Child abuse, depression, and methylation in genes involved with stress, neural plasticity, and brain circuitry

J Am Acad Child Adolesc Psychiatry. 2014 Apr;53(4):417-24.e5. doi: 10.1016/j.jaac.2013.12.025. Epub 2014 Jan 27.


Objectives: To determine whether epigenetic markers predict dimensional ratings of depression in maltreated children.

Method: A genome-wide methylation study was completed using the Illumina 450K BeadChip array in 94 maltreated and 96 healthy nontraumatized children with saliva-derived DNA. The 450K BeadChip does not include any methylation sites in the exact location as sites in candidate genes previously examined in the literature, so a test for replication of prior research findings was not feasible.

Results: Methylation in 3 genes emerged as genome-wide-significant predictors of depression: DNA-Binding Protein Inhibitor ID-3 (ID3); Glutamate Receptor, Ionotropic N-methyl-D-aspartate (NMDA) 1 (GRIN1); and Tubulin Polymerization Promoting Protein (TPPP) (p < 5.0 × 10(-7), all analyses). These genes are all biologically relevant with ID3 involved in the stress response, GRIN1 involved in neural plasticity, and TPPP involved in neural circuitry development. Methylation in CpG sites in candidate genes were not predictors of depression at significance levels corrected for whole genome testing, but maltreated and control children did have significantly different β values after Bonferroni correction at multiple methylation sites in these candidate genes (e.g., BDNF, NR3C1, FKBP5).

Conclusions: This study suggests that epigenetic changes in ID3, GRIN1, and TPPP genes, in combination with experiences of maltreatment, may confer risk for depression in children. The study adds to a growing body of literature supporting a role for epigenetic mechanisms in the pathophysiology of stress-related psychiatric disorders. Although epigenetic changes are frequently long lasting, they are not necessarily permanent. Consequently, interventions to reverse the negative biological and behavioral sequelae associated with child maltreatment are briefly discussed.

Keywords: child abuse; depression; epigenetics; methylation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adolescent
  • Child
  • Child Abuse*
  • Child, Preschool
  • DNA Methylation / genetics
  • Depression / genetics*
  • Epigenesis, Genetic / genetics*
  • Female
  • Genome-Wide Association Study
  • Humans
  • Inhibitor of Differentiation Proteins / genetics*
  • Male
  • Neoplasm Proteins / genetics*
  • Nerve Net / metabolism
  • Nerve Tissue Proteins / genetics*
  • Neuronal Plasticity / genetics
  • Receptors, N-Methyl-D-Aspartate / genetics*
  • Stress, Psychological / genetics*
  • Stress, