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Almodóvar-Payá C, París-Gómez I, Latorre-Guardia M, Guardiola-Ripoll M, Catalán R, Arias B, Penadés R, Fatjó-Vilas M. NRN1 genetic variability and methylation changes as biomarkers for cognitive remediation therapy response in schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2024:111175. [PMID: 39426559 DOI: 10.1016/j.pnpbp.2024.111175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/20/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
Abstract
Cognitive remediation therapy (CRT) demonstrates potential in enhancing cognitive function in schizophrenia (SZ), though the identification of molecular biomarkers remains challenging. The Neuritin-1 gene (NRN1) emerges as a promising candidate gene due to its association with SZ, cognitive performance and response to neurotherapeutic treatments. We aimed to investigate whether NRN1 genetic variability and methylation changes following CRT are related to cognitive improvements. Twenty-five SZ patients were randomly assigned to CRT or treatment-as-usual (TAU) groups, with cognitive function and NRN1 methylation assessed pre- and post-intervention using the MATRICS Consensus Cognitive Battery and EpiTYPER. Besides, eleven NRN1 polymorphisms were genotyped. Methylation changes (Δm = post - pre) were analyzed via sparse Partial Least Square Discriminant Analysis (sPLS-DA) to identify latent components (LCs) distinguishing CRT from TAU. To further explore methylation patterns of these LCs, CpG units were grouped into two subsets, yielding Δm means for those with increased and decreased methylation. Cognitive changes (Δcog = post - pre) were used to identify CRT improvers (CRTI, Δcog ≥1), and the association between methylation changes and cognitive improvements post-therapy was also tested. We identified two LCs that differentiated CRT from TAU with a classification error rate of 0.28. The main component, LC1, included 25 CpG units. The subsets of CpG units with increased and decreased post-therapy methylation differed significantly between the two treatment arms, suggesting that differences were not merely data-driven but reflected meaningful biological variation. Additionally, CpG units linked to therapy were also associated with cognitive improvement, with LC1 and the subset of CpG units showing increased methylation post-therapy distinguishing CRT-I from the rest of the patients across multiple cognitive domains. Furthermore, the effect of LC1 on speed processing improvement after CRT was enhanced by considering the NRN1-rs9405890 polymorphism. Notably, these CpG units, particularly those with increased methylation after CRT, overlapped with key gene regulatory elements. Our model, integrating genetics and epigenetics, boosts the understanding of CRT response variability and highlights this multi-level approach as a promising strategy for identifying potential NRN1-related biomarkers of CRT effects, though further studies with larger samples are needed.
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Affiliation(s)
- Carmen Almodóvar-Payá
- FIDMAG Germanes Hospitalàries Research Foundation, Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | | | - Mariona Latorre-Guardia
- FIDMAG Germanes Hospitalàries Research Foundation, Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | | | - Rosa Catalán
- Universitat de Barcelona Departament de Medicina-Clínic, Barcelona, Spain
| | - Bárbara Arias
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Rafael Penadés
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; Barcelona Clinic Schizophrenia Unit (BCSU), Hospital Clínic, Barcelona, Spain; Clinical Psychology and Psychobiology, University of Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | - Mar Fatjó-Vilas
- FIDMAG Germanes Hospitalàries Research Foundation, Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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3
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Nishitani S, Smith AK, Tomoda A, Fujisawa TX. Data science using the human epigenome for predicting multifactorial diseases and symptoms. Epigenomics 2024; 16:273-276. [PMID: 38312014 DOI: 10.2217/epi-2023-0321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Tweetable abstract This article reviews machine learning models that leverages epigenomic data for predicting multifactorial diseases and symptoms as well as how such models can be utilized to explore new research questions.
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Affiliation(s)
- Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, & University of Fukui, Osaka, 565-0871, Japan
- Life Science Innovation Center, School of Medical Sciences, University of Fukui, Fukui, 910-8507, Japan
| | - Alicia K Smith
- Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, & University of Fukui, Osaka, 565-0871, Japan
- Life Science Innovation Center, School of Medical Sciences, University of Fukui, Fukui, 910-8507, Japan
- Department of Child & Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, 910-1193, Japan
| | - Takashi X Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, & University of Fukui, Osaka, 565-0871, Japan
- Life Science Innovation Center, School of Medical Sciences, University of Fukui, Fukui, 910-8507, Japan
- Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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Obradovic B, Roberts O, Owen A, Milosevic I, Milic N, Ranin J, Dragovic G. Expression of CYP2B6 Enzyme in Human Liver Tissue of HIV and HCV Patients. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1207. [PMID: 37512019 PMCID: PMC10385124 DOI: 10.3390/medicina59071207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
Background and Objectives: Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) infections present significant public health challenges worldwide. The management of these infections is complicated by the need for antiviral and antiretroviral therapies, which are influenced by drug metabolism mediated by metabolic enzymes and transporters. This study focuses on the gene expression of CYP2B6, CYP3A4, and ABCB1 transporters in patients with HIV, HCV, and HIV/HCV co-infection, aiming to assess their potential association with the choice of therapy, patohistological and clinical parameters of liver damage such as the stage of liver fibrosis, serum levels of ALT and AST, as well as the grade of liver inflammation and other available biochemical parameters. Materials and Methods: The study included 54 patients who underwent liver biopsy, divided into HIV-infected, HCV-infected, and co-infected groups. The mRNA levels of CYP2B6, CYP3A4, and ABCB1 was quantified and compared between the groups, along with the analysis of liver fibrosis and inflammation levels. Results: The results indicated a significant increase in CYP2B6 mRNA levels in co-infected patients, a significant association with the presence of HIV infection with an increase in CYP3A4 mRNA levels. A trend towards downregulation of ABCB1 expression was observed in patients using lamivudine. Conclusions: This study provides insight into gene expression of CYP2B6 CYP3A4, and ABCB1 in HIV, HCV, and HIV/HCV co-infected patients. The absence of correlation with liver damage, inflammation, and specific treatment interventions emphasises the need for additional research to elucidate the complex interplay between gene expression, viral co-infection, liver pathology, and therapeutic responses in these particular patients population.
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Affiliation(s)
- Bozana Obradovic
- University of Belgrade, Faculty of Medicine, Department of Pharmacology, Clinical Pharmacology and Toxicology, 11000 Belgrade, Serbia
| | - Owain Roberts
- University of Buckingham Medical School, Faculty of Medicine and Health Sciences, University of Buckingham, Buckingham MK18 1EG, UK
| | - Andrew Owen
- Centre of Excellence in Long-Acting Therapeutics (CELT), Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ivana Milosevic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Infectious and Tropical Diseases, Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Natasa Milic
- University of Belgrade, Faculty of Medicine, Department of Medical Statistics & Informatics, 11000 Belgrade, Serbia
| | - Jovan Ranin
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Infectious and Tropical Diseases, Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Gordana Dragovic
- University of Belgrade, Faculty of Medicine, Department of Pharmacology, Clinical Pharmacology and Toxicology, 11000 Belgrade, Serbia
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Chundru VK, Marioni RE, Prendergast JGD, Lin T, Beveridge AJ, Martin NG, Montgomery GW, Hume DA, Deary IJ, Visscher PM, Wray NR, McRae AF. Rare genetic variants underlie outlying levels of DNA methylation and gene-expression. Hum Mol Genet 2023; 32:1912-1921. [PMID: 36790133 PMCID: PMC10196672 DOI: 10.1093/hmg/ddad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Testing the effect of rare variants on phenotypic variation is difficult due to the need for extremely large cohorts to identify associated variants given expected effect sizes. An alternative approach is to investigate the effect of rare genetic variants on DNA methylation (DNAm) as effect sizes are expected to be larger for molecular traits compared with complex traits. Here, we investigate DNAm in healthy ageing populations-the Lothian Birth Cohorts of 1921 and 1936-and identify both transient and stable outlying DNAm levels across the genome. We find an enrichment of rare genetic single nucleotide polymorphisms (SNPs) within 1 kb of DNAm sites in individuals with stable outlying DNAm, implying genetic control of this extreme variation. Using a family-based cohort, the Brisbane Systems Genetics Study, we observed increased sharing of DNAm outliers among more closely related individuals, consistent with these outliers being driven by rare genetic variation. We demonstrated that outlying DNAm levels have a functional consequence on gene expression levels, with extreme levels of DNAm being associated with gene expression levels toward the tails of the population distribution. This study demonstrates the role of rare SNPs in the phenotypic variation of DNAm and the effect of extreme levels of DNAm on gene expression.
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Affiliation(s)
- V Kartik Chundru
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Allan J Beveridge
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, The University of Glasgow, Glasgow G61 1QH, UK
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David A Hume
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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6
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Yazar V, Ruf WP, Knehr A, Günther K, Ammerpohl O, Danzer KM, Ludolph AC. DNA Methylation Analysis in Monozygotic Twins Discordant for ALS in Blood Cells. Epigenet Insights 2023; 16:25168657231172159. [PMID: 37152709 PMCID: PMC10161312 DOI: 10.1177/25168657231172159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/09/2023] [Indexed: 05/09/2023] Open
Abstract
ALS is a fatal motor neuron disease that displays a broad variety of phenotypes ranging from early fatal courses to slowly progressing and rather benign courses. Such divergence can also be seen in genetic ALS cases with varying phenotypes bearing specific mutations, suggesting epigenetic mechanisms like DNA methylation act as disease modifiers. However, the epigenotype dictated by, in addition to other mechanisms, DNA methylation is also strongly influenced by the individual's genotype. Hence, we performed a DNA methylation study using EPIC arrays on 7 monozygotic (MZ) twin pairs discordant for ALS in whole blood, which serves as an ideal model for eliminating the effects of the genetic-epigenetic interplay to a large extent. We found one CpG site showing intra-pair hypermethylation in the affected co-twins, which maps to the Glutamate Ionotropic Receptor Kainate Type Subunit 1 gene (GRIK1). Additionally, we found 4 DMPs which were subsequently confirmed using 2 different statistical approaches. Differentially methylated regions or blocks could not be detected within the scope of this work. In conclusion, we revealed that despite a low sample size, monozygotic twin studies discordant for the disease can bring new insights into epigenetic processes in ALS, pointing to new target loci for further investigations.
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Affiliation(s)
- Volkan Yazar
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), German Center for Neurodegenerative Diseases, Ulm, Germany
| | - Wolfgang P Ruf
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Antje Knehr
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Kornelia Günther
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Karin M Danzer
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), German Center for Neurodegenerative Diseases, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
| | - Albert C Ludolph
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), German Center for Neurodegenerative Diseases, Ulm, Germany
- Department of Neurology, Ulm University, Ulm, Baden-Württemberg, Germany
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Wu Y, Montrose L, Kochmanski JK, Dolinoy DC, Téllez-Rojo MM, Cantoral A, Mercado-García A, Peterson KE, Goodrich JM. Is adiposity related to repeat measures of blood leukocyte DNA methylation across childhood and adolescence? Clin Obes 2023; 13:e12566. [PMID: 36416295 PMCID: PMC9991944 DOI: 10.1111/cob.12566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 11/24/2022]
Abstract
Epigenetic modifications such as DNA methylation may influence gene expression and phenotypes, including obesity in childhood. The directionality of this relationship is nevertheless unclear, and some evidence suggests that adiposity modifies the epigenome, rather than the other way around. In this pilot study, we utilize data from the Early Life Exposures in Mexico to Environmental Toxicants (ELEMENT) study to examine whether measures of adiposity in childhood and early adolescence are associated with repeated measures of blood leukocyte DNA methylation at LINE-1 repetitive elements and two genes implicated in growth and adiposity: H19 and HSD11B2. Longitudinal epigenetic data were generated from cord blood and blood from follow-up visits in early and late adolescence. We assessed interactions between age and measures of body mass index (BMI) at 5 years of age and weight, BMI and waist circumference in early adolescence to infer whether adiposity deflects age-related DNA methylation changes throughout childhood. Applying linear mixed-effects models, we found an inverse association between measures of childhood BMI (kg/m2 ) and early-teen weight (kg) with repeat measures of H19 DNA methylation. We did not observe any statistically significant associations (p-value <.05) between any anthropometric measures and DNA methylation at LINE-1 or HSD11B2. We did not demonstrate statistically significant evidence in support of deflection of age-related DNA methylation trajectories by adiposity-related measures (age by adiposity interaction term). Given the pilot nature of this study, the relationships between repeat measures of DNA methylation and adiposity-measures across childhood merit further exploration in larger study populations.
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Affiliation(s)
- Yue Wu
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, CN
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Luke Montrose
- Department of Community and Environmental Health, Boise State University, Boise, ID, USA
| | - Joseph K. Kochmanski
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Martha M Téllez-Rojo
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, MX
| | | | - Adriana Mercado-García
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, MX
| | - Karen E. Peterson
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
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Nabais MF, Gadd DA, Hannon E, Mill J, McRae AF, Wray NR. An overview of DNA methylation-derived trait score methods and applications. Genome Biol 2023; 24:28. [PMID: 36797751 PMCID: PMC9936670 DOI: 10.1186/s13059-023-02855-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites ("probes") and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data.
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Colwell ML, Townsel C, Petroff RL, Goodrich JM, Dolinoy DC. Epigenetics and the Exposome: DNA Methylation as a Proxy for Health Impacts of Prenatal Environmental Exposures. EXPOSOME 2023; 3:osad001. [PMID: 37333730 PMCID: PMC10275510 DOI: 10.1093/exposome/osad001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The accumulation of every day exposures can impact health across the life course, but our understanding of such exposures is impeded by our ability to delineate the relationship between an individual's early life exposome and later life health effects. Measuring the exposome is challenging. Exposure assessed at a given time point captures a snapshot of the exposome but does not represent the full spectrum of exposures across the life course. In addition, the assessment of early life exposures and their effects is often further challenged by lack of relevant samples and the time gap between exposures and related health outcomes in later life. Epigenetics, specifically DNA methylation, has the potential to overcome these barriers as environmental epigenetic perturbances can be retained through time. In this review, we describe how DNA methylation can be framed in the world of the exposome. We offer three compelling examples of common environmental exposures, including cigarette smoke, the endocrine active compound bisphenol A (BPA), and the metal lead (Pb), to illustrate the application of DNA methylation as a proxy to measure the exposome. We discuss areas for future explorations and current limitations of this approach. Epigenetic profiling is a promising and rapidly developing tool and field of study, offering us a unique and powerful way to assess the early life exposome and its effects across different life stages.
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Affiliation(s)
- Mathia L. Colwell
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Courtney Townsel
- Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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Svoboda LK, Wang K, Goodrich JM, Jones TR, Colacino JA, Peterson KE, Tellez-Rojo MM, Sartor MA, Dolinoy DC. Perinatal Lead Exposure Promotes Sex-Specific Epigenetic Programming of Disease-Relevant Pathways in Mouse Heart. TOXICS 2023; 11:85. [PMID: 36668811 PMCID: PMC9860846 DOI: 10.3390/toxics11010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Environmental contaminants such as the metal lead (Pb) are associated with cardiovascular disease, but the underlying molecular mechanisms are poorly understood. In particular, little is known about how exposure to Pb during early development impacts the cardiac epigenome at any point across the life course and potential differences between sexes. In a mouse model of human-relevant perinatal exposures, we utilized RNA-seq and Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) to investigate the effects of Pb exposure during gestation and lactation on gene expression and DNA methylation, respectively, in the hearts of male and female mice at weaning. For ERRBS, we identified differentially methylated CpGs (DMCs) or differentially methylated 1000 bp regions (DMRs) based on a minimum absolute change in methylation of 10% and an FDR < 0.05. For gene expression data, an FDR < 0.05 was considered significant. No individual genes met the FDR cutoff for gene expression; however, we found that Pb exposure leads to significant changes in the expression of gene pathways relevant to cardiovascular development and disease. We further found that Pb promotes sex-specific changes in DNA methylation at hundreds of gene loci (280 DMCs and 99 DMRs in males, 189 DMCs and 121 DMRs in females), and pathway analysis revealed that these CpGs and regions collectively function in embryonic development. In males, differential methylation also occurred at genes related to immune function and metabolism. We then investigated whether genes exhibiting differential methylation at weaning were also differentially methylated in hearts from a cohort of Pb-exposed mice at adulthood. We found that a single gene, Galnt2, showed differential methylation in both sexes and time points. In a human cohort investigating the influence of prenatal Pb exposure on the epigenome, we also observed an inverse association between first trimester Pb concentrations and adolescent blood leukocyte DNA methylation at a locus in GALNT2, suggesting that this gene may represent a biomarker of Pb exposure across species. Together, these data, across two time points in mice and in a human birth cohort study, collectively demonstrate that Pb exposure promotes sex-specific programming of the cardiac epigenome, and provide potential mechanistic insight into how Pb causes cardiovascular disease.
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Affiliation(s)
- Laurie K. Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jaclyn M. Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tamara R. Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Karen E. Peterson
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Martha M. Tellez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca 62100, Mexico
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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11
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Devall MA, Sun X, Eaton S, Cooper GS, Willis JE, Weisenberger DJ, Casey G, Li L. A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer. Cancers (Basel) 2022; 15:cancers15010045. [PMID: 36612042 PMCID: PMC9817986 DOI: 10.3390/cancers15010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the important role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA) and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epigenome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n = 140 samples). We identified increased epigenetic age acceleration in EA than AA rectum (p = 3.91 × 10-4) using linear regression. We also identified differentially methylated regions (DMRs) associated with chronological aging in AA and EA, separately using DMRcate. Next, a consensus set of regions associated with cancer was identified through DMR analysis of two rectal cancer cohorts. The vast majority of AA DMRs were present in our analysis of aging in rectum of EA subjects, though rates of epigenetic drift were significantly greater in AA (p = 1.94 × 10-45). However, 3.66-fold more DMRs were associated with aging in rectum of EA subjects, many of which were also associated with rectal cancer. Our findings reveal a novel relationship between race, age, DNA methylation and rectal cancer risk that warrants further investigation.
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Affiliation(s)
- Matthew A. Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gregory S. Cooper
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: ; Tel.: +1-434-982-3975
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12
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Baranyi G, Deary IJ, McCartney DL, Harris SE, Shortt N, Reis S, Russ TC, Ward Thompson C, Vieno M, Cox SR, Pearce J. Life-course exposure to air pollution and biological ageing in the Lothian Birth Cohort 1936. ENVIRONMENT INTERNATIONAL 2022; 169:107501. [PMID: 36126422 DOI: 10.1016/j.envint.2022.107501] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Exposure to air pollution is associated with a range of diseases. Biomarkers derived from DNA methylation (DNAm) offer potential mechanistic insights into human health differences, connecting disease pathogenesis and biological ageing. However, little is known about sensitive periods during the life course where air pollution might have a stronger impact on DNAm, or whether effects accumulate over time. We examined associations between air pollution exposure across the life course and DNAm-based markers of biological ageing. METHODS Data were derived from the Scotland-based Lothian Birth Cohort 1936. Participants' residential history was linked to annual levels of fine particle (PM2.5), sulphur dioxide (SO2), nitrogen dioxide (NO2), and ozone (O3) around 1935, 1950, 1970, 1980, 1990, and 2001; pollutant concentrations were estimated using the EMEP4UK atmospheric chemistry transport model. Blood samples were obtained between ages of 70 and 80 years, and Horvath DNAmAge, Hannum DNAmAge, DNAmPhenoAge, DNAmGrimAge, and DNAm telomere length (DNAmTL) were computed. We applied the structured life-course modelling approach: least angle regression identified best-fit life-course models for a composite measure of air pollution (air quality index [AQI]), and mixed-effects regression estimated selected models for AQI and single pollutants. RESULTS We included 525 individuals with 1782 observations. In the total sample, increased air pollution around 1970 was associated with higher epigenetic age (AQI: b = 0.322 year, 95 %CI: 0.088, 0.555) measured with Horvath DNAmAge in late adulthood. We found shorter DNAmTL among males with higher air pollution around 1980 (AQI: b = -0.015 kilobase, 95 %CI: -0.027, -0.004) and among females with higher exposure around 1935 (AQI: b = -0.017 kilobase, 95 %CI: -0.028, -0.006). Findings were more consistent for the pollutants PM2.5, SO2 and NO2. DISCUSSION We tested the life-course relationship between air pollution and DNAm-based biomarkers. Air pollution around birth and in young-to-middle adulthood is linked to accelerated epigenetic ageing and telomere-associated ageing in later life.
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Affiliation(s)
- Gergő Baranyi
- Centre for Research on Environment, Society and Health, School of GeoSciences, The University of Edinburgh, Edinburgh, UK.
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Niamh Shortt
- Centre for Research on Environment, Society and Health, School of GeoSciences, The University of Edinburgh, Edinburgh, UK
| | - Stefan Reis
- UK Centre for Ecology & Hydrology (UKCEH), Bush Estate, Penicuik, UK; University of Exeter Medical School, Knowledge Spa, Truro TR1 3HD, UK; The University of Edinburgh, School of Chemistry, Edinburgh EH9 3BF, UK
| | - Tom C Russ
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, UK
| | | | - Massimo Vieno
- UK Centre for Ecology & Hydrology (UKCEH), Bush Estate, Penicuik, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Jamie Pearce
- Centre for Research on Environment, Society and Health, School of GeoSciences, The University of Edinburgh, Edinburgh, UK
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13
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Stevenson AJ, McCartney DL, Gadd DA, Shireby G, Hillary RF, King D, Tzioras M, Wrobel N, McCafferty S, Murphy L, McColl BW, Redmond P, Taylor AM, Harris SE, Russ TC, McIntosh AM, Mill J, Smith C, Deary IJ, Cox SR, Marioni RE, Spires‐Jones TL. A comparison of blood and brain-derived ageing and inflammation-related DNA methylation signatures and their association with microglial burdens. Eur J Neurosci 2022; 56:5637-5649. [PMID: 35362642 PMCID: PMC9525452 DOI: 10.1111/ejn.15661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022]
Abstract
Inflammation and ageing-related DNA methylation patterns in the blood have been linked to a variety of morbidities, including cognitive decline and neurodegenerative disease. However, it is unclear how these blood-based patterns relate to patterns within the brain and how each associates with central cellular profiles. In this study, we profiled DNA methylation in both the blood and in five post mortem brain regions (BA17, BA20/21, BA24, BA46 and hippocampus) in 14 individuals from the Lothian Birth Cohort 1936. Microglial burdens were additionally quantified in the same brain regions. DNA methylation signatures of five epigenetic ageing biomarkers ('epigenetic clocks'), and two inflammatory biomarkers (methylation proxies for C-reactive protein and interleukin-6) were compared across tissues and regions. Divergent associations between the inflammation and ageing signatures in the blood and brain were identified, depending on region assessed. Four out of the five assessed epigenetic age acceleration measures were found to be highest in the hippocampus (β range = 0.83-1.14, p ≤ 0.02). The inflammation-related DNA methylation signatures showed no clear variation across brain regions. Reactive microglial burdens were found to be highest in the hippocampus (β = 1.32, p = 5 × 10-4 ); however, the only association identified between the blood- and brain-based methylation signatures and microglia was a significant positive association with acceleration of one epigenetic clock (termed DNAm PhenoAge) averaged over all five brain regions (β = 0.40, p = 0.002). This work highlights a potential vulnerability of the hippocampus to epigenetic ageing and provides preliminary evidence of a relationship between DNA methylation signatures in the brain and differences in microglial burdens.
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Affiliation(s)
- Anna J. Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Gemma Shireby
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Declan King
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Makis Tzioras
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Nicola Wrobel
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Sarah McCafferty
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Lee Murphy
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Barry W. McColl
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Paul Redmond
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
| | | | - Sarah E. Harris
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Tom C. Russ
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Alzheimer Scotland Dementia Research Centre, 7 George SquareUniversity of EdinburghEdinburghUK
- Division of PsychiatryUniversity of Edinburgh, Royal Edinburgh HospitalEdinburghUK
| | - Andrew M. McIntosh
- Division of PsychiatryUniversity of Edinburgh, Royal Edinburgh HospitalEdinburghUK
| | - Jonathan Mill
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Colin Smith
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Ian J. Deary
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Simon R. Cox
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
| | - Tara L. Spires‐Jones
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
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14
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Higham J, Kerr L, Zhang Q, Walker RM, Harris SE, Howard DM, Hawkins EL, Sandu AL, Steele JD, Waiter GD, Murray AD, Evans KL, McIntosh AM, Visscher PM, Deary IJ, Cox SR, Sproul D. Local CpG density affects the trajectory and variance of age-associated DNA methylation changes. Genome Biol 2022; 23:216. [PMID: 36253871 PMCID: PMC9575273 DOI: 10.1186/s13059-022-02787-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Altered rates of aging inferred from these clocks are observed in human disease. However, the molecular mechanisms underpinning age-associated DNA methylation changes remain unknown. Local DNA sequence can program steady-state DNA methylation levels, but how it influences age-associated methylation changes is unknown. RESULTS We analyze longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs. We show that changes in methylation with age occur at 182,760 loci largely independently of variation in cell type proportions. These changes are especially apparent at 8322 low CpG density loci. Using SNP data from the same individuals, we demonstrate that methylation trajectories are affected by local sequence polymorphisms at 1487 low CpG density loci. More generally, we find that low CpG density regions are particularly prone to change and do so variably between individuals in people aged over 65. This differs from the behavior of these regions in younger individuals where they predominantly lose methylation. CONCLUSIONS Our results, which we reproduce in two independent groups of individuals, demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.
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Affiliation(s)
- Jonathan Higham
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Present address: Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Present address: School of Psychology, University of Exeter, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Emma L Hawkins
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca-Larisa Sandu
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - J Douglas Steele
- Division of Imaging Science and Technology, Medical School, University of Dundee, Dundee, UK
| | - Gordon D Waiter
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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15
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Abstract
Over the course of a human lifespan, genome integrity erodes, leading to an increased abundance of several types of chromatin changes. The abundance of DNA lesions (chemical perturbations to nucleotides) increases with age, as does the number of genomic mutations and transcriptional disruptions caused by replication or transcription of those lesions, respectively. At the epigenetic level, precise DNA methylation patterns degrade, likely causing increasingly stochastic variations in gene expression. Similarly, the tight regulation of histone modifications begins to unravel. The genomic instability caused by these mechanisms allows transposon element reactivation and remobilization, further mutations, gene dysregulation, and cytoplasmic chromatin fragments. This cumulative genomic instability promotes cell signaling events that drive cell fate decisions and extracellular communications known to disrupt tissue homeostasis and regeneration. In this Review, we focus on age-related epigenetic changes and their interactions with age-related genomic changes that instigate these events.
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Affiliation(s)
- Carolina Soto-Palma
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Christopher D. Faulk
- Institute on the Biology of Aging and Metabolism
- Department of Animal Science, and
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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16
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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17
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Fennell L, Kane A, Liu C, McKeone D, Hartel G, Su C, Bond C, Bettington M, Leggett B, Whitehall V. Braf mutation induces rapid neoplastic transformation in the aged and aberrantly methylated intestinal epithelium. Gut 2022; 71:1127-1140. [PMID: 34230216 PMCID: PMC9120393 DOI: 10.1136/gutjnl-2020-322166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Sessile serrated lesions (SSLs) are common across the age spectrum, but the BRAF mutant cancers arising occur predominantly in the elderly. Aberrant DNA methylation is uncommon in SSL from young patients. Here, we interrogate the role of ageing and DNA methylation in SSL initiation and progression. DESIGN We used an inducible model of Braf mutation to direct recombination of the oncogenic Braf V637E allele to the murine intestine. BRAF mutation was activated after periods of ageing, and tissue was assessed for histological, DNA methylation and gene expression changes thereafter. We also investigated DNA methylation alterations in human SSLs. RESULTS Inducing Braf mutation in aged mice was associated with a 10-fold relative risk of serrated lesions compared with young mice. There were extensive differences in age-associated DNA methylation between animals induced at 9 months versus wean, with relatively little differential Braf-specific methylation. DNA methylation at WNT pathway genes scales with age and Braf mutation accelerated age-associated DNA methylation. In human SSLs, increased epigenetic age was associated with high-risk serrated colorectal neoplasia. CONCLUSIONS SSLs arising in the aged intestine are at a significantly higher risk of spontaneous neoplastic progression. These findings provide support for a new conceptual model for serrated colorectal carcinogenesis, whereby risk of Braf-induced neoplastic transformation is dependent on age and may be related to age-associated molecular alterations that accumulate in the ageing intestine, including DNA methylation. This may have implications for surveillance and chemopreventive strategies targeting the epigenome.
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Affiliation(s)
- Lochlan Fennell
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Alexandra Kane
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
- Conjoint Internal Medical Laboratory, Chemical Pathology, Health Support Queensland Pathology Queensland, Herston, Queensland, Australia
| | - Cheng Liu
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Diane McKeone
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Gunter Hartel
- Statistics Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chang Su
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Catherine Bond
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
| | - Mark Bettington
- Envoi Specialist Pathologists, Brisbane, Queensland, Australia
| | - Barbara Leggett
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
- Department of Gastroenterology and Hepatology, The Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vicki Whitehall
- The Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Saint Lucia, Queensland, Australia
- Conjoint Internal Medical Laboratory, Chemical Pathology, Health Support Queensland Pathology Queensland, Herston, Queensland, Australia
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18
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Staley JR, Windmeijer F, Suderman M, Lyon MS, Davey Smith G, Tilling K. A robust mean and variance test with application to high-dimensional phenotypes. Eur J Epidemiol 2022; 37:377-387. [PMID: 34651232 PMCID: PMC9187575 DOI: 10.1007/s10654-021-00805-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 09/06/2021] [Indexed: 12/01/2022]
Abstract
Most studies of continuous health-related outcomes examine differences in mean levels (location) of the outcome by exposure. However, identifying effects on the variability (scale) of an outcome, and combining tests of mean and variability (location-and-scale), could provide additional insights into biological mechanisms. A joint test could improve power for studies of high-dimensional phenotypes, such as epigenome-wide association studies of DNA methylation at CpG sites. One possible cause of heterogeneity of variance is a variable interacting with exposure in its effect on outcome, so a joint test of mean and variability could help in the identification of effect modifiers. Here, we review a scale test, based on the Brown-Forsythe test, for analysing variability of a continuous outcome with respect to both categorical and continuous exposures, and develop a novel joint location-and-scale score (JLSsc) test. These tests were compared to alternatives in simulations and used to test associations of mean and variability of DNA methylation with gender and gestational age using data from the Accessible Resource for Integrated Epigenomics Studies (ARIES). In simulations, the Brown-Forsythe and JLSsc tests retained correct type I error rates when the outcome was not normally distributed in contrast to the other approaches tested which all had inflated type I error rates. These tests also identified > 7500 CpG sites for which either mean or variability in cord blood methylation differed according to gender or gestational age. The Brown-Forsythe test and JLSsc are robust tests that can be used to detect associations not solely driven by a mean effect.
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Affiliation(s)
- James R Staley
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Frank Windmeijer
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Department of Statistics and Nuffield College, University of Oxford, Oxford, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Matthew S Lyon
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Kate Tilling
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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19
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Shen X, Caramaschi D, Adams MJ, Walker RM, Min JL, Kwong A, Hemani G, Barbu MC, Whalley HC, Harris SE, Deary IJ, Morris SW, Cox SR, Relton CL, Marioni RE, Evans KL, McIntosh AM. DNA methylome-wide association study of genetic risk for depression implicates antigen processing and immune responses. Genome Med 2022; 14:36. [PMID: 35354486 PMCID: PMC8969265 DOI: 10.1186/s13073-022-01039-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Depression is a disabling and highly prevalent condition where genetic and epigenetic, such as DNA methylation (DNAm), differences contribute to disease risk. DNA methylation is influenced by genetic variation but the association between polygenic risk of depression and DNA methylation is unknown. METHODS We investigated the association between polygenic risk scores (PRS) for depression and DNAm by conducting a methylome-wide association study (MWAS) in Generation Scotland (N = 8898, mean age = 49.8 years) with replication in the Lothian Birth Cohorts of 1921 and 1936 and adults in the Avon Longitudinal Study of Parents and Children (ALSPAC) (Ncombined = 2049, mean age = 79.1, 69.6 and 47.2 years, respectively). We also conducted a replication MWAS in the ALSPAC children (N = 423, mean age = 17.1 years). Gene ontology analysis was conducted for the cytosine-guanine dinucleotide (CpG) probes significantly associated with depression PRS, followed by Mendelian randomisation (MR) analysis to infer the causal relationship between depression and DNAm. RESULTS Widespread associations (NCpG = 71, pBonferroni < 0.05, p < 6.3 × 10-8) were found between PRS constructed using genetic risk variants for depression and DNAm in CpG probes that localised to genes involved in immune responses and neural development. The effect sizes for the significant associations were highly correlated between the discovery and replication samples in adults (r = 0.79) and in adolescents (r = 0.82). Gene Ontology analysis showed that significant CpG probes are enriched in immunological processes in the human leukocyte antigen system. Additional MWAS was conducted for each lead genetic risk variant. Over 47.9% of the independent genetic risk variants included in the PRS showed associations with DNAm in CpG probes located in both the same (cis) and distal (trans) locations to the genetic loci (pBonferroni < 0.045). Subsequent MR analysis showed that there are a greater number of causal effects found from DNAm to depression than vice versa (DNAm to depression: pFDR ranged from 0.024 to 7.45 × 10-30; depression to DNAm: pFDR ranged from 0.028 to 0.003). CONCLUSIONS PRS for depression, especially those constructed from genome-wide significant genetic risk variants, showed methylome-wide differences associated with immune responses. Findings from MR analysis provided evidence for causal effect of DNAm to depression.
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Affiliation(s)
- Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK.
| | - Doretta Caramaschi
- College of Life and Environmental Sciences, Psychology, University of Exeter, Exeter, UK
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
| | - Josine L Min
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Alex Kwong
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts group, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK.
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20
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Silver MJ, Saffari A, Kessler NJ, Chandak GR, Fall CHD, Issarapu P, Dedaniya A, Betts M, Moore SE, Routledge MN, Herceg Z, Cuenin C, Derakhshan M, James PT, Monk D, Prentice AM. Environmentally sensitive hotspots in the methylome of the early human embryo. eLife 2022; 11:e72031. [PMID: 35188105 PMCID: PMC8912923 DOI: 10.7554/elife.72031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed three datasets covering two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin-specific methylation and germline differentially methylated regions, supporting a periconceptional environmental influence. Many SoC-associated CpGs overlapped enhancers or sites of active transcription in H1 embryonic stem cells and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental 'hotspots' providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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Affiliation(s)
- Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Ayden Saffari
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Noah J Kessler
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Gririraj R Chandak
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Caroline HD Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General HospitalSouthamptonUnited Kingdom
| | - Prachand Issarapu
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Modupeh Betts
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
- Department of Women and Children's Health, King's College LondonLondonUnited Kingdom
| | - Michael N Routledge
- School of Medicine, University of LeedsLeedsUnited Kingdom
- School of Food and Biological Engineering, Jiangsu UniversityZhenjiangChina
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Maria Derakhshan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - David Monk
- Biomedical Research Centre, University of East AngliaNorwichUnited Kingdom
- Bellvitge Institute for Biomedical ResearchBarcelonaSpain
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
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21
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A Gadd D, I McGeachan R, F Hillary R, L McCartney D, E Harris S, A Sherwood R, Abbott NJ, R Cox S, E Marioni R. The genetic and epigenetic profile of serum S100β in the Lothian Birth Cohort 1936 and its relationship to Alzheimer’s disease. Wellcome Open Res 2022; 6:306. [PMID: 35028426 PMCID: PMC8686327 DOI: 10.12688/wellcomeopenres.17322.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Circulating S100 calcium-binding protein (S100β) is a marker of brain inflammation that has been associated with a range of neurological conditions. To provide insight into the molecular regulation of S100β and its potential causal associations with Alzheimer’s disease, we carried out genome- and epigenome-wide association studies (GWAS/EWAS) of serum S100β levels in older adults and performed Mendelian randomisation with Alzheimer’s disease. Methods: GWAS (N=769, mean age 72.5 years, sd = 0.7) and EWAS (N=722, mean age 72.5 years, sd = 0.7) of S100β levels were performed in participants from the Lothian Birth Cohort 1936. Conditional and joint analysis (COJO) was used to identify independent loci. Expression quantitative trait locus (eQTL) analyses were performed for lead loci that had genome-wide significant associations with S100β. Bidirectional, two-sample Mendelian randomisation was used to test for causal associations between S100β and Alzheimer’s disease. Colocalisation between S100β and Alzheimer’s disease GWAS loci was also examined. Results: We identified 154 SNPs from chromosome 21 that associated (P<5x10-8) with S100β protein levels. The lead variant was located in the S100β gene (rs8128872, P=5.0x10-17). We found evidence that two independent causal variants existed for both transcription of S100β and S100β protein levels in our eQTL analyses. No CpG sites were associated with S100β levels at the epigenome-wide significant level (P<3.6x10-8); the lead probe was cg06833709 (P=5.8x10-6), which mapped to the LGI1 gene. There was no evidence of a causal association between S100β levels and Alzheimer’s disease or vice versa and no evidence for colocalisation between S100β and Alzheimer’s disease loci. Conclusions: These data provide insight into the molecular regulators of S100β levels. This context may aid in understanding the role of S100β in brain inflammation and neurological disease.
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Affiliation(s)
- Danni A Gadd
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Robert I McGeachan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Robert F Hillary
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Daniel L McCartney
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Roy A Sherwood
- Department of Clinical Biochemistry, King's College Hospital NHS Foundation Trust, London, Other (Non-U.S.), SE5 9RS, UK
| | - N Joan Abbott
- Institute of Pharmaceutical Science, King's College London, London, Other (Non-U.S.), WC2R 2LS, UK
| | - Simon R Cox
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Riccardo E Marioni
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
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22
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McCartney DL, Hillary RF, Conole ELS, Banos DT, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Maniega SM, Valdés-Hernández MDC, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. Blood-based epigenome-wide analyses of cognitive abilities. Genome Biol 2022; 23:26. [PMID: 35039062 PMCID: PMC8762878 DOI: 10.1186/s13059-021-02596-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia. RESULTS Using blood-based epigenome-wide analyses of general cognitive function, we show that individual differences in DNA methylation (DNAm) explain 35.0% of the variance in general cognitive function (g). A DNAm predictor explains ~4% of the variance, independently of a polygenic score, in two external cohorts. It also associates with circulating levels of neurology- and inflammation-related proteins, global brain imaging metrics, and regional cortical volumes. CONCLUSIONS As sample sizes increase, the ability to assess cognitive function from DNAm data may be informative in settings where cognitive testing is unreliable or unavailable.
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Affiliation(s)
- Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Eleanor L. S. Conole
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Daniel Trejo Banos
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Robin Flaig
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, Scotland, UK
| | - Susana Muñoz Maniega
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - María del C. Valdés-Hernández
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Mathew A. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Mark E. Bastin
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Joanna M. Wardlaw
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Elliot M. Tucker-Drob
- Department of Psychology, University of Texas, Austin, TX USA
- Population Research Center and Center on Aging and Population Sciences, University of Texas, Austin, TX USA
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | | | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
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23
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A Gadd D, I McGeachan R, F Hillary R, L McCartney D, E Harris S, A Sherwood R, Abbott NJ, R Cox S, E Marioni R. The genetic and epigenetic profile of serum S100β in the Lothian Birth Cohort 1936 and its relationship to Alzheimer's disease. Wellcome Open Res 2022; 6:306. [PMID: 35028426 DOI: 10.12688/wellcomeopenres.17322.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Circulating S100 calcium-binding protein (S100β) is a marker of brain inflammation that has been associated with a range of neurological conditions. To provide insight into the molecular regulation of S100β and its potential causal associations with Alzheimer's disease, we carried out genome- and epigenome-wide association studies (GWAS/EWAS) of serum S100β levels in older adults and performed Mendelian randomisation with Alzheimer's disease. Methods: GWAS (N=769, mean age 72.5 years, sd = 0.7) and EWAS (N=722, mean age 72.5 years, sd = 0.7) of S100β levels were performed in participants from the Lothian Birth Cohort 1936. Conditional and joint analysis (COJO) was used to identify independent loci. Expression quantitative trait locus (eQTL) analyses were performed for lead loci that had genome-wide significant associations with S100β. Bidirectional, two-sample Mendelian randomisation was used to test for causal associations between S100β and Alzheimer's disease. Colocalisation between S100β and Alzheimer's disease GWAS loci was also examined. Results: We identified 154 SNPs from chromosome 21 that associated (P<5x10 -8) with S100β protein levels. The lead variant was located in the S100β gene (rs8128872, P=5.0x10 -17). We found evidence that two independent causal variants existed for both transcription of S100β and S100β protein levels in our eQTL analyses . No CpG sites were associated with S100β levels at the epigenome-wide significant level (P<3.6x10 -8); the lead probe was cg06833709 (P=5.8x10 -6), which mapped to the LGI1 gene. There was no evidence of a causal association between S100β levels and Alzheimer's disease or vice versa and no evidence for colocalisation between S100β and Alzheimer's disease loci. Conclusions: These data provide insight into the molecular regulators of S100β levels. This context may aid in understanding the role of S100β in brain inflammation and neurological disease.
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Affiliation(s)
- Danni A Gadd
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Robert I McGeachan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Robert F Hillary
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Daniel L McCartney
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Roy A Sherwood
- Department of Clinical Biochemistry, King's College Hospital NHS Foundation Trust, London, Other (Non-U.S.), SE5 9RS, UK
| | - N Joan Abbott
- Institute of Pharmaceutical Science, King's College London, London, Other (Non-U.S.), WC2R 2LS, UK
| | - Simon R Cox
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Riccardo E Marioni
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
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24
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Gadd DA, Hillary RF, McCartney DL, Zaghlool SB, Stevenson AJ, Cheng Y, Fawns-Ritchie C, Nangle C, Campbell A, Flaig R, Harris SE, Walker RM, Shi L, Tucker-Drob EM, Gieger C, Peters A, Waldenberger M, Graumann J, McRae AF, Deary IJ, Porteous DJ, Hayward C, Visscher PM, Cox SR, Evans KL, McIntosh AM, Suhre K, Marioni RE. Epigenetic scores for the circulating proteome as tools for disease prediction. eLife 2022; 11:e71802. [PMID: 35023833 PMCID: PMC8880990 DOI: 10.7554/elife.71802] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Protein biomarkers have been identified across many age-related morbidities. However, characterising epigenetic influences could further inform disease predictions. Here, we leverage epigenome-wide data to study links between the DNA methylation (DNAm) signatures of the circulating proteome and incident diseases. Using data from four cohorts, we trained and tested epigenetic scores (EpiScores) for 953 plasma proteins, identifying 109 scores that explained between 1% and 58% of the variance in protein levels after adjusting for known protein quantitative trait loci (pQTL) genetic effects. By projecting these EpiScores into an independent sample (Generation Scotland; n = 9537) and relating them to incident morbidities over a follow-up of 14 years, we uncovered 137 EpiScore-disease associations. These associations were largely independent of immune cell proportions, common lifestyle and health factors, and biological aging. Notably, we found that our diabetes-associated EpiScores highlighted previous top biomarker associations from proteome-wide assessments of diabetes. These EpiScores for protein levels can therefore be a valuable resource for disease prediction and risk stratification.
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Affiliation(s)
- Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Shaza B Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education CityDohaQatar
- Computer Engineering Department, Virginia TechBlacksburgUnited States
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Chloe Fawns-Ritchie
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Robin Flaig
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Sarah E Harris
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
- Lothian Birth Cohorts, University of EdinburghEdinburghUnited Kingdom
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor’s Building, University of EdinburghEdinburghUnited Kingdom
| | - Liu Shi
- Department of Psychiatry, University of OxfordOxfordUnited Kingdom
| | - Elliot M Tucker-Drob
- Department of Psychology, The University of Texas at AustinAustinUnited States
- Population Research Center, The University of Texas at AustinAustinUnited States
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart AllianceMunichGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart AllianceMunichGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart AllianceMunichGermany
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff InstituteBad NauheimGermany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Max Planck Institute of Heart and Lung ResearchBad NauheimGermany
| | - Allan F McRae
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Ian J Deary
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
- Lothian Birth Cohorts, University of EdinburghEdinburghUnited Kingdom
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Simon R Cox
- Department of Psychology, University of EdinburghEdinburghUnited Kingdom
- Lothian Birth Cohorts, University of EdinburghEdinburghUnited Kingdom
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh HospitalEdinburghUnited Kingdom
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education CityDohaQatar
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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25
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Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol 2022; 14:1295-1310. [PMID: 36038072 PMCID: PMC9703134 DOI: 10.1016/j.jcmgh.2022.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. METHODS Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. RESULTS Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. CONCLUSIONS Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.
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Affiliation(s)
- Rachel D Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - April R Foster
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sophia Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Aurélie Cenier
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kai O Hensel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany
| | - Rebecca Harris
- Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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26
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Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, van IJzendoorn MH, Uitterlinden AG, Jaddoe VWV, Haley C, McIntosh AM, Evans KL, Murray A, Räikkönen K, Lahti J, Nohr EA, Sørensen TIA, Hansen T, Morgen CS, Binder EB, Lucae S, Gonzalez JR, Bustamante M, Sunyer J, Holloway JW, Karmaus W, Zhang H, Deary IJ, Wray NR, Starr JM, Beekman M, van Heemst D, Slagboom PE, Morange PE, Trégouët DA, Veldink JH, Davies GE, de Geus EJC, Boomsma DI, Vonk JM, Brunekreef B, Koppelman GH, Alarcón-Riquelme ME, Huang RC, Pennell CE, van Meurs J, Ikram MA, Hughes AD, Tillin T, Chaturvedi N, Pausova Z, Paus T, Spector TD, Kumari M, Schalkwyk LC, Visscher PM, Davey Smith G, Bock C, Gaunt TR, Bell JT, Heijmans BT, Mill J, Relton CL. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nat Genet 2021; 53:1311-1321. [PMID: 34493871 PMCID: PMC7612069 DOI: 10.1038/s41588-021-00923-x] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022]
Abstract
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.
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Affiliation(s)
- Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Koen F Dekkers
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | - René Luijk
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Gemma Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Biostatistics and Health Informatics, King's College London, London, UK
| | - Wendy L McArdle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Karen M Ho
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Chronic Disease Epidemiology unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Soriano-Tárraga
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Karen Sugden
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Silva Kasela
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexia Cardona
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Felix R Day
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giovanni Cugliari
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Michael Lerro
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Richa Gupta
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pooja Mandaviya
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Toni-Kim Clarke
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Vanessa Schmoll
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Yvonne Awaloff
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Marine Germain
- INSERM UMR_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Dylan Aïssi
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Ramona Zwamborn
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kristel van Eijk
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annelot Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
- CiiM and TWINCORE, Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Guillermo Barturen
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Francesc Català-Moll
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Martin Kerick
- Instituto de Parasitología y Biomedicina López Neyra, CSIC, Granada, Spain
| | - Carol Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Phillip Melton
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
- School of Global Population Health, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Manon Bernard
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | | | - Chris Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
| | - Ammar Al Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
- United Kingdom Dementia Research Institute, King's College London, London, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jaume Roquer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford, UK
| | | | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Terrie E Moffitt
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Carlotta Sacerdote
- Italian Institute for Genomic Medicine, Turin, Italy
- Piemonte Centre for Cancer Prevention, Turin, Italy
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico II University, Naples, Italy
| | - Avshalom Caspi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Miina Ollikainen
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Clinical, Educational and Health Psychology, Division on Psychology and Language Sciences, Faculty of Brain Sciences, University College London, London, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Alison Murray
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical research, University of Southern Denmark, Odense, Denmark
- Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health (Section of Epidemiology), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla S Morgen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - 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
| | - Susanne Lucae
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Juan Ramon Gonzalez
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Sunyer
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Universiteit Utrecht, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Marta E Alarcón-Riquelme
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | | | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Tomas Paus
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, Canada
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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27
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Hillary RF, Stevenson AJ, Cox SR, McCartney DL, Harris SE, Seeboth A, Higham J, Sproul D, Taylor AM, Redmond P, Corley J, Pattie A, Hernández MDCV, Muñoz-Maniega S, Bastin ME, Wardlaw JM, Horvath S, Ritchie CW, Spires-Jones TL, McIntosh AM, Evans KL, Deary IJ, Marioni RE. An epigenetic predictor of death captures multi-modal measures of brain health. Mol Psychiatry 2021; 26:3806-3816. [PMID: 31796892 PMCID: PMC8550950 DOI: 10.1038/s41380-019-0616-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 11/08/2022]
Abstract
Individuals of the same chronological age exhibit disparate rates of biological ageing. Consequently, a number of methodologies have been proposed to determine biological age and primarily exploit variation at the level of DNA methylation (DNAm). A novel epigenetic clock, termed 'DNAm GrimAge' has outperformed its predecessors in predicting the risk of mortality as well as many age-related morbidities. However, the association between DNAm GrimAge and cognitive or neuroimaging phenotypes remains unknown. We explore these associations in the Lothian Birth Cohort 1936 (n = 709, mean age 73 years). Higher DNAm GrimAge was strongly associated with all-cause mortality over the eighth decade (Hazard Ratio per standard deviation increase in GrimAge: 1.81, P < 2.0 × 10-16). Higher DNAm GrimAge was associated with lower age 11 IQ (β = -0.11), lower age 73 general cognitive ability (β = -0.18), decreased brain volume (β = -0.25) and increased brain white matter hyperintensities (β = 0.17). There was tentative evidence for a longitudinal association between DNAm GrimAge and cognitive decline from age 70 to 79. Sixty-nine of 137 health- and brain-related phenotypes tested were significantly associated with GrimAge. Adjusting all models for childhood intelligence attenuated to non-significance a small number of associations (12/69 associations; 6 of which were cognitive traits), but not the association with general cognitive ability (33.9% attenuation). Higher DNAm GrimAge associates with lower cognitive ability and brain vascular lesions in older age, independently of early-life cognitive ability. This epigenetic predictor of mortality associates with different measures of brain health and may aid in the prediction of age-related cognitive decline.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Anne Seeboth
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jon Higham
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Adele M Taylor
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Janie Corley
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Alison Pattie
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Maria Del C Valdés Hernández
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Neuroimaging Sciences, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Susana Muñoz-Maniega
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Neuroimaging Sciences, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark E Bastin
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Neuroimaging Sciences, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Joanna M Wardlaw
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Neuroimaging Sciences, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
| | - Craig W Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Tara L Spires-Jones
- UK Dementia Research Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
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28
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Rossetti MF, Canesini G, Lorenz V, Milesi MM, Varayoud J, Ramos JG. Epigenetic Changes Associated With Exposure to Glyphosate-Based Herbicides in Mammals. Front Endocrinol (Lausanne) 2021; 12:671991. [PMID: 34093442 PMCID: PMC8177816 DOI: 10.3389/fendo.2021.671991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/03/2021] [Indexed: 01/01/2023] Open
Abstract
Glyphosate is a phosphonomethyl amino acid derivative present in a number of non-selective and systemic herbicides. During the last years the use of glyphosate-based herbicide (GBH) has been increasing exponentially around the world, including Argentina. This fact added to the detection of glyphosate, and its main metabolite, amino methylphosphonic acid (AMPA), in environmental matrices such as soil, sediments, and food, has generated great concern about its risks for humans, animals, and environment. During the last years, there were controversy and intense debate regarding the toxicological effects of these compounds associated with the endocrine system, cancer, reproduction, and development. The mechanisms of action of GBH and their metabolites are still under investigation, although recent findings have shown that they could comprise epigenetic modifications. These are reversible mechanisms linked to tissue-specific silencing of gene expression, genomic imprinting, and tumor growth. Particularly, glyphosate, GBH, and AMPA have been reported to produce changes in global DNA methylation, methylation of specific genes, histone modification, and differential expression of non-coding RNAs in human cells and rodents. Importantly, the epigenome could be heritable and could lead to disease long after the exposure has ended. This mini-review summarizes the epigenetic changes produced by glyphosate, GBHs, and AMPA in humans and rodents and proposes it as a potential mechanism of action through which these chemical compounds could alter body functions.
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Affiliation(s)
- María Florencia Rossetti
- Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Guillermina Canesini
- Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Cátedra de Patología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Virginia Lorenz
- Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - María Mercedes Milesi
- Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jorgelina Varayoud
- Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Cátedra de Fisiología Humana, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jorge Guillermo Ramos
- Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
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29
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Gadd DA, Stevenson AJ, Hillary RF, McCartney DL, Wrobel N, McCafferty S, Murphy L, Russ TC, Harris SE, Redmond P, Taylor AM, Smith C, Rose J, Millar T, Spires-Jones TL, Cox SR, Marioni RE. Epigenetic predictors of lifestyle traits applied to the blood and brain. Brain Commun 2021; 3:fcab082. [PMID: 34041477 PMCID: PMC8134833 DOI: 10.1093/braincomms/fcab082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/02/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
Modifiable lifestyle factors influence the risk of developing many neurological diseases. These factors have been extensively linked with blood-based genome-wide DNA methylation, but it is unclear if the signatures from blood translate to the target tissue of interest-the brain. To investigate this, we apply blood-derived epigenetic predictors of four lifestyle traits to genome-wide DNA methylation from five post-mortem brain regions and the last blood sample prior to death in 14 individuals in the Lothian Birth Cohort 1936. Using these matched samples, we found that correlations between blood and brain DNA methylation scores for smoking, high-density lipoprotein cholesterol, alcohol and body mass index were highly variable across brain regions. Smoking scores in the dorsolateral prefrontal cortex had the strongest correlations with smoking scores in blood (r = 0.5, n = 14, P = 0.07) and smoking behaviour (r = 0.56, n = 9, P = 0.12). This was also the brain region which exhibited the largest correlations for DNA methylation at site cg05575921 - the single strongest correlate of smoking in blood-in relation to blood (r = 0.61, n = 14, P = 0.02) and smoking behaviour (r = -0.65, n = 9, P = 0.06). This suggested a particular vulnerability to smoking-related differential methylation in this region. Our work contributes to understanding how lifestyle factors affect the brain and suggest that lifestyle-related DNA methylation is likely to be both brain region dependent and in many cases poorly proxied for by blood. Though these pilot data provide a rarely-available opportunity for the comparison of methylation patterns across multiple brain regions and the blood, due to the limited sample size available our results must be considered as preliminary and should therefore be used as a basis for further investigation.
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Affiliation(s)
- Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sarah McCafferty
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Tom C Russ
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh EH8 9JZ, UK
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Paul Redmond
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Adele M Taylor
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Colin Smith
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Jamie Rose
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Tracey Millar
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Tara L Spires-Jones
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh 2XU, UK
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30
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Nabais MF, Laws SM, Lin T, Vallerga CL, Armstrong NJ, Blair IP, Kwok JB, Mather KA, Mellick GD, Sachdev PS, Wallace L, Henders AK, Zwamborn RAJ, Hop PJ, Lunnon K, Pishva E, Roubroeks JAY, Soininen H, Tsolaki M, Mecocci P, Lovestone S, Kłoszewska I, Vellas B, Furlong S, Garton FC, Henderson RD, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson G, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Anderson TJ, Bentley SR, Dalrymple-Alford J, Fowder J, Gratten J, Halliday G, Hickie IB, Kennedy M, Lewis SJG, Montgomery GW, Pearson J, Pitcher TL, Silburn P, Zhang F, Visscher PM, Yang J, Stevenson AJ, Hillary RF, Marioni RE, Harris SE, Deary IJ, Jones AR, Shatunov A, Iacoangeli A, van Rheenen W, van den Berg LH, Shaw PJ, Shaw CE, Morrison KE, Al-Chalabi A, Veldink JH, Hannon E, Mill J, Wray NR, McRae AF. Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol 2021; 22:90. [PMID: 33771206 PMCID: PMC8004462 DOI: 10.1186/s13059-021-02275-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment. In this study, we aim to identify shared blood DNAm differences between controls and people with Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. RESULTS We use a mixed-linear model method (MOMENT) that accounts for the effect of (un)known confounders, to test for the association of each DNAm site with each disorder. While only three probes are found to be genome-wide significant in each MOMENT association analysis of amyotrophic lateral sclerosis and Parkinson's disease (and none with Alzheimer's disease), a fixed-effects meta-analysis of the three disorders results in 12 genome-wide significant differentially methylated positions. Predicted immune cell-type proportions are disrupted across all neurodegenerative disorders. Protein inflammatory markers are correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy aging cohort. In contrast, they are not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights. CONCLUSIONS We identify shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.
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Grants
- U24 AG021886 NIA NIH HHS
- U01 AG016976 NIA NIH HHS
- Department of Health
- U01 AG024904 NIA NIH HHS
- 108890/Z/15/Z Wellcome Trust
- 503480 Medical Research Council
- TURNER/OCT15/972-797 Motor Neurone Disease Association
- U01 AG032984 NIA NIH HHS
- R01 HL105756 NHLBI NIH HHS
- 082604/2/07/Z Wellcome Trust
- R01 AG033193 NIA NIH HHS
- National Health and Medical Research Council
- Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge
- Medical Research Council (UK)
- Economic and Social Research Council
- National Institute for Health Research (NIHR)
- the European Community’s Health Seventh Framework Programme
- Horizon 2020 Programme
- MND Association and the Wellcome Trust.
- European Research Council (ERC)
- EU Joint Programme – Neurodegenerative Disease Research ()
- EU Joint Programme - Neurodegenerative Disease Research (JPND)
- Australian Research Council
- Mater Foundation
- ForeFront - NHMRC
- Australian National Health and Medical Research Council
- University of Otago Research Grant, together with financial support from the Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd
- National Health and Medical Research Council and the Dementia Collaborative Research Centres program (DCRC2), as well as funding from the Science and Industry Endowment Fund (SIEF) and the Cooperative Research Centre (CRC) for Mental Health – funded throug
- EU Joint Programme - Neurodegenerative Disease Research (JPND), co-funded through the Australian National Health and Medical Research (NHMRC) Council, Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge,
- EU Joint Programme - Neurodegenerative Disease Research (JPND), United Kingdom Medical Research Council, Economic and Social Research Council, Motor Neuro Disease Association (GB), National Institute for Health Research (NIHR) Biomedical Research Centre at
- EU Joint Programme - Neurodegenerative Disease Research (JPND), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, PPP Allowance made available by Health~Holland, Top Sector Life Sciences & Health, Unit
- National Health and Medical Research Council, Australian Research Council, Mater Foundation,
- Australian National Health and Medical Research Council (
- University of Otago Research Grant, Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd., National Health and Medical Research Counc
- EFPIA companies and SMEs as part of InnoMed (Innovative Medicines in Europe), an Integrated Project funded by the European Union of the Sixth Framework program
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Simon M Laws
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Costanza L Vallerga
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Internal Medicine, Erasmus MC, University Medical Center, 3015GD, Rotterdam, The Netherlands
| | | | - Ian P Blair
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - John B Kwok
- Brain and Mind Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW, 2031, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuropsychiatric Institute, The Prince of Wales Hospital, UNSW, Randwick, NSW, 2031, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ramona A J Zwamborn
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Paul J Hop
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Ehsan Pishva
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Patrizia Mecocci
- Department of Medicine, Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | | | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fleur C Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert D Henderson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC, 3195, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA, 6150, Australia
- Notre Dame University, Fremantle, WA, 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 6150, Australia
| | - Shyuan T Ngo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW, 2139, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tim J Anderson
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Steven R Bentley
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - John Dalrymple-Alford
- New Zealand Brain Research Institute, Christchurch, New Zealand
- School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand
| | - Javed Fowder
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Jacob Gratten
- Mater Research, Translational Research Institute, Brisbane, Australia
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Glenda Halliday
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ian B Hickie
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Martin Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simon J G Lewis
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - John Pearson
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Toni L Pitcher
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Peter Silburn
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Cristopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Stevenson AJ, Gadd DA, Hillary RF, McCartney DL, Campbell A, Walker RM, Evans KL, Harris SE, Spires-Jones TL, McRae AF, Visscher PM, McIntosh AM, Deary IJ, Marioni RE. Creating and validating a DNA methylation-based proxy for interleukin-6. J Gerontol A Biol Sci Med Sci 2021; 76:2284-2292. [PMID: 33595649 PMCID: PMC8599002 DOI: 10.1093/gerona/glab046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 01/28/2023] Open
Abstract
Background Studies evaluating the relationship between chronic inflammation and cognitive functioning have produced heterogeneous results. A potential reason for this is the variability of inflammatory mediators which could lead to misclassifications of individuals’ persisting levels of inflammation. DNA methylation (DNAm) has shown utility in indexing environmental exposures and could be leveraged to provide proxy signatures of chronic inflammation. Method We conducted an elastic net regression of interleukin-6 (IL-6) in a cohort of 875 older adults (Lothian Birth Cohort 1936; mean age: 70 years) to develop a DNAm-based predictor. The predictor was tested in an independent cohort (Generation Scotland; N = 7028 [417 with measured IL-6], mean age: 51 years). Results A weighted score from 35 CpG sites optimally predicted IL-6 in the independent test set (Generation Scotland; R2 = 4.4%, p = 2.1 × 10−5). In the independent test cohort, both measured IL-6 and the DNAm proxy increased with age (serum IL-6: n = 417, β = 0.02, SE = 0.004, p = 1.3 × 10−7; DNAm IL-6 score: N = 7028, β = 0.02, SE = 0.0009, p < 2 × 10−16). Serum IL-6 did not associate with cognitive ability (n = 417, β = −0.06, SE = 0.05, p = .19); however, an inverse association was identified between the DNAm score and cognitive functioning (N = 7028, β = −0.16, SE = 0.02, pFDR < 2 × 10−16). Conclusions These results suggest methylation-based predictors can be used as proxies for inflammatory markers, potentially allowing for further insight into the relationship between inflammation and pertinent health outcomes.
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Affiliation(s)
- Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Clinical Brain Sciences, Chancellor's Building, Little France Crescent, Edinburgh BioQuarter, Edinburgh
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tara L Spires-Jones
- UK Dementia Research Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK.,Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
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32
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Epigenetic Markers Associated with Schistosomiasis. Helminthologia 2021; 58:28-40. [PMID: 33664616 PMCID: PMC7912237 DOI: 10.2478/helm-2021-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
It is important to consider the use of the epigenome as source of complementary data for genome knowledge, which is suitable for the diagnosis of schistosomiasis. Usually, a laboratory diagnosis of schistosomiasis is performed by means of 1. Egg detection in the stool or urine by microscopy remains with limited sensitivity; 2. Immunological screening, in which positivity persists after treatment, and 3. Molecular appraisals prevail over the disadvantages of the currently used methods. In this sense, molecular methodologies are being developed based on epigenetic biomarkers, aiming to improve the diagnosis of the disease and clinical treatment as early as possible to prevent the occurrence of serious liver damage.
