Inter-individual differentially methylated region-targeted EWAS reveals epigenetic signatures of early childhood adversity

Adverse childhood experiences (ACEs), especially in early life, can affect psychosocial development and increase lifelong risk for mental disorders. ACEs are also known to induce persistent epigenetic changes. This study aimed to explore ACE-associated DNA methylation signatures using an epigenome-wide association study (EWAS) targeting inter-individual differentially methylated regions (DMRs). We developed a targeted capture probe system covering ~1.3 million CpG sites within inter-individual DMRs. This system was applied to salivary DNA from drug-naïve children aged 6–12 years with exposure to multiple early-life ACEs (n = 23) or who had no ACEs (n = 21). We identified 15 novel DMRs significantly associated with ACEs. A cluster of six CpG sites within an exon of the EIF4G2 gene showed consistently increased methylation in children with ACEs, with strong inter-site correlations. Enrichment analysis indicated that genes near these DMRs are involved in neurodevelopmental disorders, suggesting that early adversity may influence brain development through epigenetic mechanisms. Our findings suggest that early adversity may contribute to lasting epigenetic modifications in children. The identified DMRs may serve as noninvasive biomarkers for retrospective ACE assessment and provide insights into the biological embedding of early-life stress. Children who have hard experiences early in life – like abuse, neglect, or stress – may be more likely to have problems with their mental health later. These experiences can leave lasting effects on the body. One way this happens is through DNA methylation, a process that can switch genes on or off without changing the DNA itself. In our study, we looked at saliva from children aged 6 to 12. We found 15 places in the DNA where children who had stressful experiences were different from those who did not. One important gene, EIF4G2, showed higher methylation in children with early stress. Other differences were near genes important for brain development. This shows that early stress can leave biological marks. In the future, these marks may help us understand how stress affects children and identify those who might need extra support.