Epigenetic timing effects on child developmental outcomes: A longitudinal meta-regression of findings from the Pregnancy And Childhood Epigenetics Consortium

DNA methylation (DNAm) is a developmentally dynamic epigenetic process, yet we still know little about how epigenetic effects on health outcomes vary over time; whether DNAm alterations during certain periods of development are more informative than others; and whether epigenetic timing effects differ by outcome. To address these questions, we applied longitudinal meta-regression to published meta-analyses from the PACE consortium that examine DNAm at multiple time points (prospectively at birth and cross-sectionally in childhood) in relation to the same child outcome (ADHD, general psychopathology, sleep, BMI, asthma). Our findings reveal three new insights: (i) across outcomes, effects sizes are larger when DNAm is measured in childhood compared to at birth; (ii) higher effect sizes do not necessarily translate into more significant findings, as associations also become noisier in childhood for most outcomes (i.e. showing larger standard errors); and (iii) DNAm signals are highly time-specific while showing pleiotropy across health outcomes. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The work of AN and CAMC was supported by the European Research Council (TEMPO; grant agreement No 101039672) and the European Union’s HorizonEurope Research and Innovation Programme (FAMILY, grant agreement No 101057529). The work of CAMC is further supported by the European Union’s Horizon 2020 Research and Innovation Programme (EarlyCause, grant agreement No 848158; HappyMums, grant agreement No 101057390). CAMC and JFF are supported by the European Union’s Horizon Europe Programme (STAGE project, grant agreement no.101137146). This research was conducted while CAMC was a Hevolution/AFAR New Investigator Awardee in Aging Biology and Geroscience Research. LST was supported by the CAPICE (Childhood and Adolescence Psychopathology: unravelling the complex etiology by a large Interdisciplinary Collaboration in Europe) project, the European Union’s Horizon 2020 research and innovation programme, Marie Sklodowska Curie Actions MSCA-ITN-2016 Innovative Training Networks under grant agreement number 721567. SJL was supported in part by the Intramural Research Program of the NIH, NIEHS Z01 ES49019. SEH and CMP was partly supported by The Norwegian Research council no 262700 and the Norwegian Cancer Society project no 244291. See supplementary information for cohort specific acknowledgments and funding. ### 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: This work reports a meta-analysis of EWAS summary statistics generated in previous studies. Summary statistics were requested from the original authors. The Erasmus MC Medical Ethics Review Committee and respective local ethics committees previously approved the included studies. See original studies for full details. 1. Neumann, A. et al. Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis. Transl. Psychiatry 10, 398 (2020). 2. Rijlaarsdam, J. et al. DNA methylation and general psychopathology in childhood: an epigenome-wide meta-analysis from the PACE consortium. Mol. Psychiatry 28, (2023). 3. Sammallahti, S. et al. Longitudinal associations of DNA methylation and sleep in children: a meta-analysis. Clin. Epigenetics 14, 83 (2022). 4. Vehmeijer, F. O. L. et al. DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies. Genome Med. 12, 105 (2020). 5. Reese, S. E. et al. Epigenome-wide meta-analysis of DNA methylation and childhood asthma. J. Allergy Clin. Immunol. 143 (2019). 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 Original analysis code and example data can be found at https://github.com/aneumann-science/epigenetic\_timing\_effects. Full meta-analysis summary statistics can be downloaded at https://doi.org/10.5281/zenodo.10720466 (Will be made public after acceptance). For individual cohort summary statistics or individual-level data, please see original publications for details on how to request them. 1. Neumann, A. et al. Association between DNA methylation and ADHD symptoms from birth to school age: a prospective meta-analysis. Transl. Psychiatry 10, 398 (2020). 2. Rijlaarsdam, J. et al. DNA methylation and general psychopathology in childhood: an epigenome-wide meta-analysis from the PACE consortium. Mol. Psychiatry 28, (2023). 3. Sammallahti, S. et al. Longitudinal associations of DNA methylation and sleep in children: a meta-analysis. Clin. Epigenetics 14, 83 (2022). 4. Vehmeijer, F. O. L. et al. DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies. Genome Med. 12, 105 (2020). 5. Reese, S. E. et al. Epigenome-wide meta-analysis of DNA methylation and childhood asthma. J. Allergy Clin. Immunol. 143 (2019).