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33
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Mulder RH, Neumann A, Cecil CAM, Walton E, Houtepen LC, Simpkin AJ, Rijlaarsdam J, Heijmans BT, Gaunt TR, Felix JF, Jaddoe VWV, Bakermans-Kranenburg MJ, Tiemeier H, Relton CL, van IJzendoorn MH, Suderman M. Epigenome-wide change and variation in DNA methylation in childhood: trajectories from birth to late adolescence. Hum Mol Genet 2021; 30:119-134. [PMID: 33450751 PMCID: PMC8033147 DOI: 10.1093/hmg/ddaa280] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/03/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
DNA methylation (DNAm) is known to play a pivotal role in childhood health and development, but a comprehensive characterization of genome-wide DNAm trajectories across this age period is currently lacking. We have therefore performed a series of epigenome-wide association studies in 5019 blood samples collected at multiple time-points from birth to late adolescence from 2348 participants of two large independent cohorts. DNAm profiles of autosomal CpG sites (CpGs) were generated using the Illumina Infinium HumanMethylation450 BeadChip. Change over time was widespread, observed at over one-half (53%) of CpGs. In most cases, DNAm was decreasing (36% of CpGs). Inter-individual variation in linear trajectories was similarly widespread (27% of CpGs). Evidence for non-linear change and inter-individual variation in non-linear trajectories was somewhat less common (11 and 8% of CpGs, respectively). Very little inter-individual variation in change was explained by sex differences (0.4% of CpGs) even though sex-specific DNAm was observed at 5% of CpGs. DNAm trajectories were distributed non-randomly across the genome. For example, CpGs with decreasing DNAm were enriched in gene bodies and enhancers and were annotated to genes enriched in immune-developmental functions. In contrast, CpGs with increasing DNAm were enriched in promoter regions and annotated to genes enriched in neurodevelopmental functions. These findings depict a methylome undergoing widespread and often non-linear change throughout childhood. They support a developmental role for DNA methylation that extends beyond birth into late adolescence and has implications for understanding life-long health and disease. DNAm trajectories can be visualized at http://epidelta.mrcieu.ac.uk.
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Affiliation(s)
- Rosa H Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Institute of Education and Child Studies, Leiden University, Leiden, The Netherlands
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Psychology, Institute of Psychology, Psychiatry and Neuroscience, King's College London, London, UK
| | - Esther Walton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Department of Psychology, University of Bath, Bath, UK
| | - Lotte C Houtepen
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew J Simpkin
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Jolien Rijlaarsdam
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands.,School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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Hazard D, Plisson-Petit F, Moreno-Romieux C, Fabre S, Drouilhet L. Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep. Front Genet 2021; 11:616960. [PMID: 33424937 PMCID: PMC7786236 DOI: 10.3389/fgene.2020.616960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 01/21/2023] Open
Abstract
Recent studies showed that epigenetic marks, including DNA methylation, influence production and adaptive traits in plants and animals. So far, most studies dealing with genetics and epigenetics considered DNA methylation sites independently. However, the genetic basis of the global DNA methylation rate (GDMR) remains unknown. The main objective of the present study was to investigate genetic determinism of GDMR in sheep. The experiment was conducted on 1,047 Romane sheep allocated into 10 half-sib families. After weaning, all the lambs were phenotyped for global GDMR in blood as well as for production and adaptive traits. GDMR was measured by LUminometric Methylation Analysis (LUMA) using a pyrosequencing approach. Association analyses were conducted on some of the lambs (n = 775) genotyped by using the Illumina OvineSNP50 BeadChip. Blood GDMR varied among the animals (average 70.7 ± 6.0%). Female lambs had significantly higher GDMR than male lambs. Inter-individual variability of blood GDMR had an additive genetic component and heritability was moderate (h2 = 0.20 ± 0.05). No significant genetic correlation was found between GDMR and growth or carcass traits, birthcoat, or social behaviors. Association analyses revealed 28 QTLs associated with blood GDMR. Seven genomic regions on chromosomes 1, 5, 11, 17, 24, and 26 were of most interest due to either high significant associations with GDMR or to the relevance of genes located close to the QTLs. QTL effects were moderate. Genomic regions associated with GDMR harbored several genes not yet described as being involved in DNA methylation, but some are already known to play an active role in gene expression. In addition, some candidate genes, CHD1, NCO3A, KDM8, KAT7, and KAT6A have previously been described to be involved in epigenetic modifications. In conclusion, the results of the present study indicate that blood GDMR in domestic sheep is under polygenic influence and provide new insights into DNA methylation genetic determinism.
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Affiliation(s)
- Dominique Hazard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | | | | | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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35
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Terzikhan N, Xu H, Edris A, Bracke KR, Verhamme FM, Stricker BH, Dupuis J, Lahousse L, O'Connor GT, Brusselle GG. Epigenome-wide association study on diffusing capacity of the lung. ERJ Open Res 2021; 7:00567-2020. [PMID: 33748261 PMCID: PMC7957297 DOI: 10.1183/23120541.00567-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Epigenetics may play an important role in the pathogenesis of lung diseases. However, little is known about the epigenetic factors that influence impaired gas exchange at the lung. AIM To identify the epigenetic signatures of the diffusing capacity of the lung measured by carbon monoxide uptake (the diffusing capacity of the lung for carbon monoxide (D LCO)). METHODS An epigenome-wide association study (EWAS) was performed on diffusing capacity, measured by carbon monoxide uptake (D LCO) and per alveolar volume (V A) (as D LCO/V A), using the single-breath technique in 2674 individuals from two population-based cohort studies. These were the Rotterdam Study (RS, the "discovery panel") and the Framingham Heart Study (FHS, the "replication panel"). We assessed the clinical relevance of our findings by investigating the identified sites in whole blood and by lung tissue specific gene expression. RESULTS We identified and replicated two CpG sites (cg05575921 and cg05951221) that were significantly associated with D LCO/V A and one (cg05575921) suggestively associated with D LCO. Furthermore, we found a positive association between aryl hydrocarbon receptor repressor (AHRR) gene (cg05575921) hypomethylation and gene expression of exocyst complex component 3 (EXOC3) in whole blood. We confirmed that the expression of EXOC3 in lung tissue is positively associated with D LCO/V A and D LCO. CONCLUSIONS We report on epigenome-wide associations with diffusing capacity in the general population. Our results suggest EXOC3 to be an excellent candidate, through which smoking-induced hypomethylation of AHRR might affect pulmonary gas exchange.
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Affiliation(s)
- Natalie Terzikhan
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Dept of Epidemiology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
- These authors contributed equally
| | - Hanfei Xu
- Dept of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- These authors contributed equally
| | - Ahmed Edris
- Dept of Epidemiology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
- Dept of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Ken R. Bracke
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Fien M. Verhamme
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bruno H.C. Stricker
- Dept of Epidemiology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Josée Dupuis
- Dept of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- These authors contributed equally
| | - Lies Lahousse
- Dept of Epidemiology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
- Dept of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- These authors contributed equally
| | - George T. O'Connor
- Pulmonary Center, Boston University Schools of Medicine and Public Health, Boston, MA, USA
- These authors contributed equally
| | - Guy G. Brusselle
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Dept of Epidemiology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
- Dept of Respiratory Medicine, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
- These authors contributed equally
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36
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Barth E, Sieber P, Stark H, Schuster S. Robustness during Aging-Molecular Biological and Physiological Aspects. Cells 2020; 9:E1862. [PMID: 32784503 PMCID: PMC7465392 DOI: 10.3390/cells9081862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.
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Affiliation(s)
- Emanuel Barth
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Patricia Sieber
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Heiko Stark
- Institute of Zoology and Evolutionary Research with Phyletic Museum, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Stefan Schuster
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
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37
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Wagner J, Orth U, Bleidorn W, Hopwood CJ, Kandler C. Toward an Integrative Model of Sources of Personality Stability and Change. CURRENT DIRECTIONS IN PSYCHOLOGICAL SCIENCE 2020. [DOI: 10.1177/0963721420924751] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
There is now compelling evidence that people’s typical patterns of thinking, feeling, striving, and behaving are both consistent and malleable. Therefore, researchers have begun to examine the distinct sources of personality stability and change. In this article, we discuss traditional classifications of sources, review key findings, and highlight limitations and open questions in research on personality stability and change. We conclude by describing an integrative model and by outlining important directions for future research.
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Affiliation(s)
| | - Ulrich Orth
- Department of Psychology, University of Bern
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38
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The multifaceted functional role of DNA methylation in immune-mediated rheumatic diseases. Clin Rheumatol 2020; 40:459-476. [PMID: 32613397 DOI: 10.1007/s10067-020-05255-5] [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] [Received: 04/03/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
Genomic predisposition cannot explain the onset of complex diseases, as well illustrated by the largely incomplete concordance among monozygotic twins. Epigenetic mechanisms, including DNA methylation, chromatin remodelling and non-coding RNA, are considered to be the link between environmental stimuli and disease onset on a permissive genetic background in autoimmune and chronic inflammatory diseases. The paradigmatic cases of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc), Sjogren's syndrome (SjS) and type-1 diabetes (T1D) share the loss of immunological tolerance to self-antigen influenced by several factors, with a largely incomplete role of individual genomic susceptibility. The most widely investigated epigenetic mechanism is DNA methylation which is associated with gene silencing and is due to the binding of methyl-CpG binding domain (MBD)-containing proteins, such as MECP2, to 5-methylcytosine (5mC). Indeed, a causal relationship occurs between DNA methylation and transcription factors occupancy and recruitment at specific genomic locus. In most cases, the results obtained in different studies are controversial in terms of DNA methylation comparison while fascinating evidence comes from the comparison of the epigenome in clinically discordant monozygotic twins. In this manuscript, we will review the mechanisms of epigenetics and DNA methylation changes in specific immune-mediated rheumatic diseases to highlight remaining unmet needs and to identify possible shared mechanisms beyond different tissue involvements with common therapeutic opportunities. Key Points • DNA methylation has a crucial role in regulating and tuning the immune system. • Evidences suggest that dysregulation of DNA methylation is pivotal in the context of immune-mediated rheumatic diseases. • DNA methylation dysregulation in FOXP3 and interferons-related genes is shared within several autoimmune diseases. • DNA methylation is an attractive marker for diagnosis and therapy.
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39
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Taylor AM, Ritchie SJ, Madden C, Deary IJ. Associations between Brief Resilience Scale scores and ageing-related domains in the Lothian Birth Cohort 1936. Psychol Aging 2020; 35:329-344. [PMID: 31682139 PMCID: PMC7161361 DOI: 10.1037/pag0000419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/07/2023]
Abstract
[Correction Notice: An Erratum for this article was reported online in Psychology and Aging on Mar 5 2020 (see record 2020-16850-001). This article should have been published under the terms of the Creative Commons Attribution License (CC BY 3.0). Therefore, the article was amended to list the authors as copyright holders, and information about the terms of the CC BY 3.0 was added to the author note. In addition, the article is now open access. All versions of this article have been corrected.] It is unclear how scores on self-report resilience scales relate to key ageing-related domains in older age and if they truly measure resilience. We examined antecedents and outcomes of age-76 Brief Resilience Scale (BRS) scores in participants of the Lothian Birth Cohort 1936 (n = 655). We found bivariate associations between age-76 BRS scores and ageing-relevant antecedent variables measured at least 3 years earlier, from domains of cognitive ability, physical fitness, and wellbeing and, additionally, sociodemographics and personality (absolute r's from .082 to .49). Biological health variables were not associated with BRS scores. Age-73 cognitive ability (largest β = 0.14), physical fitness (largest β = 0.084), and wellbeing variables (largest β = 0.26) made positive independent contributions to age-76 BRS scores in multivariate models. In a conservative model including all variables as covariates, corrected for multiple comparisons, only emotional stability (neuroticism) significantly independently contributed to BRS score (β = 0.33). An exploratory backward elimination model indicated more wellbeing and personality associates of BRS scores (βs from .087 to .32). We used latent difference score modeling to assess outcomes of BRS scores; we examined associations between age-76 BRS and change in latent factors of age-related domains between age 76 and 79. Whereas BRS scores were related cross-sectionally to levels of latent cognitive ability (r = .19), physical fitness (r = .20), and wellbeing (r = .60) factors, they were not related to declines in these domains. The independence of the BRS construct from established wellbeing and personality factors is unclear. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
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Affiliation(s)
| | | | | | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology
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40
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Westerman K, Fernández‐Sanlés A, Patil P, Sebastiani P, Jacques P, Starr JM, J. Deary I, Liu Q, Liu S, Elosua R, DeMeo DL, Ordovás JM. Epigenomic Assessment of Cardiovascular Disease Risk and Interactions With Traditional Risk Metrics. J Am Heart Assoc 2020; 9:e015299. [PMID: 32308120 PMCID: PMC7428544 DOI: 10.1161/jaha.119.015299] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/10/2020] [Indexed: 12/16/2022]
Abstract
Background Epigenome-wide association studies for cardiometabolic risk factors have discovered multiple loci associated with incident cardiovascular disease (CVD). However, few studies have sought to directly optimize a predictor of CVD risk. Furthermore, it is challenging to train multivariate models across multiple studies in the presence of study- or batch effects. Methods and Results Here, we analyzed existing DNA methylation data collected using the Illumina HumanMethylation450 microarray to create a predictor of CVD risk across 3 cohorts: Women's Health Initiative, Framingham Heart Study Offspring Cohort, and Lothian Birth Cohorts. We trained Cox proportional hazards-based elastic net regressions for incident CVD separately in each cohort and used a recently introduced cross-study learning approach to integrate these individual scores into an ensemble predictor. The methylation-based risk score was associated with CVD time-to-event in a held-out fraction of the Framingham data set (hazard ratio per SD=1.28, 95% CI, 1.10-1.50) and predicted myocardial infarction status in the independent REGICOR (Girona Heart Registry) data set (odds ratio per SD=2.14, 95% CI, 1.58-2.89). These associations remained after adjustment for traditional cardiovascular risk factors and were similar to those from elastic net models trained on a directly merged data set. Additionally, we investigated interactions between the methylation-based risk score and both genetic and biochemical CVD risk, showing preliminary evidence of an enhanced performance in those with less traditional risk factor elevation. Conclusions This investigation provides proof-of-concept for a genome-wide, CVD-specific epigenomic risk score and suggests that DNA methylation data may enable the discovery of high-risk individuals who would be missed by alternative risk metrics.
