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Dwaraka VB, Aronica L, Carreras-Gallo N, Robinson JL, Hennings T, Carter MM, Corley MJ, Lin A, Turner L, Smith R, Mendez TL, Went H, Ebel ER, Sonnenburg ED, Sonnenburg JL, Gardner CD. Unveiling the epigenetic impact of vegan vs. omnivorous diets on aging: insights from the Twins Nutrition Study (TwiNS). BMC Med 2024; 22:301. [PMID: 39069614 DOI: 10.1186/s12916-024-03513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Geroscience focuses on interventions to mitigate molecular changes associated with aging. Lifestyle modifications, medications, and social factors influence the aging process, yet the complex molecular mechanisms require an in-depth exploration of the epigenetic landscape. The specific epigenetic clock and predictor effects of a vegan diet, compared to an omnivorous diet, remain underexplored despite potential impacts on aging-related outcomes. METHODS This study examined the impact of an entirely plant-based or healthy omnivorous diet over 8 weeks on blood DNA methylation in paired twins. Various measures of epigenetic age acceleration (PC GrimAge, PC PhenoAge, DunedinPACE) were assessed, along with system-specific effects (Inflammation, Heart, Hormone, Liver, and Metabolic). Methylation surrogates of clinical, metabolite, and protein markers were analyzed to observe diet-specific shifts. RESULTS Distinct responses were observed, with the vegan cohort exhibiting significant decreases in overall epigenetic age acceleration, aligning with anti-aging effects of plant-based diets. Diet-specific shifts were noted in the analysis of methylation surrogates, demonstrating the influence of diet on complex trait prediction through DNA methylation markers. An epigenome-wide analysis revealed differentially methylated loci specific to each diet, providing insights into the affected pathways. CONCLUSIONS This study suggests that a short-term vegan diet is associated with epigenetic age benefits and reduced calorie intake. The use of epigenetic biomarker proxies (EBPs) highlights their potential for assessing dietary impacts and facilitating personalized nutrition strategies for healthy aging. Future research should explore the long-term effects of vegan diets on epigenetic health and overall well-being, considering the importance of proper nutrient supplementation. TRIAL REGISTRATION Clinicaltrials.gov identifier: NCT05297825.
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Affiliation(s)
- Varun B Dwaraka
- TruDiagnostic, Inc, 881 Corporate Dr, Lexington, KY, 40503, USA.
| | - Lucia Aronica
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, 3180 Porter Dr, Palo Alto, Stanford, CA, 94305, USA
| | | | - Jennifer L Robinson
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, 3180 Porter Dr, Palo Alto, Stanford, CA, 94305, USA
| | - Tayler Hennings
- Seattle Children's Research Institute, Seattle, WA, 98101, USA
| | - Matthew M Carter
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, CA, USA
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Aaron Lin
- TruDiagnostic, Inc, 881 Corporate Dr, Lexington, KY, 40503, USA
| | - Logan Turner
- TruDiagnostic, Inc, 881 Corporate Dr, Lexington, KY, 40503, USA
| | - Ryan Smith
- TruDiagnostic, Inc, 881 Corporate Dr, Lexington, KY, 40503, USA
| | - Tavis L Mendez
- TruDiagnostic, Inc, 881 Corporate Dr, Lexington, KY, 40503, USA
| | - Hannah Went
- TruDiagnostic, Inc, 881 Corporate Dr, Lexington, KY, 40503, USA
| | - Emily R Ebel
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, CA, USA
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, CA, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford University, Palo Alto, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher D Gardner
- Stanford Prevention Research Center, Department of Medicine, School of Medicine, Stanford University, 3180 Porter Dr, Palo Alto, Stanford, CA, 94305, USA.
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Hellbach F, Freuer D, Meisinger C, Peters A, Winkelmann J, Costeira R, Hauner H, Baumeister SE, Bell JT, Waldenberger M, Linseisen J. Usual dietary intake and change in DNA methylation over years: EWAS in KORA FF4 and KORA fit. Front Nutr 2024; 10:1295078. [PMID: 38249614 PMCID: PMC10799384 DOI: 10.3389/fnut.2023.1295078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Changes in DNA methylation can increase or suppress the expression of health-relevant genes. We investigated for the first time the relationship between habitual food consumption and changes in DNA methylation. Methods The German KORA FF4 and KORA Fit studies were used to study the change in methylation over a median follow-up of 4 years. Only subjects participating in both surveys and with available dietary and methylation data were included in the analysis (n = 465). DNA methylation was measured using the Infinium MethylationEPIC BeadChip (Illumina), resulting in 735,527 shared CpGs across both studies. Generalized estimating equation models with an interaction term of exposure and time point were used to analyze the association of 34 food groups, folic acid, and two dietary patterns with changes in DNA methylation over time. Results The results were corrected for genomic inflation. Significant interaction terms indicate different effects between both time points. We observed only a few significant associations between food intake and change in DNA methylation, except for cream and spirit consumption. The annotated genes include CLN3, PROM1, DLEU7, TLL2, and UGT1A10. Discussion We identified weak associations between food consumption and DNA methylation change. The differential results for cream and spirits, both consumed in low quantities, require replication in independent studies.
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Affiliation(s)
- Fabian Hellbach
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Dennis Freuer
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Christa Meisinger
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Annette Peters
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Technical University of Munich, Institute of Human Genetics, Klinikum Rechts der Isar, Munich, Germany
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- School of Medicine, Institute of Nutritional Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian-Edgar Baumeister
- Medical Faculty, Institute of Health Services Research in Dentistry, University of Münster, Münster, Germany
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jakob Linseisen
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
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Costeira R, Evangelista L, Wilson R, Yan X, Hellbach F, Sinke L, Christiansen C, Villicaña S, Masachs OM, Tsai PC, Mangino M, Menni C, Berry SE, Beekman M, van Heemst D, Slagboom PE, Heijmans BT, Suhre K, Kastenmüller G, Gieger C, Peters A, Small KS, Linseisen J, Waldenberger M, Bell JT. Metabolomic biomarkers of habitual B vitamin intakes unveil novel differentially methylated positions in the human epigenome. Clin Epigenetics 2023; 15:166. [PMID: 37858220 PMCID: PMC10588110 DOI: 10.1186/s13148-023-01578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND B vitamins such as folate (B9), B6, and B12 are key in one carbon metabolism, which generates methyl donors for DNA methylation. Several studies have linked differential methylation to self-reported intakes of folate and B12, but these estimates can be imprecise, while metabolomic biomarkers can offer an objective assessment of dietary intakes. We explored blood metabolomic biomarkers of folate and vitamins B6 and B12, to carry out epigenome-wide analyses across up to three European cohorts. Associations between self-reported habitual daily B vitamin intakes and 756 metabolites (Metabolon Inc.) were assessed in serum samples from 1064 UK participants from the TwinsUK cohort. The identified B vitamin metabolomic biomarkers were then used in epigenome-wide association tests with fasting blood DNA methylation levels at 430,768 sites from the Infinium HumanMethylation450 BeadChip in blood samples from 2182 European participants from the TwinsUK and KORA cohorts. Candidate signals were explored for metabolite associations with gene expression levels in a subset of the TwinsUK sample (n = 297). Metabolomic biomarker epigenetic associations were also compared with epigenetic associations of self-reported habitual B vitamin intakes in samples from 2294 European participants. RESULTS Eighteen metabolites were associated with B vitamin intakes after correction for multiple testing (Bonferroni-adj. p < 0.05), of which 7 metabolites were available in both cohorts and tested for epigenome-wide association. Three metabolites - pipecolate (metabolomic biomarker of B6 and folate intakes), pyridoxate (marker of B6 and folate) and docosahexaenoate (DHA, marker of B6) - were associated with 10, 3 and 1 differentially methylated positions (DMPs), respectively. The strongest association was observed between DHA and DMP cg03440556 in the SCD gene (effect = 0.093 ± 0.016, p = 4.07E-09). Pyridoxate, a catabolic product of vitamin B6, was inversely associated with CpG methylation near the SLC1A5 gene promoter region (cg02711608 and cg22304262) and with SLC7A11 (cg06690548), but not with corresponding changes in gene expression levels. The self-reported intake of folate and vitamin B6 had consistent but non-significant associations with the epigenetic signals. CONCLUSION Metabolomic biomarkers are a valuable approach to investigate the effects of dietary B vitamin intake on the human epigenome.
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Affiliation(s)
- Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
| | - Laila Evangelista
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Rory Wilson
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Xinyu Yan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Fabian Hellbach
- Epidemiology, Medical Faculty, University Augsburg, University Hospital Augsburg, 86156, Augsburg, Germany
| | - Lucy Sinke
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Olatz M Masachs
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, SE1 9NH, UK
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Karsten Suhre
- Department of Biophysics and Physiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, 80802, Munich, Germany
| | - Annette Peters
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, 80802, Munich, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jakob Linseisen
- Epidemiology, Medical Faculty, University Augsburg, University Hospital Augsburg, 86156, Augsburg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, 80802, Munich, Germany
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
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