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Prospects of Genetics and Epigenetics of Alcohol Use Disorder. CURRENT ADDICTION REPORTS 2020. [DOI: 10.1007/s40429-020-00331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
Purpose of Review
In this study, we illustrate recent findings regarding the genetics and epigenetics of alcohol use disorder (AUD). We further outline the future direction of genetic and epigenetic research in AUD.
Recent Findings
Recent genome- and epigenome-wide studies allow new insight into genetic and epigenetic variation associated with AUD. The largest EWAS of AUD so far/to date found evidence for altered glucocorticoid receptor regulation. Longitudinal studies provide insight into the dynamics of the disease. Analyses of postmortem brain tissue reveal the impact of chronic alcohol consumption on DNA methylation in the brain.
Summary
Genetic and environmental factors—mediated via epigenetic mechanisms—play an important role in AUD. Although knowledge of the biological underpinnings of AUD is still limited, ongoing research will ultimately lead to the development of biomarkers for disease classification, course of disease, and treatment response to support personalized medicine in the future.
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Smigielski L, Jagannath V, Rössler W, Walitza S, Grünblatt E. Epigenetic mechanisms in schizophrenia and other psychotic disorders: a systematic review of empirical human findings. Mol Psychiatry 2020; 25:1718-1748. [PMID: 31907379 DOI: 10.1038/s41380-019-0601-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/26/2022]
Abstract
Schizophrenia and other psychotic disorders are highly debilitating psychiatric conditions that lack a clear etiology and exhibit polygenic inheritance underlain by pleiotropic genes. The prevailing explanation points to the interplay between predisposing genes and environmental exposure. Accumulated evidence suggests that epigenetic regulation of the genome may mediate dynamic gene-environment interactions at the molecular level by modulating the expression of psychiatric phenotypes through transcription factors. This systematic review summarizes the current knowledge linking schizophrenia and other psychotic disorders to epigenetics, based on PubMed and Web of Science database searches conducted according to the PRISMA guidelines. Three groups of mechanisms in case-control studies of human tissue (i.e., postmortem brain and bio-fluids) were considered: DNA methylation, histone modifications, and non-coding miRNAs. From the initial pool of 3,204 records, 152 studies met our inclusion criteria (11,815/11,528, 233/219, and 2,091/1,827 cases/controls for each group, respectively). Many of the findings revealed associations with epigenetic modulations of genes regulating neurotransmission, neurodevelopment, and immune function, as well as differential miRNA expression (e.g., upregulated miR-34a, miR-7, and miR-181b). Overall, actual evidence moderately supports an association between epigenetics and schizophrenia and other psychotic disorders. However, heterogeneous results and cross-tissue extrapolations call for future work. Integrating epigenetics into systems biology may critically enhance research on psychosis and thus our understanding of the disorder. This may have implications for psychiatry in risk stratification, early recognition, diagnostics, precision medicine, and other interventional approaches targeting epigenetic fingerprints.
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Affiliation(s)
- Lukasz Smigielski
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland. .,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.
| | - Vinita Jagannath
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,Merck Sharp & Dohme (MSD) R&D Innovation Centre, London, UK
| | - Wulf Rössler
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin, Berlin, Germany.,Laboratory of Neuroscience, Institute of Psychiatry, Universidade de São Paulo, São Paulo, Brazil
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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Novel candidate genes for ECT response prediction-a pilot study analyzing the DNA methylome of depressed patients receiving electroconvulsive therapy. Clin Epigenetics 2020; 12:114. [PMID: 32727556 PMCID: PMC7388224 DOI: 10.1186/s13148-020-00891-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/23/2020] [Indexed: 01/07/2023] Open
Abstract
Background Major depressive disorder (MDD) represents a serious global health concern. The urge for efficient MDD treatment strategies is presently hindered by the incomplete knowledge of its underlying pathomechanism. Despite recent progress (highlighting both genetics and the environment, and thus DNA methylation, to be relevant for its development), 30–50% of MDD patients still fail to reach remission with standard treatment approaches. Electroconvulsive therapy (ECT) is one of the most powerful options for the treatment of pharmacoresistant depression; nevertheless, ECT remission rates barely reach 50% in large-scale naturalistic population-based studies. To optimize MDD treatment strategies and enable personalized medicine in the long- term, prospective indicators of ECT response are thus in great need. Because recent target-driven analyses revealed DNA methylation baseline differences between ECT responder groups, we analyzed the DNA methylome of depressed ECT patients using next-generation sequencing. In this pilot study, we did not only aim to find novel targets for ECT response prediction but also to get a deeper insight into its possible mechanism of action. Results Longitudinal DNA methylation analysis of peripheral blood mononuclear cells isolated from a cohort of treatment-resistant MDD patients (n = 12; time points: before and after 1st and last ECT, respectively) using a TruSeq-Methyl Capture EPIC Kit for library preparation, led to the following results: (1) The global DNA methylation differed neither between the four measured time points nor between ECT responders (n = 8) and non-responders (n = 4). (2) Analyzing the DNA methylation variance for every probe (=1476812 single CpG sites) revealed eight novel candidate genes to be implicated in ECT response (protein-coding genes: RNF175, RNF213, TBC1D14, TMC5, WSCD1; genes encoding for putative long non-coding RNA transcripts: AC018685.2, AC098617.1, CLCN3P1). (3) In addition, DNA methylation of two CpG sites (located within AQP10 and TRERF1) was found to change during the treatment course. Conclusions We suggest ten novel candidate genes to be implicated in either ECT response or its possible mechanism. Because of the small sample size of our pilot study, our findings must be regarded as preliminary.
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Krause BJ, Artigas R, Sciolla AF, Hamilton J. Epigenetic mechanisms activated by childhood adversity. Epigenomics 2020; 12:1239-1255. [PMID: 32706263 DOI: 10.2217/epi-2020-0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adverse childhood experiences (ACE) impair health and life expectancy and may result in an epigenetic signature that drives increased morbidity primed during early stages of life. This literature review focuses on the current evidence for epigenetic-mediated programming of brain and immune function resulting from ACE. To address this aim, a total of 88 articles indexed in PubMed before August 2019 concerning ACE and epigenetics were surveyed. Current evidence partially supports epigenetic programming of the hypothalamic-pituitary-adrenal axis, but convincingly shows that ACE impairs immune function. Additionally, the needs and challenges that face this area are discussed in order to provide a framework that may help to clarify the role of epigenetics in the long-lasting effects of ACE.
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Affiliation(s)
- Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O''Higgins, Rancagua, Chile.,CUIDA - Centro de Investigación del Abuso y la Adversidad Temprana, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Rocio Artigas
- CUIDA - Centro de Investigación del Abuso y la Adversidad Temprana, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Andres F Sciolla
- Department of Psychiatry & Behavioral Sciences, University of California, Davis, CA 95834, USA
| | - James Hamilton
- CUIDA - Centro de Investigación del Abuso y la Adversidad Temprana, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, Chile.,Fundación Para la Confianza, Pérez Valenzuela 1264, Providencia, Santiago, Chile
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105
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Marie-Claire C, Lejeune FX, Mundwiller E, Ulveling D, Moszer I, Bellivier F, Etain B. A DNA methylation signature discriminates between excellent and non-response to lithium in patients with bipolar disorder type 1. Sci Rep 2020; 10:12239. [PMID: 32699220 PMCID: PMC7376060 DOI: 10.1038/s41598-020-69073-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
Lithium (Li) is the cornerstone maintenance treatment for bipolar disorders (BD), but response rates are highly variable. To date, no clinical or biological marker is available to reliably define eligibility criteria for a maintenance treatment with Li. We examined whether the prophylactic response to Li (assessed retrospectively) is associated with distinct blood DNA methylation profiles. Bisulfite-treated total blood DNA samples from individuals with BD type 1 (15 excellent-responders (LiERs) versus 11 non-responders (LiNRs)) were used for targeted enrichment of CpG rich genomic regions followed by high-resolution next-generation sequencing to identify differentially methylated regions (DMRs). After controlling for potential confounders we identified 111 DMRs that significantly differ between LiERs and LiNRs with a significant enrichment in neuronal cell components. Logistic regression and receiver operating curves identified a combination of 7 DMRs with a good discriminatory power for response to Li (Area Under the Curve 0.806). Annotated genes associated with these DMRs include Eukaryotic Translation Initiation Factor 2B Subunit Epsilon (EIF2B5), Von Willebrand Factor A Domain Containing 5B2 (VWA5B2), Ral GTPase Activating Protein Catalytic Alpha Subunit 1 (RALGAPA1). Although preliminary and deserving replication, these results suggest that biomarkers of response to Li may be identified through peripheral epigenetic measures.
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Affiliation(s)
- C Marie-Claire
- Optimisation thérapeutique en Neurospsychopharmacologie, INSERM U1144, Université de Paris, Paris, France.
| | - F X Lejeune
- Bioinformatics and Biostatistics Core Facility iCONICS, Inserm U 1127, CNRS UMR 7225, Sorbonne Université UMR S 1127, Institut du Cerveau Et de La Moelle Épinière, Paris, France
| | - E Mundwiller
- IGenSeq, Institut du Cerveau Et de La Moelle Épinière, Paris, France
| | - D Ulveling
- Bioinformatics and Biostatistics Core Facility iCONICS, Inserm U 1127, CNRS UMR 7225, Sorbonne Université UMR S 1127, Institut du Cerveau Et de La Moelle Épinière, Paris, France
| | - I Moszer
- Bioinformatics and Biostatistics Core Facility iCONICS, Inserm U 1127, CNRS UMR 7225, Sorbonne Université UMR S 1127, Institut du Cerveau Et de La Moelle Épinière, Paris, France
| | - F Bellivier
- Optimisation thérapeutique en Neurospsychopharmacologie, INSERM U1144, Université de Paris, Paris, France.,AP-HP, GH Saint-Louis-Lariboisière-F. Widal, Pole de Psychiatrie Et de Médecine Addictologique, Paris, France.,Fondation FondaMental, Créteil, France.,Faculté de Médecine, Université de Paris, Paris, France
| | - B Etain
- Optimisation thérapeutique en Neurospsychopharmacologie, INSERM U1144, Université de Paris, Paris, France.,AP-HP, GH Saint-Louis-Lariboisière-F. Widal, Pole de Psychiatrie Et de Médecine Addictologique, Paris, France.,Fondation FondaMental, Créteil, France.,Faculté de Médecine, Université de Paris, Paris, France
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106
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Ciuculete DM, Voisin S, Kular L, Jonsson J, Rask-Andersen M, Mwinyi J, Schiöth HB. meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes. Clin Epigenetics 2020; 12:99. [PMID: 32616021 PMCID: PMC7333393 DOI: 10.1186/s13148-020-00884-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Little is known about how genetics and epigenetics interplay in depression. Evidence suggests that genetic variants may change vulnerability to depression by modulating DNA methylation (DNAm) and non-coding RNA (ncRNA) levels. Therefore, the aim of the study was to investigate the effect of the genetic variation, previously identified in the largest genome-wide association study for depression, on proximal DNAm and ncRNA levels. RESULTS We performed DNAm quantitative trait locus (meQTL) analysis in two independent cohorts (total n = 435 healthy individuals), testing associations between 102 single-nucleotide polymorphisms (SNPs) and DNAm levels in whole blood. We identified and replicated 64 SNP-CpG pairs (padj. < 0.05) with meQTL effect. Lower DNAm at cg02098413 located in the HACE1 promoter conferred by the risk allele (C allele) at rs1933802 was associated with higher risk for depression (praw = 0.014, DNAm = 2.3%). In 1202 CD14+ cells sorted from blood, DNAm at cg02088412 positively correlated with HACE1 mRNA expression. Investigation in postmortem brain tissue of adults diagnosed with major depressive disorder (MDD) indicated 1% higher DNAm at cg02098413 in neurons and lower HACE1 mRNA expression in CA1 hippocampus of MDD patients compared with healthy controls (p = 0.008 and 0.012, respectively). Expression QTL analysis in blood of 74 adolescent revealed that hsa-miR-3664-5p was associated with rs7117514 (SHANK2) (padj. = 0.015, mRNA difference = 5.2%). Gene ontology analysis of the miRNA target genes highlighted implication in neuronal processes. CONCLUSIONS Collectively, our findings from a multi-tissue (blood and brain) and multi-layered (genetic, epigenetic, transcriptomic) approach suggest that genetic factors may influence depression by modulating DNAm and miRNA levels. Alterations at HACE1 and SHANK2 loci imply potential mechanisms, such as oxidative stress in the brain, underlying depression. Our results deepened the knowledge of molecular mechanisms in depression and suggest new epigenetic targets that should be further evaluated.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76, Stockholm, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetic and Pathology, Uppsala University, Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, Husargatan 3, 753124, Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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107
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Vasanthakumar A, Davis JW, Idler K, Waring JF, Asque E, Riley-Gillis B, Grosskurth S, Srivastava G, Kim S, Nho K, Nudelman KNH, Faber K, Sun Y, Foroud TM, Estrada K, Apostolova LG, Li QS, Saykin AJ. Harnessing peripheral DNA methylation differences in the Alzheimer's Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease. Clin Epigenetics 2020; 12:84. [PMID: 32539856 PMCID: PMC7294637 DOI: 10.1186/s13148-020-00864-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a chronic progressive neurodegenerative disease impacting an estimated 44 million adults worldwide. The causal pathology of AD (accumulation of amyloid-beta and tau), precedes hallmark symptoms of dementia by more than a decade, necessitating development of early diagnostic markers of disease onset, particularly for new drugs that aim to modify disease processes. To evaluate differentially methylated positions (DMPs) as novel blood-based biomarkers of AD, we used a subset of 653 individuals with peripheral blood (PB) samples in the Alzheimer's disease Neuroimaging Initiative (ADNI) consortium. The selected cohort of AD, mild cognitive impairment (MCI), and age-matched healthy controls (CN) all had imaging, genetics, transcriptomics, cerebrospinal protein markers, and comprehensive clinical records, providing a rich resource of concurrent multi-omics and phenotypic information on a well-phenotyped subset of ADNI participants. RESULTS In this manuscript, we report cross-diagnosis differential peripheral DNA methylation in a cohort of AD, MCI, and age-matched CN individuals with longitudinal DNA methylation measurements. Epigenome-wide association studies (EWAS) were performed using a mixed model with repeated measures over time with a P value cutoff of 1 × 10-5 to test contrasts of pairwise differential peripheral methylation in AD vs CN, AD vs MCI, and MCI vs CN. The most highly significant differentially methylated loci also tracked with Mini Mental State Examination (MMSE) scores. Differentially methylated loci were enriched near brain and neurodegeneration-related genes (e.g., BDNF, BIN1, APOC1) validated using the genotype tissue expression project portal (GTex). CONCLUSIONS Our work shows that peripheral differential methylation between age-matched subjects with AD relative to healthy controls will provide opportunities to further investigate and validate differential methylation as a surrogate of disease. Given the inaccessibility of brain tissue, the PB-associated methylation marks may help identify the stage of disease and progression phenotype, information that would be central to bringing forward successful drugs for AD.
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Affiliation(s)
| | - Justin W Davis
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | - Kenneth Idler
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | | | | | | | | | | | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Electrical and Computer Engineering, State University of New York, Oswego, NY, 13126, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kelly N H Nudelman
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kelley Faber
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yu Sun
- Neuroscience Therapeutic Area, Janssen Research & Development, Pennington, NJ, 08534, USA
- Research Information Technology, Janssen Research & Development, Pennington, NJ, 08534, USA
| | - Tatiana M Foroud
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Karol Estrada
- Biogen, Cambridge, MA, 02142, USA
- Currently at Biomarin Pharmaceuticals, Novato, CA, 94949, USA
| | - Liana G Apostolova
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research & Development, Pennington, NJ, 08534, USA
- Research Information Technology, Janssen Research & Development, Pennington, NJ, 08534, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
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108
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Chen J, Zang Z, Braun U, Schwarz K, Harneit A, Kremer T, Ma R, Schweiger J, Moessnang C, Geiger L, Cao H, Degenhardt F, Nöthen MM, Tost H, Meyer-Lindenberg A, Schwarz E. Association of a Reproducible Epigenetic Risk Profile for Schizophrenia With Brain Methylation and Function. JAMA Psychiatry 2020; 77:628-636. [PMID: 32049268 PMCID: PMC7042900 DOI: 10.1001/jamapsychiatry.2019.4792] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
IMPORTANCE Schizophrenia is a severe mental disorder in which epigenetic mechanisms may contribute to illness risk. Epigenetic profiles can be derived from blood cells, but to our knowledge, it is unknown whether these predict established brain alterations associated with schizophrenia. OBJECTIVE To identify an epigenetic signature (quantified as polymethylation score [PMS]) of schizophrenia using machine learning applied to genome-wide blood DNA-methylation data; evaluate whether differences in blood-derived PMS are mirrored in data from postmortem brain samples; test whether the PMS is associated with alterations of dorsolateral prefrontal cortex hippocampal (DLPFC-HC) connectivity during working memory in healthy controls (HC); explore the association between interactions between polygenic and epigenetic risk with DLPFC-HC connectivity; and test the specificity of the signature compared with other serious psychiatric disorders. DESIGN, SETTING, AND PARTICIPANTS In this case-control study conducted from 2008 to 2018 in sites in Germany, the United Kingdom, the United States, and Australia, blood DNA-methylation data from 2230 whole-blood samples from 6 independent cohorts comprising HC (1238 [55.5%]) and participants with schizophrenia (803 [36.0%]), bipolar disorder (39 [1.7%]), major depressive disorder 35 [1.6%]), and autism (27 [1.2%]), and first-degree relatives of all patient groups (88 [3.9%]) were analyzed. DNA-methylation data were further explored from 244 postmortem DLPFC samples from 136 HC and 108 patients with schizophrenia. Neuroimaging and genome-wide association data were available for 393 HC. The latter data was used to calculate a polygenic risk score (PRS) for schizophrenia. The data were analyzed in 2019. MAIN OUTCOMES AND MEASURES The accuracy of schizophrenia control classification based on machine learning using epigenetic data; association of schizophrenia PMS scores with DLPFC-HC connectivity; and association of the interaction between PRS and PMS with DLPFC-HC connectivity. RESULTS This study included 7488 participants (4395 men [58.7%]), of whom 3158 (2230 men [70.6%]) received a diagnosis of schizophrenia. The PMS signature was associated with schizophrenia across 3 independent data sets (area under the curve [AUC] from 0.69 to 0.78; P value from 0.049 to 1.24 × 10-7) and data from postmortem DLPFC samples (AUC = 0.63; P = 1.42 × 10-4), but not with major depressive disorder (AUC = 0.51; P = .16), autism (AUC = 0.53; P = .66), or bipolar disorder (AUC = 0.58; P = .21). Pathways contributing most to the classification included synaptic processes. Healthy controls with schizophrenia-like PMS showed significantly altered DLPFC-HC connectivity (validation methylation/magnetic resonance imaging, t < -3.81; P for familywise error, <.04; validation magnetic resonance imaging, t < -3.54; P for familywise error, <.02), mirroring the lack of functional decoupling in schizophrenia. There was no significant association of the interaction between PMS and PRS with DLPFC-HC connectivity (P > .19). CONCLUSIONS AND RELEVANCE We identified a reproducible blood DNA-methylation signature specific for schizophrenia that was correlated with altered functional DLPFC-HC coupling during working memory and mapped to methylation differences found in DLPFC postmortem samples. This indicates a possible epigenetic contribution to a schizophrenia intermediate phenotype and suggests that PMS could be of interest to be studied in the context of multimodal biomarkers for disease stratification and treatment personalization.
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Affiliation(s)
- Junfang Chen
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Zhenxiang Zang
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Urs Braun
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kristina Schwarz
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anais Harneit
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Kremer
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ren Ma
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Janina Schweiger
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carolin Moessnang
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lena Geiger
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Han Cao
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Franziska Degenhardt
- School of Medicine & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus M. Nöthen
- School of Medicine & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany,Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
| | - Heike Tost
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Meyer-Lindenberg
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Emanuel Schwarz
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Boehm I, Walton E, Alexander N, Batury VL, Seidel M, Geisler D, King JA, Weidner K, Roessner V, Ehrlich S. Peripheral serotonin transporter DNA methylation is linked to increased salience network connectivity in females with anorexia nervosa. J Psychiatry Neurosci 2020; 45:206-213. [PMID: 31823595 PMCID: PMC7828979 DOI: 10.1503/jpn.190016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Epigenetic variation in the serotonin transporter gene (SLC6A4) has been shown to modulate the functioning of brain circuitry associated with the salience network and may heighten the risk for mental illness. This study is, to our knowledge, the first to test this epigenome–brain–behaviour pathway in patients with anorexia nervosa. METHODS We obtained resting-state functional connectivity (rsFC) data and blood samples from 55 acutely underweight female patients with anorexia nervosa and 55 age-matched female healthy controls. We decomposed imaging data using independent component analysis. We used bisulfite pyrosequencing to analyze blood DNA methylation within the promoter region of SLC6A4. We then explored salience network rsFC patterns in the group × methylation interaction. RESULTS We identified a positive relationship between SLC6A4 methylation levels and rsFC between the dorsolateral prefrontal cortex and the salience network in patients with anorexia nervosa compared to healthy controls. Increased rsFC in the salience network mediated the link between SLC6A4 methylation and eating disorder symptoms in patients with anorexia nervosa. We confirmed findings of rsFC alterations for CpG-specific methylation at a locus with evidence of methylation correspondence between brain and blood tissue. LIMITATIONS This study was cross-sectional in nature, the sample size was modest for the method and methylation levels were measured peripherally, so findings cannot be fully generalized to brain tissue. CONCLUSION This study sheds light on the neurobiological process of how epigenetic variation in the SLC6A4 gene may relate to rsFC in the salience network that is linked to psychopathology in anorexia nervosa.
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Affiliation(s)
- Ilka Boehm
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Esther Walton
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Nina Alexander
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Victoria-Luise Batury
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Maria Seidel
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Daniel Geisler
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Joseph A. King
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Kerstin Weidner
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Veit Roessner
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
| | - Stefan Ehrlich
- From the Division of Psychological and Social Medicine and Developmental Neurosciences, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Boehm, Walton, Batury, Seidel, Geisler, King, Ehrlich); the Department of Psychology, University of Bath, Bath, UK (Walton); the Department of Psychology, Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany (Alexander); the Department of Psychotherapy and Psychosomatic Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Weidner); the Department of Child and Adolescent Psychiatry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany (Roessner); and the Eating Disorders Research and Treatment Center at the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany (Ehrlich)
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Mur J, McCartney DL, Walker RM, Campbell A, Bermingham ML, Morris SW, Porteous DJ, McIntosh AM, Deary IJ, Evans KL, Marioni RE. DNA methylation in APOE: The relationship with Alzheimer's and with cardiovascular health. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2020; 6:e12026. [PMID: 32346601 PMCID: PMC7185210 DOI: 10.1002/trc2.12026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/16/2019] [Accepted: 01/01/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Genetic variation in the apolipoprotein E (APOE) gene is associated with Alzheimer's disease (AD) and risk factors for cardiovascular disease (CVD). DNA methylationat APOE has been associated with altered cognition and AD. It is unclear if epigenetic marks could be used for predicting future disease. METHODS We assessed blood-based DNA methylation at 13 CpGs in the APOE gene in 5828 participants from the Generation Scotland (GS) cohort. Using linear mixed models regression, we examined the relationships among APOE methylation, cognition, cholesterol, the family history of AD and the risk for CVD. RESULTS DNA methylation at two CpGs was associated with the ratio of total cholesterol and HDL cholesterol, but not with cognition, family history of AD, or the risk of CVD. DISCUSSION APOE methylation is associated with the levels of blood cholesterol, but there is no evidence for the utility of APOE methylation as a biomarker for predicting AD or CVD.
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Affiliation(s)
- Jure Mur
- Department of PsychologyUniversity of EdinburghEdinburghUK
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Rosie M. Walker
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Archie Campbell
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Stewart W. Morris
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - David J. Porteous
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Division of PsychiatryCentre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Ian J. Deary
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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111
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Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects. Sci Rep 2020; 10:4704. [PMID: 32170143 PMCID: PMC7069985 DOI: 10.1038/s41598-020-61671-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
Interrogating DNA methylation within schizophrenia risk loci holds promise to identify mechanisms by which genes influence the disease. Based on the hypothesis that allele specific methylation (ASM) of a single CpG, or perhaps CpH, might mediate or mark the effects of genetic variants on disease risk and phenotypes, we explored haplotype specific methylation levels of individual cytosines within a genomic region harbouring the BAG5, APOPT1 and KLC1 genes in peripheral blood of schizophrenia patients and healthy controls. Three DNA fragments located in promoter, intronic and intergenic areas were studied by single-molecule real-time bisulfite sequencing enabling the analysis of long reads of DNA with base-pair resolution and the determination of haplotypes directly from sequencing data. Among 1,012 cytosines studied, we did not find any site where methylation correlated with the disease or cognitive deficits after correction for multiple testing. At the same time, we determined the methylation profile associated with the schizophrenia risk haplotype within the KLC1 fourth intron and confirmed ASM for cytosines located in the vicinity of rs67899457. These genetically associated DNA methylation variations may be related to the pathophysiological mechanism differentiating the risk and non-risk haplotypes and merit further investigation.
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112
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Güiza F, Vanhorebeek I, Verstraete S, Verlinden I, Derese I, Ingels C, Dulfer K, Verbruggen SC, Garcia Guerra G, Joosten KF, Wouters PJ, Van den Berghe G. Effect of early parenteral nutrition during paediatric critical illness on DNA methylation as a potential mediator of impaired neurocognitive development: a pre-planned secondary analysis of the PEPaNIC international randomised controlled trial. THE LANCET RESPIRATORY MEDICINE 2020; 8:288-303. [DOI: 10.1016/s2213-2600(20)30046-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022]
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113
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Chan RF, Shabalin AA, Montano C, Hannon E, Hultman CM, Fallin MD, Feinberg AP, Mill J, van den Oord EJCG, Aberg KA. Independent Methylome-Wide Association Studies of Schizophrenia Detect Consistent Case-Control Differences. Schizophr Bull 2020; 46:319-327. [PMID: 31165892 PMCID: PMC7442362 DOI: 10.1093/schbul/sbz056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Methylome-wide association studies (MWASs) are promising complements to sequence variation studies. We used existing sequencing-based methylation data, which assayed the majority of all 28 million CpGs in the human genome, to perform an MWAS for schizophrenia in blood, while controlling for cell-type heterogeneity with a recently generated platform-specific reference panel. Next, we compared the MWAS results with findings from 3 existing large-scale array-based schizophrenia methylation studies in blood that assayed up to ~450 000 CpGs. Our MWAS identified 22 highly significant loci (P < 5 × 10-8) and 852 suggestively significant loci (P < 1 × 10-5). The top finding (P = 5.62 × 10-11, q = 0.001) was located in MFN2, which encodes mitofusin-2 that regulates Ca2+ transfer from the endoplasmic reticulum to mitochondria in cooperation with DISC1. The second-most significant site (P = 1.38 × 10-9, q = 0.013) was located in ALDH1A2, which encodes an enzyme for astrocyte-derived retinoic acid-a key neuronal morphogen with relevance for schizophrenia. Although the most significant MWAS findings were not assayed on the arrays, we observed significant enrichment of overlapping findings with 2 of the 3 array datasets (P = 0.0315, 0.0045, 0.1946). Overrepresentation analysis of Gene Ontology terms for the genes in the significant overlaps suggested high similarity in the biological functions detected by the different datasets. Top terms were related to immune and/or stress responses, cell adhesion and motility, and a broad range of processes essential for neurodevelopment.
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Affiliation(s)
- Robin F Chan
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | | | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Margaret D Fallin
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA
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Abstract
Epigenetic mechanisms govern the transcription of the genome. Research with model systems reveals that environmental conditions can directly influence epigenetic mechanisms that are associated with interindividual differences in gene expression in brain and neural function. In this review, we provide a brief overview of epigenetic mechanisms and research with relevant rodent models. We emphasize more recent translational research programs in epigenetics as well as the challenges inherent in the integration of epigenetics into developmental and clinical psychology. Our objectives are to present an update with respect to the translational relevance of epigenetics for the study of psychopathology and to consider the state of current research with respect to its potential importance for clinical research and practice in mental health.
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Affiliation(s)
- Kieran J O'Donnell
- Department of Psychiatry and Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec H4H 1R3, Canada; .,Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3H 1R4, Canada.,Child and Brain Development Program, CIFAR, Toronto, Ontario M5G 1M1, Canada
| | - Michael J Meaney
- Department of Psychiatry and Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec H4H 1R3, Canada; .,Child and Brain Development Program, CIFAR, Toronto, Ontario M5G 1M1, Canada.,Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 117609 Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
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115
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Cecil CAM, Zhang Y, Nolte T. Childhood maltreatment and DNA methylation: A systematic review. Neurosci Biobehav Rev 2020; 112:392-409. [PMID: 32081689 DOI: 10.1016/j.neubiorev.2020.02.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 12/20/2022]
Abstract
DNA methylation (DNAm) - an epigenetic process that regulates gene expression - may represent a mechanism for the biological embedding of early traumatic experiences, including childhood maltreatment. Here, we conducted the first systematic review of human studies linking childhood maltreatment to DNAm. In total, 72 studies were included in the review (2008-2018). The majority of extant studies (i) were based on retrospective data in adults, (ii) employed a candidate gene approach (iii) focused on global maltreatment, (iv) were based on easily accessible peripheral tissues, typically blood; and (v) were cross-sectional. Two-thirds of studies (n = 48) also examined maltreatment-related outcomes, such as stress reactivity and psychiatric symptoms. While findings generally support an association between childhood maltreatment and altered patterns of DNAm, factors such as the lack of longitudinal data, low comparability across studies as well as potential genetic and 'pre-exposure' environmental confounding currently limit the conclusions that can be drawn. Key challenges are discussed and concrete recommendations for future research are provided to move the field forward.
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Affiliation(s)
- Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry, Erasmus Medical Centre, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands; Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.
| | - Yuning Zhang
- Centre for Innovation in Mental Health, University of Southampton; State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Tobias Nolte
- The Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom; Anna Freud National Centre for Children and Families, London, United Kingdom
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116
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Schiele MA, Gottschalk MG, Domschke K. The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention. Clin Psychol Rev 2020; 77:101830. [PMID: 32163803 DOI: 10.1016/j.cpr.2020.101830] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/11/2022]
Abstract
Mental disorders are highly complex and multifactorial in origin, comprising an elaborate interplay of genetic and environmental factors. Epigenetic mechanisms such as DNA modifications (e.g. CpG methylation), histone modifications (e.g. acetylation) and microRNAs function as a translator between genes and the environment. Indeed, environmental influences such as exposure to stress shape epigenetic patterns, and lifetime experiences continue to alter the function of the genome throughout the lifespan. Here, we summarize the recently burgeoning body of research regarding the involvement of aberrant epigenetic signatures in mediating an increased vulnerability to a wide range of mental disorders. We review the current knowledge of epigenetic changes to constitute useful markers predicting the clinical response to psychotherapeutic interventions, and of psychotherapy to alter - and potentially reverse - epigenetic risk patterns. Given first evidence pointing to a transgenerational transmission of epigenetic information, epigenetic alterations arising from successful psychotherapy might be transferred to future generations and thus contribute to the prevention of mental disorders. Findings are integrated into a multi-level framework highlighting challenges pertaining to the mechanisms of action and clinical implications of epigenetic research. Promising future directions regarding the prediction, prevention, and personalized treatment of mental disorders in line with a 'precision medicine' approach are discussed.
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Affiliation(s)
- Miriam A Schiele
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstrasse 5, D-79104 Freiburg, Germany
| | - Michael G Gottschalk
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstrasse 5, D-79104 Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstrasse 5, D-79104 Freiburg, Germany; Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Breisacher Straße 64, D-79106 Freiburg, Germany.
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117
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Garcia-Ruiz B, Moreno L, Muntané G, Sánchez-Gistau V, Gutiérrez-Zotes A, Martorell L, Labad J, Vilella E. Leukocyte and brain DDR1 hypermethylation is altered in psychosis and is correlated with stress and inflammatory markers. Epigenomics 2020; 12:251-265. [PMID: 31920096 DOI: 10.2217/epi-2019-0191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: To investigate DDR1 methylation in blood and brain DNA in psychosis and its relationship with stress markers. Materials & methods: Saliva cortisol, blood neutrophil and lymphocyte counts, leukocyte DNA and psychological variables were collected from 60 patients with nonaffective psychosis and 40 healthy controls (HC). Brain dorsolateral prefrontal cortex DNA from 35 patients with schizophrenia and 34 HC was studied. DDR1 methylation at 43 CpG sites was measured using the MassARRAY EpiTYPER platform. Results: We describe leukocyte DDR1 hypermethylation in patients with psychosis compared with HC; this hypermethylation is associated with psychological stress, neutrophil-to-lymphocyte ratios, and, in the dorsolateral prefrontal cortex, DDR1 methylation correlated with DDR1 isoform expression. Conclusion: We confirmed a relationship between stress and blood and brain DDR1 methylation in psychosis.
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Affiliation(s)
- Beatriz Garcia-Ruiz
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain.,Universitat Rovira i Virgili, C/ Sant Llorenç, 21. 43201, Reus, Spain
| | - Lorena Moreno
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain
| | - Gerard Muntané
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain.,Universitat Rovira i Virgili, C/ Sant Llorenç, 21. 43201, Reus, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Vanessa Sánchez-Gistau
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain.,Universitat Rovira i Virgili, C/ Sant Llorenç, 21. 43201, Reus, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Alfonso Gutiérrez-Zotes
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain.,Universitat Rovira i Virgili, C/ Sant Llorenç, 21. 43201, Reus, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain.,Universitat Rovira i Virgili, C/ Sant Llorenç, 21. 43201, Reus, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Javier Labad
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain.,Hospital Parc Taulí, C/ Parc Taulí, 1, 08208, Sabadell, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, Ctra de l'Institut Pere Mata, s/, 43206, Reus, Spain.,Institut d'Investigació Sanitària Pere Virgili, C/ Escorxador s/n, 42003, Tarragona, Spain.,Universitat Rovira i Virgili, C/ Sant Llorenç, 21. 43201, Reus, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
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118
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Caramaschi D, Hatcher C, Mulder RH, Felix JF, Cecil CAM, Relton CL, Walton E. Epigenome-wide association study of seizures in childhood and adolescence. Clin Epigenetics 2020; 12:8. [PMID: 31915053 PMCID: PMC6950851 DOI: 10.1186/s13148-019-0793-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/02/2019] [Indexed: 12/31/2022] Open
Abstract
The occurrence of seizures in childhood is often associated with neurodevelopmental impairments and school underachievement. Common genetic variants associated with epilepsy have been identified and epigenetic mechanisms have also been suggested to play a role. In this study, we analyzed the association of genome-wide blood DNA methylation with the occurrence of seizures in ~ 800 children from the Avon Longitudinal Study of Parents and Children, UK, at birth (cord blood), during childhood, and adolescence (peripheral blood). We also analyzed the association between the lifetime occurrence of any seizures before age 13 with blood DNA methylation levels. We sought replication of the findings in the Generation R Study and explored causality using Mendelian randomization, i.e., using genetic variants as proxies. The results showed five CpG sites which were associated cross-sectionally with seizures either in childhood or adolescence (1-5% absolute methylation difference at pFDR < 0.05), although the evidence of replication in an independent study was weak. One of these sites was located in the BDNF gene, which is highly expressed in the brain, and showed high correspondence with brain methylation levels. The Mendelian randomization analyses suggested that seizures might be causal for changes in methylation rather than vice-versa. In conclusion, we show a suggestive link between seizures and blood DNA methylation while at the same time exploring the limitations of conducting such study.
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Affiliation(s)
- Doretta Caramaschi
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK. .,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Charlie Hatcher
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Rosa H Mulder
- Institute of Education and Child Studies, Leiden University, Pieter de la Court building, Wassenaarseweg 52, 2333, AK, Leiden, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Caroline L Relton
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Esther Walton
- Bristol Medical School, Population Health Sciences, University of Bristol, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Department of Psychology, University of Bath, Bath, BA2 7AY, UK
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119
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García-Gutiérrez MS, Navarrete F, Sala F, Gasparyan A, Austrich-Olivares A, Manzanares J. Biomarkers in Psychiatry: Concept, Definition, Types and Relevance to the Clinical Reality. Front Psychiatry 2020; 11:432. [PMID: 32499729 PMCID: PMC7243207 DOI: 10.3389/fpsyt.2020.00432] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
During the last years, an extraordinary effort has been made to identify biomarkers as potential tools for improving prevention, diagnosis, drug response and drug development in psychiatric disorders. Contrary to other diseases, mental illnesses are classified by diagnostic categories with a broad variety list of symptoms. Consequently, patients diagnosed from the same psychiatric illness present a great heterogeneity in their clinical presentation. This fact together with the incomplete knowledge of the neurochemical alterations underlying mental disorders, contribute to the limited efficacy of current pharmacological options. In this respect, the identification of biomarkers in psychiatry is becoming essential to facilitate diagnosis through the developing of markers that allow to stratify groups within the syndrome, which in turn may lead to more focused treatment options. In order to shed light on this issue, this review summarizes the concept and types of biomarkers including an operational definition for therapeutic development. Besides, the advances in this field were summarized and sorted into five categories, which include genetics, transcriptomics, proteomics, metabolomics, and epigenetics. While promising results were achieved, there is a lack of biomarker investigations especially related to treatment response to psychiatric conditions. This review includes a final conclusion remarking the future challenges required to reach the goal of developing valid, reliable and broadly-usable biomarkers for psychiatric disorders and their treatment. The identification of factors predicting treatment response will reduce trial-and-error switches of medications facilitating the discovery of new effective treatments, being a crucial step towards the establishment of greater personalized medicine.
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Affiliation(s)
- Maria Salud García-Gutiérrez
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.,Red Temática de Investigación Cooperativa en Salud (RETICS), Red de Trastornos Adictivos, Instituto de Salud Carlos III, MICINN and FEDER, Madrid, Spain
| | - Francisco Navarrete
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.,Red Temática de Investigación Cooperativa en Salud (RETICS), Red de Trastornos Adictivos, Instituto de Salud Carlos III, MICINN and FEDER, Madrid, Spain
| | - Francisco Sala
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain
| | - Ani Gasparyan
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.,Red Temática de Investigación Cooperativa en Salud (RETICS), Red de Trastornos Adictivos, Instituto de Salud Carlos III, MICINN and FEDER, Madrid, Spain
| | | | - Jorge Manzanares
- Instituto de Neurociencias, Universidad Miguel Hernández-CSIC, Alicante, Spain.,Red Temática de Investigación Cooperativa en Salud (RETICS), Red de Trastornos Adictivos, Instituto de Salud Carlos III, MICINN and FEDER, Madrid, Spain
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120
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Gardini ES, Fiacco S, Mernone L, Ehlert U. Sleep and Methylation of Estrogen Receptor Genes, ESR1 and GPER, in Healthy Middle-Aged and Older Women: Findings from the Women 40+ Healthy Aging Study. Nat Sci Sleep 2020; 12:525-536. [PMID: 32801978 PMCID: PMC7394583 DOI: 10.2147/nss.s256102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/06/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Sleep problems in middle-aged and older women are very common and have been associated with menopause-related changes in estrogen levels. However, not all women experience sleep problems as they enter perimenopause, and epigenetic mechanisms might contribute to the differences in sleep quality within this population. In this study, we hypothesized that increased methylation of two estrogen receptor (ER) genes (ESR1 and GPER) would be associated with increased sleep problems in healthy pre-, peri-, and postmenopausal women, either directly or indirectly through the experience of vasomotor symptoms (VMS). MATERIALS AND METHODS In 130 healthy women aged 40-73 years, we assessed DNA methylation from dried blood spots (DBS). Women rated their sleep quality using the Pittsburgh Sleep Quality Index (PSQI), and VMS using the Menopause Rating Scale (MRS). RESULTS Higher percentage methylation of ESR1 was associated with increased sleep problems, mediated by VMS, even after controlling for age, menopausal status, body mass index, estradiol levels, depressive symptoms, and caffeine consumption. There was no significant association between GPER methylation and either sleep problems or VMS. CONCLUSION The study findings support an association between increased ESR1 methylation and sleep problems through increased VMS among healthy women aged 40-73 years.