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Affiliation(s)
- Kenneth Westerman
- JM‐USDA Human Nutrition Research Center on Aging at Tufts UniversityBostonMA
| | - Alba Fernández‐Sanlés
- Cardiovascular Epidemiology and Genetics Research GroupREGICOR Study GroupIMIM (Hospital del Mar Medical Research Institute)BarcelonaCataloniaSpain
- Pompeu Fabra University (UPF)BarcelonaCataloniaSpain
| | - Prasad Patil
- Department of BiostatisticsBoston University School of Public HealthBostonMA
| | - Paola Sebastiani
- Department of BiostatisticsBoston University School of Public HealthBostonMA
| | - Paul Jacques
- JM‐USDA Human Nutrition Research Center on Aging at Tufts UniversityBostonMA
| | - John M. Starr
- Department of PsychologyUniversity of EdinburghUnited Kingdom
- Centre for Cognitive Ageing and Cognitive EpidemiologyUniversity of EdinburghUnited Kingdom
| | - Ian J. Deary
- Department of PsychologyUniversity of EdinburghUnited Kingdom
- Centre for Cognitive Ageing and Cognitive EpidemiologyUniversity of EdinburghUnited Kingdom
| | - Qing Liu
- Department of EpidemiologyBrown University School of Public HealthProvidenceRI
| | - Simin Liu
- Department of EpidemiologyBrown University School of Public HealthProvidenceRI
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research GroupREGICOR Study GroupIMIM (Hospital del Mar Medical Research Institute)BarcelonaCataloniaSpain
- CIBER Cardiovascular Diseases (CIBERCV)MadridSpain
- Medicine DepartmentMedical SchoolUniversity of Vic‐Central University of Catalonia (UVic‐UCC)VicCataloniaSpain
| | - Dawn L. DeMeo
- Channing Division of Network MedicineDepartment of MedicineBrigham and Women’s HospitalBostonMA
| | - José M. Ordovás
- JM‐USDA Human Nutrition Research Center on Aging at Tufts UniversityBostonMA
- IMDEA AlimentaciónCEIUAMMadridSpain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC)MadridSpain
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41
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Seeboth A, McCartney DL, Wang Y, Hillary RF, Stevenson AJ, Walker RM, Campbell A, Evans KL, McIntosh AM, Hägg S, Deary IJ, Marioni RE. DNA methylation outlier burden, health, and ageing in Generation Scotland and the Lothian Birth Cohorts of 1921 and 1936. Clin Epigenetics 2020; 12:49. [PMID: 32216821 PMCID: PMC7098133 DOI: 10.1186/s13148-020-00838-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND DNA methylation outlier burden has been suggested as a potential marker of biological age. An outlier is typically defined as DNA methylation levels at any one CpG site that are three times beyond the inter-quartile range from the 25th or 75th percentiles compared to the rest of the population. DNA methylation outlier burden (the number of such outlier sites per individual) increases exponentially with age. However, these findings have been observed in small samples. RESULTS Here, we showed an association between age and log10-transformed DNA methylation outlier burden in a large cross-sectional cohort, the Generation Scotland Family Health Study (N = 7010, β = 0.0091, p < 2 × 10-16), and in two longitudinal cohort studies, the Lothian Birth Cohorts of 1921 (N = 430, β = 0.033, p = 7.9 × 10-4) and 1936 (N = 898, β = 0.0079, p = 0.074). Significant confounders of both cross-sectional and longitudinal associations between outlier burden and age included white blood cell proportions, body mass index (BMI), smoking, and batch effects. In Generation Scotland, the increase in epigenetic outlier burden with age was not purely an artefact of an increase in DNA methylation level variability with age (epigenetic drift). Log10-transformed DNA methylation outlier burden in Generation Scotland was not related to self-reported, or family history of, age-related diseases, and it was not heritable (SNP-based heritability of 4.4%, p = 0.18). Finally, DNA methylation outlier burden was not significantly related to survival in either of the Lothian Birth Cohorts individually or in the meta-analysis after correction for multiple testing (HRmeta = 1.12; 95% CImeta = [1.02; 1.21]; pmeta = 0.021). CONCLUSIONS These findings suggest that, while it does not associate with ageing-related health outcomes, DNA methylation outlier burden does track chronological ageing and may also relate to survival. DNA methylation outlier burden may thus be useful as a marker of biological ageing.
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Affiliation(s)
- Anne Seeboth
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
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42
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Borkowska J, Domaszewska-Szostek A, Kołodziej P, Wicik Z, Połosak J, Buyanovskaya O, Charzewski L, Stańczyk M, Noszczyk B, Puzianowska-Kuznicka M. Alterations in 5hmC level and genomic distribution in aging-related epigenetic drift in human adipose stem cells. Epigenomics 2020; 12:423-437. [PMID: 32031421 DOI: 10.2217/epi-2019-0131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: To clarify mechanisms affecting the level and distribution of 5-hydroxymethylcytosine (5hmC) during aging. Materials & methods: We examined levels and genomic distribution of 5hmC along with the expression of ten-eleven translocation methylcytosine dioxygenases (TETs) in adipose stem cells in young and age-advanced individuals. Results: 5hmC levels were higher in adipose stem cells of age-advanced than young individuals (p = 0.0003), but were not associated with age-related changes in expression of TETs. 5hmC levels correlated with population doubling time (r = 0.62; p = 0.01). We identified 58 differentially hydroxymethylated regions. Hypo-hydroxymethylated differentially hydroxymethylated regions were approximately twofold enriched in CCCTC-binding factor binding sites. Conclusion: Accumulation of 5hmC in aged cells can result from inefficient active demethylation due to altered TETs activity and reduced passive demethylation due to slower proliferation.
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Affiliation(s)
- Joanna Borkowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Anna Domaszewska-Szostek
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Paulina Kołodziej
- Department of Geriatrics & Gerontology, Medical Centre of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
| | - Zofia Wicik
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Jacek Połosak
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Olga Buyanovskaya
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Lukasz Charzewski
- Faculty of Physics, University of Warsaw, 5 Pasteur Street, 02-093 Warsaw, Poland
| | - Marek Stańczyk
- Department of General Surgery, Wolski Hospital, 17 Kasprzaka Street, 01-211 Warsaw, Poland
| | - Bartłomiej Noszczyk
- Department of Plastic Surgery, Medical Centre of Postgraduate Education, 99/103 Marymoncka Street, 01-813 Warsaw, Poland
| | - Monika Puzianowska-Kuznicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland.,Department of Geriatrics & Gerontology, Medical Centre of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
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43
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McLachlan KJJ, Cole JH, Harris SE, Marioni RE, Deary IJ, Gale CR. Attitudes to ageing, biomarkers of ageing and mortality: the Lothian Birth Cohort 1936. J Epidemiol Community Health 2020; 74:377-383. [PMID: 31992610 PMCID: PMC7079194 DOI: 10.1136/jech-2019-213462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 11/30/2022]
Abstract
Objective To investigate whether people with more positive attitudes to ageing are biologically younger as defined by leucocyte telomere length, accelerated DNA methylation GrimAge (AgeAccelGrim) and brain-predicted age difference, and whether these biomarkers explain relationships between attitudes to ageing and mortality. Methods We used linear regression to examine cross-sectionally attitudes to ageing (measured using the Attitudes to Ageing Questionnaire) and the three biomarkers in 758 adults, mean age 72.5 years, from the Lothian Birth Cohort 1936. We used Cox proportional hazards models to examine longitudinally attitudes to ageing and mortality and the role of the biomarkers. Results More positive attitude to physical change was associated with younger biological age, as measured by AgeAccelGrim and brain-predicted age difference in age-adjusted and sex-adjusted models: for an SD higher score, AgeAccelGrim was lower by -0.73 (95% CI -1.03 to -0.42) of a year, and brain-predicted age difference was lower by -0.87 (1.51 to 0.23) of a year. Both associations were attenuated by adjustment for covariates and not significant after simultaneous adjustment for all covariates and correction for multiple testing. More positive attitudes to physical change were associated with lower mortality: for an SD higher score the age-adjusted and sex-adjusted HR (95% CI) was 0.66 (0.56 to 0.78). Adjustment for AgeAccelGrim or brain-predicted age difference attenuated this association slightly. It remained significant after adjustment for all covariates. Conclusion We found partial evidence that attitudes to ageing are linked with ageing biomarkers but they accounted for only a little of the association between attitudes and mortality.
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Affiliation(s)
| | - James H Cole
- Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- Centre for Medical Imaging Computing, Computer Science, University College London, London, UK
- Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | | | - Riccardo E Marioni
- Psychology, The University of Edinburgh, Edinburgh, UK
- MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Psychology, The University of Edinburgh, Edinburgh, UK
| | - Catharine R Gale
- Psychology, The University of Edinburgh, Edinburgh, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, Hampshire, UK
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44
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Stevenson AJ, McCartney DL, Hillary RF, Redmond P, Taylor AM, Zhang Q, McRae AF, Spires-Jones TL, McIntosh AM, Deary IJ, Marioni RE. Childhood intelligence attenuates the association between biological ageing and health outcomes in later life. Transl Psychiatry 2019; 9:323. [PMID: 31780646 PMCID: PMC6883059 DOI: 10.1038/s41398-019-0657-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/09/2019] [Accepted: 10/09/2019] [Indexed: 01/14/2023] Open
Abstract
The identification of biomarkers that discriminate individual ageing trajectories is a principal target of ageing research. Some of the most promising predictors of biological ageing have been developed using DNA methylation. One recent candidate, which tracks age-related phenotypes in addition to chronological age, is 'DNAm PhenoAge'. Here, we performed a phenome-wide association analysis of this biomarker in a cohort of older adults to assess its relationship with a comprehensive set of both historical, and contemporaneously-measured, phenotypes. Higher than expected DNAm PhenoAge compared with chronological age, known as epigenetic age acceleration, was found to associate with a number of blood, cognitive, physical fitness and lifestyle variables, and with mortality. Notably, DNAm PhenoAge, assessed at age 70, was associated with cognitive ability at age 11, and with educational attainment. Adjusting for age 11 cognitive ability attenuated the majority of the cross-sectional later-life associations between DNAm PhenoAge and health outcomes. These results highlight the importance of early life factors on healthy older ageing.
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Affiliation(s)
- Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Department for Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele M Taylor
- Department for Psychology, University of Edinburgh, Edinburgh, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Tara L Spires-Jones
- UK Dementia Research Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Department for Psychology, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
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45
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Wikenius E, Moe V, Smith L, Heiervang ER, Berglund A. DNA methylation changes in infants between 6 and 52 weeks. Sci Rep 2019; 9:17587. [PMID: 31772264 PMCID: PMC6879561 DOI: 10.1038/s41598-019-54355-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Infants undergo extensive developments during their first year of life. Although the biological mechanisms involved are not yet fully understood, changes in the DNA methylation in mammals are believed to play a key role. This study was designed to investigate changes in infant DNA methylation that occurs between 6 and 52 weeks. A total of 214 infant saliva samples from 6 or 52 weeks were assessed using principal component analyses and t-distributed stochastic neighbor-embedding algorithms. Between the two time points, there were clear differences in DNA methylation. To further investigate these findings, paired two-sided student’s t-tests were performed. Differently methylated regions were defined as at least two consecutive probes that showed significant differences, with a q-value < 0.01 and a mean difference > 0.2. After correcting for false discovery rates, changes in the DNA methylation levels were found in 42 genes. Of these, 36 genes showed increased and six decreased DNA methylation. The overall DNA methylation changes indicated decreased gene expression. This was surprising because infants undergo such profound developments during their first year of life. The results were evaluated by taking into consideration the extensive development that occurs during pregnancy. During the first year of life, infants have an overall three-fold increase in weight, while the fetus develops from a single cell into a viable infant in 9 months, with an 875-million-fold increase in weight. It is possible that the findings represent a biological slowing mechanism in response to extensive fetal development. In conclusion, our study provides evidence of DNA methylation changes during the first year of life, representing a possible biological slowing mechanism. We encourage future studies of DNA methylation changes in infants to replicate the findings by using a repeated measures model and less stringent criteria to see if the same genes can be found, as well as investigating whether other genes are involved in development during this period.
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Affiliation(s)
- Ellen Wikenius
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Vibeke Moe
- Department of Psychology, Faculty of Social Sciences, University of Oslo, Oslo, Norway.,The Center for Child and Adolescent Mental Health, Eastern and Southern Norway (RBUP), Oslo, Norway
| | - Lars Smith
- Department of Psychology, Faculty of Social Sciences, University of Oslo, Oslo, Norway
| | - Einar R Heiervang
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Oslo University Hospital, Oslo, Norway
| | - Anders Berglund
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
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Wu X, Chen W, Lin F, Huang Q, Zhong J, Gao H, Song Y, Liang H. DNA methylation profile is a quantitative measure of biological aging in children. Aging (Albany NY) 2019; 11:10031-10051. [PMID: 31756171 PMCID: PMC6914436 DOI: 10.18632/aging.102399] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/26/2019] [Indexed: 12/21/2022]
Abstract
DNA methylation changes within the genome can be used to predict human age. However, the existing biological age prediction models based on DNA methylation are predominantly adult-oriented. We established a methylation-based age prediction model for children (9-212 months old) using data from 716 blood samples in 11 DNA methylation datasets. Our elastic net model includes 111 CpG sites, mostly in genes associated with development and aging. The model performed well and exhibited high precision, yielding a 98% correlation between the DNA methylation age and the chronological age, with an error of only 6.7 months. When we used the model to assess age acceleration in children based on their methylation data, we observed the following: first, the aging rate appears to be fastest in mid-childhood, and this acceleration is more pronounced in autistic children; second, lead exposure early in life increases the aging rate in boys, but not in girls; third, short-term recombinant human growth hormone treatment has little effect on the aging rate of children. Our child-specific methylation-based age prediction model can effectively detect epigenetic changes and health imbalances early in life. This may thus be a useful model for future studies of epigenetic interventions for age-related diseases.
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Affiliation(s)
- Xiaohui Wu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China
| | - Weidan Chen
- Department of Cardiovascular Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fangqin Lin
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qingsheng Huang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiayong Zhong
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huan Gao
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanyan Song
- The Guangdong Early Childhood Development Applied Engineering and Technology Research Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Gibson J, Russ TC, Clarke TK, Howard DM, Hillary RF, Evans KL, Walker RM, Bermingham ML, Morris SW, Campbell A, Hayward C, Murray AD, Porteous DJ, Horvath S, Lu AT, McIntosh AM, Whalley HC, Marioni RE. A meta-analysis of genome-wide association studies of epigenetic age acceleration. PLoS Genet 2019; 15:e1008104. [PMID: 31738745 PMCID: PMC6886870 DOI: 10.1371/journal.pgen.1008104 10.1371/journal.pgen.1008104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 12/02/2019] [Accepted: 08/16/2019] [Indexed: 12/20/2023] Open
Abstract
'Epigenetic age acceleration' is a valuable biomarker of ageing, predictive of morbidity and mortality, but for which the underlying biological mechanisms are not well established. Two commonly used measures, derived from DNA methylation, are Horvath-based (Horvath-EAA) and Hannum-based (Hannum-EAA) epigenetic age acceleration. We conducted genome-wide association studies of Horvath-EAA and Hannum-EAA in 13,493 unrelated individuals of European ancestry, to elucidate genetic determinants of differential epigenetic ageing. We identified ten independent SNPs associated with Horvath-EAA, five of which are novel. We also report 21 Horvath-EAA-associated genes including several involved in metabolism (NHLRC, TPMT) and immune system pathways (TRIM59, EDARADD). GWAS of Hannum-EAA identified one associated variant (rs1005277), and implicated 12 genes including several involved in innate immune system pathways (UBE2D3, MANBA, TRIM46), with metabolic functions (UBE2D3, MANBA), or linked to lifespan regulation (CISD2). Both measures had nominal inverse genetic correlations with father's age at death, a rough proxy for lifespan. Nominally significant genetic correlations between Hannum-EAA and lifestyle factors including smoking behaviours and education support the hypothesis that Hannum-based epigenetic ageing is sensitive to variations in environment, whereas Horvath-EAA is a more stable cellular ageing process. We identified novel SNPs and genes associated with epigenetic age acceleration, and highlighted differences in the genetic architecture of Horvath-based and Hannum-based epigenetic ageing measures. Understanding the biological mechanisms underlying individual differences in the rate of epigenetic ageing could help explain different trajectories of age-related decline.
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Affiliation(s)
- Jude Gibson
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom C. Russ
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Dementia Prevention, University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Toni-Kim Clarke
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David M. Howard
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stewart W. Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United Kingdom
| | - David J. Porteous
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, United States of America
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, United States of America
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, United States of America
| | - Andrew M. McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Heather C. Whalley
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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Gibson J, Russ TC, Clarke TK, Howard DM, Hillary RF, Evans KL, Walker RM, Bermingham ML, Morris SW, Campbell A, Hayward C, Murray AD, Porteous DJ, Horvath S, Lu AT, McIntosh AM, Whalley HC, Marioni RE. A meta-analysis of genome-wide association studies of epigenetic age acceleration. PLoS Genet 2019; 15:e1008104. [PMID: 31738745 PMCID: PMC6886870 DOI: 10.1371/journal.pgen.1008104] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 12/02/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022] Open
Abstract
'Epigenetic age acceleration' is a valuable biomarker of ageing, predictive of morbidity and mortality, but for which the underlying biological mechanisms are not well established. Two commonly used measures, derived from DNA methylation, are Horvath-based (Horvath-EAA) and Hannum-based (Hannum-EAA) epigenetic age acceleration. We conducted genome-wide association studies of Horvath-EAA and Hannum-EAA in 13,493 unrelated individuals of European ancestry, to elucidate genetic determinants of differential epigenetic ageing. We identified ten independent SNPs associated with Horvath-EAA, five of which are novel. We also report 21 Horvath-EAA-associated genes including several involved in metabolism (NHLRC, TPMT) and immune system pathways (TRIM59, EDARADD). GWAS of Hannum-EAA identified one associated variant (rs1005277), and implicated 12 genes including several involved in innate immune system pathways (UBE2D3, MANBA, TRIM46), with metabolic functions (UBE2D3, MANBA), or linked to lifespan regulation (CISD2). Both measures had nominal inverse genetic correlations with father's age at death, a rough proxy for lifespan. Nominally significant genetic correlations between Hannum-EAA and lifestyle factors including smoking behaviours and education support the hypothesis that Hannum-based epigenetic ageing is sensitive to variations in environment, whereas Horvath-EAA is a more stable cellular ageing process. We identified novel SNPs and genes associated with epigenetic age acceleration, and highlighted differences in the genetic architecture of Horvath-based and Hannum-based epigenetic ageing measures. Understanding the biological mechanisms underlying individual differences in the rate of epigenetic ageing could help explain different trajectories of age-related decline.
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Affiliation(s)
- Jude Gibson
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom C. Russ
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Dementia Prevention, University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Toni-Kim Clarke
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David M. Howard
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stewart W. Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United Kingdom
| | - David J. Porteous
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, United States of America
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, United States of America
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, United States of America
| | - Andrew M. McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Heather C. Whalley
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing & Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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49
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Corley J, Cox SR, Harris SE, Hernandez MV, Maniega SM, Bastin ME, Wardlaw JM, Starr JM, Marioni RE, Deary IJ. Epigenetic signatures of smoking associate with cognitive function, brain structure, and mental and physical health outcomes in the Lothian Birth Cohort 1936. Transl Psychiatry 2019; 9:248. [PMID: 31591380 PMCID: PMC6779733 DOI: 10.1038/s41398-019-0576-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/29/2019] [Indexed: 12/18/2022] Open
Abstract
Recent advances in genome-wide DNA methylation (DNAm) profiling for smoking behaviour have given rise to a new, molecular biomarker of smoking exposure. It is unclear whether a smoking-associated DNAm (epigenetic) score has predictive value for ageing-related health outcomes which is independent of contributions from self-reported (phenotypic) smoking measures. Blood DNA methylation levels were measured in 895 adults aged 70 years in the Lothian Birth Cohort 1936 (LBC1936) study using the Illumina 450K assay. A DNA methylation score based on 230 CpGs was used as a proxy for smoking exposure. Associations between smoking variables and health outcomes at age 70 were modelled using general linear modelling (ANCOVA) and logistic regression. Additional analyses of smoking with brain MRI measures at age 73 (n = 532) were performed. Smoking-DNAm scores were positively associated with self-reported smoking status (P < 0.001, eta-squared ɳ2 = 0.63) and smoking pack years (r = 0.69, P < 0.001). Higher smoking DNAm scores were associated with variables related to poorer cognitive function, structural brain integrity, physical health, and psychosocial health. Compared with phenotypic smoking, the methylation marker provided stronger associations with all of the cognitive function scores, especially visuospatial ability (P < 0.001, partial eta-squared ɳp2 = 0.022) and processing speed (P < 0.001, ɳp2 = 0.030); inflammatory markers (all P < 0.001, ranges from ɳp2 = 0.021 to 0.030); dietary patterns (healthy diet (P < 0.001, ɳp2 = 0.052) and traditional diet (P < 0.001, ɳp2 = 0.032); stroke (P = 0.006, OR 1.48, 95% CI 1.12, 1.96); mortality (P < 0.001, OR 1.59, 95% CI 1.42, 1.79), and at age 73; with MRI volumetric measures (all P < 0.001, ranges from ɳp2 = 0.030 to 0.052). Additionally, education was the most important life-course predictor of lifetime smoking tested. Our results suggest that a smoking-associated methylation biomarker typically explains a greater proportion of the variance in some smoking-related morbidities in older adults, than phenotypic measures of smoking exposure, with some of the accounted-for variance being independent of phenotypic smoking status.
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Affiliation(s)
- Janie Corley
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.
| | - Simon R Cox
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Maria Valdéz Hernandez
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Susana Muñoz Maniega
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Mark E Bastin
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Joanna M Wardlaw
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Brain Research Imaging Centre, Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Royal Victoria Building, Western General Hospital, Porterfield Road, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
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50
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Starr JM. Ageing and epigenetics: linking neurodevelopmental and neurodegenerative disorders. Dev Med Child Neurol 2019; 61:1134-1138. [PMID: 30883719 DOI: 10.1111/dmcn.14210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
Epigenetics has classically been recognized as crucial to neurodevelopment and neurodevelopmental disorders. More recently its role in ageing processes, including neurodegenerative disorders has emerged, although far more research is required in this area, particularly in humans. Epigenetic processes that regulate gene expression comprise strata of DNA modification (e.g. methylation), histone modification (e.g. histone acetylation), and mRNA translation (e.g. by microRNAs). These strata are progressively more fluid whereby changes in DNA methylation may persist for many years whilst expression of microRNAs fluctuates over short periods. There is considerable 'cross-talk' between these epigenetic strata. Epigenetic mechanisms are open to parental imprinting and thus they are candidates for linking diseases, not just over the life course, but also intergenerationally. There is a genetic overlap between intellectual disability and cognitive ageing. Epigenetic pathways may strengthen the links between neurodevelopmental disorders and neurodegenerative diseases. WHAT THIS PAPER ADDS: DNA methylation has relevance to both neurological development and neurodegeneration. Links between epigenetics, genotype and phenotype are emerging.
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Affiliation(s)
- John M Starr
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
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