Blood-based DNA methylation study of alcohol consumption

Alcohol consumption is an important risk factor for multiple diseases. It is typically assessed via self-report, which is open to measurement error and bias. Instead, molecular data such as blood-based DNA methylation (DNAm) could be used to derive a more objective measure of alcohol consumption by incorporating information from cytosine-phosphate-guanine (CpG) sites known to be linked to the trait. Here, we explore the epigenetic architecture of self-reported weekly units of alcohol consumption in the Generation Scotland study. We first create a blood-based epigenetic score (EpiScore) of alcohol consumption using elastic net penalised linear regression. We explore the effect of pre-filtering for CpG features ahead of elastic net, as well as differential patterns by sex and by units consumed in the last week relative to an average week. The final EpiScore was trained on 16,717 individuals and tested in four external cohorts: the Lothian Birth Cohorts (LBC) of 1921 and 1936, the Sister Study, and the Avon Longitudinal Study of Parents and Children (total N across studies > 10,000). The maximum Pearson correlation between the EpiScore and self-reported alcohol consumption within cohort ranged from 0.41 to 0.53. In LBC1936, higher EpiScore levels had significant associations with poorer global brain imaging metrics, whereas self-reported alcohol consumption did not. Finally, we identified two novel CpG loci via a Bayesian penalized regression epigenome-wide association study (EWAS) of alcohol consumption. Together, these findings show how DNAm can objectively characterize patterns of alcohol consumption that associate with brain health, unlike self-reported estimates. ### Competing Interest Statement R.E.M has received a speaker fee from Illumina and is an advisor to the Epigenetic Clock Development Foundation. R.F.H. has received consultant fees from Illumina. R.E.M and R.F.H. have received consultant fees from Optima partners. M.R.R. receives research funding from Boehringer Ingelheim. All other authors declare no competing interests. ### Funding Statement Generation Scotland: Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and DNA methylation profiling of the Generation Scotland samples was carried out by the Genetics Core Laboratory at the Edinburgh Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award STratifying Resilience and Depression Longitudinally (STRADL; Reference 104036/Z/14/Z). The DNA methylation data assayed for Generation Scotland was partially funded by a 2018 NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation (Ref: 27404; awardee: Dr David M Howard) and by a JMAS SIM fellowship from the Royal College of Physicians of Edinburgh (Awardee: Dr Heather C Whalley). Lothian Birth Cohorts: We thank the LBC1921 and LBC1936 participants and team members who contributed to these studies. The LBC1921 was supported by the UK's Biotechnology and Biological Sciences Research Council (BBSRC), The Royal Society, and The Chief Scientist Office of the Scottish Government. The LBC1936 is supported by the BBSRC, and the Economic and Social Research Council \[BB/W008793/1\] (which supports S.E.H.), Age UK (Disconnected Mind project), the Milton Damerel Trust, the Medical Research Council (MR/M01311/1), and the University of Edinburgh. Methylation typing of LBC1936 was supported by the Centre for Cognitive Ageing and Cognitive Epidemiology (Pilot Fund award), Age UK, The Wellcome Trust Institutional Strategic Support Fund, The University of Edinburgh, and The University of Queensland. Genotyping was funded by the BBSRC (BB/F019394/1). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant Number 221890/Z/20/Z). ALSPAC: The UK Medical Research Council and Wellcome (Grant ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors and Matthew Suderman will serve as guarantors for the contents of this paper. A comprehensive list of grants funding is available on the ALSPAC website (http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf). Funding for ALSPAC DNAm measurements were supported bythe Wellcome (102215/2/13/2); the University of Bristol; the UK Economic and Social Research Council (ES/N000498/1); the UK Medical Research Council (MC\_UU\_12013/1, MC\_UU\_12013/2); and the John Templeton Foundation (60828). MS and PY work within the MRC Integrative Epidemiology Unit at the University of Bristol, which is supported by the Medical Research Council (MC\_UU\_00011/5). R.F.H is supported by an MRC IEU Fellowship. M.R.R. was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181 and by core funding from the Institute of Science and Technology Austria. E.B. and R.E.M. are supported by Alzheimer's Society major project grant AS-PG-19b-010. This research was funded in whole, or in part, by the Wellcome Trust (104036/Z/14/Z, 108890/Z/15/Z, 220857/Z/20/Z, and 221890/Z/20/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. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All components of Generation Scotland received ethical approval from the NHS Tayside Committee on Medical Research Ethics (REC Reference Number: 05/S1401/89). All participants provided broad and enduring written informed consent for biomedical research. Generation Scotland has also been granted Research Tissue Bank status by the East of Scotland Research Ethics Service (REC Reference Number: 15/0040/ES), providing generic ethical approval for a wide range of uses within medical research. This study was performed in accordance with the Helsinki declaration. Ethical approval for the LBC1921 and LBC1936 studies was obtained from the Multi-Centre Research Ethics Committee for Scotland (MREC/01/0/56) and the Lothian Research Ethics committee (LREC/1998/4/183; LREC/2003/2/29). In both studies, all participants provided written informed consent. These studies were performed in accordance with the Helsinki declaration. Ethical approval for the ALSPAC study was obtained from the ALSPAC Ethics and Law Committee and the Local Research Ethics Committees. Consent for biological samples has been collected in accordance with the Human Tissue Act (2004). Informed consent for the use of data collected via questionnaires and clinics was obtained from participants following the recommendations of the ALSPAC Ethics and Law Committee at the time. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All custom R (version 4.3.0), Python (version 3.9.7), and bash code is available with open access at the following GitHub repository: https://github.com/elenabernabeu/methylomics_alcohol EWAS summary statistics will be made available on Edinburgh DataShare on publication.