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Affiliation(s)
- Elena S Gardini
- Clinical Psychology and Psychotherapy, University of Zurich, Zurich, Switzerland.,University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, Zurich, Switzerland
| | - Serena Fiacco
- Clinical Psychology and Psychotherapy, University of Zurich, Zurich, Switzerland.,University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, Zurich, Switzerland
| | - Laura Mernone
- Clinical Psychology and Psychotherapy, University of Zurich, Zurich, Switzerland.,University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, Zurich, Switzerland
| | - Ulrike Ehlert
- Clinical Psychology and Psychotherapy, University of Zurich, Zurich, Switzerland.,University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, Zurich, Switzerland
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121
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Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
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122
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Ziegler C, Grundner-Culemann F, Schiele MA, Schlosser P, Kollert L, Mahr M, Gajewska A, Lesch KP, Deckert J, Köttgen A, Domschke K. The DNA methylome in panic disorder: a case-control and longitudinal psychotherapy-epigenetic study. Transl Psychiatry 2019; 9:314. [PMID: 31754096 PMCID: PMC6872551 DOI: 10.1038/s41398-019-0648-6] [Citation(s) in RCA: 18] [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: 05/09/2019] [Revised: 09/23/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
In panic disorder (PD), epigenetic mechanisms such as DNA methylation of candidate genes have been suggested to play a key role at the intersection of genetic and environmental factors. On an epigenome-wide level, however, only two studies in PD patients have been published so far, while to date no study has intra-individually analyzed dynamic epigenetic correlates of treatment-response in PD on a DNA methylome level. Here, an epigenome-wide association study (EWAS) was performed in a sample of 57 PD patients and matched healthy controls using the Illumina MethylationEPIC BeadChip, along with a longitudinal approach assessing changes on the DNA methylome level corresponding to clinical effects of a manualized six-week cognitive-behavioral therapy (CBT) in PD. While no epigenome-wide significant hits could be discerned, top suggestive evidence was observed for decreased methylation in PD at cg19917903 in the Cilia and Flagella Associated Protein 46 (CFAP46) gene, and for an increase in methylation after CBT at cg06943668 in the Interleukin 1 Receptor Type 1 (IL1R1) gene in treatment responders to CBT. Additional exploratory analyses based on biological validity and a combined statistical/biological ranking point to further new potential PD risk genes such as the CCL4L1 or GMNN genes, and suggest dynamic methylation of, e.g., the ZFP622 and the SLC43A2 genes along with response to CBT. These EWAS and first longitudinal epigenome-wide pilot data in PD add to the emerging candidate gene-based body of evidence for epigenetic mechanisms to be involved in PD pathogenesis and to possibly constitute dynamic biological correlates of therapeutic interventions.
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Affiliation(s)
- Christiane Ziegler
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Franziska Grundner-Culemann
- 0000 0000 9428 7911grid.7708.8Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center – University of Freiburg, Freiburg, Germany
| | - Miriam A. Schiele
- Department of Psychiatry and Psychotherapy, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pascal Schlosser
- 0000 0000 9428 7911grid.7708.8Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center – University of Freiburg, Freiburg, Germany
| | - Leonie Kollert
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Marina Mahr
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Agnieszka Gajewska
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Klaus-Peter Lesch
- 0000 0001 1958 8658grid.8379.5Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany ,0000 0001 2288 8774grid.448878.fLaboratory of Psychiatric Neurobiology, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, Russia ,0000 0001 0481 6099grid.5012.6Department of Neuroscience, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Jürgen Deckert
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Anna Köttgen
- 0000 0000 9428 7911grid.7708.8Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center – University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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123
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Hudon Thibeault AA, Laprise C. Cell-Specific DNA Methylation Signatures in Asthma. Genes (Basel) 2019; 10:E932. [PMID: 31731604 PMCID: PMC6896152 DOI: 10.3390/genes10110932] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering the role of environmental exposure on asthma development, an increasing amount of literature has been published on epigenetic modifications associated with this pathology and especially on DNA methylation, in an attempt to better understand its missing heritability. These studies have been conducted in different tissues, but mainly in blood or its peripheral mononuclear cells. However, there is growing evidence that epigenetic changes that occur in one cell type cannot be directly translated into another one. In this review, we compare alterations in DNA methylation from different cells of the immune system and of the respiratory tract. The cell types in which data are obtained influences the global status of alteration of DNA methylation in asthmatic individuals compared to control (an increased or a decreased DNA methylation). Given that several genes were cell-type-specific, there is a great need for comparative studies on DNA methylation from different cells, but from the same individuals in order to better understand the role of epigenetics in asthma pathophysiology.
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Affiliation(s)
- Andrée-Anne Hudon Thibeault
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
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124
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Madrid A, Hogan KJ, Papale LA, Clark LR, Asthana S, Johnson SC, Alisch RS. DNA Hypomethylation in Blood Links B3GALT4 and ZADH2 to Alzheimer's Disease. J Alzheimers Dis 2019; 66:927-934. [PMID: 30372681 DOI: 10.3233/jad-180592] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Differentially methylated positions (DMPs) between persons with and without late-onset Alzheimer's disease (LOAD) were observed at 477 of 769,190 loci in a plurality of genes. Of these, 17 were shared with DMPs identified using clinical LOAD markers analyzed independently as continuous variables comprising Rey Auditory Verbal Learning Test scores, cerebrospinal fluid total tau (t-tau) and phosphorylated tau 181 (p-tau181) levels, and t-tau/Aβ1-42 (Aβ42), p-tau181/Aβ42, and Aβ42/Aβ1-40 (Aβ40) ratios. In patients with LOAD, 12 of the shared 17 DMPs were hypomethylated in B3GALT4 (Beta-1,3-galatcosyltransferase 4) (EC 2.4.1.62), and 5 were hypomethylated in ZADH2 (Prostaglandin reductase 3) (EC 1.3.1.48).
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R Clark
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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125
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Jiang S, Postovit L, Cattaneo A, Binder EB, Aitchison KJ. Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma. Front Psychiatry 2019; 10:808. [PMID: 31780969 PMCID: PMC6857662 DOI: 10.3389/fpsyt.2019.00808] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Adverse childhood experiences (ACEs) may be referred to by other terms (e.g., early life adversity or stress and childhood trauma) and have a lifelong impact on mental and physical health. For example, childhood trauma has been associated with posttraumatic stress disorder (PTSD), anxiety, depression, bipolar disorder, diabetes, and cardiovascular disease. The heritability of ACE-related phenotypes such as PTSD, depression, and resilience is low to moderate, and, moreover, is very variable for a given phenotype, which implies that gene by environment interactions (such as through epigenetic modifications) may be involved in the onset of these phenotypes. Currently, there is increasing interest in the investigation of epigenetic contributions to ACE-induced differential health outcomes. Although there are a number of studies in this field, there are still research gaps. In this review, the basic concepts of epigenetic modifications (such as methylation) and the function of the hypothalamic-pituitary-adrenal (HPA) axis in the stress response are outlined. Examples of specific genes undergoing methylation in association with ACE-induced differential health outcomes are provided. Limitations in this field, e.g., uncertain clinical diagnosis, conceptual inconsistencies, and technical drawbacks, are reviewed, with suggestions for advances using new technologies and novel research directions. We thereby provide a platform on which the field of ACE-induced phenotypes in mental health may build.
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Affiliation(s)
- Shui Jiang
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Lynne Postovit
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Annamaria Cattaneo
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Elisabeth B. Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States
| | - Katherine J. Aitchison
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
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126
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van Dongen J, Zilhão NR, Sugden K, Hannon EJ, Mill J, Caspi A, Agnew-Blais J, Arseneault L, Corcoran DL, Moffitt TE, Poulton R, Franke B, Boomsma DI. Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults. Biol Psychiatry 2019; 86:599-607. [PMID: 31003786 PMCID: PMC6717697 DOI: 10.1016/j.biopsych.2019.02.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Previous studies have reported associations between attention-deficit/hyperactivity disorder symptoms and DNA methylation in children. We report the first epigenome-wide association study meta-analysis of adult attention-deficit/hyperactivity disorder symptoms, based on peripheral blood DNA methylation (Infinium HumanMethylation450K array) in three population-based adult cohorts. METHODS An epigenome-wide association study was performed in the Netherlands Twin Register (N = 2258, mean age 37 years), Dunedin Multidisciplinary Health and Development Study (N = 800, age 38 years), and Environmental Risk Longitudinal Twin Study (N = 1631, age 18 years), and results were combined through meta-analysis (total sample size N = 4689). Region-based analyses accounting for the correlation between nearby methylation sites were also performed. RESULTS One epigenome-wide significant differentially methylated position was detected in the Dunedin study, but meta-analysis did not detect differentially methylated positions that were robustly associated across cohorts. In region-based analyses, six significant differentially methylation regions (DMRs) were identified in the Netherlands Twin Register, 19 in the Dunedin study, and none in the Environmental Risk Longitudinal Twin Study. Of these DMRs, 92% were associated with methylation quantitative trait loci, and 68% showed moderate to large blood-brain correlations for DNA methylation levels. DMRs included six nonoverlapping DMRs (three in the Netherlands Twin Register, three in the Dunedin study) in the major histocompatibility complex, which were associated with expression of genes in the major histocompatibility complex, including C4A and C4B, previously implicated in schizophrenia. CONCLUSIONS Our findings point at new candidate loci involved in immune and neuronal functions that await further replication. Our work also illustrates the need for further research to examine to what extent epigenetic associations with psychiatric traits depend on characteristics such as age, comorbidities, exposures, and genetic background.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam.
| | - Nuno R Zilhão
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Eilis J Hannon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jessica Agnew-Blais
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, North Carolina; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam
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127
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Maussion G, Demirova I, Gorwood P, Ramoz N. Induced Pluripotent Stem Cells; New Tools for Investigating Molecular Mechanisms in Anorexia Nervosa. Front Nutr 2019; 6:118. [PMID: 31457016 PMCID: PMC6700384 DOI: 10.3389/fnut.2019.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022] Open
Abstract
Anorexia nervosa (AN) is a dramatic psychiatric disorder characterized by dysregulations in food intake and reward processing, involving molecular and cellular changes in several peripheral cell types and central neuronal networks. Genomic and epigenomic analyses have allowed the identification of multiple genetic and epigenetic modifications highlighting the complex pathophysiology of AN. Behavioral and genetic rodent models have been used to recapitulate and investigate, with some limitations, the cellular and molecular changes that potentially underlie eating disorders. In the last 5 years, the use of induced pluripotent stem cells (IPSCs), combined with CRISPR-Cas9 technology, has led to the generation of specific neuronal cell subtypes engineered from human somatic samples, representing a powerful tool to complement observations made in human samples and data collected from animal models. Systems biology using IPSCs has indeed proved to be a valuable approach for the study of metabolic disorders, in addition to neurodevelopmental and psychiatric disorders. The manuscript, while reviewing the main findings related to the genetic, epigenetic, and cellular bases of AN, will present how new studies published, or to be performed, in the field of IPSC-derived cells should improve our current understanding of the pathophysiology of AN and provide potential therapeutic strategies addressing specific endophenotypes.
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Affiliation(s)
- Gilles Maussion
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Iveta Demirova
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Philip Gorwood
- INSERM U1266, Institute of Psychiatry and Neuroscience of Paris, Paris, France.,Hôpital Sainte-Anne (CMME), University Paris-Descartes, Paris, France
| | - Nicolas Ramoz
- INSERM U1266, Institute of Psychiatry and Neuroscience of Paris, Paris, France
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128
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DNA methylation fingerprint of monozygotic twins and their singleton sibling with intellectual disability carrying a novel KDM5C mutation. Eur J Med Genet 2019; 63:103737. [PMID: 31419599 DOI: 10.1016/j.ejmg.2019.103737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 06/25/2019] [Accepted: 08/11/2019] [Indexed: 01/12/2023]
Abstract
Mutations in KDM5C (lysine (K)-specific demethylase 5C) were causally associated with up to 3% of X-linked intellectual disability (ID) in males. By exome and Sanger sequencing, a novel frameshift KDM5C variant, predicted to eliminate the JmjC catalytic domain from the protein, was identified in two monozygotic twins and their older brother, which was inherited from their clinically normal mother, who had completely skewed X-inactivation. DNA methylation (DNAm) data were evaluated using the Illumina 450 K Methylation Beadchip arrays. Comparison of methylation levels between the three patients and male controls identified 399 differentially methylated CpG sites, which were enriched among those CpG sites modulated during brain development. Most of them were hypomethylated (72%), and located mainly in shores, whereas the hypermethylated CpGs were more represented in open sea regions. The DNAm changes did not differ between the monozygotic twins nor between them and their older sibling, all presenting a global hypomethylation, similar to other studies that associated DNA methylation changes to different KDM5C mutations. The 38 differentially methylated regions (DMRs) were enriched for H3K4me3 marks identified in developing brains. The remarkable similarity between the methylation changes in the monozygotic twins and their older brother is indicative that these epigenetic changes were mostly driven by the KDM5C mutation.
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Abstract
Increasing numbers of studies implicate abnormal DNA methylation in cancer and many non-malignant diseases. This is consistent with numerous findings about differentiation-associated changes in DNA methylation at promoters, enhancers, gene bodies, and sites that control higher-order chromatin structure. Abnormal increases or decreases in DNA methylation contribute to or are markers for cancer formation and tumour progression. Aberrant DNA methylation is also associated with neurological diseases, immunological diseases, atherosclerosis, and osteoporosis. In this review, I discuss DNA hypermethylation in disease and its interrelationships with normal development as well as proposed mechanisms for the origin of and pathogenic consequences of disease-associated hypermethylation. Disease-linked DNA hypermethylation can help drive oncogenesis partly by its effects on cancer stem cells and by the CpG island methylator phenotype (CIMP); atherosclerosis by disease-related cell transdifferentiation; autoimmune and neurological diseases through abnormal perturbations of cell memory; and diverse age-associated diseases by age-related accumulation of epigenetic alterations.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center and Tulane Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA
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130
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He Y, de Witte LD, Houtepen LC, Nispeling DM, Xu Z, Yu Q, Yu Y, Hol EM, Kahn RS, Boks MP. DNA methylation changes related to nutritional deprivation: a genome-wide analysis of population and in vitro data. Clin Epigenetics 2019; 11:80. [PMID: 31097004 PMCID: PMC6524251 DOI: 10.1186/s13148-019-0680-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DNA methylation has recently been identified as a mediator between in utero famine exposure and a range of metabolic and psychiatric traits. However, genome-wide analyses are scarce and cross-sectional analyses are hampered by many potential confounding factors. Moreover, causal relations are hard to identify due to the lack of controlled experimental designs. In the current study, we therefore combined a comprehensive assessment of genome-wide DNA methylation differences in people exposed to the great Chinese famine in utero with an in vitro study in which we deprived fibroblasts of nutrition. METHODS We compared whole blood DNA methylation differences between 25 individuals in utero exposed to famine and 54 healthy control individuals using the HumanMethylation450 platform. In vitro, we analyzed DNA methylation changes in 10 fibroblast cultures that were nutritionally deprived for 72 h by withholding fetal bovine serum. RESULTS We identified three differentially methylated regions (DMRs) in four genes (ENO2, ZNF226, CCDC51, and TMA7) that were related to famine exposure in both analyses. Pathway analysis with data from both Chinese famine samples and fibroblasts highlighted the nervous system and neurogenesis pathways as the most affected by nutritional deprivation. CONCLUSIONS The combination of cross-sectional and experimental data provides indications that biological adaptation to famine leads to DNA methylation changes in genes involved in the central nervous system.
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Affiliation(s)
- Yujie He
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
- Brain Center University Medical Center Utrecht, Department of Translational Neuroscience, Utrecht University, Utrecht, The Netherlands
| | - Lot D de Witte
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - Lotte C Houtepen
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
| | - Danny M Nispeling
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
| | - Zhida Xu
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Yaqin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Elly M Hol
- Brain Center University Medical Center Utrecht, Department of Translational Neuroscience, Utrecht University, Utrecht, The Netherlands
- Department of Neuroimmunology, Netherlands Institute for Neuroscience, an Institute of the Royal Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - René S Kahn
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - Marco P Boks
- Brain Center University Medical Center Utrecht, Department of Psychiatry, Utrecht University, A01.468, PO Box 85500, 3508, GA, Utrecht, The Netherlands.
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131
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Toepfer P, O'Donnell KJ, Entringer S, Garg E, Heim CM, Lin DTS, MacIsaac JL, Kobor MS, Meaney MJ, Provençal N, Binder EB, Wadhwa PD, Buss C. Dynamic DNA methylation changes in the maternal oxytocin gene locus (OXT) during pregnancy predict postpartum maternal intrusiveness. Psychoneuroendocrinology 2019; 103:156-162. [PMID: 30690225 PMCID: PMC6554513 DOI: 10.1016/j.psyneuen.2019.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 01/21/2023]
Abstract
Maternal behavior (MB) is observable across mammals and represents an important feature of environmental variation during early postnatal development. Oxytocin (OT) plays a crucial role in MB. Even prior to childbirth, pregnancy induces epigenetic and other downstream changes in the maternal OT-system, likely mediated by the actions of steroid hormones. However, little is known about the nature and consequences of epigenetic modifications in the maternal OT-encoding gene (OXT) during pregnancy. Our study aims to investigate temporal dynamics of OXT promoter DNA methylation (DNAm) throughout pregnancy in predicting MB in humans. In 107 mother-child dyads, maternal OXT DNAm was serially analyzed in whole blood in early, mid and late pregnancy. MB was coded based on standardized mother-child interactions at six months postpartum. After controlling for cellular heterogeneity, race/ethnicity, age, and socioeconomic status, OXT-promoter DNAm exhibited a dynamic profile during pregnancy (b = 0.026, t=-3.37, p < .001), with decreases in DNAm from early to mid-pregnancy and no further change until late pregnancy. Moreover, dynamic DNAm trajectories of the OXT-promoter region predicted MB (intrusiveness) at six months postpartum (b = 0.006, t = 2.0, p < 0.05), with 6% higher OXT DNAm in late pregnancy in intrusive compared to non-intrusive mothers. We here demonstrate that OXT promoter DNAm changes significantly throughout gestation in peripheral blood and that these changes are associated with variability in MB, providing a novel potential biomarker predicting postnatal MB.
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Affiliation(s)
- Philipp Toepfer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany
| | - Kieran J O'Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada; Sackler Program for Epigenetics and Psychobiology at McGill University, Montreal, QC, Canada
| | - Sonja Entringer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany; University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Elika Garg
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Christine M Heim
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany; Department of Biobehavioral Health, Pennsylvania State University, University Park, PA, USA
| | - David T S Lin
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Michael J Meaney
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada; Sackler Program for Epigenetics and Psychobiology at McGill University, Montreal, QC, Canada; Singapore Institute for Clinical Sciences, Singapore
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany; Simon Fraser University, Faculty of Health Sciences, Vancouver, BC, Canada
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Pathik D Wadhwa
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA; Departments of Psychiatry and Human Behavior, Obstetrics and Gynecology, and Epidemiology, University of California, Irvine, School of Medicine, Irvine, CA, USA
| | - Claudia Buss
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Institute of Medical Psychology, Berlin, Germany; University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA.
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Ramo-Fernández L, Boeck C, Koenig AM, Schury K, Binder EB, Gündel H, Fegert JM, Karabatsiakis A, Kolassa IT. The effects of childhood maltreatment on epigenetic regulation of stress-response associated genes: an intergenerational approach. Sci Rep 2019; 9:983. [PMID: 31000782 PMCID: PMC7052131 DOI: 10.1038/s41598-018-36689-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022] Open
Abstract
While biological alterations associated with childhood maltreatment (CM) have been found in affected individuals, it remains unknown to what degree these alterations are biologically transmitted to the next generation. We investigated intergenerational effects of maternal CM on DNA methylation and gene expression in N = 113 mother-infant dyads shortly after parturition, additionally accounting for the role of the FKBP5 rs1360780 genotype. Using mass array spectrometry, we assessed the DNA methylation of selected stress-response-associated genes (FK506 binding protein 51 [FKBP5], glucocorticoid receptor [NR3C1], corticotropin-releasing hormone receptor 1 [CRHR1]) in isolated immune cells from maternal blood and neonatal umbilical cord blood. In mothers, CM was associated with decreased levels of DNA methylation of FKBP5 and CRHR1 and increased NR3C1 methylation, but not with changes in gene expression profiles. Rs1360780 moderated the FKBP5 epigenetic CM-associated regulation profiles in a gene × environment interaction. In newborns, we found no evidence for any intergenerational transmission of CM-related methylation profiles for any of the investigated epigenetic sites. These findings support the hypothesis of a long-lasting impact of CM on the biological epigenetic regulation of stress-response mediators and suggest for the first time that these specific epigenetic patterns might not be directly transmitted to the next generation.
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Affiliation(s)
- Laura Ramo-Fernández
- Department of Clinical & Biological Psychology, Institute of Psychology and Education, Ulm University, Albert-Einstein-Allee 47, Ulm, 89081, Germany.
| | - Christina Boeck
- Department of Clinical & Biological Psychology, Institute of Psychology and Education, Ulm University, Albert-Einstein-Allee 47, Ulm, 89081, Germany
| | - Alexandra M Koenig
- Department of Clinical & Biological Psychology, Institute of Psychology and Education, Ulm University, Albert-Einstein-Allee 47, Ulm, 89081, Germany
| | - Katharina Schury
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Ulm, 89075, Ulm, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, 80804, Germany.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Harald Gündel
- Department of Psychosomatic Medicine and Psychotherapy, University Hospital Ulm, 89081, Ulm, Germany
| | - Jöerg M Fegert
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Ulm, 89075, Ulm, Germany
| | - Alexander Karabatsiakis
- Department of Clinical & Biological Psychology, Institute of Psychology and Education, Ulm University, Albert-Einstein-Allee 47, Ulm, 89081, Germany
| | - Iris-Tatjana Kolassa
- Department of Clinical & Biological Psychology, Institute of Psychology and Education, Ulm University, Albert-Einstein-Allee 47, Ulm, 89081, Germany.
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133
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Hack LM, Fries GR, Eyre HA, Bousman CA, Singh AB, Quevedo J, John VP, Baune BT, Dunlop BW. Moving pharmacoepigenetics tools for depression toward clinical use. J Affect Disord 2019; 249:336-346. [PMID: 30802699 PMCID: PMC6763314 DOI: 10.1016/j.jad.2019.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) is a leading cause of disability worldwide, and over half of patients do not achieve symptom remission following an initial antidepressant course. Despite evidence implicating a strong genetic basis for the pathophysiology of MDD, there are no adequately validated biomarkers of treatment response routinely used in clinical practice. Pharmacoepigenetics is an emerging field that has the potential to combine both genetic and environmental information into treatment selection and further the goal of precision psychiatry. However, this field is in its infancy compared to the more established pharmacogenetics approaches. METHODS We prepared a narrative review using literature searches of studies in English pertaining to pharmacoepigenetics and treatment of depressive disorders conducted in PubMed, Google Scholar, PsychINFO, and Ovid Medicine from inception through January 2019. We reviewed studies of DNA methylation and histone modifications in both humans and animal models of depression. RESULTS Emerging evidence from human and animal work suggests a key role for epigenetic marks, including DNA methylation and histone modifications, in the prediction of antidepressant response. The challenges of heterogeneity of patient characteristics and loci studied as well as lack of replication that have impacted the field of pharmacogenetics also pose challenges to the development of pharmacoepigenetic tools. Additionally, given the tissue specific nature of epigenetic marks as well as their susceptibility to change in response to environmental factors and aging, pharmacoepigenetic tools face additional challenges to their development. LIMITATIONS This is a narrative and not systematic review of the literature on the pharmacoepigenetics of antidepressant response. We highlight key studies pertaining to pharmacoepigenetics and treatment of depressive disorders in humans and depressive-like behaviors in animal models, regardless of sample size or methodology. While we discuss DNA methylation and histone modifications, we do not cover microRNAs, which have been reviewed elsewhere recently. CONCLUSIONS Utilization of genome-wide approaches and reproducible epigenetic assays, careful selection of the tissue assessed, and integration of genetic and clinical information into pharmacoepigenetic tools will improve the likelihood of developing clinically useful tests.
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Affiliation(s)
- Laura M Hack
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 401 Quarry Road, Palo Alto, CA 94305, USA; Sierra Pacific Mental Illness Research Education and Clinical Centers, VA Palo Alto Health Care System, Palo Alto, CA, USA.
| | - Gabriel R Fries
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Harris A Eyre
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 401 Quarry Road, Palo Alto, CA 94305, USA; Innovation Institute, Texas Medical Center, Houston, TX, USA; IMPACT SRC, School of Medicine, Deakin University, Geelong, Victoria, Australia; Department of Psychiatry, University of Melbourne, Melbourne, Victoria, Australia
| | - Chad A Bousman
- Departments of Medical Genetics, Psychiatry, Physiology & Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Ajeet B Singh
- IMPACT SRC, School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Joao Quevedo
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Vineeth P John
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Bernhard T Baune
- Department of Psychiatry, University of Melbourne, Melbourne, Victoria, Australia
| | - Boadie W Dunlop
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA, USA
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134
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Sadikovic B, Aref-Eshghi E, Levy MA, Rodenhiser D. DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype. Epigenomics 2019; 11:563-575. [PMID: 30875234 DOI: 10.2217/epi-2018-0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). We propose that these episignatures be considered as echoes and/or legacies of the initiating mutational events within proteins of the so-called epigenetic machinery. As well, we discuss approaches to directly confirm the functional consequences and the implications of these episignatures to patient management and treatment.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - David Rodenhiser
- Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.,Children's Health Research Institute & Lawson Health Research Institute, London, ON, N6C 2V5, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, ON, N6A 5W9, Canada
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135
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Bakulski KM, Dou J, Lin N, London SJ, Colacino JA. DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood. Sci Rep 2019; 9:4576. [PMID: 30872662 PMCID: PMC6418160 DOI: 10.1038/s41598-019-40963-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
Smoking impacts DNA methylation genome-wide in blood of newborns from maternal smoking during pregnancy and adults from personal smoking. We compared smoking-related DNA methylation in lung adenocarcinoma (61 never smokers, 91 current smokers, and 238 former smokers) quantified with the Illumina450k BeadArray in The Cancer Genome Atlas with published large consortium meta-analyses of newborn and adult blood. We assessed whether CpG sites related to smoking in blood from newborns and adults were enriched in the lung adenocarcinoma methylation signal. Testing CpGs differentially methylated by smoke exposure, we identified 296 in lung adenocarcinoma meeting a P < 10-4 cutoff, while previous meta-analyses identified 3,042 in newborn blood, and 8,898 in adult blood meeting the same P < 10-4 cutoff. Lung signals were highly enriched for those seen in newborn (24 overlapping CpGs, Penrichment = 1.2 × 10-18) and adult blood (66 overlapping CpGs, Penrichment = 1.2 × 10-48). The 105 genes annotated to CpGs differentially methylated in lung tumors, but not blood, were enriched for RNA processing ontologies. Some epigenetic alterations associated with cigarette smoke exposure are tissue specific, but others are common across tissues. These findings support the value of blood-based methylation biomarkers for assessing exposure effects in target tissues.
