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Meta-Analysis
. 2025 Apr 14;17(1):39.
doi: 10.1186/s13073-025-01451-7.

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

Alexander Neumann  1 Sara Sammallahti  2   3 Marta Cosin-Tomas  4   5   6 Sarah E Reese  7 Matthew Suderman  8 Silvia Alemany  9   10   11 Catarina Almqvist  12 Sandra Andrusaityte  13 Syed H Arshad  14 Marian J Bakermans-Kranenburg  15 Lawrence Beilin  16 Carrie Breton  17 Mariona Bustamante  4   5   6 Darina Czamara  18 Dana Dabelea  19 Celeste Eng  20 Brenda Eskenazi  21 Bernard F Fuemmeler  22 Frank D Gilliland  23 Regina Grazuleviciene  13 Siri E Håberg  24 Gunda Herberth  25 Nina Holland  26 Amy Hough  27 Donglei Hu  28 Karen Huen  26 Anke Hüls  29   30   31 Marjo-Riitta Jarvelin  32   33   34   35 Jianping Jin  36 Jordi Julvez  37 Berthold V Koletzko  38 Gerard H Koppelman  39 Inger Kull  40 Xueling Lu  41 Léa Maitre  42   5   43 Dan Mason  27 Erik Melén  44 Simon K Merid  44 Peter L Molloy  45 Trevor A Mori  16 Rosa H Mulder  46 Christian M Page  47 Rebecca C Richmond  8 Stefan Röder  25 Jason P Ross  48 Laura Schellhas  49 Sylvain Sebert  50 Dean Sheppard  51 Harold Snieder  41 Anne P Starling  52 Dan J Stein  53 Gwen Tindula  54 Marinus H van IJzendoorn  55   56   57 Judith Vonk  58   59 Esther Walton  60 Jonathan Witonsky  61 Cheng-Jian Xu  62   63 Ivana V Yang  64 Paul D Yousefi  8 Heather J Zar  65 Ana C Zenclussen  25 Hongmei Zhang  66 Henning Tiemeier  67   68 Stephanie J London  69 Janine F Felix  70   71 Charlotte Cecil  67   72   73
Affiliations
Meta-Analysis

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

Alexander Neumann et al. Genome Med. .

Abstract

Background: DNA methylation (DNAm) is a developmentally dynamic epigenetic process; yet, most epigenome-wide association studies (EWAS) have examined DNAm at only one timepoint or without systematic comparisons between timepoints. Thus, it is unclear whether DNAm alterations during certain developmental periods are more informative than others for health outcomes, how persistent epigenetic signals are across time, and whether epigenetic timing effects differ by outcome.

Methods: We applied longitudinal meta-regression models to published meta-analyses from the PACE consortium that examined DNAm at two timepoints-prospectively at birth and cross-sectionally in childhood-in relation to the same child outcome (ADHD symptoms, general psychopathology, sleep duration, BMI, asthma). These models allowed systematic comparisons of effect sizes and statistical significance between timepoints. Furthermore, we tested correlations between DNAm regression coefficients to assess the consistency of epigenetic signals across time and outcomes. Finally, we performed robustness checks, estimated between-study heterogeneity, and tested pathway enrichment.

Results: Our findings reveal three new insights: (i) across outcomes, DNAm effect sizes are consistently larger in childhood cross-sectional analyses compared to prospective analyses at birth; (ii) higher effect sizes do not necessarily translate into more significant findings, as associations also become noisier in childhood for most outcomes (showing larger standard errors in cross-sectional vs prospective analyses); and (iii) DNAm signals are highly time-specific, while also showing evidence of shared associations across health outcomes (ADHD symptoms, general psychopathology, and asthma). Notably, these observations could not be explained by sample size differences and only partly to differential study-heterogeneity. DNAm sites changing associations were enriched for neural pathways.

Conclusions: Our results highlight developmentally-specific associations between DNAm and child health outcomes, when assessing DNAm at birth vs childhood. This implies that EWAS results from one timepoint are unlikely to generalize to another. Longitudinal studies with repeated epigenetic assessments are direly needed to shed light on the dynamic relationship between DNAm, development and health, as well as to enable the creation of more reliable and generalizable epigenetic biomarkers. More broadly, this study underscores the importance of considering the time-varying nature of DNAm in epigenetic research and supports the potential existence of epigenetic "timing effects" on child health.

Keywords: ADHD; Asthma; BMI; Child psychiatry; DNA methylation; Epigenetics; Longitudinal analysis; Meta-analysis; Pediatrics; Sleep.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: The Erasmus MC Medical Ethics Review Committee (approval number MEC-2012-165) and respective local ethics committees approved the studies included in the meta-analysis and all studies obtained informed consent, only publicly available data has been used for the analyses. See original publications for details [7–9, 18, 19]. This research confirms with the principles of the Helsinki Declaration. Consent for publication: Not applicable. Competing interests: The authors declare that they do not have any competing interests.

Figures

Fig. 1
Fig. 1
Mean effect sizes and statistical significance for DNAm at birth and in childhood. Mean effect sizes (left column) and mean statistical significance (right column) across all tested autosomal DNAm sites per outcome (color) and timepoint. Upper row displays results from analyses utilizing the maximum available sample sizes. Lower row displays results from analyses with cohorts removed to achieve equal sample sizes at both timepoints. Effect size is given as absolute regression coefficient (|‾β|), representing the difference in child health outcomes in SD between full or no methylation in the case of continuous outcomes (ADHD, general psychopathology, sleep duration, and BMI), or log(odds ratio) for categorical outcomes (asthma diagnosis). Statistical significance is given as mean absolute Z-values
Fig. 2
Fig. 2
QQ-plots. Distribution of observed p-values (y-axis) vs expected (x-axis). Diagonal represents the expected distribution of p-values by chance. Upwards deviations indicate a higher presence of lower p-values than expected assuming a null effect. Distributions are given for DNAm effects at birth (left), in childhood (middle), and for change in effect between birth and childhood (right) per outcome (color). Gray displays the 95% confidence interval of the null distribution
Fig. 3
Fig. 3
Correlations between DNAm effects at birth and childhood and across outcomes. This correlation matrix displays Spearman correlations between regression coefficients for DNAm at birth and childhood and across outcomes. Intensity of red represents higher positive correlations and blue lower negative correlations

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