DNA METHYLOME PROFILE CAN DISTINGUISH MOLECULAR PATHOLOGIES OF SUICIDE AMONG DEPRESSED PATIENTS
Authors: Dwivedi *Yogesh 
Published: February 2025

Background

Major depressive disorder (MDD) is a debilitating disorder affecting 8.4% of the US population and globally about 5% of the adult population. It is the single most important risk factor for suicide, where more than 60% of those who die by suicide meet the diagnostic criteria for MDD. Suicide attempt is 5-times higher in MDD patients than in the general population. Interestingly, even with a high prevalence of suicidality, not all MDD patients develop suicidal thoughts or complete suicide. Thus, it is important to study the risk factors that can distinguish suicidality among MDD patients.

Aims and Objectives

Although the molecular correlates of depression and suicide remain poorly understood, it has been hypothesized that epigenetic marks, such as DNA methylation, which can be influenced by the environment, might play a critical role in developing depression and suicidal behavior. A few studies have examined DNA methylation changes in the brains of depressed suicide subjects or suicide subjects with various mental illnesses. So far, no study has examined suicide-specific DNA methylation marks in the brains of depressed subjects. The present study examined genome-wide DNA methylation in the prefrontal cortex of depressed suicide (DS), depressed non-suicide (DNS), and nonpsychiatric control subjects.

Methods

Genome-wide DNA methylation was examined in the prefrontal cortex of age- and sex-matched depressed suicide (DS; n=15), depressed non-suicide (DNS; n=17), and nonpsychiatric control (NC; n=16) subjects using 850K Infinium Methylation EPIC BeadChip. Signal intensities and raw methylation β values were extracted from Illumina’ s Genome-Studio software R package ChAMP. The methylation β values were generated based on normalized signal intensities and background subtraction using negative control probes and were derived as the ratio of methylation probe intensity to the overall intensity. The hyper and hypo-methylated sites were also mapped across 22 autosomes using PhenoGram Plot. The significantly differentially methylated gene lists were used to determine the functional enrichment of genes for ontological clustering and pathway analysis.

Results

The chromosome-wise methylation sites and mapping of methylated sites based on the number of CpG content and their relative distribution from specific landmark regions of genes varied significantly between NC, DS, and DNS groups. 32958 methylation sites were identified across 12574 genes in NC vs. all MDD subjects, 30852 methylation sites across 12019 genes in NC vs. DNS, 41648 methylation sites across 13941 genes in NC vs. DS, and 49848 methylation sites across 15015 genes in DNS vs. DS groups. A comparison of methylation sites showed 33129 unique methylation sites and 5451 genes in the DNS group compared to the DS group. Functional analysis suggested Oxytocin, GABA, VGFA, TNFA, and MTOR pathways associated with suicide in the MDD group.

Discussion & Conclusion

Our data show a discrete pattern of DNA methylation, the genomic distribution of differentially methylated sites, gene enrichment, and pathways in MDD subjects who died by suicide compared to non-suicide MDD subjects and suggest that epigenetic DNA modifications could be used to distinguish suicidality in MDD patients.