Association Study on Multi-Timepoint DNA Methylation Levels of Serotonin Transporter Gene and Adolescent Psychological-Behavioral Development

Comprehensive Summary

This study aims to see whether there is an association between levels of DNA methylation at multiple points in the serotonin promoter pathway with deep-learning-based psychopathological symptom clusters. Methylation was measured with bisulfite pyrosequencing on saliva samples collected in the Tokyo Teen Cohort (TTC) study with adolescent participants. 3171 pairs of children and their caregivers were included in the study, from which 122 gave 3 saliva samples at ages 11, 13, and 15. From this saliva, average methylation levels between 2 functional CpG sites (part of the SLC6A4/serotonin gene promoter) were measured and integrated into 1 index. TTC data was previously collected using questionnaires that were given for both children and caregivers to complete about the child’s psychosocial profile and grouped into minimal, internalizing, discrepant, externalizing, and severe psychological clusters by a deep-learning model. Linear mixed-effects models (LMMs), using the minimal cluster as a reference, examined the association of the psychopathological symptom clusters with the DNA methylation index. Sex-stratified LMMs were also conducted as a result of previously observed studies demonstrating increased methylation levels in females. Males overall had a statistically significant decrease in DNA methylation compared to females (p<0.001) consistent with prior studies, had statistically significant differences in DNA methylation by age, and had a statistically significant difference in DNA methylation of the externalizing psychological cluster compared with the minimal cluster (p-value= 0.041). Comparatively, in females there were no statistically significant differences between psychopathological clusters or ages. In the discussion, the authors explain that the different effects of hypermethylation found in this study may explain prior associations with hypermethylation at CpG3 sites in males with bipolar disorder/schizophrenia and lower serotonin receptor density in females from hypermethylation of gene transcriptions Limitations of this study included the small sample size, difference in IQ between the subsection and general sample group, lack of ethnic diversity in the sample (all participants being Japanese), and small age range of participants. In the future, researchers would like to confirm an association between polymorphisms in a promoter found within the SLC6A4 gene and DNA methylation levels, as they found that the current study’s small sample size stopped them from proving this.

Outcomes and Implications

It is important to study changes in adolescence because they may impact psychopathological disorder progression into adulthood. One facet of this progression is thought to be linked to changes in serotonergic pathways, which provides an opportunity to apply machine learning algorithms to both epigenetics and psychosocial behaviors. While this article demonstrated a few statistically significant differences in DNA methylation at sites involved in serotonergic pathways, particularly in males, more research is needed to find stronger associations between these epigenetic changes and different emotions/behaviors so that different disorders can be identified and treated earlier.