Dataset Information

Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.

ABSTRACT: Coffee and tea are extensively consumed beverages worldwide which have received considerable attention regarding health. Intake of these beverages is consistently linked to, among others, reduced risk of diabetes and liver diseases; however, the mechanisms of action remain elusive. Epigenetics is suggested as a mechanism mediating the effects of dietary and lifestyle factors on disease onset. Here we report the results from epigenome-wide association studies (EWAS) on coffee and tea consumption in 15,789 participants of European and African-American ancestries from 15 cohorts. EWAS meta-analysis of coffee consumption reveals 11 CpGs surpassing the epigenome-wide significance threshold (P-value <1.1×10^-7), which annotated to the AHRR, F2RL3, FLJ43663, HDAC4, GFI1 and PHGDH genes. Among them, cg14476101 is significantly associated with expression of the PHGDH and risk of fatty liver disease. Knockdown of PHGDH expression in liver cells shows a correlation with expression levels of genes associated with circulating lipids, suggesting a role of PHGDH in hepatic-lipid metabolism. EWAS meta-analysis on tea consumption reveals no significant association, only two CpGs annotated to CACNA1A and PRDM16 genes show suggestive association (P-value <5.0×10^-6). These findings indicate that coffee-associated changes in DNA methylation levels may explain the mechanism of action of coffee consumption in conferring risk of diseases.

SUBMITTER: Karabegovic I

PROVIDER: S-EPMC8121846 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.

Karabegović Irma I Portilla-Fernandez Eliana E Li Yang Y Ma Jiantao J Maas Silvana C E SCE Sun Daokun D Hu Emily A EA Kühnel Brigitte B Zhang Yan Y Ambatipudi Srikant S Fiorito Giovanni G Huang Jian J Castillo-Fernandez Juan E JE Wiggins Kerri L KL de Klein Niek N Grioni Sara S Swenson Brenton R BR Polidoro Silvia S Treur Jorien L JL Cuenin Cyrille C Tsai Pei-Chien PC Costeira Ricardo R Chajes Veronique V Braun Kim K Verweij Niek N Kretschmer Anja A Franke Lude L van Meurs Joyce B J JBJ Uitterlinden André G AG de Knegt Robert J RJ Ikram M Arfan MA Dehghan Abbas A Peters Annette A Schöttker Ben B Gharib Sina A SA Sotoodehnia Nona N Bell Jordana T JT Elliott Paul P Vineis Paolo P Relton Caroline C Herceg Zdenko Z Brenner Hermann H Waldenberger Melanie M Rebholz Casey M CM Voortman Trudy T Pan Qiuwei Q Fornage Myriam M Levy Daniel D Kayser Manfred M Ghanbari Mohsen M

Nature communications 20210514 1

Coffee and tea are extensively consumed beverages worldwide which have received considerable attention regarding health. Intake of these beverages is consistently linked to, among others, reduced risk of diabetes and liver diseases; however, the mechanisms of action remain elusive. Epigenetics is suggested as a mechanism mediating the effects of dietary and lifestyle factors on disease onset. Here we report the results from epigenome-wide association studies (EWAS) on coffee and tea consumption ...[more]

PMID: 33990564

Similar Datasets

Project description:ObjectivesThis meta-analysis aims to quantify the relationship between coffee and tea consumption and the risk of osteoporosis and explore whether such consumption positively or negatively impacts this risk, thereby providing a scientific basis for understanding the effects of coffee and tea on bone health.MethodsWe systematically searched PubMed, the Cochrane Library, and Embase for observational studies published up to November 5, 2024, using medical subject headings (MeSH) and keywords related to "osteoporosis, tea, and coffee." Statistical analyses were conducted using Stata software version 14.0. A fixed-effects model was used when heterogeneity was low (I 2 ≤ 50% and p > 0.1). A random-effects model was used for greater heterogeneity (I 2 > 50%). Publication bias was assessed using funnel plots and Egger's regression tests.ResultsThis meta-analysis included 14 observational studies comprising 562,838 participants published between 2008 and 2024. The pooled analysis showed that coffee consumption is significantly associated with a reduced risk of osteoporosis (odds ratio [OR] = 0.79, 95% confidence interval [CI]: 0.73-0.84, I 2 = 28.9%, p < 0.05). Tea consumption also demonstrated a protective effect, with a lower risk of osteoporosis (OR = 0.75, 95% CI: 0.62-0.91, I 2 = 80.4%, p < 0.05). Subgroup analysis revealed that high-frequency coffee consumption (more than one cup per day) was associated with a greater reduction in osteoporosis risk (OR = 0.83, 95% CI: 0.74-0.93, p = 0.001) compared to low-frequency consumption (less than one cup per day), which showed no statistically significant reduction (OR = 0.86, 95% CI: 0.68-1.07, p = 0.171). Similarly, high-frequency tea consumption (more than four times per week) exhibited a slightly stronger protective effect against osteoporosis compared to low-frequency consumption (OR = 0.82, 95% CI: 0.70-0.97, p = 0.02).ConclusionThis meta-analysis suggests that long-term coffee and tea consumption is associated with a reduced risk of osteoporosis. Moreover, a higher frequency of consumption within a moderate range appeared to enhance the protective effect against osteoporosis.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42024612101, PROSPERO CRD42024612101.

Project description:BackgroundPanic disorder (PD) is considered to be a multifactorial disorder emerging from interactions among multiple genetic and environmental factors. To date, although genetic studies reported several susceptibility genes with PD, few of them were replicated and the pathogenesis of PD remains to be clarified. Epigenetics is considered to play an important role in etiology of complex traits and diseases, and DNA methylation is one of the major forms of epigenetic modifications. In this study, we performed an epigenome-wide association study of PD using DNA methylation arrays so as to investigate the possibility that different levels of DNA methylation might be associated with PD.MethodsThe DNA methylation levels of CpG sites across the genome were examined with genomic DNA samples (PD, N = 48, control, N = 48) extracted from peripheral blood. Methylation arrays were used for the analysis. β values, which represent the levels of DNA methylation, were normalized via an appropriate pipeline. Then, β values were converted to M values via the logit transformation for epigenome-wide association study. The relationship between each DNA methylation site and PD was assessed by linear regression analysis with adjustments for the effects of leukocyte subsets.ResultsForty CpG sites showed significant association with PD at 5% FDR correction, though the differences of the DNA methylation levels were relatively small. Most of the significant CpG sites (37/40 CpG sites) were located in or around CpG islands. Many of the significant CpG sites (27/40 CpG sites) were located upstream of genes, and all such CpG sites with the exception of two were hypomethylated in PD subjects. A pathway analysis on the genes annotated to the significant CpG sites identified several pathways, including "positive regulation of lymphocyte activation."ConclusionsAlthough future studies with larger number of samples are necessary to confirm the small DNA methylation abnormalities associated with PD, there is a possibility that several CpG sites might be associated, together as a group, with PD.

Dataset Information

Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.

Publications

Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets