Abstract
Background: DNA methylation (DNAm) is associated with time-varying environmental factors that contribute to major depressive disorder (MDD) risk. We sought to test whether DNAm signatures of lifestyle and biochemical factors were associated with MDD to reveal dynamic biomarkers of MDD risk that may be amenable to lifestyle interventions. Methods: Here, we calculated methylation scores (MS) at multiple p-value thresholds for lifestyle (BMI, smoking, alcohol consumption, and educational attainment) and biochemical (high-density lipoprotein (HDL) and total cholesterol) factors in Generation Scotland (GS) (N=9,502) and in a replication cohort (ALSPACadults, N=565), using CpG sites reported in previous well-powered methylome-wide association studies. We also compared their predictive accuracy for MDD to a MDD MS in an independent GS sub-sample (N=4,432). Findings: Each trait MS was significantly associated with its corresponding phenotype in GS (βrange=0.089–1.457) and in ALSPAC (βrange=0.078–2.533). Each MS was also significantly associated with MDD before and after adjustment for its corresponding phenotype in GS (βrange=0.053–0.145). After accounting for relevant lifestyle factors, MS for educational attainment (β=0.094) and alcohol consumption (MSp-value<0.01–0.5; βrange=-0.069–0.083) remained significantly associated with MDD in GS. Smoking (AUC=0.569) and educational attainment (AUC=0.585) MSs could discriminate MDD from controls better than the MDD MS (AUC=0.553) in the independent GS sub-sample. Analyses implicating MDD did not replicate across ALSPAC, although the direction of effect was consistent for all traits when adjusting for the MS corresponding phenotypes. Interpretation: We showed that lifestyle and biochemical MS were associated with MDD before and after adjustment for their corresponding phenotypes (pnominal<0.05), but not when smoking, alcohol consumption, and BMI were also included as covariates. MDD results did not replicate in the smaller, female-only independent ALSPAC cohort (NALSPAC=565; NGS=9,502), potentially due to demographic differences or low statistical power, but effect sizes were consistent with the direction reported in GS. DNAm scores for modifiable MDD risk factors may contribute to disease vulnerability and, in some cases, explain additional variance to their observed phenotypes. Funding: Wellcome Trust.
Original language | English |
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Article number | 104000 |
Pages (from-to) | 1-19 |
Number of pages | 19 |
Journal | Ebiomedicine |
Volume | 79 |
Early online date | 28 Apr 2022 |
DOIs | |
Publication status | Published - May 2022 |
Bibliographical note
Funding Information:MCB has received financial support from Edinburgh Neuroscience Researcher's Fund, Wellcome Trust Institutional Translational Partnership Award Innovation Competition, and Research Adaptation Fund to attend courses and conferences in the past. RMW has received financial support from Alzheimer's Research UK (ARUK) to attend the ARUK annual conference (2021 and 2022). JLM is supported by the UK Medical Research Council Integrative Epidemiology Unit at the University of Bristol. AC is a University of Edinburgh Medical Research Ethics Committee member. JvdD was supported by NWO Large Scale infrastructures, X-Omics (184.034.019). Remaining authors report no conflicts of interest.
Funding Information:
This research was funded in whole, or in part, by the Wellcome Trust [216767/Z/19/Z]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Generation Scotland is currently supported by the Wellcome Trust [216767/Z/19/Z] and by the Wellcome Trust Investigator Award in Science 01/06/2021 to 31/05/26 ‘Exploiting genomic approaches to identify the environmental basis of depression’. (Reference: 220857/Z/20/Z) to McIntosh AM (PI). The DNA methylation profiling and data preparation was supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI for both grants: McIntosh AM) and through funding from NARSAD (Ref: 27404; PI: Dr DM Howard and Ref: 21956; PI Dr Kathryn Evans) and the Royal College of Physicians of Edinburgh (Sim Fellowship; PI: Dr HC Whalley). Genotyping of the GS:SFHS samples was funded by the MRC and Wellcome Trust [104036/Z/14/Z]. Generation Scotland also receives support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. Dr DM Howard is supported by a Sir Henry Wellcome Postdoctoral Fellowship (Reference 213674/Z/18/Z). Dr M Barbu is supported by a Guarantors of Brain Non-clinical Post-Doctoral Fellowship.
Funding Information:
The UK Medical Research Council and Wellcome (Grant Ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. A comprehensive list of grants funding is available on the ALSPAC website ( http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf ).
Publisher Copyright:
© 2022 The Authors
Funding
MCB has received financial support from Edinburgh Neuroscience Researcher's Fund, Wellcome Trust Institutional Translational Partnership Award Innovation Competition, and Research Adaptation Fund to attend courses and conferences in the past. RMW has received financial support from Alzheimer's Research UK (ARUK) to attend the ARUK annual conference (2021 and 2022). JLM is supported by the UK Medical Research Council Integrative Epidemiology Unit at the University of Bristol. AC is a University of Edinburgh Medical Research Ethics Committee member. JvdD was supported by NWO Large Scale infrastructures, X-Omics (184.034.019). Remaining authors report no conflicts of interest. This research was funded in whole, or in part, by the Wellcome Trust [216767/Z/19/Z]. For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. Generation Scotland is currently supported by the Wellcome Trust [216767/Z/19/Z] and by the Wellcome Trust Investigator Award in Science 01/06/2021 to 31/05/26 ‘Exploiting genomic approaches to identify the environmental basis of depression’. (Reference: 220857/Z/20/Z) to McIntosh AM (PI). The DNA methylation profiling and data preparation was supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI for both grants: McIntosh AM) and through funding from NARSAD (Ref: 27404; PI: Dr DM Howard and Ref: 21956; PI Dr Kathryn Evans) and the Royal College of Physicians of Edinburgh (Sim Fellowship; PI: Dr HC Whalley). Genotyping of the GS:SFHS samples was funded by the MRC and Wellcome Trust [104036/Z/14/Z]. Generation Scotland also receives support from the Chief Scientist Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish Funding Council [HR03006]. Dr DM Howard is supported by a Sir Henry Wellcome Postdoctoral Fellowship (Reference 213674/Z/18/Z). Dr M Barbu is supported by a Guarantors of Brain Non-clinical Post-Doctoral Fellowship. The UK Medical Research Council and Wellcome (Grant Ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. A comprehensive list of grants funding is available on the ALSPAC website ( http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf ).
Funders | Funder number |
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University of Otago | |
Det Sundhedsvidenskabelige Fakultet, Københavns Universitet | |
Health and Medical Sciences, University of Copenhagen | |
Broad Institute | |
Sir Henry Wellcome Postdoctoral Fellowship | |
Menzies Institute for Medical Research | |
Bradford Institute for Health Research | |
College of Health and Medicine, University of Tasmania | |
80 Hospital del Mar Medical Research Institute | |
Bellvitge Biomedical Research Institute | |
Louise Arseneault60 | |
Leids Universitair Medisch Centrum | |
Beatrix Children's Hospital | |
Barcelona Institute of Science and Technology | |
Erasmus Universiteit Rotterdam | |
University of Edinburgh | |
Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford University | |
74 Centre of Women's, Family and Child Health, University of South-Eastern Norway | |
Instituto de Parasitología y Biomedicina López Neyra | |
Zhongshan School of Medicine, Sun Yat-Sen University | |
Institut Hospital del Mar d'Investigacions Mèdiques | |
King's College Hospital, London, UK, 56 United Kingdom Dementia Research Institute | |
Institut national de la santé et de la recherche médicale | |
Royal College of Physicians of Edinburgh | |
31 Guangdong Province Key Laboratory of Brain Function and Disease | |
College of Medicine and Health, University of Exeter | |
Avera Institute for Human Genetics, Sioux Falls | |
Institute of Genetics and Molecular Medicine, Western General Hospital | |
University of Toronto | |
68 Department of Social and Behavioral Science | |
National Institute of Public Health, University of Southern Denmark | |
Harvard T.H. Chan School of Public Health | |
School of Medicine, Emory University | |
College of Health, Medicine and Wellbeing | |
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement | |
University of Granada - Andalusian Government Center for Genomics and Oncological Research | |
Rijksuniversiteit Groningen | |
Illinois Department of Public Health | |
Dorret I Boomsma43 | |
Helsingin Yliopisto | |
Children's Health | |
Tartu Ülikool | |
Universitair Medisch Centrum Groningen | |
Department of Pediatric Pulmonology and Pediatric Allergology | |
Aix-Marseille Université | |
Telethon Kids Institute | |
83 Division of Epidemiology, Biostatistics, and Environmental Health Sciences | |
University of Newcastle, Newcastle, Australia | |
Consejo Superior de Investigaciones Científicas | |
University of Southampton | |
University of Queensland | |
Universität Basel | |
Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológic | |
Karolinska Institutet | |
University of Aberdeen | |
Helmholtz Centre for Infection Research | |
Department of Biomedical Data Sciences | |
Syddansk Universitet | |
Institute of Genetics and Molecular Medicine, University of Edinburgh | |
Sun Yat-Sen University | |
Medizinischen Hochschule Hannover | |
Österreichischen Akademie der Wissenschaften | |
TWINCORE | |
University of Western Australia | |
3 University of Exeter Medical School | |
Institute for Molecular Bioscience | |
Hospital for Sick Children | |
Department of Biostatistics and Health Informatics, King's College London | |
Novo Nordisk Fonden | |
Queensland Brain Institute | |
University of Bristol | |
King's College London | |
Public Health Institute | |
Hacettepe Üniversitesi | |
85 Alzheimer Scotland Dementia Research Centre | |
Department of Epidemiology | |
Bristol Medical School, University of Bristol | |
81 Human Development and Health, Faculty of Medicine, University of Southampton | |
Medizinische Universität Wien | |
Wellcome Trust | 104036/Z/14/Z, 220857, 213674, 216767/Z/19/Z, 217065, 01/06/2021, 220857/Z/20/Z |
Scottish Funding Council | HR03006, 213674/Z/18/Z |
Allan F McRae18 | W Montgomery18 |
Medical Research Council | 217065/Z/19/Z |
Alzheimer’s Research UK | 2022 |
National Alliance for Research on Schizophrenia and Depression | 27404, 21956 |
Chief Scientist Office of the Scottish Government Health Directorates | CZD/16/6 |
NWO | 184.034.019 |
Keywords
- Avon longitudinal study of parents and children
- DNA methylation
- Environmental factors
- Generation Scotland
- Major depressive disorder
- Methylation score