Caffeic acid phenethyl ester, a coffee polyphenol, inhibits DNA methylation in vitro and in vivo

Nutrition, DNA methylation and obesity across life stages and generations

Obesity is a complex multifactorial condition that often manifests in early life with a lifelong burden on metabolic health. Diet, including pre-pregnancy maternal diet, in utero nutrition and dietary patterns in early and late life, can shape obesity development. Growing evidence suggests that epigenetic modifications, specifically DNA methylation, might mediate or accompany these effects across life stages and generations. By reviewing human observational and intervention studies conducted over the past 10 years, this work provides a comprehensive overview of the evidence linking nutrition to DNA methylation and its association with obesity across different age periods, spanning from preconception to adulthood and identify future research directions in the field.

Genomic targets and selective inhibition of DNA methyltransferase isoforms

Background

DNA methylation in the human genome is established and maintained by DNA methyltransferases (DNMTs). DNMT isoforms show differential expression by cell lineage and during development, but much remains to be elucidated about their shared and unique genomic targets.

Results

We examined changes in the epigenome following overexpression of 13 DNMT isoforms in HEK293T cells. We observed increased methylation (Δβ > 0.2) at 43,405 CpG sites, with expression of DNMT3A2, DNMTΔ3B4 and DNMTΔ3B2 associated with the greatest impact. De novo methylation occurred primarily within open sea regions and at loci with intermediate methylation levels (β: 0.2–0.6). 53% of differentially methylated loci showed specificity towards a single DNMT subfamily, primarily DNMTΔ3B and DNMT3A and 39% towards a single isoform. These loci were significantly enriched for pathways related to neuronal development (DNMTΔ3B4), calcium homeostasis (DNMTΔ3B3) and ion transport (DNMT3L). Repetitive elements did not display differential sensitivity to overexpressed DNMTs, but hypermethylation of Alu elements was associated with their evolutionary age following overexpression of DNMT3A2, DNMT3B1, DNMT3B2 and DNMT3L. Differential methylation (Δβ > 0.1) was observed at 121 of the 353 loci associated with the Horvath ‘epigenetic clock’ model of ageing, with 51 showing isoform specificity, and was associated with reduction of epigenetic age by 5–15 years following overexpression of seven isoforms. Finally, we demonstrate the potential for dietary constituents to modify epigenetic marks through isoform-specific inhibition of methylation activity.

Conclusions

Our results provide insight into regions of the genome methylated uniquely by specific DNMT isoforms and demonstrate the potential for dietary intervention to modify the epigenome.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-022-01325-4.

Implication of the Mediterranean diet on the human epigenome

Epigenetics, defined as "hereditary changes in gene expression that occur without any change in the DNA sequence", consists of various epigenetic marks, including DNA methylation, histone modifications, and non-coding RNAs. The epigenome, which has a dynamic structure in response to intracellular and extracellular stimuli, has a key role in the control of gene activity, since it is located at the intersection of cellular information encoded in the genome and molecular/chemical information of extracellular origin. The focus shift of studies to epigenetic reprogramming has led to the formation and progressive importance of a concept called "nutriepigenetics", whose aim is to prevent diseases by intervening on nutrition style. Among the diet types adopted in the world, the renowned Mediterranean Diet (MD), being rich in unsaturated fatty acids and containing high levels of whole grain foods and large quantities of fruits, vegetables, and legumes, has shown numerous advantages in excluding chronic diseases. Additionally, the fact that this diet is rich in polyphenols with high antioxidant and anti-inflammatory properties has an undeniable effect in turning some cellular pathways against the disease. It is also apparent that the effects of polyphenols on the epigenome cause changes in mechanisms such as DNA methylation and histone acetylation/deacetylation, which have a regulatory effect on gene regulation. This review presents the effects of long-term consumption of nutrients from the MD on the epigenome and discusses the benefits of this diet in the treatment and even prevention of chronic diseases.

Nutrition and Rheumatoid Arthritis Onset: A Prospective Analysis Using the UK Biobank

Rheumatoid arthritis (RA) is a chronic inflammatory disease that affects the joints. The multifactorial etiopathogenesis of RA has been heavily investigated, but is still only partially understood. Diet can represent both a risk factor and a protective factor, based on some evidence that suggests specific properties of certain foods and their ability to increase/reduce inflammation. To date, the studies done on this topic provide discordant results and are heterogeneous in terms of design and cohort size. In this work, we investigated for the first time the relationship between nutrition and the risk of RA onset using a sample size of about half a million subjects from one of the largest publicly available biobanks that is the UK biobank. Results showed that oily fish, alcohol, coffee and breakfast cereals have protective roles in RA; whereas, tea can increase the risk of RA. In conclusion, the obtained results confirm that diet plays key roles in RA, either by promoting or by preventing RA onset and development. Future research should focus on unravelling the effects of dietary habits on immune-mediated diseases to establish better preventive strategies.

Beverages in Rheumatoid Arthritis: What to Prefer or to Avoid

Background: The role of nutrition in the pathogenesis of rheumatic diseases, including rheumatoid arthritis (RA), has gained increasing attention in recent years. A growing number of studies have focussed on the diverse nutritional contents of beverages, and their possible role in the development and progression of RA. Main body: We aimed to summarise the current knowledge on the role of a range of beverages in the context of RA. Beverages have a key role within the mosaic of autoimmunity in RA and potential to alter the microbiome, leading to downstream effects on inflammatory pathways. The molecular contents of beverages, including coffee, tea, and wine, have similarly been found to interfere with immune signalling pathways, some beneficial for disease progression and others less so. Finally, we consider beverages in the context of wider dietary patterns, and how this growing body of evidence may be harnessed by the multidisciplinary team in patient management. Conclusions: While there is increasing work focussing on the role of beverages in RA, integration of discussions around diet and lifestyle in our management of patients remains sparse. Nutrition in RA remains a controversial topic, but future studies, especially on the role of beverages, are likely to shed further light on this in coming years.