 2:33-45. [PMID: 29276780 DOI: 10.1080/23808993.2017.1284557] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction Epigenetics is the study of reversible modifications to chromatin and their extensive and profound effects on gene regulation. To date, the role of epigenetics in personalized medicine has been under-explored. Therefore, this review aims to highlight the vast potential that epigenetics holds. Areas covered We first review the cell-specific nature of epigenetic states and how these can vary with developmental stage and in response to environmental factors. We then summarize epigenetic biomarkers of disease, with a focus on diagnostic tests, followed by a detailed description of current and pipeline drugs with epigenetic modes of action. Finally, we discuss epigenetic biomarkers of drug response. Expert commentary Epigenetic variation can yield information on cellular states and developmental histories in ways that genotype information cannot. Furthermore, in contrast to fixed genome sequence, epigenetic patterns are plastic, so correcting aberrant, disease-causing epigenetic marks holds considerable therapeutic promise. While just six epigenetic drugs are currently approved for use in the United States, a larger number is being developed. However, a drawback to current therapeutics is their non-specific effects. Development of locus-specific epigenetic modifiers, used in conjunction with epigenetic biomarkers of response, will enable truly precision interventions.
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Affiliation(s)
- Mohamad M Kronfol
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University School of Pharmacy, Richmond, Virginia, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Rong Huang
- Department of Medicinal Chemistry, Virginia Commonwealth University School of Pharmacy, Richmond, Virginia, USA
| | - Patricia W Slattum
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University School of Pharmacy, Richmond, Virginia, USA
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University School of Pharmacy, Richmond, Virginia, USA
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Chatterton Z, Hartley BJ, Seok MH, Mendelev N, Chen S, Milekic M, Rosoklija G, Stankov A, Trencevsja-Ivanovska I, Brennand K, Ge Y, Dwork AJ, Haghighi F. In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain. Epigenetics Chromatin 2017; 10:4. [PMID: 28149327 PMCID: PMC5270321 DOI: 10.1186/s13072-017-0111-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of cortical gray matter in childhood, indicating that prenatal exposure to tobacco may impact cortical development and manifest as behavioral problems. Cellular development is mediated by changes in epigenetic modifications such as DNA methylation, which can be affected by exposure to tobacco. Results In this study, we sought to ascertain how maternal smoking during pregnancy affects global DNA methylation profiles of the developing dorsolateral prefrontal cortex (DLPFC) during the second trimester of gestation. When DLPFC methylation profiles (assayed via Illumina, HM450) of smoking-exposed and unexposed fetuses were compared, no differentially methylated regions (DMRs) passed the false discovery correction (FDR ≤ 0.05). However, the most significant DMRs were hypomethylated CpG Islands within the promoter regions of GNA15 and SDHAP3 of smoking-exposed fetuses. Interestingly, the developmental up-regulation of SDHAP3 mRNA was delayed in smoking-exposed fetuses. Interaction analysis between gestational age and smoking exposure identified significant DMRs annotated to SYCE3, C21orf56/LSS, SPAG1 and RNU12/POLDIP3 that passed FDR. Furthermore, utilizing established methods to estimate cell proportions by DNA methylation, we found that exposed DLPFC samples contained a lower proportion of neurons in samples from fetuses exposed to maternal smoking. We also show through in vitro experiments that nicotine impedes the differentiation of neurons independent of cell death. Conclusions We found evidence that intrauterine smoking exposure alters the developmental patterning of DNA methylation and gene expression and is associated with reduced mature neuronal content, effects that are likely driven by nicotine. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0111-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zac Chatterton
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Brigham J Hartley
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Man-Ho Seok
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Natalia Mendelev
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Sean Chen
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Maria Milekic
- Department of Psychiatry, Columbia University, New York, NY 10032 USA
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, New York, NY 10032 USA.,Macedonian Academy of Sciences and Arts, Skopje, Macedonia.,School of Medicine, Skopje, Macedonia
| | | | | | - Kristen Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY 10032 USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY 10032 USA.,Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Fatemeh Haghighi
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029 USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Floor 10, Room 10-70D, New York, NY 10029 USA.,Medical Epigenetics, James J. Peters VA Medical Center, Bronx, NY 10468 USA
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162
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Epigenetic regulation and chromatin remodeling in learning and memory. Exp Mol Med 2017; 49:e281. [PMID: 28082740 PMCID: PMC5291841 DOI: 10.1038/emm.2016.140] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/21/2016] [Accepted: 09/25/2016] [Indexed: 01/12/2023] Open
Abstract
Understanding the underlying mechanisms of memory formation and maintenance has been a major goal in the field of neuroscience. Memory formation and maintenance are tightly controlled complex processes. Among the various processes occurring at different levels, gene expression regulation is especially crucial for proper memory processing, as some genes need to be activated while some genes must be suppressed. Epigenetic regulation of the genome involves processes such as DNA methylation and histone post-translational modifications. These processes edit genomic properties or the interactions between the genome and histone cores. They then induce structural changes in the chromatin and lead to transcriptional changes of different genes. Recent studies have focused on the concept of chromatin remodeling, which consists of 3D structural changes in chromatin in relation to gene regulation, and is an important process in learning and memory. In this review, we will introduce three major epigenetic processes involved in memory regulation: DNA methylation, histone methylation and histone acetylation. We will also discuss general mechanisms of long-term memory storage and relate the epigenetic control of learning and memory to chromatin remodeling. Finally, we will discuss how epigenetic mechanisms can contribute to the pathologies of neurological disorders and cause memory-related symptoms.
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163
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Bak ST, Staunstrup NH, Starnawska A, Daugaard TF, Nyengaard JR, Nyegaard M, Børglum A, Mors O, Dorph-Petersen KA, Nielsen AL. Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples. Mol Neurobiol 2016; 55:668-681. [PMID: 27995571 DOI: 10.1007/s12035-016-0345-x] [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: 08/03/2016] [Accepted: 12/05/2016] [Indexed: 01/14/2023]
Abstract
We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.
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Affiliation(s)
- Stine T Bak
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark
| | - Nicklas H Staunstrup
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Tina F Daugaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark
| | - Jens R Nyengaard
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
| | - Anders Børglum
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karl-Anton Dorph-Petersen
- Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark.,Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
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164
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Schroeder DI, Schmidt RJ, Crary-Dooley FK, Walker CK, Ozonoff S, Tancredi DJ, Hertz-Picciotto I, LaSalle JM. Placental methylome analysis from a prospective autism study. Mol Autism 2016; 7:51. [PMID: 28018572 PMCID: PMC5159983 DOI: 10.1186/s13229-016-0114-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/28/2016] [Indexed: 11/10/2022] Open
Abstract
Background Autism spectrum disorders (ASD) are increasingly prevalent neurodevelopmental disorders that are behaviorally diagnosed in early childhood. Most ASD cases likely arise from a complex mixture of genetic and environmental factors, an interface where the epigenetic marks of DNA methylation may be useful as risk biomarkers. The placenta is a potentially useful surrogate tissue characterized by a methylation pattern of partially methylated domains (PMDs) and highly methylated domains (HMDs) reflective of methylation patterns observed in the early embryo. Methods In this study, we investigated human term placentas from the MARBLES (Markers of Autism Risk in Babies: Learning Early Signs) prospective study by whole genome bisulfite sequencing. We also examined the utility of PMD/HMDs in detecting methylation differences consistent with ASD diagnosis at age three. Results We found that while human placental methylomes have highly reproducible PMD and HMD locations, there is a greater variation between individuals in methylation levels over PMDs than HMDs due to both sampling and individual variability. In a comparison of methylation differences in placental samples from 24 ASD and 23 typically developing (TD) children, a HMD containing a putative fetal brain enhancer near DLL1 was found to reach genome-wide significance and was validated for significantly higher methylation in ASD by pyrosequencing. Conclusions These results suggest that the placenta could be an informative surrogate tissue for predictive ASD biomarkers in high-risk families. Electronic supplementary material The online version of this article (doi:10.1186/s13229-016-0114-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diane I Schroeder
- Department of Medical Microbiology and Immunology, Genome Center, Davis, CA 95616 USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, University of California, Davis, CA 95616 USA ; MIND Institute, University of California, Davis, CA 95616 USA
| | | | - Cheryl K Walker
- Department of Obstetrics and Gynecology, University of California, Davis, CA 95616 USA ; MIND Institute, University of California, Davis, CA 95616 USA
| | - Sally Ozonoff
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95616 USA ; MIND Institute, University of California, Davis, CA 95616 USA
| | - Daniel J Tancredi
- Department of Pediatrics, University of California, Davis, CA 95616 USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, University of California, Davis, CA 95616 USA ; MIND Institute, University of California, Davis, CA 95616 USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, Davis, CA 95616 USA ; MIND Institute, University of California, Davis, CA 95616 USA
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165
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Dunaway KW, Islam MS, Coulson RL, Lopez SJ, Vogel Ciernia A, Chu RG, Yasui DH, Pessah IN, Lott P, Mordaunt C, Meguro-Horike M, Horike SI, Korf I, LaSalle JM. Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes. Cell Rep 2016; 17:3035-3048. [PMID: 27974215 PMCID: PMC5206988 DOI: 10.1016/j.celrep.2016.11.058] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/14/2016] [Accepted: 11/20/2016] [Indexed: 12/17/2022] Open
Abstract
Rare variants enriched for functions in chromatin regulation and neuronal synapses have been linked to autism. How chromatin and DNA methylation interact with environmental exposures at synaptic genes in autism etiologies is currently unclear. Using whole-genome bisulfite sequencing in brain tissue and a neuronal cell culture model carrying a 15q11.2-q13.3 maternal duplication, we find that significant global DNA hypomethylation is enriched over autism candidate genes and affects gene expression. The cumulative effect of multiple chromosomal duplications and exposure to the pervasive persistent organic pollutant PCB 95 altered methylation of more than 1,000 genes. Hypomethylated genes were enriched for H2A.Z, increased maternal UBE3A in Dup15q corresponded to reduced levels of RING1B, and bivalently modified H2A.Z was altered by PCB 95 and duplication. These results demonstrate the compounding effects of genetic and environmental insults on the neuronal methylome that converge upon dysregulation of chromatin and synaptic genes.
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Affiliation(s)
- Keith W Dunaway
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - M Saharul Islam
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Rochelle L Coulson
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - S Jesse Lopez
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Annie Vogel Ciernia
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Roy G Chu
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Dag H Yasui
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Isaac N Pessah
- Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA; Veterinary Molecular Biosciences, UC Davis, Davis, CA 95616, USA
| | - Paul Lott
- Genome Center, UC Davis, Davis, CA 95616, USA
| | - Charles Mordaunt
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Makiko Meguro-Horike
- Advanced Science Research Center, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Japan
| | - Ian Korf
- Genome Center, UC Davis, Davis, CA 95616, USA
| | - Janine M LaSalle
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA.
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166
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"Gap hunting" to characterize clustered probe signals in Illumina methylation array data. Epigenetics Chromatin 2016; 9:56. [PMID: 27980682 PMCID: PMC5142147 DOI: 10.1186/s13072-016-0107-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/25/2016] [Indexed: 12/16/2022] Open
Abstract
Background The Illumina 450k array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple mapping locations. An additional set of potentially problematic probes are those with DNA methylation distributions characterized by two or more distinct clusters separated by gaps. Data-driven identification of such probes may offer additional insights for downstream analyses. Results We developed a procedure, termed “gap hunting,” to identify probes showing clustered distributions. Among 590 peripheral blood samples from the Study to Explore Early Development, we identified 11,007 “gap probes.” The vast majority (9199) are likely attributed to an underlying SNP(s) or other variant in the probe, although SNP-affected probes exist that do not produce a gap signals. Specific factors predict which SNPs lead to gap signals, including type of nucleotide change, probe type, DNA strand, and overall methylation state. These expected effects are demonstrated in paired genotype and 450k data on the same samples. Gap probes can also serve as a surrogate for the local genetic sequence on a haplotype scale and can be used to adjust for population stratification. Conclusions The characteristics of gap probes reflect potentially informative biology. QC pipelines may benefit from an efficient data-driven approach that “flags” gap probes, rather than filtering such probes, followed by careful interpretation of downstream association analyses. Our results should translate directly to the recently released Illumina EPIC array given the similar chemistry and content design. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0107-z) contains supplementary material, which is available to authorized users.
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167
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Svendsen AJ, Gervin K, Lyle R, Christiansen L, Kyvik K, Junker P, Nielsen C, Houen G, Tan Q. Differentially Methylated DNA Regions in Monozygotic Twin Pairs Discordant for Rheumatoid Arthritis: An Epigenome-Wide Study. Front Immunol 2016; 7:510. [PMID: 27909437 PMCID: PMC5112246 DOI: 10.3389/fimmu.2016.00510] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/02/2016] [Indexed: 12/29/2022] Open
Abstract
Objectives In an explorative epigenome-wide association study (EWAS) to search for gene independent, differentially methylated DNA positions and regions (DMRs) associated with rheumatoid arthritis (RA) by studying monozygotic (MZ) twin pairs discordant for RA. Methods Genomic DNA was isolated from whole blood samples from 28 MZ twin pairs discordant for RA. DNA methylation was measured using the HumanMethylation450 BeadChips. Smoking, anti-cyclic citrullinated peptide antibodies, and immunosuppressive treatment were included as covariates. Pathway analysis was performed using GREAT. Results Smoking was significantly associated with hypomethylation of a DMR overlapping the promoter region of the RNF5 and the AGPAT1, which are implicated in inflammation and autoimmunity, whereas DMARD treatment induced hypermethylation of the same region. Additionally, the promotor region of both S100A6 and EFCAB4B were hypomethylated, and both genes have previously been associated with RA. We replicated several candidate genes identified in a previous EWAS in treatment-naïve RA singletons. Gene-set analysis indicated the involvement of immunologic signatures and cancer-related pathways in RA. Conclusion We identified several differentially methylated regions associated with RA, which may represent environmental effects or consequences of the disease and plausible biological pathways pertinent to the pathogenesis of RA.
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Affiliation(s)
- Anders J Svendsen
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark , Odense , Denmark
| | - Kristina Gervin
- Department of Medical Genetics, Oslo University Hospital, University of Oslo , Oslo , Norway
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, University of Oslo , Oslo , Norway
| | - Lene Christiansen
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark , Odense , Denmark
| | - Kirsten Kyvik
- Denmark and Odense Patient data Explorative Network (OPEN), Institute of Clinical Research, Odense University Hospital, University of Southern Denmark , Odense , Denmark
| | - Peter Junker
- Department of Rheumatology, Odense University Hospital, University of Southern Denmark , Odense , Denmark
| | - Christian Nielsen
- Department of Clinical Immunology, Odense University Hospital , Odense , Denmark
| | - Gunnar Houen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institute , Copenhagen , Denmark
| | - Qihua Tan
- The Danish Twin Registry, Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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168
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Atsem S, Reichenbach J, Potabattula R, Dittrich M, Nava C, Depienne C, Böhm L, Rost S, Hahn T, Schorsch M, Haaf T, El Hajj N. Paternal age effects on sperm FOXK1 and KCNA7 methylation and transmission into the next generation. Hum Mol Genet 2016; 25:4996-5005. [PMID: 28171595 PMCID: PMC5418740 DOI: 10.1093/hmg/ddw328] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 01/27/2023] Open
Abstract
Children of older fathers carry an increased risk for developing autism and other disorders. To elucidate the underlying mechanisms, we investigated the correlation of sperm DNA methylation with paternal age and its impact on the epigenome of the offspring. Methylation levels of nine candidate genes and LINE-1 repeats were quantified by bisulfite pyrosequencing in sperm DNA of 162 donors and 191 cord blood samples of resulting children (conceived by IVF/ICSI with the same sperm samples). Four genes showed a significant negative correlation between sperm methylation and paternal age. For FOXK1 and KCNA7, the age effect on the sperm epigenome was replicated in an independent cohort of 188 sperm samples. For FOXK1, paternal age also significantly correlated with foetal cord blood (FCB) methylation. Deep bisulfite sequencing and allele-specific pyrosequencing allowed us to distinguish between maternal and paternal alleles in FCB samples with an informative SNP. FCB methylation of the paternal FOXK1 allele was negatively correlated with paternal age, whereas maternal allele was unaffected by maternal age. Since FOXK1 duplication has been associated with autism, we studied blood FOXK1 methylation in 74 children with autism and 41 age-matched controls. The FOXK1 promoter showed a trend for accelerated demethylation in the autism group. Dual luciferase reporter assay revealed that FOXK1 methylation influences gene expression. Collectively, our study demonstrates that age-related DNA methylation changes in sperm can be transmitted to the next generation and may contribute to the increased disease risk in offspring of older fathers.
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Affiliation(s)
- Stefanie Atsem
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Juliane Reichenbach
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Caroline Nava
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Christel Depienne
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Lena Böhm
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius-Maximilians University, Würzburg, Germany
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169
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Hannon E, Lunnon K, Schalkwyk L, Mill J. Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics 2016; 10:1024-32. [PMID: 26457534 PMCID: PMC4844197 DOI: 10.1080/15592294.2015.1100786] [Citation(s) in RCA: 310] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Given the tissue-specific nature of epigenetic processes, the assessment of disease-relevant tissue is an important consideration for epigenome-wide association studies (EWAS). Little is known about whether easily accessible tissues, such as whole blood, can be used to address questions about interindividual epigenomic variation in inaccessible tissues, such as the brain. We quantified DNA methylation in matched DNA samples isolated from whole blood and 4 brain regions (prefrontal cortex, entorhinal cortex, superior temporal gyrus, and cerebellum) from 122 individuals. We explored co-variation between tissues and the extent to which methylomic variation in blood is predictive of interindividual variation identified in the brain. For the majority of DNA methylation sites, interindividual variation in whole blood is not a strong predictor of interindividual variation in the brain, although the relationship with cortical regions is stronger than with the cerebellum. Variation at a subset of probes is strongly correlated across tissues, even in instances when the actual level of DNA methylation is significantly different between them. A substantial proportion of this co-variation, however, is likely to result from genetic influences. Our data suggest that for the majority of the genome, a blood-based EWAS for disorders where brain is presumed to be the primary tissue of interest will give limited information relating to underlying pathological processes. These results do not, however, discount the utility of using a blood-based EWAS to identify biomarkers of disease phenotypes manifest in the brain. We have generated a searchable database for the interpretation of data from blood-based EWAS analyses (http://epigenetics.essex.ac.uk/bloodbrain/).
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Affiliation(s)
- Eilis Hannon
- a University of Exeter Medical School; University of Exeter ; Devon , UK
| | - Katie Lunnon
- a University of Exeter Medical School; University of Exeter ; Devon , UK
| | - Leonard Schalkwyk
- b School of Biological Sciences; University of Essex ; Wivenhoe Park, Colchester , UK
| | - Jonathan Mill
- a University of Exeter Medical School; University of Exeter ; Devon , UK.,c Institute of Psychiatry; Psychology & Neuroscience; King's College London ; De Crespigny Park, London , UK
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170
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Okazaki S, Boku S, Otsuka I, Mouri K, Aoyama S, Shiroiwa K, Sora I, Fujita A, Shirai Y, Shirakawa O, Kokai M, Hishimoto A. The cell cycle-related genes as biomarkers for schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2016; 70:85-91. [PMID: 27216283 DOI: 10.1016/j.pnpbp.2016.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Recent studies suggest that genomic abnormalities such as single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) may elevate the risk of schizophrenia. Such genomic abnormalities often occur during chromosomal DNA replication in the S phase of cell cycle. In addition, several studies showed that abnormal expressions of several cell cycle-related genes are associated with schizophrenia. Therefore, here we compared mRNA expression levels of cell cycle-related genes in peripheral blood cells between patients with schizophrenia and healthy controls. METHOD mRNA expression levels of cell cycle-related genes in peripheral blood cells from patients with schizophrenia and healthy controls were measured with quantitative reverse transcription polymerase chain reaction (Q-RT-PCR). The discovery, replication and intervention studies with Q-RT-PCR were performed as follows: discovery (40 cases and 20 controls), replication (82 cases and 74 controls) and intervention (22 cases and 18 controls). RESULT Nine genes were identified in the discovery and replication stages as schizophrenia-associated genes. Moreover, the combination of mRNA expression levels of CDK4, MCM7 and POLD4 was identified as a potential biomarker for schizophrenia with multivariate logistic regression analysis. The intervention stage revealed that the mRNA expression levels of these three genes were significantly decreased in the acute state of schizophrenia, and CDK4 was significantly recovered in the remission state of schizophrenia. CONCLUSION The combination of mRNA expression levels of three cell cycle-related genes such as CDK4, MCM7 and POLD4 is expected to be a candidate for useful biomarkers for schizophrenia. Especially, the mRNA expression changes of CDK4 may be potential as both trait and state markers for schizophrenia.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shuken Boku
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Mouri
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinsuke Aoyama
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kyoichi Shiroiwa
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ichiro Sora
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Aiko Fujita
- Department of Psychiatry, Hyogo Prefectural Kofu Hospital, Kobe, Japan
| | - Yutaka Shirai
- Department of Psychiatry, Shoseikai Minatogawa Hospital, Kobe, Japan
| | - Osamu Shirakawa
- Department of Neuropsychiatry, Kinki University School of Medicine, Osaka, Japan
| | - Masahiro Kokai
- Department of Neuropsychiatry, Hyogo College of Medicine, Hyogo, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
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171
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Salehi M, Kamali E, Karahmadi M, Mousavi SM. RORA and Autism in The Isfahan Population: Is There An Epigenetic Relationship. CELL JOURNAL 2016; 18:540-546. [PMID: 28042538 PMCID: PMC5086332 DOI: 10.22074/cellj.2016.4720] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/09/2016] [Indexed: 01/05/2023]
Abstract
Objective Autism is a neurodevelopmental disorder characterized by difficulty in verbal
and non-verbal communication, impaired social interaction, and restricted and repetitive
behavior. It has been recently introduced as a multigenic disorder with significant epigenetic effects on its pathology. Recently, epigenetic silencing of retinoic acid receptor-
related orphan receptor alpha (RORα) gene (which has an essential role in neural tissue
development) was shown to have occurred in autistic children due to methylation of its
promoter region. This may thus explain a significant part of the molecular pathogenesis
of autism. Therefore, we aimed to confirm this finding by implementing a case-control
(experimental) study in the population of Isfahan.
Materials and Methods The methylation status of a 136 bp sequence of a GpG island
(encompassing 13 CpG sites) in the RORA promoter region (positions -200 to -64) as an
experimental study was examined in the lymphocyte cells of 30 autistic children after sodium bisulfite treatment using the melting curve analysis-methylation (MCA-Meth) assay
compared with normal children. Also, quantitative reverse transcriptase-polymerase chain
reaction (qRT-PCR) analysis was used to estimate the level of mRNA transcripts and to
evaluate MCA-Meth analysis results.
Results This study revealed no methylation in the examined promoter regions in both
autistic and normal children, with the melting curve of all studied samples being comparable to that of the non-methylated control. The results of MCA-Meth analysis were also
consistent with qRT-PCR results. We therefore observed no significant difference in the
levels of RORα transcripts in the blood lymphocytes between autistic and healthy children.
Conclusion The methylation of the RORA promoter region may not be considered as a
common epigenetic risk factor for autism in all populations. Hence, the molecular pathogenesis of autism remains unclear in the population investigated.
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Affiliation(s)
- Mansoor Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elahe Kamali
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran
| | - Mojgan Karahmadi
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyyed Mohammad Mousavi
- Genetic and Identification Lab, Legal Medicine Center, Isfahan, Iran; Cellular and Molecular Research Center, School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
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172
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Tsang SY, Ahmad T, Mat FWK, Zhao C, Xiao S, Xia K, Xue H. Variation of global DNA methylation levels with age and in autistic children. Hum Genomics 2016; 10:31. [PMID: 27663196 PMCID: PMC5035466 DOI: 10.1186/s40246-016-0086-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/07/2016] [Indexed: 11/22/2022] Open
Abstract
Background The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2–97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us. Results Genome-wide or global DNA methylation levels proceeded through multiple phases of variation with age, consisting of a steady increase from age 2 to 25 (r = 0.382) and another rise from age 41 to 55 to reach a peak level of ~80 % (r = 0.265), followed by a sharp decrease to ~40 % in the mid-1970s (age 56 to 75; r = −0.395) and leveling off thereafter. Significant gender effect in methylation levels was observed only for the 41–55 age group in which methylation in females was significantly higher than in males (p = 0.010). In addition, global methylation level was significantly higher in autistic children than in age-matched healthy children (p < 0.001). Conclusions The multiphasic nature of changes in global methylation levels with age was delineated, and investigation into the factors underlying this profile will be essential to a proper understanding of the aging process. Furthermore, this first report of global hypermethylation in autistic children also illustrates the importance of age-matched controls in characterization of disease-associated variations in DNA methylation. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0086-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shui-Ying Tsang
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tanveer Ahmad
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Flora W K Mat
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cunyou Zhao
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Department of Medical Genetics, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Shifu Xiao
- Department of Geriatric Psychiatry, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200030, China.
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410078, China.
| | - Hong Xue
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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173
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Genetic architecture, epigenetic influence and environment exposure in the pathogenesis of Autism. SCIENCE CHINA-LIFE SCIENCES 2016; 58:958-67. [PMID: 26490976 DOI: 10.1007/s11427-015-4941-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) is a spectral neurodevelopment disorder affecting approximately 1% of the population. ASD is characterized by impairments in reciprocal social interaction, communication deficits and restricted patterns of behavior. Multiple factors, including genetic/genomic, epigenetic/epigenomic and environmental, are thought to be necessary for autism development. Recent reviews have provided further insight into the genetic/genomic basis of ASD. It has long been suspected that epigenetic mechanisms, including DNA methylation, chromatin structures and long non-coding RNAs may play important roles in the pathology of ASD. In addition to genetic/genomic alterations and epigenetic/epigenomic influences, environmental exposures have been widely accepted as an important role in autism etiology, among which immune dysregulation and gastrointestinal microbiota are two prominent ones.
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174
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Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD. Epigenetic Research in Neuropsychiatric Disorders: the "Tissue Issue". Curr Behav Neurosci Rep 2016; 3:264-274. [PMID: 28093577 DOI: 10.1007/s40473-016-0083-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Evidence has linked neuropsychiatric disorders with epigenetic marks as either a biomarker of disease, biomarker of exposure, or mechanism of disease processes. Neuropsychiatric epidemiologic studies using either target brain tissue or surrogate blood tissue each have methodological challenges and distinct advantages. RECENT FINDINGS Brain tissue studies are challenged by small sample sizes of cases and controls, incomplete phenotyping, post-mortem timing, and cellular heterogeneity, but the use of a primary disease relevant tissue is critical. Blood-based studies have access to much larger sample sizes and more replication opportunities, as well as the potential for longitudinal measurements, both prior to onset and during the course of treatments. Yet, blood studies also are challenged by cell-type heterogeneity, and many question the validity of using peripheral tissues as a brain biomarker. Emerging evidence suggests that these limitations to blood-based epigenetic studies are surmountable, but confirmation in target tissue remains important. SUMMARY Epigenetic mechanisms have the potential to help elucidate biology connecting experiential risk factors with neuropsychiatric disease manifestation. Cross-tissue studies as well as advanced epidemiologic methods should be employed to more effectively conduct neuropsychiatric epigenetic research.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Alycia Halladay
- Autism Science Foundation, New York City, New York, USA; Department of Pharmacology and Toxicology, Rutgers University, New Brunswick, New Jersey, USA
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK; Institute for Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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175
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Schneider E, Dittrich M, Böck J, Nanda I, Müller T, Seidmann L, Tralau T, Galetzka D, El Hajj N, Haaf T. CpG sites with continuously increasing or decreasing methylation from early to late human fetal brain development. Gene 2016; 592:110-118. [PMID: 27468947 DOI: 10.1016/j.gene.2016.07.058] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/28/2016] [Accepted: 07/23/2016] [Indexed: 01/03/2023]
Abstract
Normal human brain development is dependent on highly dynamic epigenetic processes for spatial and temporal gene regulation. Recent work identified wide-spread changes in DNA methylation during fetal brain development. We profiled CpG methylation in frontal cortex of 27 fetuses from gestational weeks 12-42, using Illumina 450K methylation arrays. Sites showing genome-wide significant correlation with gestational age were compared to a publicly available data set from gestational weeks 3-26. Altogether, we identified 2016 matching developmentally regulated differentially methylated positions (m-dDMPs): 1767m-dDMPs were hypermethylated and 1149 hypomethylated during fetal development. M-dDMPs are underrepresented in CpG islands and gene promoters, and enriched in gene bodies. They appear to cluster in certain chromosome regions. M-dDMPs are significantly enriched in autism-associated genes and CpGs. Our results promote the idea that reduced methylation dynamics during fetal brain development may predispose to autism. In addition, m-dDMPs are enriched in genes with human-specific brain expression patterns and/or histone modifications. Collectively, we defined a subset of dDMPs exhibiting constant methylation changes from early to late pregnancy. The same epigenetic mechanisms involving methylation changes in cis-regulatory regions may have been adopted for human brain evolution and ontogeny.
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Affiliation(s)
- Eberhard Schneider
- 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
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Larissa Seidmann
- Department of Pathology, University Medical Center, 55131 Mainz, Germany
| | - Tim Tralau
- Department of Pathology, University Medical Center, 55131 Mainz, Germany; Rehabilitation Clinic for Children and Adolescents, 25980 Westerland/Sylt, Germany
| | - Danuta Galetzka
- Department of Radiation Oncology and Radiotherapy, University Medical Center, 55131 Mainz, Germany
| | - Nady El Hajj
- 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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176
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Nardone S, Elliott E. The Interaction between the Immune System and Epigenetics in the Etiology of Autism Spectrum Disorders. Front Neurosci 2016; 10:329. [PMID: 27462204 PMCID: PMC4940387 DOI: 10.3389/fnins.2016.00329] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/29/2016] [Indexed: 12/24/2022] Open
Abstract
Recent studies have firmly established that the etiology of autism includes both genetic and environmental components. However, we are only just beginning to elucidate the environmental factors that might be involved in the development of autism, as well as the molecular mechanisms through which they function. Mounting epidemiological and biological evidence suggest that prenatal factors that induce a more activated immune state in the mother are involved in the development of autism. In parallel, molecular studies have highlighted the role of epigenetics in brain development as a process susceptible to environmental influences and potentially causative of autism spectrum disorders (ASD). In this review, we will discuss converging evidence for a multidirectional interaction between immune system activation in the mother during pregnancy and epigenetic regulation in the brain of the fetus that may cooperate to produce an autistic phenotype. This interaction includes immune factor-induced changes in epigenetic signatures in the brain, dysregulation of epigenetic modifications specifically in genomic regions that encode immune functions, and aberrant epigenetic regulation of microglia. Overall, the interaction between immune system activation in the mother and the subsequent epigenetic dysregulation in the developing fetal brain may be a main consideration for the environmental factors that cause autism.
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Affiliation(s)
| | - Evan Elliott
- Faculty of Medicine, Bar Ilan University Safed, Israel
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177
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Vogel Ciernia A, LaSalle J. The landscape of DNA methylation amid a perfect storm of autism aetiologies. Nat Rev Neurosci 2016; 17:411-23. [PMID: 27150399 PMCID: PMC4966286 DOI: 10.1038/nrn.2016.41] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increasing evidence points to a complex interplay between genes and the environment in autism spectrum disorder (ASD), including rare de novo mutations in chromatin genes such as methyl-CpG binding protein 2 (MECP2) in Rett syndrome. Epigenetic mechanisms such as DNA methylation act at this interface, reflecting the plasticity in metabolic and neurodevelopmentally regulated gene pathways. Genome-wide studies of gene sequences, gene pathways and DNA methylation are providing valuable mechanistic insights into ASD. The dynamic developmental landscape of DNA methylation is vulnerable to numerous genetic and environmental insults: therefore, understanding pathways that are central to this 'perfect storm' will be crucial to improving the diagnosis and treatment of ASD.
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Affiliation(s)
- Annie Vogel Ciernia
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
| | - Janine LaSalle
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
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178
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Homs A, Codina-Solà M, Rodríguez-Santiago B, Villanueva CM, Monk D, Cuscó I, Pérez-Jurado LA. Genetic and epigenetic methylation defects and implication of the ERMN gene in autism spectrum disorders. Transl Psychiatry 2016; 6:e855. [PMID: 27404287 PMCID: PMC5545709 DOI: 10.1038/tp.2016.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 04/01/2016] [Accepted: 05/08/2016] [Indexed: 12/11/2022] Open
Abstract
Autism spectrum disorders (ASD) are highly heritable and genetically complex conditions. Although highly penetrant mutations in multiple genes have been identified, they account for the etiology of <1/3 of cases. There is also strong evidence for environmental contribution to ASD, which can be mediated by still poorly explored epigenetic modifications. We searched for methylation changes on blood DNA of 53 male ASD patients and 757 healthy controls using a methylomic array (450K Illumina), correlated the variants with transcriptional alterations in blood RNAseq data, and performed a case-control association study of the relevant findings in a larger cohort (394 cases and 500 controls). We found 700 differentially methylated CpGs, most of them hypomethylated in the ASD group (83.9%), with cis-acting expression changes at 7.6% of locations. Relevant findings included: (1) hypomethylation caused by rare genetic variants (meSNVs) at six loci (ERMN, USP24, METTL21C, PDE10A, STX16 and DBT) significantly associated with ASD (q-value <0.05); and (2) clustered epimutations associated to transcriptional changes in single-ASD patients (n=4). All meSNVs and clustered epimutations were inherited from unaffected parents. Resequencing of the top candidate genes also revealed a significant load of deleterious mutations affecting ERMN in ASD compared with controls. Our data indicate that inherited methylation alterations detectable in blood DNA, due to either genetic or epigenetic defects, can affect gene expression and contribute to ASD susceptibility most likely in an additive manner, and implicate ERMN as a novel ASD gene.
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Affiliation(s)
- A Homs
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - M Codina-Solà
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | | | - C M Villanueva
- Center for Research in Environmental Epidemiology, Barcelona, Spain,Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Barcelona, Spain
| | - D Monk
- Cancer Epigenetics Group, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - I Cuscó
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain,Genetics Unit, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Dr. Aiguader 88, Barcelona 08003, Spain. E-mails: and
| | - L A Pérez-Jurado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain,Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain,Genetics Unit, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Dr. Aiguader 88, Barcelona 08003, Spain. E-mails: and
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179
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Portales-Casamar E, Lussier AA, Jones MJ, MacIsaac JL, Edgar RD, Mah SM, Barhdadi A, Provost S, Lemieux-Perreault LP, Cynader MS, Chudley AE, Dubé MP, Reynolds JN, Pavlidis P, Kobor MS. DNA methylation signature of human fetal alcohol spectrum disorder. Epigenetics Chromatin 2016; 9:25. [PMID: 27358653 PMCID: PMC4926300 DOI: 10.1186/s13072-016-0074-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/17/2016] [Indexed: 02/06/2023] Open
Abstract
Background Prenatal alcohol exposure is the leading preventable cause of behavioral and cognitive deficits, which may affect between 2 and 5 % of children in North America. While the underlying mechanisms of alcohol’s effects on development remain relatively unknown, emerging evidence implicates epigenetic mechanisms in mediating the range of symptoms observed in children with fetal alcohol spectrum disorder (FASD). Thus, we investigated the effects of prenatal alcohol exposure on genome-wide DNA methylation in the NeuroDevNet FASD cohort, the largest cohort of human FASD samples to date. Methods Genome-wide DNA methylation patterns of buccal epithelial cells (BECs) were analyzed using the Illumina HumanMethylation450 array in a Canadian cohort of 206 children (110 FASD and 96 controls). Genotyping was performed in parallel using the Infinium HumanOmni2.5-Quad v1.0 BeadChip. Results After correcting for the effects of genetic background, we found 658 significantly differentially methylated sites between FASD cases and controls, with 41 displaying differences in percent methylation change >5 %. Furthermore, 101 differentially methylated regions containing two or more CpGs were also identified, overlapping with 95 different genes. The majority of differentially methylated genes were highly expressed at the level of mRNA in brain samples from the Allen Brain Atlas, and independent DNA methylation data from cortical brain samples showed high correlations with BEC DNA methylation patterns. Finally, overrepresentation analysis of genes with up-methylated CpGs revealed a significant enrichment for neurodevelopmental processes and diseases, such as anxiety, epilepsy, and autism spectrum disorders. Conclusions These findings suggested that prenatal alcohol exposure is associated with distinct DNA methylation patterns in children and adolescents, raising the possibility of an epigenetic biomarker of FASD. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0074-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alexandre A Lussier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Sarah M Mah
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Amina Barhdadi
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada
| | | | - Max S Cynader
- Brain Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Manitoba, Winnipeg, MB Canada.,Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, MB Canada
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada.,Faculty of Medicine, Université de Montréal, Montreal, QC Canada
| | - James N Reynolds
- Centre for Neuroscience Studies, Queen's University, Kingston, ON Canada
| | - Paul Pavlidis
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada.,Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia Canada
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180
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Kubota T, Mochizuki K. Epigenetic Effect of Environmental Factors on Autism Spectrum Disorders. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13050504. [PMID: 27187441 PMCID: PMC4881129 DOI: 10.3390/ijerph13050504] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/23/2016] [Accepted: 05/10/2016] [Indexed: 12/22/2022]
Abstract
Both environmental factors and genetic factors are involved in the pathogenesis of autism spectrum disorders (ASDs). Epigenetics, an essential mechanism for gene regulation based on chemical modifications of DNA and histone proteins, is also involved in congenital ASDs. It was recently demonstrated that environmental factors, such as endocrine disrupting chemicals and mental stress in early life, can change epigenetic status and gene expression, and can cause ASDs. Moreover, environmentally induced epigenetic changes are not erased during gametogenesis and are transmitted to subsequent generations, leading to changes in behavior phenotypes. However, epigenetics has a reversible nature since it is based on the addition or removal of chemical residues, and thus the original epigenetic status may be restored. Indeed, several antidepressants and anticonvulsants used for mental disorders including ASDs restore the epigenetic state and gene expression. Therefore, further epigenetic understanding of ASDs is important for the development of new drugs that take advantages of epigenetic reversibility.
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Affiliation(s)
- Takeo Kubota
- Department of Epigenetic Medicine, Faculty of Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Kazuki Mochizuki
- Department of Local Produce and Food Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu-City, Yamanashi 400-8510, Japan.
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181
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Lintas C, Sacco R, Persico AM. Differential methylation at the RELN gene promoter in temporal cortex from autistic and typically developing post-puberal subjects. J Neurodev Disord 2016; 8:18. [PMID: 27134686 PMCID: PMC4850686 DOI: 10.1186/s11689-016-9151-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/12/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Reelin plays a pivotal role in neurodevelopment and in post-natal synaptic plasticity and has been implicated in the pathogenesis of autism spectrum disorder (ASD). The reelin (RELN) gene expression is significantly decreased in ASD, both in the brain and peripherally. Methylation at the RELN gene promoter is largely triggered at puberty, and hypermethylation has been found in post-mortem brains of schizophrenic and bipolar patients. METHODS In this study, we assessed RELN gene methylation status in post-mortem temporocortical tissue samples (BA41/42 or 22) of six pairs of post-puberal individuals with ASD and typically developing subjects, matched for sex (male:female, M:F = 5:1), age, and post-mortem interval. RESULTS ASD patients display a significantly higher number of methylated CpG islands and heavier methylation in the 5' region of the RELN gene promoter, spanning from -458 to -223 bp, whereas controls have more methylated CpG positions and greater extent of methylation at the 3' promoter region, spanning from -222 to +1 bp. The most upstream promoter region (-458 to -364 bp) is methylated only in ASD brains, while the most downstream region (-131 to +1 bp) is methylated exclusively in control brains. Within this general framework, three different methylation patterns are discernible, each correlated with different extents of reduction in reelin gene expression among ASD individuals compared to controls. CONCLUSIONS The methylation pattern is different in ASD and control post-mortem brains. ASD-specific CpG positions, located in the most upstream gene promoter region, may exert a functional role potentially conferring ASD risk by blunting RELN gene expression.
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Affiliation(s)
- Carla Lintas
- Unit of Child and Adolescent Neuropsychiatry, University Campus Bio-Medico, Rome, Italy ; Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
| | - Roberto Sacco
- Unit of Child and Adolescent Neuropsychiatry, University Campus Bio-Medico, Rome, Italy ; Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
| | - Antonio M Persico
- Unit of Child and Adolescent Neuropsychiatry, "Gaetano Martino" University Hospital, University of Messina, via Consolare Valeria 1, I-98125 Messina, Italy ; Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
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182
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Vijayakumar NT, Judy MV. Autism spectrum disorders: Integration of the genome, transcriptome and the environment. J Neurol Sci 2016; 364:167-76. [PMID: 27084239 DOI: 10.1016/j.jns.2016.03.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/18/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Autism spectrum disorders denote a series of lifelong neurodevelopmental conditions characterized by an impaired social communication profile and often repetitive, stereotyped behavior. Recent years have seen the complex genetic architecture of the disease being progressively unraveled with advancements in gene finding technology and next generation sequencing methods. However, a complete elucidation of the molecular mechanisms behind autism is necessary for potential diagnostic and therapeutic applications. A multidisciplinary approach should be adopted where the focus is not only on the 'genetics' of autism but also on the combinational roles of epigenetics, transcriptomics, immune system disruption and environmental factors that could all influence the etiopathogenesis of the disease. ASD is a clinically heterogeneous disorder with great genetic complexity; only through an integrated multidimensional effort can modern autism research progress further.
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Affiliation(s)
- N Thushara Vijayakumar
- Department of Computer Science & IT., Amrita School of Arts & Sciences, Amrita Vishwa Vidyapeetham, Amrita University, Kochi, India.
| | - M V Judy
- Department of Computer Science & IT., Amrita School of Arts & Sciences, Amrita Vishwa Vidyapeetham, Amrita University, Kochi, India
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183
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Lahiri DK, Maloney B, Bayon BL, Chopra N, White FA, Greig NH, Nurnberger JI. Transgenerational latent early-life associated regulation unites environment and genetics across generations. Epigenomics 2016; 8:373-87. [PMID: 26950428 DOI: 10.2217/epi.15.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The origin of idiopathic diseases is still poorly understood. The latent early-life associated regulation (LEARn) model unites environmental exposures and gene expression while providing a mechanistic underpinning for later-occurring disorders. We propose that this process can occur across generations via transgenerational LEARn (tLEARn). In tLEARn, each person is a 'unit' accumulating preclinical or subclinical 'hits' as in the original LEARn model. These changes can then be epigenomically passed along to offspring. Transgenerational accumulation of 'hits' determines a sporadic disease state. Few significant transgenerational hits would accompany conception or gestation of most people, but these may suffice to 'prime' someone to respond to later-life hits. Hits need not produce symptoms or microphenotypes to have a transgenerational effect. Testing tLEARn requires longitudinal approaches. A recently proposed longitudinal epigenome/envirome-wide association study would unite genetic sequence, epigenomic markers, environmental exposures, patient personal history taken at multiple time points and family history.
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Affiliation(s)
- Debomoy K Lahiri
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Bryan Maloney
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Baindu L Bayon
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Nipun Chopra
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Fletcher A White
- Department of Anesthesia, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
| | - Nigel H Greig
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - John I Nurnberger
- Department of Psychiatry, Stark Neurosciences Research Institute, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA.,Department of Medical & Molecular Genetics, Indiana University School of Medicine, 320 West 15th Street, Indianapolis, IN 46202, USA
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184
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Yang ZL, Sun GL. [Research advances in candidate genes for autism spectrum disorder]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:282-287. [PMID: 26975830 PMCID: PMC7390002 DOI: 10.7499/j.issn.1008-8830.2016.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
Autism spectrum disorder (ASD) is a kind of neurodevelopmental multigenic disorder. More than one hundred of candidate genes for ASD have been reported. The candidate gene research for ASD involves in chromosome loci and screening of candidate genes and epigenetic abnormalities for candidate genes. The reported genes encode neural adhesion molecules, ion channels, scaffold proteins, protein kinases, receptor protein and carrier protein, signaling modulate molecules and circadian relevant proteins. The research of mutation screening and expression regulation of candidate genes can help to elucidate genetic mechanisms for ASD, and may provide new approaches for the diagnosis and treatment of this disorder. This article reviews the research advance in candidate genes for ASD.
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Affiliation(s)
- Zhi-Liang Yang
- Department of Pediatrics, First Affiliated Hospital of China Medical University, Shenyang 110001, China.
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185
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Lunnon K, Hannon E, Smith RG, Dempster E, Wong C, Burrage J, Troakes C, Al-Sarraj S, Kepa A, Schalkwyk L, Mill J. Variation in 5-hydroxymethylcytosine across human cortex and cerebellum. Genome Biol 2016; 17:27. [PMID: 26883014 PMCID: PMC4756397 DOI: 10.1186/s13059-016-0871-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/05/2016] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND The most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite; however, this method cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Previous studies have shown that 5hmC is enriched in the brain, although little is known about its genomic distribution and how it differs between anatomical regions and individuals. In this study, we combine oxidative bisulfite (oxBS) treatment with the Illumina Infinium 450K BeadArray to quantify genome-wide patterns of 5hmC in two distinct anatomical regions of the brain from multiple individuals. RESULTS We identify 37,145 and 65,563 sites passing our threshold for detectable 5hmC in the prefrontal cortex and cerebellum respectively, with 23,445 loci common across both brain regions. Distinct patterns of 5hmC are identified in each brain region, with notable differences in the genomic location of the most hydroxymethylated loci between these brain regions. Tissue-specific patterns of 5hmC are subsequently confirmed in an independent set of prefrontal cortex and cerebellum samples. CONCLUSIONS This study represents the first systematic analysis of 5hmC in the human brain, identifying tissue-specific hydroxymethylated positions and genomic regions characterized by inter-individual variation in DNA hydroxymethylation. This study demonstrates the utility of combining oxBS-treatment with the Illumina 450k methylation array to systematically quantify 5hmC across the genome and the potential utility of this approach for epigenomic studies of brain disorders.
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Affiliation(s)
- Katie Lunnon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.
| | - Eilis Hannon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Rebecca G Smith
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Emma Dempster
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Chloe Wong
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Joe Burrage
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Agnieszka Kepa
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, UK
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186
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Zhang Y, Hodgson NW, Trivedi MS, Abdolmaleky HM, Fournier M, Cuenod M, Do KQ, Deth RC. Decreased Brain Levels of Vitamin B12 in Aging, Autism and Schizophrenia. PLoS One 2016; 11:e0146797. [PMID: 26799654 PMCID: PMC4723262 DOI: 10.1371/journal.pone.0146797] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022] Open
Abstract
Many studies indicate a crucial role for the vitamin B12 and folate-dependent enzyme methionine synthase (MS) in brain development and function, but vitamin B12 status in the brain across the lifespan has not been previously investigated. Vitamin B12 (cobalamin, Cbl) exists in multiple forms, including methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), serving as cofactors for MS and methylmalonylCoA mutase, respectively. We measured levels of five Cbl species in postmortem human frontal cortex of 43 control subjects, from 19 weeks of fetal development through 80 years of age, and 12 autistic and 9 schizophrenic subjects. Total Cbl was significantly lower in older control subjects (> 60 yrs of age), primarily reflecting a >10-fold age-dependent decline in the level of MeCbl. Levels of inactive cyanocobalamin (CNCbl) were remarkably higher in fetal brain samples. In both autistic and schizophrenic subjects MeCbl and AdoCbl levels were more than 3-fold lower than age-matched controls. In autistic subjects lower MeCbl was associated with decreased MS activity and elevated levels of its substrate homocysteine (HCY). Low levels of the antioxidant glutathione (GSH) have been linked to both autism and schizophrenia, and both total Cbl and MeCbl levels were decreased in glutamate-cysteine ligase modulatory subunit knockout (GCLM-KO) mice, which exhibit low GSH levels. Thus our findings reveal a previously unrecognized decrease in brain vitamin B12 status across the lifespan that may reflect an adaptation to increasing antioxidant demand, while accelerated deficits due to GSH deficiency may contribute to neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
- Yiting Zhang
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115, United States of America
| | - Nathaniel W. Hodgson
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115, United States of America
- Department of Surgery, Laboratory of Nutrition and Metabolism at BIDMC, Harvard Medical School, Boston, MA, 02215, United States of America
| | - Malav S. Trivedi
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115, United States of America
- Department of Pharmaceutical Sciences, Nova Southeastern University College of Pharmacy, Fort Lauderdale, FL, 33328, United States of America
| | - Hamid M. Abdolmaleky
- Department of Medicine (Biomedical Genetics Section), Genetics & Genomics, Boston University School of Medicine, Boston, MA, 02118, United States of America
| | - Margot Fournier
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
| | - Michel Cuenod
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
| | - Kim Quang Do
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
| | - Richard C. Deth
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115, United States of America
- Department of Pharmaceutical Sciences, Nova Southeastern University College of Pharmacy, Fort Lauderdale, FL, 33328, United States of America
- * E-mail:
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187
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Sparrow S, Manning JR, Cartier J, Anblagan D, Bastin ME, Piyasena C, Pataky R, Moore EJ, Semple SI, Wilkinson AG, Evans M, Drake AJ, Boardman JP. Epigenomic profiling of preterm infants reveals DNA methylation differences at sites associated with neural function. Transl Psychiatry 2016; 6:e716. [PMID: 26784970 PMCID: PMC5068883 DOI: 10.1038/tp.2015.210] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 12/13/2022] Open
Abstract
DNA methylation (DNAm) plays a determining role in neural cell fate and provides a molecular link between early-life stress and neuropsychiatric disease. Preterm birth is a profound environmental stressor that is closely associated with alterations in connectivity of neural systems and long-term neuropsychiatric impairment. The aims of this study were to examine the relationship between preterm birth and DNAm, and to investigate factors that contribute to variance in DNAm. DNA was collected from preterm infants (birth<33 weeks gestation) and healthy controls (birth>37 weeks), and a genome-wide analysis of DNAm was performed; diffusion magnetic resonance imaging (dMRI) data were acquired from the preterm group. The major fasciculi were segmented, and fractional anisotropy, mean diffusivity and tract shape were calculated. Principal components (PC) analysis was used to investigate the contribution of MRI features and clinical variables to variance in DNAm. Differential methylation was found within 25 gene bodies and 58 promoters of protein-coding genes in preterm infants compared with controls; 10 of these have neural functions. Differences detected in the array were validated with pyrosequencing. Ninety-five percent of the variance in DNAm in preterm infants was explained by 23 PCs; corticospinal tract shape associated with 6th PC, and gender and early nutritional exposure associated with the 7th PC. Preterm birth is associated with alterations in the methylome at sites that influence neural development and function. Differential methylation analysis has identified several promising candidate genes for understanding the genetic/epigenetic basis of preterm brain injury.
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Affiliation(s)
- S Sparrow
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, UK
| | - J R Manning
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - J Cartier
- University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - D Anblagan
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - M E Bastin
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - C Piyasena
- University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - R Pataky
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, UK
| | - E J Moore
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, UK
| | - S I Semple
- Clinical Research Imaging Centre, University of Edinburgh, Edinburgh, UK
| | | | - M Evans
- Department of Pathology, NHS Lothian, Edinburgh, UK
| | - A J Drake
- University/BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - J P Boardman
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, UK,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK,MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Room W1.26, Edinburgh EH16 4TJ, UK. E-mail:
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188
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Pediatric asthma and autism-genomic perspectives. Clin Transl Med 2015; 4:37. [PMID: 26668064 PMCID: PMC4678135 DOI: 10.1186/s40169-015-0078-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/29/2015] [Indexed: 02/06/2023] Open
Abstract
High-throughput technologies, ranging from microarrays to NexGen sequencing of RNA and genomic DNA, have opened new avenues for exploration of the pathobiology of human disease. Comparisons of the architecture of the genome, identification of mutated or modified sequences, and pre-and post- transcriptional regulation of gene expression as disease specific biomarkers are revolutionizing our understanding of the causes of disease and are guiding the development of new therapies. There is enormous heterogeneity in types of genomic variation that occur in human disease. Some are inherited, while others are the result of new somatic or germline mutations or errors in chromosomal replication. In this review, we provide examples of changes that occur in the human genome in two of the most common chronic pediatric disorders, autism and asthma. The incidence and economic burden of both of these disorders are increasing worldwide. Genomic variations have the potential to serve as biomarkers for personalization of therapy and prediction of outcomes.
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189
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Trivedi MS, Hodgson NW, Walker SJ, Trooskens G, Nair V, Deth RC. Epigenetic effects of casein-derived opioid peptides in SH-SY5Y human neuroblastoma cells. Nutr Metab (Lond) 2015; 12:54. [PMID: 26664459 PMCID: PMC4673759 DOI: 10.1186/s12986-015-0050-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022] Open
Abstract
Background Casein-free, gluten-free diets have been reported to mitigate some of the inflammatory gastrointestinal and behavioral traits associated with autism, but the mechanism for this palliative effect has not been elucidated. We recently showed that the opioid peptide beta-casomorphin-7, derived from bovine (bBCM7) milk, decreases cysteine uptake, lowers levels of the antioxidant glutathione (GSH) and decreases the methyl donor S-adenosylmethionine (SAM) in both Caco-2 human GI epithelial cells and SH-SY5Y human neuroblastoma cells. While human breast milk can also release a similar peptide (hBCM-7), the bBCM7 and hBCM-7 vary greatly in potency; as the bBCM-7 is highly potent and similar to morphine in it's effects. Since SAM is required for DNA methylation, we wanted to further investigate the epigenetic effects of these food-derived opioid peptides. In the current study the main objective was to characterize functional pathways and key genes responding to DNA methylation effects of food-derived opioid peptides. Methods SH-SY5Y neuroblastoma cells were treated with 1 μM hBCM7 and bBCM7 and RNA and DNA were isolated after 4 h with or without treatment. Transcriptional changes were assessed using a microarray approach and CpG methylation status was analyzed at 450,000 CpG sites. Functional implications from both endpoints were evaluated via Ingenuity Pathway Analysis 4.0 and KEGG pathway analysis was performed to identify biological interactions between transcripts that were significantly altered at DNA methylation or transcriptional levels (p < 0.05, FDR <0.1). Results Here we show that hBCM7 and bBCM7, as well as morphine, cause epigenetic changes affecting gene pathways related to gastrointestinal disease and inflammation. These epigenetic consequences exhibited the same potency order as opiate inhibition of cysteine uptake insofar as hBCM7 was less potent than bBCM7, which was less potent than morphine. Conclusion Our findings indicate that epigenetic effects of milk-derived opiate peptides may contribute to GI dysfunction and inflammation in sensitive individuals. While the current study was performed using SH-SY5Y neuronal cellular models, similar actions on other cells types might combine to cause symptoms of intolerance. These actions may provide a potential contributing mechanism for the beneficial effects of a casein-free diet in alleviating gastrointestinal symptoms in neurological conditions including autism and other conditions. Lastly, our study also contributes to the evolving awareness of a “gut-brain connection”. Electronic supplementary material The online version of this article (doi:10.1186/s12986-015-0050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malav S Trivedi
- Department of Pharmaceutical Sciences, Nova Southeastern University, Rm # 3103, HPD building, Fort Lauderdale, FL USA
| | - Nathaniel W Hodgson
- Department of Molecular and Cellular Biology, Harvard Medical School, Boston, MA USA
| | - Stephen J Walker
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston Salem, NC USA
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium
| | - Vineeth Nair
- Department of Pharmaceutical Sciences, Nova Southeastern University, Rm # 3103, HPD building, Fort Lauderdale, FL USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Rm # 3103, HPD building, Fort Lauderdale, FL USA
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190
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Kratsman N, Getselter D, Elliott E. Sodium butyrate attenuates social behavior deficits and modifies the transcription of inhibitory/excitatory genes in the frontal cortex of an autism model. Neuropharmacology 2015; 102:136-45. [PMID: 26577018 DOI: 10.1016/j.neuropharm.2015.11.003] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/26/2015] [Accepted: 11/03/2015] [Indexed: 02/08/2023]
Abstract
The core behavioral symptoms of Autism Spectrum Disorders (ASD) include dysregulation of social communication and the presence of repetitive behaviors. However, there is no pharmacological agent that is currently used to target these core symptoms. Epigenetic dysregulation has been implicated in the etiology of ASD, and may present a pharmacological target. The effect of sodium butyrate, a histone deacetylase inhibitor, on social behavior and repetitive behavior, and the frontal cortex transcriptome, was examined in the BTBR autism mouse model. A 100 mg/kg dose, but not a 1200 mg/kg dose, of sodium butyrate attenuated social deficits in the BTBR mouse model. In addition, both doses decreased marble burying, an indication of repetitive behavior, but had no significant effect on self-grooming. Using RNA-seq, we determined that the 100 mg/kg dose of sodium butyrate induced changes in many behavior-related genes in the prefrontal cortex, and particularly affected genes involved in neuronal excitation or inhibition. The decrease in several excitatory neurotransmitter and neuronal activation marker genes, including cFos Grin2b, and Adra1, together with the increase in inhibitory neurotransmitter genes Drd2 and Gabrg1, suggests that sodium butyrate promotes the transcription of inhibitory pathway transcripts. Finally, DMCM, a GABA reverse agonist, decreased social behaviors in sodium-butyrate treated BTBR mice, suggesting that sodium butyrate increases social behaviors through modulation of the excitatory/inhibitory balance. Therefore, transcriptional modulation by sodium butyrate may have beneficial effects on autism related behaviors.
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Affiliation(s)
- Neta Kratsman
- Bar Ilan University Faculty of Medicine, Safed, Israel
| | | | - Evan Elliott
- Bar Ilan University Faculty of Medicine, Safed, Israel.
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191
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Li J, You Y, Yue W, Yu H, Lu T, Wu Z, Jia M, Ruan Y, Liu J, Zhang D, Wang L. Chromatin remodeling gene EZH2 involved in the genetic etiology of autism in Chinese Han population. Neurosci Lett 2015; 610:182-6. [PMID: 26552012 DOI: 10.1016/j.neulet.2015.10.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 01/17/2023]
Abstract
Autism spectrum disorder (ASD) is a group of severe neurodevelopmental disorders. Epigenetic factors play a critical role in the etiology of ASD. Enhancer of zest homolog 2 (EZH2), which encodes a histone methyltransferase, plays an important role in the process of chromatin remodeling during neurodevelopment. Further, EZH2 is located in chromosome 7q35-36, which is one of the linkage regions for autism. However, the genetic relationship between autism and EZH2 remains unclear. To investigate the association between EZH2 and autism in Chinese Han population, we performed a family-based association study between autism and three tagged single nucleotide polymorphisms (SNPs) that covered 95.4% of the whole region of EZH2. In the discovery cohort of 239 trios, two SNPs (rs740949 and rs6464926) showed a significant association with autism. To decrease false positive results, we expanded the sample size to 427 trios. A SNP (rs6464926) was significantly associated with autism even after Bonferroni correction (p=0.008). Haplotype G-T (rs740949 and rs6464926) was a risk factor for autism (Z=2.655, p=0.008, Global p=0.024). In silico function prediction for SNPs indicated that these two SNPs might be regulatory SNPs. Expression pattern of EZH2 showed that it is highly expressed in human embryonic brains. In conclusion, our findings demonstrate that EZH2 might contribute to the genetic etiology of autism in Chinese Han population.
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Affiliation(s)
- Jun Li
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Yang You
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Weihua Yue
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Hao Yu
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PR China
| | - Tianlan Lu
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Zhiliu Wu
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Meixiang Jia
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Yanyan Ruan
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China
| | - Jing Liu
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China.
| | - Dai Zhang
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PR China; PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, PR China.
| | - Lifang Wang
- Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, PR China; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), Beijing, PR China.
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192
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Grayson DR, Guidotti A. Merging data from genetic and epigenetic approaches to better understand autistic spectrum disorder. Epigenomics 2015; 8:85-104. [PMID: 26551091 PMCID: PMC4864049 DOI: 10.2217/epi.15.92] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that is characterized by a wide range of cognitive and behavioral abnormalities. Genetic research has identified large numbers of genes that contribute to ASD phenotypes. There is compelling evidence that environmental factors contribute to ASD through influences that differentially impact the brain through epigenetic mechanisms. Both genetic mutations and epigenetic influences alter gene expression in different cell types of the brain. Mutations impact the expression of large numbers of genes and also have downstream consequences depending on specific pathways associated with the mutation. Environmental factors impact the expression of sets of genes by altering methylation/hydroxymethylation patterns, local histone modification patterns and chromatin remodeling. Herein, we discuss recent developments in the research of ASD with a focus on epigenetic pathways as a complement to current genetic screening.
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Affiliation(s)
- Dennis R Grayson
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60607, USA
| | - Alessandro Guidotti
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60607, USA
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193
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Wockner LF, Morris CP, Noble EP, Lawford BR, Whitehall VLJ, Young RM, Voisey J. Brain-specific epigenetic markers of schizophrenia. Transl Psychiatry 2015; 5:e680. [PMID: 26575221 PMCID: PMC5068768 DOI: 10.1038/tp.2015.177] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/22/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetics plays a crucial role in schizophrenia susceptibility. In a previous study, we identified over 4500 differentially methylated sites in prefrontal cortex (PFC) samples from schizophrenia patients. We believe this was the first genome-wide methylation study performed on human brain tissue using the Illumina Infinium HumanMethylation450 Bead Chip. To understand the biological significance of these results, we sought to identify a smaller number of differentially methylated regions (DMRs) of more functional relevance compared with individual differentially methylated sites. Since our schizophrenia whole genome methylation study was performed, another study analysing two separate data sets of post-mortem tissue in the PFC from schizophrenia patients has been published. We analysed all three data sets using the bumphunter function found in the Bioconductor package minfi to identify regions that are consistently differentially methylated across distinct cohorts. We identified seven regions that are consistently differentially methylated in schizophrenia, despite considerable heterogeneity in the methylation profiles of patients with schizophrenia. The regions were near CERS3, DPPA5, PRDM9, DDX43, REC8, LY6G5C and a region on chromosome 10. Of particular interest is PRDM9 which encodes a histone methyltransferase that is essential for meiotic recombination and is known to tag genes for epigenetic transcriptional activation. These seven DMRs are likely to be key epigenetic factors in the aetiology of schizophrenia and normal brain neurodevelopment.
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Affiliation(s)
- L F Wockner
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - C P Morris
- Department of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - E P Noble
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - B R Lawford
- Department of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - V L J Whitehall
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - R M Young
- Department of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - J Voisey
- Department of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia,Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, 2 George Street, Kelvin Grove, QLD 4000, Australia. E-mail:
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194
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Autism-Like Behavior and Epigenetic Changes Associated with Autism as Consequences of In Utero Exposure to Environmental Pollutants in a Mouse Model. Behav Neurol 2015; 2015:426263. [PMID: 26586927 PMCID: PMC4637446 DOI: 10.1155/2015/426263] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/01/2015] [Accepted: 10/01/2015] [Indexed: 12/31/2022] Open
Abstract
We tested the hypothesis that in utero exposure to heavy metals increases autism-like behavioral phenotypes in adult animals and induces epigenetic changes in genes that have roles in the etiology of autism. Mouse dams were treated with cadmium, lead, arsenate, manganese, and mercury via drinking water from gestational days (E) 1–10. Valproic acid (VPA) injected intraperitoneally once on (E) 8.5 served as a positive control. Young male offspring were tested for behavioral deficits using four standardized behavioral assays. In this study, in utero exposure to heavy metals resulted in multiple behavioral abnormalities that persisted into adulthood. VPA and manganese induced changes in perseverative/impulsive behavior and social dominance behavior, arsenic caused changes only in perseverative/impulsive behavior, and lead induced abnormalities in social interaction in comparison to the control animals. Brain samples from Mn, Pb, and VPA treated and control animals were evaluated for changes in CpG island methylation in promoter regions and associated changes in gene expression. The Chd7 gene, essential for neural crest cell migration and patterning, was found to be hypomethylated in each experimental animal tested compared to water-treated controls. Furthermore, distinct patterns of CpG island methylation yielded novel candidate genes for further investigation.
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195
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Yang J, Yu L, Gaiteri C, Srivastava GP, Chibnik LB, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA. Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies. Int J Biochem Cell Biol 2015; 67:58-64. [PMID: 26003740 PMCID: PMC4564337 DOI: 10.1016/j.biocel.2015.05.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 11/18/2022]
Abstract
DNA methylation plays a crucial role in the regulation of gene expression, cell differentiation and development. Previous studies have reported age-related alterations of methylation levels in the human brain across the lifespan, but little is known about whether the observed association with age is confounded by common neuropathologies among older persons. Using genome-wide DNA methylation data from 740 postmortem brains, we interrogated 420,132 CpG sites across the genome in a cohort of individuals with ages from 66 to 108 years old, a range of ages at which many neuropathologic indices become quite common. We compared the association of DNA methylation prior to and following adjustment for common neuropathologies using a series of linear regression models. In the simplest model adjusting for technical factors including batch effect and bisulfite conversion rate, we found 8156 CpGs associated with age. The number of CpGs associated with age dropped by more than 10% following adjustment for sex. Notably, after adjusting for common neuropathologies, the total number of CpGs associated with age was reduced by approximately 40%, compared to the sex-adjusted model. These data illustrate that the association of methylation changes in the brain with age is inflated if one does not account for age-related brain pathologies. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Christopher Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Gyan P Srivastava
- Program in Translational NeuroPsychiatric Genomics, Departments of Neurology & Psychiatry, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics, Departments of Neurology & Psychiatry, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Sue E Leurgans
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA; Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Departments of Neurology & Psychiatry, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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196
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Varadinova M, Boyadjieva N. Epigenetic mechanisms: A possible link between autism spectrum disorders and fetal alcohol spectrum disorders. Pharmacol Res 2015; 102:71-80. [PMID: 26408203 DOI: 10.1016/j.phrs.2015.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/12/2015] [Accepted: 09/13/2015] [Indexed: 01/26/2023]
Abstract
The etiology of autism spectrum disorders (ASDs) still remains unclear and seems to involve a considerable overlap between polygenic, epigenetic and environmental factors. We have summarized the current understanding of the interplay between gene expression dysregulation via epigenetic modifications and the potential epigenetic impact of environmental factors in neurodevelopmental deficits. Furthermore, we discuss the scientific controversies of the relationship between prenatal exposure to alcohol and alcohol-induced epigenetic dysregulations, and gene expression alterations which are associated with disrupted neural plasticity and causal pathways for ASDs. The review of the literature suggests that a better understanding of developmental epigenetics should contribute to furthering our comprehension of the etiology and pathogenesis of ASDs and fetal alcohol spectrum disorders.
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Affiliation(s)
- Miroslava Varadinova
- Department of Pharmacology and Toxicology, Medical Faculty, Medical University, Sofia, Bulgaria.
| | - Nadka Boyadjieva
- Department of Pharmacology and Toxicology, Medical Faculty, Medical University, Sofia, Bulgaria.
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197
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Berko ER, Greally JM. How might epigenetic dysregulation in early embryonic life contribute to autism spectrum disorder? Epigenomics 2015; 7:1-4. [PMID: 25687459 DOI: 10.2217/epi.14.86] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Esther R Berko
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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198
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Mor M, Nardone S, Sams DS, Elliott E. Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex. Mol Autism 2015; 6:46. [PMID: 26273428 PMCID: PMC4535255 DOI: 10.1186/s13229-015-0040-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 08/04/2015] [Indexed: 12/03/2022] Open
Abstract
Background MicroRNAs are small RNA molecules that regulate the translation of protein from gene transcripts and are a powerful mechanism to regulate gene networks. Next-generation sequencing technologies have produced important insights into gene transcription changes that occur in the brain of individuals diagnosed with autism spectrum disorder (asd). However, these technologies have not yet been employed to uncover changes in microRNAs in the brain of individuals diagnosed with asd. Methods Small RNA next-generation sequencing was performed on RNA extracted from 12 human autism brain samples and 12 controls. Real-time PCR was used to validate a sample of the differentially expressed microRNAs, and bioinformatic analysis determined common pathways of gene targets. MicroRNA expression data was correlated to genome-wide DNA methylation data to determine if there is epigenetic regulation of dysregulated microRNAs in the autism brain. Luciferase assays, real-time PCR, and Western blot analysis were used to determine how dysregulated microRNAs may regulate the expression and translation of an autism-related gene transcript. Results We determined that miR-142-5p, miR-142-3p, miR-451a, miR-144-3p, and miR-21-5p are overexpressed in the asd brain. Furthermore, the promoter region of the miR-142 gene is hypomethylated in the same brain samples, suggesting that epigenetics plays a role in dysregulation of microRNAs in the brain. Bioinformatic analysis revealed that these microRNAs target genes that are involved in synaptic function. Further bioinformatic analysis, coupled with in vitro luciferase assays, determined that miR-451a and miR-21-5p can target the oxytocin receptor (OXTR) gene. OXTR gene expression is increased in these same brain samples, and there is a positive correlation between miR-21-5p and OXTR expression. However, miR-21-5p expression negatively correlates to production of OXTR protein from the OXTR transcript. Therefore, we suggest that miR-21-5p may attenuate OXTR expression in the human autism brain. Conclusions Our data suggests that dysregulation of microRNAs may play a biological role in the brain of individuals of autism. In addition, we suggest an interaction between epigenetic mechanisms and microRNA dysregulation in the brain. Overall, this data adds an important link in our understanding of the molecular events that are dysregulated in the brain of individuals diagnosed with autism. Electronic supplementary material The online version of this article (doi:10.1186/s13229-015-0040-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michal Mor
- Bar Ilan University Faculty of Medicine, Hanrieta Sold 8, Safed, 13215 Israel
| | - Stefano Nardone
- Bar Ilan University Faculty of Medicine, Hanrieta Sold 8, Safed, 13215 Israel
| | - Dev Sharan Sams
- Bar Ilan University Faculty of Medicine, Hanrieta Sold 8, Safed, 13215 Israel
| | - Evan Elliott
- Bar Ilan University Faculty of Medicine, Hanrieta Sold 8, Safed, 13215 Israel
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199
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Strong E, Butcher D, Singhania R, Mervis C, Morris C, De Carvalho D, Weksberg R, Osborne L. Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23. Am J Hum Genet 2015; 97:216-27. [PMID: 26166478 DOI: 10.1016/j.ajhg.2015.05.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022] Open
Abstract
Epigenetic dysfunction has been implicated in a growing list of disorders that include cancer, neurodevelopmental disorders, and neurodegeneration. Williams syndrome (WS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders with broad phenotypic spectra caused by deletion and duplication, respectively, of a 1.5-Mb region that includes several genes with a role in epigenetic regulation. We have identified striking differences in DNA methylation across the genome between blood cells from children with WS or Dup7 and blood cells from typically developing (TD) children. Notably, regions that were differentially methylated in both WS and Dup7 displayed a significant and symmetrical gene-dose-dependent effect, such that WS typically showed increased and Dup7 showed decreased DNA methylation. Differentially methylated genes were significantly enriched with genes in pathways involved in neurodevelopment, autism spectrum disorder (ASD) candidate genes, and imprinted genes. Using alignment with ENCODE data, we also found the differentially methylated regions to be enriched with CCCTC-binding factor (CTCF) binding sites. These findings suggest that gene(s) within 7q11.23 alter DNA methylation at specific sites across the genome and result in dose-dependent DNA-methylation profiles in WS and Dup7. Given the extent of DNA-methylation changes and the potential impact on CTCF binding and chromatin regulation, epigenetic mechanisms most likely contribute to the complex neurological phenotypes of WS and Dup7. Our findings highlight the importance of DNA methylation in the pathogenesis of WS and Dup7 and provide molecular mechanisms that are potentially shared by WS, Dup7, and ASD.
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200
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Gardner RM, Lee BK, Magnusson C, Rai D, Frisell T, Karlsson H, Idring S, Dalman C. Maternal body mass index during early pregnancy, gestational weight gain, and risk of autism spectrum disorders: Results from a Swedish total population and discordant sibling study. Int J Epidemiol 2015; 44:870-83. [PMID: 26045508 PMCID: PMC4521130 DOI: 10.1093/ije/dyv081] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Prenatal environmental factors such as maternal adiposity may influence the risk of offspring autism spectrum disorders (ASD), though current evidence is inconsistent. The objective of this study was to assess the relationship of parental BMI and gestational weight gain (GWG) with risk of offspring ASD in a population-based cohort study using family-based study designs. METHODS The cohort was based in Stockholm County, Sweden, including 333,057 individuals born 1984-2007, of whom 6420 were diagnosed with an ASD. We evaluated maternal body mass index (BMI) at first antenatal visit, GWG and paternal BMI at the time of conscription into the Swedish military as exposures using general estimating equation (GEE) models with logit link. RESULTS At the population level, maternal overweight/obesity was associated with increased risk of offspring ASD [odds ratio (OR)25 ≤ BMI < 30 1.31, 95% confidence interval = 1.21-1.41; ORBMI ≥ 30 1.94, 1.72-2.17], as was paternal underweight (ORBMI < 18.5, 1.19, 1.06-1.33) and obesity (ORBMI ≥ 30 1.47, 1.12-1.92) in mutually adjusted models. However, in matched sibling analyses, the relationship between elevated maternal BMI and ASD risk was not apparent. GWG had a U-shaped association with offspring ASD at the population level (ORinsufficient 1.22, 1.07-1.40; ORexcessive 1.23, 1.08-1.40). Matched sibling analyses were suggestive of elevated risk with excessive GWG (ORinsufficient 1.12, 0.68-1.84; ORexcessive 1.48, 0.93-2.38). CONCLUSIONS Whereas population-level results suggested that maternal BMI was associated with ASD, sibling analyses and paternal BMI analyses indicate that maternal BMI may also be a proxy marker for other familial risk factors. Evidence is stronger for a direct link between GWG and ASD risk.
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Affiliation(s)
- Renee M Gardner
- Department of Public Health Sciences, and Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden,
| | - Brian K Lee
- Department of Epidemiology and Biostatistics, Drexel University School of Public Health, Philadelphia, PA, USA, A.J. Drexel Autism Institute, Philadelphia, PA, USA
| | - Cecilia Magnusson
- Department of Public Health Sciences, and Centre for Epidemiology and Community Medicine, Stockholm County Council, Stockholm, Sweden
| | - Dheeraj Rai
- School of Social and Community Medicine, University of Bristol, Bristol, UK, Avon and Wiltshire Partnership NHS Mental Health Trust, Bristol, UK
| | - Thomas Frisell
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden and
| | - Håkan Karlsson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Selma Idring
- Department of Public Health Sciences, and Neurodevelopmental Psychiatry Unit, Child and Youth Psychiatry, Stockholm County Council, Stockholm, Sweden
| | - Christina Dalman
- Department of Public Health Sciences, and Centre for Epidemiology and Community Medicine, Stockholm County Council, Stockholm, Sweden
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