Summary: New research reveals that child maltreatment leaves measurable biological “scars” on DNA, altering brain structure and function. Using a genome-wide epigenetic analysis, scientists identified four key methylation sites—ATE1, SERPINB9P1, CHST11, and FOXP1—linked to maltreatment.
Changes in FOXP1 were especially important, correlating with reduced gray matter in brain regions tied to emotion and memory. These findings highlight how early trauma imprints itself on both biology and behavior, paving the way for early detection and trauma-informed care.
Key Facts:
- Epigenetic Evidence: Four DNA methylation sites were identified as biological markers of child maltreatment.
- FOXP1’s Role: Hypermethylation of FOXP1 was associated with brain changes in regions involved in emotional and social processing.
- Predictive Potential: A methylation risk score (MRS) successfully distinguished individuals with a history of maltreatment.
Source: University of Fukui
Child maltreatment, which includes abuse and neglect, is one of the most serious public health concerns worldwide. These adversities leave a lasting impact on the emotional well-being, memory, and social development of affected individuals.
The problem, however, reaches far beyond its psychological impact, affecting the brain and biological processes through genetic changes, which have remained unclear until now.
A recent study led by Senior Asst. Professor Shota Nishitani and Professor Akemi Tomoda from the Research Center for Child Mental Development at University of Fukui, Japan, in collaboration with Professor Masataka Nagao from the Department of Forensic Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan, reveals that child maltreatment leaves measurable biological “scars” on children’s DNA, leading to long-term alterations in the brain.
The findings of the study were published in Molecular Psychiatry on September 16, 2025.
Their research builds on earlier findings from Prof. Tomoda’s group, which had revealed that child maltreatment can alter DNA. Unlike previous studies that focused on specific candidate genes, this current work employed a broader genome-wide approach, revealing novel molecular markers and directly linking them to brain structure.
Briefly, the researchers conducted a detailed analysis of the epigenome (a set of chemical “switches” on our DNA that regulate gene activity) across three different groups to identify biological markers linked to childhood maltreatment as trauma.
Participants included those in judicial autopsy cases, as well as toddlers and adolescents who had undergone protective interventions, with the adolescents also undergoing brain MRI scans.
“We identified four DNA methylation sites that were consistently associated with child maltreatment, namely ATE1, SERPINB9P1, CHST11, and FOXP1,” explains lead author, Senior Asst. Professor Nishitani.
DNA methylation sites are key players in genetic regulation, as they can regulate the gene expressions without changing the underlying DNA sequence. While the researchers identified four different sites, the site FOXP1 was particularly significant as it acts as a “master switch” for the genes involved in brain development.
The researchers found that hypermethylation of FOXP1 was linked to changes in gray matter volume in the orbitofrontal cortex, cingulate gyrus, and occipital fusiform gyrus of the brain regions which are responsible for emotional regulation, memory retrieval, and social cognition. This highlights the biological link between early trauma, brain development, and later mental health outcomes.
“Childhood trauma is not only a painful psychological experience but also leaves lasting biological marks at the molecular and brain levels,” explains Prof. Tomoda.
“By identifying these epigenetic markers, we hope to develop new tools that can enable the detection and support of at-risk children as early as possible.”
To use their discovery for predictive analysis, the researchers created a methylation risk score (MRS) using the four identified DNA methylation sites. The score could successfully distinguish individuals with and without a history of maltreatment using external data independent of their own, suggesting its potential as an objective screening tool for identifying childhood trauma.
The significance of this discovery extends to multiple fields, including healthcare, forensic medicine, and public health policies. In healthcare, these biomarkers could help improve early diagnosis and personalized trauma-informed treatment approaches.
While in forensics, it could help support investigations and support child welfare. Furthermore, the screening tools may also drive preventive care, reducing the long-term societal impact of maltreatment.
With these implications, the study also reflects the mission of the Division of Developmental Support Research at the University of Fukui, which integrates neuroscience, clinical practice, and community-based approaches to promote resilience and well-being for children and families.
The center is dedicated to advancing the science and practice of child development and mental health, and focuses on early detection, intervention, and prevention of developmental and mental health issues.
“Childhood should be a time of safety and growth,” emphasizes Prof. Tomoda. “Understanding how childhood trauma affects us biologically can lead to better strategies for prevention, treatment, and support, helping break the cycle of maltreatment.”
Key Questions Answered:
A: It causes changes in DNA methylation, especially in genes like FOXP1, which influence brain development and emotional regulation.
A: The orbitofrontal cortex, cingulate gyrus, and occipital fusiform gyrus—areas linked to emotion, memory, and social cognition—show measurable gray matter alterations.
A: It provides biological evidence of trauma’s long-term effects and could lead to new diagnostic tools for early intervention and prevention.
About this genetics, neurodevelopment, and mental health research news
Author: Yuuka Kawamoto
Source: University of Fukui
Contact: Yuuka Kawamoto – University of Fukui
Image: The image is credited to Neuroscience News
Original Research: Open access.
“Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents” by Masataka Nagao et al. Molecular Psychiatry
Abstract
Multi-epigenome-wide analyses and meta-analysis of child maltreatment in judicial autopsies and intervened children and adolescents
Child maltreatment (CM) is associated with adverse physical, psychological, and neurodevelopmental outcomes later in life. Epigenetic modifications, particularly DNA methylation, have been proposed as potential mechanisms underlying these long-term effects.
To identify robust CM-associated methylation signatures, we conducted epigenome-wide analyses across three independent cohorts: judicial autopsy cases (CM:11, Controls:7), toddlers shortly after social intervention (CM:36, Controls:49), and adolescents who underwent brain MRI (CM:61, Controls:62).
Each cohort was analyzed separately, followed by a meta-analysis to identify common methylation sites associated with CM exposure. The meta-analysis identified four significant CpG sites located within the ATE1, SERPINB9P1, CHST11, and FOXP1 genes.
Among these, methylation of FOXP1 was consistently associated with structural brain alterations, including increased gray matter volume (GMV) in the orbitofrontal cortex (OFrC) and middle/posterior cingulate gyrus (MPCG), and decreased GMV in the occipital fusiform gyrus (OFuG).
These brain regions are implicated in emotional regulation, memory retrieval, and social cognition, suggesting a potential neurobiological mechanism linking CM to later psychopathology.
Furthermore, methylation risk scores (MRS) derived from these four CpGs successfully discriminated individuals who experienced early-life adversity in an independent validation dataset, achieving an area under the receiver operating characteristic curve (AUC) of 0.672, highlighting their potential utility as biomarkers.
Gene ontology and pathway analyses revealed enrichment of cholinergic and glutamatergic synaptic transmission pathways, supporting their involvement in traumatic memory formation.
Our findings provide novel insights into the epigenetic mechanisms underlying CM and identify potential biomarkers for early detection, prevention, and therapeutic intervention, ultimately contributing to breaking the intergenerational cycle of maltreatment.
