A meta-analysis of epigenome-wide association studies of ultra-processed food consumption with DNA methylation in European children

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• dc.contributor.author Llauradó-Pont, Joana
• dc.contributor.author Stratakis, Nikos
• dc.contributor.author Vrijheid, Martine
• dc.contributor.author Bustamante Pineda, Mariona
• dc.contributor.author Lassale, Camille
• dc.date.accessioned 2025-02-25T07:29:32Z
• dc.date.available 2025-02-25T07:29:32Z
• dc.date.issued 2025
• dc.description.abstract Background/objective: There is limited knowledge on how diet affects the epigenome of children. Ultra-processed food (UPF) consumption is emerging as an important factor impacting health, but mechanisms need to be uncovered. We therefore aimed to assess the association between UPF consumption and DNA methylation in children. Methods: We conducted a meta-analysis of epigenome-wide association studies (EWAS) from a total of 3152 children aged 5-11 years from four European studies (HELIX, Generation XXI, ALSPAC, and Generation R). UPF consumption was defined applying the Nova food classification system (group 4), and DNA methylation was measured in blood with Illumina Infinium Methylation arrays. Associations were estimated within each cohort using robust linear regression models, adjusting for relevant covariates, followed by a meta-analysis of the resulting EWAS estimates. Results: Although no CpG was significant at FDR level, we found suggestive associations (p-value < 10-5) between UPF consumption and methylation at seven CpG sites. Three of them, cg00339913 (PHYHIP), cg03041696 (intergenic), and cg03999434 (intergenic), were negatively associated, whereas the other four, cg14665028 (NHEJ1), cg18968409 (intergenic), cg24730307 (intergenic), and cg09709951 (ATF7), were positively associated with UPF intake. These CpGs have been previously associated with health outcomes such as carcinomas, and the related genes are mainly involved in pathways related to thyroid hormones and liver function. Conclusion: We only found suggestive changes in methylation at 7 CpGs associated with UPF intake in a large EWAS among children: although this shows a potential impact of UPF intake on DNAm, this might not be a key mechanism underlying the health effects of UPFs in children. There is a need for more detailed dietary assessment in children studies and of intervention studies to assess potential epigenetic changes linked to a reduction in UPF in the diet.
• dc.description.sponsorship We are grateful to participants in all cohorts included in the four studies (HELIX, Generation XXI, ALSPAC and Generation R) across countries who have generously given their time and collaborated in the studies. The HELIX cohort received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) [grant number 308333]. Joana Llauradó-Pont has received support from the European Union—NextGenerationEU and the Spanish government, under the Investigo Programme (grant ID: 2022 INV-1 00046). Camille Lassale is supported by a Ramon y Cajal Fellowship RYC2020-029599 funded by MICIU/AEI/https://doi.org/10.13039/501100011033 and the European Social Fund 'Invest in your future'. Nikos Stratakis has been supported from the European Union’s Horizon Europe research and innovation programme under the Marie Skłodowska-Curie Actions (MSCA) Postdoctoral Fellowships (grant ID: 101059245), from the Ministry of Science and Innovation and State Research Agency through the 'Centro de Excelencia Severo Ochoa 2019–2023' Program (CEX2018-000806-S) and by a Juan de la Cierva-Incorporación fellowship (IJC2020-043630-I) financed by Ministerio de Ciencia e Innovación (MCIN)/Agencia Estatal de Investigación (AEI)/https://doi.org/10.13039/501100011033 and the European Union 'NextGenerationEU/PRTR'. Oliver Robinson was supported by a UKRI Future Leaders Fellowship (MR/S03532X/1). This work received funding from the European Union’s Horizon 2020 research and innovation programme (774548, STOP; 874739, LongITools; 874583, EUCAN-Connect) and from the European Joint Programming Initiative 'A Healthy Diet for a Healthy Life' (JPI HDHL, NutriPROGRAM project, ZonMw the Netherlands no.529051022 and PREcisE project ZonMw the Netherlands no.529051023). Details of funding for each study and for contributions of individual studies can be found in Supplementary material S3. No funders listed here or in Supplementary material S3 influenced the study aim, design, analysis or interpretation of results. The results expressed here are those of the authors and not necessarily any listed funder.
• dc.format.mimetype application/pdf
• dc.identifier.citation Llauradó-Pont J, Stratakis N, Fiorito G, Handakas E, Neumann A, Barros H, et al. A meta-analysis of epigenome-wide association studies of ultra-processed food consumption with DNA methylation in European children. Clin Epigenetics. 2025 Jan 7;17(1):3. DOI: 10.1186/s13148-024-01782-z
• dc.identifier.doi http://dx.doi.org/10.1186/s13148-024-01782-z
• dc.identifier.issn 1868-7075
• dc.identifier.uri http://hdl.handle.net/10230/69726
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Clin Epigenetics. 2025 Jan 7;17(1):3
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/308333
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RYC2020-029599
• dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101059245
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/774548
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/874739
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/874583
• dc.rights © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Children
• dc.subject.keyword DNA methylation
• dc.subject.keyword Epigenome-wide association study (EWAS)
• dc.subject.keyword Nutrition
• dc.subject.keyword Ultra-processed food (UPF)
• dc.title A meta-analysis of epigenome-wide association studies of ultra-processed food consumption with DNA methylation in European children
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion