1. Introduction
Epigenetic modifications represent a possible link between dietary intake and disease risk. Several studies support the idea that diet may be actively involved in epigenetic regulation which eventually impacts the development of chronic diseases, including cardiometabolic diseases [
1]. Rather than focusing on nutrients, analyzing food groups and dietary patterns is more appropriate, as the results are easier to translate to public health recommendations. DNA methylation is one of the epigenetic regulatory mechanisms that can affect gene expression in one of two ways, either by enhancing or suppressing gene expression, for example by enhancing the binding capacity of transcription factors [
2]. About 1% of all nucleic acids in the human genome are methylated cytosines, most of which are preceded by a guanine base, called CpG sites. Enriched CpG regions, called CpG islands (CGIs), are roughly 1000 base pairs long with a higher CpG density than the remaining genome [
2].
Epigenome-wide association studies (EWAS) hypothesized a role of folic acid, vitamin B12 and methyl group donors in DNA methylation pattern trajectories [
3]. So far, however, study results are not consistent with this theory [
4,
5], instead supporting the idea that the supply of methyl groups (methionine, betaine, choline) or vitamins involved in the C1 pathway are not a major determinant of CpG site methylation. Another hypothesis refers to the impact of diet on systemic inflammation, acknowledging that inflammatory processes themselves can lead to disturbance in the balance of DNA methylation patterns [
3] and therefore might be a pathway of altering DNA methylation through diet. Dietary EWAS mostly focused on nutrients and more recent work analyzed dietary patterns [
6]. Only a few EWAS analyzing food groups have so far been performed [
7], which leaves a gap to be filled. Differential DNA methylation is strongly associated with metabolic derangements such as cancer or obesity [
3,
8]. Including information about metabolic status into a diet-DNA methylation analysis can give valuable insight about effect modification by metabolic profiles [
9]. The estimation of clusters of subjects with homogenous metabolic characteristics within each cluster (also called subgroup) is a possible approach. Pooling multiple metabolic characteristics into one cluster takes the wide facets of interactions between them into account and thus qualifies as a suitable solution to test for metabolic effect modification. Based on a few standard clinical parameters, the definition of so-called metabotypes by the k-means procedure has been described by both our group and others [
9,
10]. We hypothesize that there will be different methylation trajectories in reaction to usual dietary intake in distinct metabolic situations as characterized by metabotypes.
In this cross-sectional exploratory analysis of participants in the population-based KORA FF4 study using data from the Infinium MethylationEPIC BeadChip array, our primary research goal was to examine the effect modification of usual dietary food group intake by metabotype on DNA methylation. Further analysis included examining the basic association of food groups with DNA methylation. Various food groups were analyzed, with a particular focus on food groups that provide the nutrients involved in C1 metabolism or inflammatory processes.
3. Results
Overall, 595 male and 666 female study participants were included. The participants had a median age of 58 years, a median BMI of 26.8 kg/m
2 and had a total daily energy intake of ~1800 kcal (
Table 1 and
Table 2). Metabotypes differed by sex and age. As indicated in
Table 1 and
Table 2, participants in metabotype subgroup 3 were older and more likely to be male, while a higher proportion of women and younger participants were assigned to metabotype 1.
Table 3 shows the median usual dietary intake of food groups and nutrients stratified by sex and metabotype. We analyzed several food groups for an association with DNA methylation in the basic analysis. With a Bonferroni-adjusted
p-value (and an alpha threshold of 0.05), we found 1 statistically significant signal for the dietary intake of leafy green vegetables, one signal for root vegetables, three signals for cruciferous vegetables, one signal for onions and garlic, one signal for wine and nine signals for beer (
Table 4). Genes annotated to these CpGs were SLC7A11, PHGDH, CCDC149 and KIFC1, among others. Methylation of cg06690548 (SLC7A11) was associated with wine. The product of this gene is a sodium-independent amino acid transport system that is highly specific for cysteine and glutamate. Two CpGs, which were significantly associated with beer consumption are located in the PHGDH gene, which is translated to phosphoglycerate dehydrogenase and is involved in L-serine synthesis, an amino acid part of the C1-metabolism. We found no significant associations for other exposures. Volcano plots and a table with the results of all analyzed exposures (including hs-CRP, alcohol in g/day and folic acid, which we did for quality checking of our results) can be found in
Table S1 and Figures S1–S38.
Table S1 contains all significant signals and 10 CpGs with the lowest
p-values for food groups where no significant signals were observed at all. For a legend of all
supplementary tables, see
Tables S1–S3 legend.
In the analysis for effect modification of food groups by metabotypes, we evaluated the
p-value of the metabotype interaction terms.
Table 5 contains
p-values for the calculated marginal effect size, the marginal standard error and the interaction
p-value adjusted for genomic inflation and corrected by the FDR—for the 10 lowest
p-values per food group, if available. A table with all statistically significant results of the interaction analysis is provided in
Table S2, including data of the analysis of hs-CRP and the nutrients alcohol and folic acid. FDR-corrected
p-values below an alpha of 0.1 were regarded as statistically significant. We observed much evidence for an effect modification with metabotype for some food groups. These food groups were cruciferous vegetables with 83 signals for mainly metabotype 1 (
Figure 1), cheese with 164 signals for metabotype 3 (
Figure 2), whole grain products with 17 signals for metabotype 3, total meat with seven signals for metabotype 2, eggs with nine signals for metabotypes 2 and 3 and margarine with 81 signals for metabotype 3. Cruciferous and cheese forest plots were produced to show the wide distribution of effect sizes. See
Figures S39–S42 for the remaining forest plots. We checked for genes that appeared multiple times across food groups or in the analysis of one food group. These were ASB16, CCDC149, TMEM88B, KRTAP9-6, and MTHFD1L, which can be found in
Table S2 with color codes and as interaction plots in
Figures S43–S51 section. The most interesting finding of genes that appeared multiple times is MTHFD1L, which translates to the protein methylenetetrahydrofolate dehydrogenase-1 similar to and essentially part of the regeneration of methionine from homocysteine. We found significant signals for CpGs that were annotated to genes that are associated with eye health: RP1L1, EML1, PITPNC1, NRL (see
Figure 3 for interaction plots with calculated marginal effect sizes). Other gene annotations were retinoid X receptor gamma (RXRG), which is a nuclear receptor reacting to retinoic acid, glutathione peroxidase 2 (GPX2), which is a crucial part of the human being’s antioxidant-system and paraoxonase 3 (PON3), which inhibits the oxidation of low-density lipoprotein. The results from the sensitivity analysis, where we accounted for genomic inflation, showed that several associations were no longer statistically significant, although many persisted (see
Table S3 for all results and
Figures S52–S57 for t- and
p-value distribution). For the six food groups that we examined for stability of results, 22 associations remained significant for cruciferous vegetables, 33 associations for cheese, 16 associations for whole grain products, zero associations for total meat and eggs, and all associations remained for margarine. None of the CpG-annotated genes associated with eye health persisted. Some examples of CpG sites that were still significant are those annotated to MTHFD1L, HFE, CDH4, TLR5 and 3 of 4 CpGs that were annotated to TMEM88B. In the sensitivity analysis accounting for physical activity and menopause, the
p-value for all signals remained <0.05, except for one in the food group cruciferous for metabotype 3, see
Table S4.
4. Discussion
This is the first comprehensive diet EWAS investigating usual food group consumption and effect modification by the participants’ metabolic status as reflected by metabotype clusters. Independent of metabotype, we discovered only very few associations for leafy green vegetables, root vegetables, cruciferous vegetables, onions and garlic, and wine and beer. The main findings of this study are, however, the many interaction effects between food groups and CpG methylation for different metabotype clusters. This highlights the importance of the metabolic characteristics of participants in studies of diet and EWAS.
In our basic model (without metabotype), the most signals were found for beer. Alcohol could be one driving factor for these associations. High consumption of beer in Bavaria, Germany leads to high statistical power, which could explain why there are very few associations in wine and spirits. Additionally, the complex composition of beer, with metabolites generated by yeast and bioactive compounds of hops could be a driving factor for the many associations of DNA methylation and beer [
25]. We also tested for folic acid and showed once again that an association of folic acid and DNA methylation in EWAS is not clear [
4]. In comparison to Karabegovic et al. [
7] we found no association of DNA methylation and either coffee or tea. It is worth noting that they found 11 significant signals with a sample size tenfold of ours, therefore it is clear that the power of our study could be too small to observe these signals as well. The gene SCRIN1, annotated for a CpG signals associated with cruciferous consumption with a positive direction of the effect estimate, encodes a protein which can lead to impaired cell spreading and migration due to inhibiting SRC activity [
33]. We use the CpG features and prior knowledge to interpret this finding in this work. Since cruciferous vegetables are often associated with anti-cancer properties [
34], it can be assumed that methylation of this gene would lead to enhanced expression. In contrast, the region lies within a CGI, which is often interpreted as an indication of gene suppression if located near a transcription start site (TSS) [
35]. However, this locus lies within the gene body, and DNA methylation at loci in the gene body are sometimes interpreted as a gene expression-enhancing factor [
36]. The significant signal associated with the food group onions and garlic is cg10399824, which is annotated with the GRK5 gene. This gene is associated with different conditions, such as cartilage degradation [
37], cardiac hypertrophy [
38], and renal cell carcinoma [
39]. The literature supports the idea that components of this food group can be connected to all of these conditions [
40,
41,
42].
In our interaction model, statistically significant interactions with metabotype are apparent for many food group-CpG associations. Most of the significant findings refer to the food groups cruciferous, cheese, whole grain products, margarine, eggs, and total meat. The effect of cruciferous vegetables on changes in DNA methylation can be partially explained by the nutrient and phytochemical profile. Almost all significant signals we found for cruciferous intake were significant in metabotype cluster 1. Cg05305046 lies near the TSS of the CARD6 gene and its methylation level is positively associated with cruciferous consumption, most likely leading to repression of gene expression. Notably, the CARD6 gene can lead to activation of the transcription factor NF-kappa B [
43], which often leads to activation of genes involved in inflammation. Among the phytochemicals that could affect DNA methylation, the isothiocyanate sulforaphane was shown to down-regulate DNA methyltransferase (DNMT) activity, resulting in promoter demethylation and enhanced expression (to normal concentration) of antioxidative metabolites such as glutathione S-transferase pi 1 or erythroid 2-related factor 2 [
34,
44].
Interaction analysis of the food group cheese obtained significant signals associated with the following genes RP1L1, NRL, EML1, and PITPNC1. These are involved in the function of photoreceptors in the eye or diseases affecting the eye, such as diabetic retinopathy (DR) [
33]. Yan et al. showed an inverse association of cheese consumption with DR [
45]. Additionally, high cheese consumption is associated with lower serum UA concentration [
46] and studies have shown a direct association between UA concentration and diabetic retinopathy [
47,
48]. The NRL gene was also observed to be associated with proliferative DR [
49]. Interestingly, the study of Yan et al. has shown that the association of cheese intake and DR is enhanced in a subgroup analysis in participants with a BMI > 25, which supports our result of the interaction effects in participants attributed to metabotype cluster 3. Cheese contains a variety of nutrients and bioactive substances, including fat-soluble vitamins, minerals (especially calcium), and mostly casein as the form of protein [
50]. However, few significant signals were identified for consumption of dairy products (with a similar nutrient profile). It is possible that the antioxidative potential of cheese [
51], in combination with the high casein content, is a major component driving the significant CpG associations.
Similar to the interpretation of the associations with cheese consumption, the statistically significant findings for margarine, meat, eggs, or whole grain product consumption with DNA methylation may be driven by their effects on metabolic derangements. The consumption of meat could exert effects on DNA methylation via effects on elevated plasma metabolites, for example, and red meat may modulate plasma LDL-cholesterol and HDL cholesterol concentrations [
52].
In addition, associations between DNA methylation status and HDL cholesterol have been reported previously [
53]. Whole grain products were associated with a CpG, annotated to SMAD7 (see
Figure 4), which has a mechanistic role in the protection of the kidney in participants with diabetes [
54]. Additionally, reverse causality is possible, for example, as participants with known elevated blood non-HDL cholesterol concentrations may follow a diet rich in polyunsaturated fatty acids and low in saturated fatty acids in response. Margarine could be either part of or a proxy of such a diet. Margarine intake in our study population is low and it seems surprising that such minor intake could have effects on DNA methylation.
We did not find any significant signals for the dietary scores AHEI and MDS. We assumed substantial effects on DNA methylation based on the epidemiological evidence regarding these scores and chronic diseases [
19], especially in participants at high risk [
55]. One explanation could be that their favorable effects are not mediated by modification of DNA methylation. Since the metabotype clustering is based on five metabolic parameters, i.e., fasting serum HDL cholesterol, non-HDL cholesterol, plasma glucose, UA and BMI, the question of whether there are some driving variables is valid. We did another interaction analysis using a metabotype clustering approach, replacing UA by triglycerides. The obtained results (not shown) support the idea that UA is a driver of some of the effect modification by metabotype on DNA methylation as observed here. However, the clusters represent the complex metabolic characteristic of the individuals.
Our study has several strengths. First, we calculated habitual dietary data using a blended approach, i.e., combining repeated 24-h recalls and FFQ data, leading to more valid and precise intake estimates as compared to FFQ data alone [
56]. Second, we investigated interaction terms instead of stratification of our population, resulting in increased statistical power due to the inclusion of the data of all selected confounders for all participants. Third, to avoid effects being present due to genomic inflation, we used the bacon package in the sensitivity analysis to estimate the empirical null distribution and reduce bias and inflation [
28]. Fourth, we saw very consistent results in our interaction analysis, with almost exclusively one metabotype per food group.
Our study also presents some limitations. Our dietary data did not include information about the origin of the food; therefore, it is possible that there is noise in the data regarding organic or conventional origins of our vegetable and meat food groups. Pesticides or different nutrient composition could affect the association of the food groups with DNA methylation [
57]. We cannot rule out that some remaining bias arose from diet affecting leukocyte composition and therefore led to changed DNA methylation patterns due to different cell type composition, though we adjusted for cell counts. Since gene expression data are lacking, observed changes in DNA methylation cannot clearly be translated to metabolic changes. We also only had access to whole blood cells, so we cannot draw any tissue-specific conclusions. On a statistical note, despite the debate about the focus on
p-values [
58], we followed this concept because of the explorative nature of this study to have an absolute threshold to decide if we should follow-up on a signal or not. Due to the cross-sectional nature of our study, we cannot conclude on causality and residual confounding cannot be excluded.
In conclusion, the effect modification by metabotype is apparent for various food groups, which underlines the importance of including information on the metabolic state of participants in diet EWAS, though different metabotype definitions may achieve different results. We tested for several food groups and there were few significant signals obtained in the analysis without metabotype. Based on the findings of the interaction analysis, many gene annotations regarding eye health, inflammation and antioxidative system were observed and should be followed up in further studies—especially longitudinal, replication and experimental studies addressing functional consequences of methylation status.