Article summary with Annual Research Review: DNA methylation as a mediator in the association between risk exposure and child and adolescent psychopathology by Barker a.o. - 2018

What is DNA methylation (DNAm)?

DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. DNAm refers to the addition of a methyl group primarily in the context of cytosine guanine (CpG) dinucleotides. CpG sites often cluster in CpG island which tend to be embedded in promoter regions of genes. When located in a gene promoter, DNA methylation typically acts to repress gene transcription, and hence can provide a mechanism that can trigger long-term alterations in phenotypes. Research suggests that DNAm can be sensitive to a range of environmental exposures and thus possibly can be influenced.

What can be the benefits of understanding the role of DNAm?

DNAm seems to be a potential mechanism through which the genome can capture the effects of environmental exposures and propagate their influence, and possibly explain altered biological processes that underlie the emergence of different forms of psychopathology. A better understanding of the role of DNAm can be used in the prevention, detection, and treatment of psychopathology (that is, if DNAm is identified as a causal link in the aetiology of a disease). If DNAm is simply a consequence of disease aetiology, it can still be used as an important biomarker of disease and have clinical utility.

What is an epigenome?

An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism. Epigenetic mechanisms influence dynamic changes in transcription independent of the genomic DNA sequence. Epigenetic modifications are fundamental for the establishment and maintenance of cellular identity and also coordinate many biological processes, such as genomic imprinting, X chromosome inactivation, stress response, immune function, and neurodevelopment. Because epigenetic processes respond to both genetic and environmental factors, they represent a potential mechanism that can help explain the gene-environmental interplay and disease susceptibility. DNAm is an epigenetic mechanism.

How can DNAm be studied?

DNAm can be studies through different approaches:

• Global DNAm is used as a proxy for the overall degree of myelination in the genome. It can be derived through high-performance liquid chromatography or mass spectrophotometry.
• Candidate gene approaches focus on preselected genes based on a priori hypotheses, for example via pyrosequencing.
• Methods to assess DNAm across the genome include whole-genome bisulphate sequencing or array, bead-type hybridization.
• Experimental animal models enable the manipulation of environmental exposures, the investigation of time- and tissue-specific effects on DNAm, and the characterization of downstream consequences on gene expression and behavior.

What effects does nutrition have on DNAm?

DNAm is highly responsive to diet, because nutrients and bioactive compounds can alter the expression of genes at the transcriptional level and result in long-term phenotypic changes. The prenatal diet can be viewed on a spectrum that ranges from undernutrition to overnutrition. Undernutrition is linked to lower DNAm of the IGF2 gene, which is implicated in foetal development, as well as changes in prenatal growth, insulin signaling, birth weight, and low-density lipoprotein cholesterol levels. Overnutrition is linked to greater concentrations of glucose, fatty acids, and inflammatory markers to the developing foetus.

How does exposure to toxins influence DNAm?

Prenatal exposure to bioactive compounds have been shown to affect DNAm patterns in neonates. Children aged 5-7 who were prenatally exposed to maternal smoking showed lower levels of global and CpG-specific methylation in buccal cells. Research shows that some of the effects to the genes are reversible, whereas others show persistently perturbed patterns. Overall, prenatal exposure to teratogens can have long-term impact on the methylome.

How does early-life stress and adversity influence DNAm?

Prenatal and postnatal stress can cause long-term elevations in hypothalamic-pituitary axis reactivity and anxiety-like behaviors. This can partially be explained by altered glucocorticoid receptor gene expression. Research regarding prenatal maternal stress shows different results and more research is required. With regards to postnatal influences, research shows that early exposure to poverty and adversity is associated with altered DNAm. Childhood maltreatment is also associated with changes in DNAm in genes that are important for stress response, immune function, and neurodevelopment. Also, the maltreated children showed different methylation levels across CpG sites which contain markers of physical and psychiatric morbidity.

How do internalizing and externalizing difficulties relate to DNAm and psychopathology?

Research supports a link between higher NR3C1 methylation and internalizing difficulties. However, NR3C1 methylation does not seem to be a significant predictor of internalizing difficulties. This suggests that, if there is an association, it is probably of small effect size. With regards to externalizing difficulties, the research results show many discrepancies. These are due to wide methodological differences across the studies, including differences in sample characteristics, phenotype operationalisation, and analytical strategy.

Does DNAm mediate associations between risk exposures and psychopathology?

Studies show that DNAm can act as a mediator between risk exposure and child psychopathology. However, the results are associational and causality cannot be inferred. Some recommendations are made that may help to move the field forward:

• A more complete and precise understanding of environmental effects on DNAm needs to be reached. A lot of environmental factors are correlated, like poverty, smoking, low quality of diet, etc. Studies should look at the extent to which epigenetic patterns may differentiate between types of exposures, whether the effects of acute exposures differ from chronic ones, and whether environmental effects may be developmentally dependent.
• Improving understanding of the methylome. Three aspects of DNAm require further investigation: variability (DNAm is dynamic over time and varies across multiple factors), scale (the methylome as a whole is only one of multiple epigenetic mechanisms that work together and many epigenetic patterns are uninvestigated), and transmission (DNAm patterns may be passed on across generations).
• Establishing the functional significance of identified loci. It remains yet unclear to what extent statistical significance overlaps with functional significance. Some effects may be highly statistically significant, but only involve a small change in methylation with unknown biological consequences.
• Maximizing comparability across studies and opportunities for replication.
• Strengthening causal inference.