Cell-type-specific DNA methylation patterns associated with suicide are enriched in excitatory neurons

Abstract

BackgroundSuicide is a major public health concern and a highly complex, heterogeneous phenotype. Increasing evidence implicates epigenetic mechanisms, particularly DNA methylation (DNAm), in suicidal behavior. MethodsBuilding on previous epigenome-wide association studies (EWASs), we conducted the largest EWAS to date in postmortem dorsolateral prefrontal cortex (Brodmann area 9), analyzing DNAm and epigenetic aging (EA) in 199 suicide decedents (SD) and 190 age- and sex-matched non-psychiatric controls (NPC) using the Infinium MethylationEPIC BeadChip Array v2.0. ResultsBulk tissue analysis identified no significant differentially methylated positions or regions. In contrast, cell type-specific analysis using DNAm-deconvoluted cell proportions identified 605 differentially methylated cytosines in individual cell types (DMCTs) in excitatory neurons, 10 in inhibitory neurons, and 28 in oligodendrocyte precursor cells. Sex-stratified analyses identified mainly male-specific DMCTs, most of which were found in excitatory neurons, while comparison of violent and non-violent suicide identified additional DMCTs in glial cell types. Excitatory neuron DMCTs were enriched for synaptic, small GTPase signaling, and neurodevelopmental pathways, and overlapped genes previously associated with suicidal behavior, including MAD1L1. No significant differences in EA acceleration were observed overall or by sex or suicide mechanism. ConclusionsThese findings indicate that suicide-associated DNAm patterns are primarily neuron-specific and may remain undetectable in bulk tissue, highlighting the importance of cell type-specific approaches to elucidate biological mechanisms underlying suicide.