Postprandial alterations in whole-blood DNA methylation are mediated by changes in white blood cell composition

Abstract

Background: DNA methylation is an essential nuclear process associated with genomic functions such as transcription factor binding and the regulation of gene expression. DNA methylation patterns can also serve as potential biomarkers for disease progression and response to therapy. However, the full dynamics of DNA methylation across daily physiologic events have not been fully elucidated. Objective: We sought to study how ingesting a standardized meal acutely affects peripheral blood DNA methylation. Design: We performed an observational study in healthy men (n = 26) on DNA methylation and gene expression in whole blood before and 160 min after the ingestion of a standardized meal. Cytosinephosphate-guanine (CpG) methylation was assayed on the HumanMethylation450k microarray, and gene expression was measured with the Human Gene 2.1 ST Array. Results: Differential methylation after food intake was detected in 13% of the analyzed probes (63,207 CpG probes) at a 5% false discovery rate (FDR). This effect was driven by changes in leukocyte fractions as estimated from comparisons against methylation datasets generated from sorted leukocytes. When methylation values were adjusted for estimated leukocyte fractions, 541 probes were observed to be altered in the postprandial state (5% FDR). Conclusions: Apparent alterations in DNA methylation 160 min after meal ingestion mainly reflect changes in the estimated leukocyte population in whole blood. These results have major methodologic implications for genome-wide methylation studies because they highlight the strong underlying effects of changes in leukocyte fractions on CpG methylation patterns as well as the potential importance of meal-standardized sampling procedures for future investigations when alterations in white blood cell fractions are unavailable. This trial was registered at clinicaltrials.gov as LSF008786.Am J Clin Nutr 2016;104:518-25.

Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes

“…The patient population was as homogenous as found reasonable, excluding subjects with psychotic illness, alcohol or drug abuse, other psychiatric disease requiring immediate treatment and other severe physical illness. However, other potential confounding factors, e.g., dietary patterns, ethnicity or prandial states may be able to induce changes in methylation patterns as well [40]. Furthermore, as the mean difference in per cent DNA methylation between HD patients and healthy volunteers was only~2.6% it can be called into question what impact such small methylation changes would have on physiology.…”

“…The association analyses between DNA methylation and hypersexuality were tested with linear models using the 'limma' package for R, applying an empirical Bayes method based on a moderated t-statistic [39,40]. These linear regressions using limma have been previously considered fitting for large-scale methylation studies [39,40]. For statistical analysis, we transformed the beta values to M-values, which have been shown to be statistically more robust [41].…”

“…Tang et al demonstrated that this cut-off resulted in a sensitivity for alcohol dependence of 98.6%, a specificity of 58.2%, a positive predictive value of 0.538 and a negative predictive value of 0.988 [38]. To exclude any potential confound from white blood cell type heterogeneity, which has been shown to impact the DNA methylation pattern [40], we compared the relative proportions of B-cells, CD4 T-cells, CD8 T-cells, granulocytes and monocytes between subjects stratified as alcohol dependent and controls using unpaired t-tests. We then considered initially the following variables as potential confounders on the association analysis between DNA methylation and alcohol dependence, i.e., age, gender, BMI, and the occurrence of any under treatment depressive disorder, anxiety disorder, bipolar disorder or post-traumatic stress disorder.…”

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score

“…More details about this healthy group as well as about preprocessing of the methylation specimens and expression patterns in this cohort can be found elsewhere. 16 …”

Imaging Genetics and Genomics in Psychiatry: A Critical Review of Progress and Potential

“…It is also important to highlight that while integrative approaches will undoubtedly lead to greater etiologic insight, unique challenges need to be actively confronted. For example, because methylation is dynamic (143), with evidence that even proximal experiences (e.g., meal consumption), shape its landscape and measurement (144), it will be important for imaging genetics studies to collect DNA samples temporally linked to imaging data.…”