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Affiliation(s)
- K M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
| | - J Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - N Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - S J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - J A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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Walton E, Relton CL, Caramaschi D. Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. Genes (Basel) 2019; 10:E193. [PMID: 30832291 PMCID: PMC6470715 DOI: 10.3390/genes10030193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
The recent focus on the role of epigenetic mechanisms in mental health has led to several studies examining the association of epigenetic processes with psychiatric conditions and neurodevelopmental traits. Some studies suggest that epigenetic changes might be causal in the development of the psychiatric condition under investigation. However, other scenarios are possible, e.g., statistical confounding or reverse causation, making it particularly challenging to derive conclusions on causality. In the present review, we examine the evidence from human population studies for a possible role of epigenetic mechanisms in neurodevelopment and mental health and discuss methodological approaches on how to strengthen causal inference, including the need for replication, (quasi-)experimental approaches and Mendelian randomization. We signpost openly accessible resources (e.g., "MR-Base" "EWAS catalog" as well as tissue-specific methylation and gene expression databases) to aid the application of these approaches.
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Affiliation(s)
- Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
- Department of Psychology, University of Bath, BA2 7AY Bath, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
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Relationship between Alzheimer's disease-associated SNPs within the CLU gene, local DNA methylation and episodic verbal memory in healthy and schizophrenia subjects. Psychiatry Res 2019; 272:380-386. [PMID: 30599442 DOI: 10.1016/j.psychres.2018.12.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/16/2018] [Accepted: 12/24/2018] [Indexed: 11/24/2022]
Abstract
Genetic variation may impact on local DNA methylation patterns. Therefore, information about allele-specific DNA methylation (ASM) within disease-related loci has been proposed to be useful for the interpretation of GWAS results. To explore mechanisms that may underlie associations between Alzheimer's disease (AD) and schizophrenia risk CLU gene and verbal memory, one of the most affected cognitive domains in both conditions, we studied DNA methylation in a region between AD-associated SNPs rs9331888 and rs9331896 in 72 healthy individuals and 73 schizophrenia patients. Using single-molecule real-time bisulfite sequencing we assessed the haplotype-dependent ASM in this region. We then investigated whether its methylation could influence episodic verbal memory measured with the Rey Auditory Verbal Learning Test in these two cohorts. The region showed a complex methylation pattern, which was similar in healthy and schizophrenia individuals and unrelated to haplotypes. The pattern predicted memory scores in controls. The results suggest that epigenetic modifications within the CLU locus may play a role in memory variation, independent of ASM.
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138
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Braun PR, Han S, Hing B, Nagahama Y, Gaul LN, Heinzman JT, Grossbach AJ, Close L, Dlouhy BJ, Howard MA, Kawasaki H, Potash JB, Shinozaki G. Genome-wide DNA methylation comparison between live human brain and peripheral tissues within individuals. Transl Psychiatry 2019; 9:47. [PMID: 30705257 PMCID: PMC6355837 DOI: 10.1038/s41398-019-0376-y] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 12/10/2018] [Accepted: 01/02/2019] [Indexed: 12/24/2022] Open
Abstract
Differential DNA methylation in the brain is associated with many psychiatric diseases, but access to brain tissues is essentially limited to postmortem samples. The use of surrogate tissues has become common in identifying methylation changes associated with psychiatric disease. In this study, we determined the extent to which peripheral tissues can be used as surrogates for DNA methylation in the brain. Blood, saliva, buccal, and live brain tissue samples from 27 patients with medically intractable epilepsy undergoing brain resection were collected (age range 5-61 years). Genome-wide methylation was assessed with the Infinium HumanMethylation450 (n = 12) and HumanMethylationEPIC BeadChip arrays (n = 21). For the EPIC methylation data averaged for each CpG across subjects, the saliva-brain correlation (r = 0.90) was higher than that for blood-brain (r = 0.86) and buccal-brain (r = 0.85) comparisons. However, within individual CpGs, blood had the highest proportion of CpGs correlated to brain at nominally significant levels (20.8%), as compared to buccal tissue (17.4%) and saliva (15.1%). For each CpG and each gene, levels of brain-peripheral tissue correlation varied widely. This indicates that to determine the most useful surrogate tissue for representing brain DNA methylation, the patterns specific to the genomic region of interest must be considered. To assist in that objective, we have developed a website, IMAGE-CpG, that allows researchers to interrogate DNA methylation levels and degree of cross-tissue correlation in user-defined locations across the genome.
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Affiliation(s)
- Patricia R Braun
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52246, USA
- Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Shizhong Han
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52246, USA
- Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Benjamin Hing
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Yasunori Nagahama
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Lindsey N Gaul
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Jonathan T Heinzman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Andrew J Grossbach
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Department of Neurological Surgery, Ohio State University, Columbus, OH, 43203, USA
| | - Liesl Close
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Brian J Dlouhy
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Matthew A Howard
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - James B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52246, USA
- Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Gen Shinozaki
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA.
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA.
- Interdisciplinary Graduate Program for Neuroscience, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA.
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139
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Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation. Epigenetics Chromatin 2019; 12:1. [PMID: 30602389 PMCID: PMC6314079 DOI: 10.1186/s13072-018-0245-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. Given that DNAm patterns in early life undergo rapid changes and have been linked to a wide range of health outcomes and environmental exposures, direct investigations of tissue-specific DNAm variation in pediatric samples may help inform the design and interpretation of DNAm analyses from early life cohorts. In this study, we present a systematic comparison of genome-wide DNAm patterns between matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages. Results BECs had greater inter-individual DNAm variability compared to PBMCs and highly the variable CpGs are more likely to be positively correlated between the matched tissues compared to less variable CpGs. These sites were enriched for CpGs under genetic influence, suggesting that a substantial proportion of DNAm covariation between tissues can be attributed to genetic variation. Finally, we demonstrated the relevance of our findings to human epigenetic studies by categorizing CpGs from published DNAm association studies of pediatric BECs and peripheral blood. Conclusions Taken together, our results highlight a number of important considerations and practical implications in the design and interpretation of EWAS analyses performed in pediatric peripheral tissues. Electronic supplementary material The online version of this article (10.1186/s13072-018-0245-6) contains supplementary material, which is available to authorized users.
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140
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Abstract
Our social environment, from the microscopic to the macro-social, affects us for the entirety of our lives. One integral line of research to examine how interpersonal and societal environments can get "under the skin" is through the lens of epigenetics. Epigenetic mechanisms are adaptations made to our genome in response to our environment which include tags placed on and removed from the DNA itself to how our DNA is packaged, affecting how our genes are read, transcribed, and interact. These tags are affected by social environments and can persist over time; this may aid us in responding to experiences and exposures, both the enriched and the disadvantageous. From memory formation to immune function, the experience-dependent plasticity of epigenetic modifications to micro- and macro-social environments may contribute to the process of learning from comfort, pain, and stress to better survive in whatever circumstances life has in store.
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Affiliation(s)
- Sarah M Merrill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada.
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141
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Lussier AA, Bodnar TS, Mingay M, Morin AM, Hirst M, Kobor MS, Weinberg J. Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues. Front Genet 2018; 9:610. [PMID: 30568673 PMCID: PMC6290329 DOI: 10.3389/fgene.2018.00610] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022] Open
Abstract
Background: Prenatal alcohol exposure (PAE) can alter the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE resulted in blood alcohol levels of ~80-150 mg/dl throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal days (P) 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing. Results: PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental period at a false-discovery rate (FDR) < 0.05. In addition, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR < 0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses. Conclusions: Persistent DNA methylation changes in the hypothalamus may be associated with the long-term physiological and neurobehavioral alterations in observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology of neurodevelopmental and mental health disorders, as they share numerous phenotypes and comorbidities.
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Affiliation(s)
- Alexandre A Lussier
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Tamara S Bodnar
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Mingay
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre M Morin
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency Research Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
| | - Joanne Weinberg
- Department of Cellular & Physiological Sciences, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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142
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Cecil CAM, Walton E, Pingault JB, Provençal N, Pappa I, Vitaro F, Côté S, Szyf M, Tremblay RE, Tiemeier H, Viding E, McCrory EJ. DRD4 methylation as a potential biomarker for physical aggression: An epigenome-wide, cross-tissue investigation. Am J Med Genet B Neuropsychiatr Genet 2018; 177:746-764. [PMID: 30411855 DOI: 10.1002/ajmg.b.32689] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 08/23/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022]
Abstract
Epigenetic processes that regulate gene expression, such as DNA methylation (DNAm), have been linked to individual differences in physical aggression. Yet, it is currently unclear whether: (a) DNAm patterns in humans associate with physical aggression independently of other co-occurring psychiatric and behavioral symptoms; (b) whether these patterns are observable across multiple tissues; and (c) whether they may function as a causal versus noncausal biomarker of physical aggression. Here, we used a multisample, cross-tissue design to address these questions. First, we examined genome-wide DNAm patterns (buccal swabs; Illumina 450k) associated with engagement in physical fights in a sample of high-risk youth (n = 119; age = 16-24 years; 53% female). We identified one differentially methylated region in DRD4, which survived genome-wide correction, associated with physical aggression above and beyond co-occurring symptomatology (e.g., ADHD, substance use), and showed strong cross-tissue concordance with both blood and brain. Second, we found that DNAm sites within this region were also differentially methylated in an independent sample of young adults, between individuals with a history of chronic-high versus low physical aggression (peripheral T cells; ages 26-28). Finally, we ran a Mendelian randomization analysis using GWAS data from the EAGLE consortium to test for a causal association of DRD4 methylation with physical aggression. Only one genetic instrument was eligible for the analysis, and results provided no evidence for a causal association. Overall, our findings lend support for peripheral DRD4 methylation as a potential biomarker of physically aggressive behavior, with no evidence yet of a causal relationship.
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Affiliation(s)
- Charlotte A M Cecil
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Jean-Baptiste Pingault
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Nadine Provençal
- Faculty of Health Sciences, Simon Fraser University, Burnaby and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Irene Pappa
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank Vitaro
- Department of Psychoeducation, Université de Montréal, Montréal, Québec, Canada
| | - Sylvana Côté
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada.,Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Québec, Canada
| | - Richard E Tremblay
- Department of Pediatrics, Université de Montréal, Montréal, Québec, Canada.,Department of Psychology, Université de Montréal, Montréal, Québec, Canada
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Essi Viding
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
| | - Eamon J McCrory
- Division of Psychology and Language Sciences, University College London, London, United Kingdom
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143
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Study Design and Rationale for the Mood and Methylation Study: A Platform for Multi-Omics Investigation of Depression in Twins. Twin Res Hum Genet 2018; 21:507-513. [DOI: 10.1017/thg.2018.64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Major depression is a complex disorder with no single, direct causal mechanism. Morbidity has been linked to genetic processes, developmental history, and unique environmental exposures. Epigenetic mechanisms, especially DNA methylation, are also likely important factors in the pathogenesis of major depressive disorder (MDD). A community-based twin sample has many advantages for epigenetic studies, given the shared genetic and developmental histories of same-sex twin pairs. This article describes the rationale and study design for the Mood and Methylation Study in which 133 twin pairs (101 monozygotic and 32 dizygotic), both discordant and concordant for lifetime history of MDD, were evaluated on a large number of variables related to MDD. The twins also provided blood samples for an epigenome-wide association study of differentially methylated regions (DMR) relevant to MDD. Although MDD is typically considered a disorder of the central nervous system, it is unfeasible to obtain a large sample of brain tissues. However, epigenetic variation is not limited to the affected tissue but can also be detected in peripheral blood leukocytes. Thus, this study focused on monocytes for the major analyses. Additional plans for the study include gene expression analysis from the same set of twins using RNA-seq and validation of significant DMRs in postmortem brain tissues from a separate sample. Moreover, sufficient samples have been collected to perform future ‘multi-omic’ analyses, including metabolome, microbiome, and transcriptome. Our long-term goal is to understand how epigenomic and other ‘omic’ factors can be manipulated for diagnostic, preventive, and therapeutic purposes for MDD and its related conditions.
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144
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Marioni RE, McRae AF, Bressler J, Colicino E, Hannon E, Li S, Prada D, Smith JA, Trevisi L, Tsai PC, Vojinovic D, Simino J, Levy D, Liu C, Mendelson M, Satizabal CL, Yang Q, Jhun MA, Kardia SLR, Zhao W, Bandinelli S, Ferrucci L, Hernandez DG, Singleton AB, Harris SE, Starr JM, Kiel DP, McLean RR, Just AC, Schwartz J, Spiro A, Vokonas P, Amin N, Ikram MA, Uitterlinden AG, van Meurs JBJ, Spector TD, Steves C, Baccarelli AA, Bell JT, van Duijn CM, Fornage M, Hsu YH, Mill J, Mosley TH, Seshadri S, Deary IJ. Meta-analysis of epigenome-wide association studies of cognitive abilities. Mol Psychiatry 2018; 23:2133-2144. [PMID: 29311653 PMCID: PMC6035894 DOI: 10.1038/s41380-017-0008-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/02/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts. CpGs that passed a Bonferroni correction, adjusting for the number of CpGs and cognitive tests, were assessed for: longitudinal change; being under genetic control (methylation QTLs); and associations with brain health (structural MRI), brain methylation and Alzheimer's disease pathology. Across the seven measures of cognitive functioning (meta-analysis n range: 2557-6809), there were epigenome-wide significant (P < 1.7 × 10-8) associations for global cognitive function (cg21450381, P = 1.6 × 10-8), and phonemic verbal fluency (cg12507869, P = 2.5 × 10-9). The CpGs are located in an intergenic region on chromosome 12 and the INPP5A gene on chromosome 10, respectively. Both probes have moderate correlations (~0.4) with brain methylation in Brodmann area 20 (ventral temporal cortex). Neither probe showed evidence of longitudinal change in late-life or associations with white matter brain MRI measures in one cohort with these data. A methylation QTL analysis suggested that rs113565688 was a cis methylation QTL for cg12507869 (P = 5 × 10-5 and 4 × 10-13 in two lookup cohorts). We demonstrate a link between blood-based DNA methylation and measures of phonemic verbal fluency and global cognitive ability. Further research is warranted to understand the mechanisms linking genomic regulatory changes with cognitive function to health and disease.
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Affiliation(s)
- Riccardo E. Marioni
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK ,0000 0000 9320 7537grid.1003.2Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD Australia
| | - Allan F. McRae
- 0000 0000 9320 7537grid.1003.2Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD Australia ,0000 0000 9320 7537grid.1003.2Queensland Brain Institute, University of Queensland, Brisbane, QLD Australia
| | - Jan Bressler
- 0000 0000 9206 2401grid.267308.8Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Elena Colicino
- 0000000419368729grid.21729.3fColumbia University Mailman School of Public Health, New York, NY USA ,0000 0001 0670 2351grid.59734.3cIcahn School of Medicine at Mount Sinai, New York, NY USA
| | - Eilis Hannon
- 0000 0004 1936 8024grid.8391.3University of Exeter Medical School, Exeter, UK
| | - Shuo Li
- 0000 0004 1936 7558grid.189504.1Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Diddier Prada
- 0000 0004 1777 1207grid.419167.cInstituto Nacional de Cancerologia, Mexico City, Mexico
| | - Jennifer A Smith
- 0000000086837370grid.214458.eDepartment of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA ,0000000086837370grid.214458.eSurvey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI USA
| | - Letizia Trevisi
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA
| | - Pei-Chien Tsai
- 0000 0001 2322 6764grid.13097.3cDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, UK ,grid.145695.aDepartment of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan ,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Dina Vojinovic
- 000000040459992Xgrid.5645.2Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeannette Simino
- 0000 0004 1937 0407grid.410721.1Department of Data Science, School of Population Health, University of Mississippi Medical Center, Jackson, MS USA ,0000 0004 1937 0407grid.410721.1MIND Center, University of Mississippi Medical Center, Jackson, MS USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA USA ,0000 0001 2293 4638grid.279885.9Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Chunyu Liu
- 0000 0004 1936 7558grid.189504.1Department of Biostatistics, Boston University School of Public Health, Boston, MA USA ,Framingham Heart Study, Framingham, MA USA ,0000 0001 2293 4638grid.279885.9Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Michael Mendelson
- Framingham Heart Study, Framingham, MA USA ,0000 0001 2293 4638grid.279885.9Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA ,0000 0004 0367 5222grid.475010.7Boston University School of Medicine, Boston, MA USA ,0000 0004 0378 8438grid.2515.3Department of Cardiology, Boston Children’s Hospital, Boston, MA USA
| | - Claudia L. Satizabal
- Framingham Heart Study, Framingham, MA USA ,0000 0004 0367 5222grid.475010.7Department of Neurology, Boston University School of Medicine, Boston, MA USA
| | - Qiong Yang
- 0000 0004 1936 7558grid.189504.1Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Min A. Jhun
- 0000000086837370grid.214458.eDepartment of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA ,0000 0001 2180 1622grid.270240.3Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Sharon L. R. Kardia
- 0000000086837370grid.214458.eDepartment of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Wei Zhao
- 0000000086837370grid.214458.eDepartment of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Stefania Bandinelli
- 0000 0004 1756 9121grid.423864.fGeriatric Unit, Azienda Sanitaria di Firenze, Florence, Italy
| | - Luigi Ferrucci
- 0000 0000 9372 4913grid.419475.aClinical Research Branch, National Institute on Aging, Baltimore, MD USA
| | - Dena G. Hernandez
- 0000 0001 2297 5165grid.94365.3dLaboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD USA
| | - Andrew B. Singleton
- 0000 0001 2297 5165grid.94365.3dLaboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD USA
| | - Sarah E. Harris
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - John M. Starr
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Douglas P. Kiel
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,000000041936754Xgrid.38142.3cHebrew SeniorLife Institute for Aging Research, Boston, MA USA
| | - Robert R. McLean
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,000000041936754Xgrid.38142.3cHebrew SeniorLife Institute for Aging Research, Boston, MA USA
| | - Allan C. Just
- 0000 0001 0670 2351grid.59734.3cIcahn School of Medicine at Mount Sinai, New York, NY USA
| | - Joel Schwartz
- 000000041936754Xgrid.38142.3cHarvard T.H. Chan School of Public Health, Boston, MA USA
| | - Avron Spiro
- 0000 0004 1936 7558grid.189504.1Boston University Schools of Public Health and Medicine, Boston, MA USA ,0000 0004 4657 1992grid.410370.1VA Boston Healthcare System, Boston, MA USA
| | - Pantel Vokonas
- 0000 0004 1936 7558grid.189504.1Boston University Schools of Public Health and Medicine, Boston, MA USA ,0000 0004 4657 1992grid.410370.1VA Boston Healthcare System, Boston, MA USA
| | - Najaf Amin
- 000000040459992Xgrid.5645.2Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M. Arfan Ikram
- 000000040459992Xgrid.5645.2Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Departments of Radiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andre G. Uitterlinden
- 000000040459992Xgrid.5645.2Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce B. J. van Meurs
- 000000040459992Xgrid.5645.2Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands ,000000040459992Xgrid.5645.2Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tim D. Spector
- 0000 0001 2322 6764grid.13097.3cDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Claire Steves
- 0000 0001 2322 6764grid.13097.3cDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Andrea A. Baccarelli
- 0000000419368729grid.21729.3fColumbia University Mailman School of Public Health, New York, NY USA
| | - Jordana T. Bell
- 0000 0001 2322 6764grid.13097.3cDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Cornelia M. van Duijn
- 000000040459992Xgrid.5645.2Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Myriam Fornage
- 0000 0000 9206 2401grid.267308.8Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA ,0000 0000 9206 2401grid.267308.8Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Yi-Hsiang Hsu
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,000000041936754Xgrid.38142.3cHebrew SeniorLife Institute for Aging Research, Boston, MA USA ,grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jonathan Mill
- 0000 0001 0670 2351grid.59734.3cIcahn School of Medicine at Mount Sinai, New York, NY USA
| | - Thomas H. Mosley
- 0000 0004 1937 0407grid.410721.1MIND Center, University of Mississippi Medical Center, Jackson, MS USA ,0000 0004 1937 0407grid.410721.1Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS USA
| | - Sudha Seshadri
- 0000 0004 0367 5222grid.475010.7Department of Neurology, Boston University School of Medicine, Boston, MA USA ,0000 0001 0629 5880grid.267309.9Glenn Biggs Institute of Alzheimer and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX USA
| | - Ian J. Deary
- 0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Department of Psychology, University of Edinburgh, Edinburgh, UK
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145
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Abstract
Prenatal adversity shapes child neurodevelopment and risk for later mental health problems. The quality of the early care environment can buffer some of the negative effects of prenatal adversity on child development. Retrospective studies, in adult samples, highlight epigenetic modifications as sentinel markers of the quality of the early care environment; however, comparable data from pediatric cohorts are lacking. Participants were drawn from the Maternal Adversity Vulnerability and Neurodevelopment (MAVAN) study, a longitudinal cohort with measures of infant attachment, infant development, and child mental health. Children provided buccal epithelial samples (mean age = 6.99, SD = 1.33 years, n = 226), which were used for analyses of genome-wide DNA methylation and genetic variation. We used a series of linear models to describe the association between infant attachment and (a) measures of child outcome and (b) DNA methylation across the genome. Paired genetic data was used to determine the genetic contribution to DNA methylation at attachment-associated sites. Infant attachment style was associated with infant cognitive development (Mental Development Index) and behavior (Behavior Rating Scale) assessed with the Bayley Scales of Infant Development at 36 months. Infant attachment style moderated the effects of prenatal adversity on Behavior Rating Scale scores at 36 months. Infant attachment was also significantly associated with a principal component that accounted for 11.9% of the variation in genome-wide DNA methylation. These effects were most apparent when comparing children with a secure versus a disorganized attachment style and most pronounced in females. The availability of paired genetic data revealed that DNA methylation at approximately half of all infant attachment-associated sites was best explained by considering both infant attachment and child genetic variation. This study provides further evidence that infant attachment can buffer some of the negative effects of early adversity on measures of infant behavior. We also highlight the interplay between infant attachment and child genotype in shaping variation in DNA methylation. Such findings provide preliminary evidence for a molecular signature of infant attachment and may help inform attachment-focused early intervention programs.
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146
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Goodman SJ, Roubinov DS, Bush NR, Park M, Farré P, Emberly E, Hertzman C, Essex MJ, Kobor MS, Boyce WT. Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood. Dev Sci 2018; 22:e12739. [PMID: 30176105 PMCID: PMC6433477 DOI: 10.1111/desc.12739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/08/2018] [Indexed: 12/21/2022]
Abstract
A growing body of research has documented associations between adverse childhood environments and DNA methylation, highlighting epigenetic processes as potential mechanisms through which early external contexts influence health across the life course. The present study tested a complementary hypothesis: indicators of children's early internal, biological, and behavioral responses to stressful challenges may also be linked to stable patterns of DNA methylation later in life. Children's autonomic nervous system reactivity, temperament, and mental health symptoms were prospectively assessed from infancy through early childhood, and principal components analysis (PCA) was applied to derive composites of biological and behavioral reactivity. Buccal epithelial cells were collected from participants at 15 and 18 years of age. Findings revealed an association between early life biobehavioral inhibition/disinhibition and DNA methylation across many genes. Notably, reactive, inhibited children were found to have decreased DNA methylation of the DLX5 and IGF2 genes at both time points, as compared to non‐reactive, disinhibited children. Results of the present study are provisional but suggest that the gene's profile of DNA methylation may constitute a biomarker of normative or potentially pathological differences in reactivity. Overall, findings provide a foundation for future research to explore relations among epigenetic processes and differences in both individual‐level biobehavioral risk and qualities of the early, external childhood environment.
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Affiliation(s)
- Sarah J Goodman
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Nicole R Bush
- Psychiatry, University of California, San Francisco, California.,Pediatrics, University of California, San Francisco, California
| | - Mina Park
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Pau Farré
- Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Eldon Emberly
- Physics, Simon Fraser University, Burnaby, BC, Canada
| | - Clyde Hertzman
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada
| | - Marilyn J Essex
- Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research, Vancouver, BC, Canada.,Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, BC, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - W Thomas Boyce
- Psychiatry, University of California, San Francisco, California.,Pediatrics, University of California, San Francisco, California.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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147
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Story Jovanova O, Nedeljkovic I, Spieler D, Walker RM, Liu C, Luciano M, Bressler J, Brody J, Drake AJ, Evans KL, Gondalia R, Kunze S, Kuhnel B, Lahti J, Lemaitre RN, Marioni RE, Swenson B, Himali JJ, Wu H, Li Y, McRae AF, Russ TC, Stewart J, Wang Z, Zhang G, Ladwig KH, Uitterlinden AG, Guo X, Peters A, Räikkönen K, Starr JM, Waldenberger M, Wray NR, Whitsel EA, Sotoodehnia N, Seshadri S, Porteous DJ, van Meurs J, Mosley TH, McIntosh AM, Mendelson MM, Levy D, Hou L, Eriksson JG, Fornage M, Deary IJ, Baccarelli A, Tiemeier H, Amin N. DNA Methylation Signatures of Depressive Symptoms in Middle-aged and Elderly Persons: Meta-analysis of Multiethnic Epigenome-wide Studies. JAMA Psychiatry 2018; 75:949-959. [PMID: 29998287 PMCID: PMC6142917 DOI: 10.1001/jamapsychiatry.2018.1725] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
IMPORTANCE Depressive disorders arise from a combination of genetic and environmental risk factors. Epigenetic disruption provides a plausible mechanism through which gene-environment interactions lead to depression. Large-scale, epigenome-wide studies on depression are missing, hampering the identification of potentially modifiable biomarkers. OBJECTIVE To identify epigenetic mechanisms underlying depression in middle-aged and elderly persons, using DNA methylation in blood. DESIGN, SETTING, AND PARTICIPANTS To date, the first cross-ethnic meta-analysis of epigenome-wide association studies (EWAS) within the framework of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium was conducted. The discovery EWAS included 7948 individuals of European origin from 9 population-based cohorts. Participants who were assessed for both depressive symptoms and whole-blood DNA methylation were included in the study. Results of EWAS were pooled using sample-size weighted meta-analysis. Replication of the top epigenetic sites was performed in 3308 individuals of African American and European origin from 2 population-based cohorts. MAIN OUTCOMES AND MEASURES Whole-blood DNA methylation levels were assayed with Illumina-Infinium Human Methylation 450K BeadChip and depressive symptoms were assessed by questionnaire. RESULTS The discovery cohorts consisted of 7948 individuals (4104 [51.6%] women) with a mean (SD) age of 65.4 (5.8) years. The replication cohort consisted of 3308 individuals (2456 [74.2%] women) with a mean (SD) age of 60.3 (6.4) years. The EWAS identified methylation of 3 CpG sites to be significantly associated with increased depressive symptoms: cg04987734 (P = 1.57 × 10-08; n = 11 256; CDC42BPB gene), cg12325605 (P = 5.24 × 10-09; n = 11 256; ARHGEF3 gene), and an intergenic CpG site cg14023999 (P = 5.99 × 10-08; n = 11 256; chromosome = 15q26.1). The predicted expression of the CDC42BPB gene in the brain (basal ganglia) (effect, 0.14; P = 2.7 × 10-03) and of ARHGEF3 in fibroblasts (effect, -0.48; P = 9.8 × 10-04) was associated with major depression. CONCLUSIONS AND RELEVANCE This study identifies 3 methylated sites associated with depressive symptoms. All 3 findings point toward axon guidance as the common disrupted pathway in depression. The findings provide new insights into the molecular mechanisms underlying the complex pathophysiology of depression. Further research is warranted to determine the utility of these findings as biomarkers of depression and evaluate any potential role in the pathophysiology of depression and their downstream clinical effects.
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Affiliation(s)
- Olivera Story Jovanova
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Derek Spieler
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Klinik und Poliklinik für Psychosomatische
Medizin und Psychotherapie des Klinikums Rechts der Isar der Technischen Universität
München, Munich, Germany
| | - Rosie M. Walker
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Centre for Genomic and Experimental Medicine, MRC
Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General
Hospital, Edinburgh, United Kingdom
| | - Chunyu Liu
- The Framingham Heart Study, Framingham,
Massachusetts,The Population Sciences Branch, Division of Intramural
Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland,Boston University School of Public Health, Boston,
Massachusetts
| | - Michelle Luciano
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Department of Psychology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Jan Bressler
- Human Genetics Center, University of Texas Health
Science Center at Houston
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle
| | - Amanda J. Drake
- University/British Heart Foundation Centre for
Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh,
Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Centre for Genomic and Experimental Medicine, MRC
Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General
Hospital, Edinburgh, United Kingdom
| | - Rahul Gondalia
- Department of Epidemiology, University of North
Carolina at Chapel Hill
| | - Sonja Kunze
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Brigitte Kuhnel
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of
Medicine, University of Helsinki, Helsinki, Finland
| | - Rozenn N. Lemaitre
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Department of Psychology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Brenton Swenson
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle,Institute for Public Health Genetics, School of
Public Health, University of Washington, Seattle
| | - Jayandra Jung Himali
- The Framingham Heart Study, Framingham,
Massachusetts,Boston University School of Public Health, Boston,
Massachusetts,Boston University School of Medicine, Boston,
Massachusetts
| | - Hongsheng Wu
- Computer Science and Networking, Wentworth Institute
of Technology, Boston, Massachusetts
| | - Yun Li
- Department of Genetics, University of North Carolina
at Chapel Hill,Department of Biostatistics, University of North
Carolina at Chapel Hill,Department of Computer Science, University of North
Carolina at Chapel Hill
| | - Allan F. McRae
- Institute for Molecular Bioscience, The University
of Queensland, Brisbane, Australia,Queensland Brain Institute, The University of
Queensland, Brisbane, Australia
| | - Tom C. Russ
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Alzheimer Scotland Dementia Research Centre,
Edinburgh, United Kingdom,Centre for Dementia Prevention, University of
Edinburgh, Edinburgh, United Kingdom
| | - James Stewart
- Department of Epidemiology, University of North
Carolina at Chapel Hill,Carolina Population Center, University of North
Carolina at Chapel Hill
| | - Zhiying Wang
- Human Genetics Center, University of Texas Health
Science Center at Houston
| | - Guosheng Zhang
- Department of Genetics, University of North Carolina
at Chapel Hill,Department of Biostatistics, University of North
Carolina at Chapel Hill,Department of Computer Science, University of North
Carolina at Chapel Hill
| | - Karl-Heinz Ladwig
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Klinik und Poliklinik für Psychosomatische
Medizin und Psychotherapie des Klinikums Rechts der Isar der Technischen Universität
München, Munich, Germany
| | - Andre G. Uitterlinden
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Internal Medicine, Erasmus Medical
Center, Rotterdam, the Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and
Population Sciences, Department of Pediatrics, Harbor-University of California Los Angeles
(UCLA) Medical Center
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of
Medicine, University of Helsinki, Helsinki, Finland
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Alzheimer Scotland Dementia Research Centre,
Edinburgh, United Kingdom
| | - Melanie Waldenberger
- Institute of Epidemiology II, Helmholtz Zentrum
München, Neuherberg, Germany,Research Unit of Molecular Epidemiology, Helmholtz
Zentrum München, Neuherberg, Germany
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University
of Queensland, Brisbane, Australia,Queensland Brain Institute, The University of
Queensland, Brisbane, Australia
| | - Eric A. Whitsel
- Department of Epidemiology, University of North
Carolina at Chapel Hill,Department of Medicine, University of North Carolina
at Chapel Hill
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham,
Massachusetts,Boston University School of Medicine, Boston,
Massachusetts
| | - David J. Porteous
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Centre for Genomic and Experimental Medicine, MRC
Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General
Hospital, Edinburgh, United Kingdom
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus Medical
Center, Rotterdam, the Netherlands
| | | | - Andrew M. McIntosh
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Division of Psychiatry, The University of Edinburgh,
Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael M. Mendelson
- The Framingham Heart Study, Framingham,
Massachusetts,The Population Sciences Branch, Division of Intramural
Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland,Department of Cardiology, Boston Children’s
Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel Levy
- The Framingham Heart Study, Framingham,
Massachusetts,The Population Sciences Branch, Division of Intramural
Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Lifang Hou
- Feinberg School of Medicine, Northwestern
University, Chicago, Illinois
| | - Johan G. Eriksson
- Department of General Practice and Primary Health
Care, University of Helsinki, Helsinki, Finland
| | - Myriam Fornage
- Human Genetics Center, University of Texas Health
Science Center at Houston,Institute of Molecular Medicine, University of Texas
Health Science Center at Houston
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive
Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom,Department of Psychology, University of Edinburgh,
Edinburgh, United Kingdom
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Harvard
T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Child and Adolescent Psychiatry,
Erasmus MC-University Medical Center Rotterdam, Rotterdam, the Netherlands,Department of Social and Behavioral Science, Harvard
T. H. Chan School of Public Health, Boston, Massachusetts
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC-University
Medical Center Rotterdam, Rotterdam, the Netherlands
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148
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Thomas M, Knoblich N, Wallisch A, Glowacz K, Becker-Sadzio J, Gundel F, Brückmann C, Nieratschker V. Increased BDNF methylation in saliva, but not blood, of patients with borderline personality disorder. Clin Epigenetics 2018; 10:109. [PMID: 30134995 PMCID: PMC6106893 DOI: 10.1186/s13148-018-0544-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022] Open
Abstract
Background The importance of epigenetic alterations in psychiatric disorders is increasingly acknowledged and the use of DNA methylation patterns as markers of disease is a topic of ongoing investigation. Recent studies suggest that patients suffering from Borderline Personality Disorder (BPD) display differential DNA methylation of various genes relevant for neuropsychiatric conditions. For example, several studies report differential methylation in the promoter region of the brain-derived neurotrophic factor gene (BDNF) in blood. However, little is known about BDNF methylation in other tissues. Results In the present study, we analyzed DNA methylation of the BDNF IV promoter in saliva and blood of 41 BPD patients and 41 matched healthy controls and found significant hypermethylation in the BPD patient’s saliva, but not blood. Further, we report that BDNF methylation in saliva of BPD patients significantly decreased after a 12-week psychotherapeutic intervention. Conclusions Providing a direct comparison of BDNF methylation in blood and saliva of the same individuals, our results demonstrate the importance of choice of tissue for the study of DNA methylation. In addition, they indicate a better suitability of saliva for the study of differential BDNF methylation in BPD patients. Further, our data appear to indicate a reversal of disease-specific alterations in BDNF methylation in response to psychotherapy, though further experiments are necessary to validate these results and determine the specificity of the effect. Electronic supplementary material The online version of this article (10.1186/s13148-018-0544-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mara Thomas
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany.,Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany
| | - Nora Knoblich
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany
| | - Annalena Wallisch
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany
| | - Katarzyna Glowacz
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany
| | - Julia Becker-Sadzio
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany
| | - Friederike Gundel
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany
| | - Christof Brückmann
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany
| | - Vanessa Nieratschker
- Department of Psychiatry and Psychotherapy, University Hospital Tübingen, Calwerstr. 14, 72076, Tübingen, Germany.
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149
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Population DNA methylation studies in the Developmental Origins of Health and Disease (DOHaD) framework. J Dev Orig Health Dis 2018; 10:306-313. [PMID: 30101736 DOI: 10.1017/s2040174418000442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic changes represent a potential mechanism underlying associations of early-life exposures and later life health outcomes. Population-based cohort studies starting in early life are an attractive framework to study the role of such changes. DNA methylation is the most studied epigenetic mechanism in population research. We discuss the application of DNA methylation in early-life population studies, some recent findings, key challenges and recommendations for future research. Studies into DNA methylation within the Developmental Origins of Health and Disease framework generally either explore associations between prenatal exposures and offspring DNA methylation or associations between offspring DNA methylation in early life and later health outcomes. Only a few studies to date have integrated prospective exposure, epigenetic and phenotypic data in order to explicitly test the role of DNA methylation as a potential biological mediator of environmental effects on health outcomes. Population epigenetics is an emerging field which has challenges in terms of methodology and interpretation of the data. Key challenges include tissue specificity, cell type adjustment, issues of power and comparability of findings, genetic influences, and exploring causality and functional consequences. Ongoing studies are working on addressing these issues. Large collaborative efforts of prospective cohorts are emerging, with clear benefits in terms of optimizing power and use of resources, and in advancing methodology. In the future, multidisciplinary approaches, within and beyond longitudinal birth and preconception cohorts will advance this complex, but highly promising, the field of research.
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150
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Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C. Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. Mol Autism 2018; 9:40. [PMID: 29988321 PMCID: PMC6022498 DOI: 10.1186/s13229-018-0224-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several reports have suggested a role for epigenetic mechanisms in ASD etiology. Epigenome-wide association studies (EWAS) in autism spectrum disorder (ASD) may shed light on particular biological mechanisms. However, studies of ASD cases versus controls have been limited by post-mortem timing and severely small sample sizes. Reports from in-life sampling of blood or saliva have also been very limited in sample size and/or genomic coverage. We present the largest case-control EWAS for ASD to date, combining data from population-based case-control and case-sibling pair studies. Methods DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. The Simons Simplex Collection (SSC) provided 450K array DNAm data on an additional 343 cases and their unaffected siblings. We performed EWAS meta-analysis across results from the two data sets, with adjustment for sex and surrogate variables that reflect major sources of biological variation and technical confounding such as cell type, batch, and ancestry. We compared top EWAS results to those from a previous brain-based analysis. We also tested for enrichment of ASD EWAS CpGs for being targets of meQTL associations using available SNP genotype data in the SEED sample. Findings In this meta-analysis of blood-based DNA from 796 cases and 858 controls, no single CpG met a Bonferroni discovery threshold of p < 1.12 × 10− 7. Seven CpGs showed differences at p < 1 × 10− 5 and 48 at 1 × 10− 4. Of the top 7, 5 showed brain-based ASD associations as well, often with larger effect sizes, and the top 48 overall showed modest concordance (r = 0.31) in direction of effect with cerebellum samples. Finally, we observed suggestive evidence for enrichment of CpG sites controlled by SNPs (meQTL targets) among the EWAS CpG hits, which was consistent across EWAS and meQTL discovery p value thresholds. Conclusions No single CpG site showed a large enough DNAm difference between cases and controls to achieve epigenome-wide significance in this sample size. However, our results suggest the potential to observe disease associations from blood-based samples. Among the seven sites achieving suggestive statistical significance, we observed consistent, and stronger, effects at the same sites among brain samples. Discovery-oriented EWAS for ASD using blood samples will likely need even larger samples and unified genetic data to further understand DNAm differences in ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0224-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan V Andrews
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Brooke Sheppard
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
| | - Gayle C Windham
- 3California Department of Public Health, Environmental Health Investigations Branch, 850 Marina Bay Parkway, Richmond, CA 94804 USA
| | - Laura A Schieve
- 4National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, MS E-86, 1600 Clifton Road, Atlanta, GA 30333 USA
| | - Diana E Schendel
- 5Deparment of Public Health, Section of Epidemiology, Aarhus University, Aarhus, Denmark.,6Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,7Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Lisa A Croen
- 8Kaiser Permanente Division of Research, 2000 Broadway, Oakland, CA 94612 USA
| | - Pankaj Chopra
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Reid S Alisch
- 10Department of Psychiatry, University of Wisconsin-Madison, 6001 Research Park Blvd, Madison, WI 53719 USA
| | - Craig J Newschaffer
- 11Department of Epidemiology and Biostatistics, Drexel University School of Public Health, 3215 Market Street, Philadelphia, PA 19104 USA.,A.J. Drexel Autism Institute, 3020 Market Street Suite 560, Philadelphia, PA 19104 USA
| | - Stephen T Warren
- 9Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,13Department of Biochemistry, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA.,14Department of Pediatrics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322 USA
| | - Andrew P Feinberg
- 15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,16Department of Medicine, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA
| | - M Daniele Fallin
- 2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA.,15Center for Epigenetics, Johns Hopkins School of Medicine, 855 N. Wolfe Street, Baltimore, MD 21205 USA.,17Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, HH850, Baltimore, MD 21205 USA
| | - Christine Ladd-Acosta
- 1Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 USA.,2Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, W6509, Baltimore, MD 21205 USA
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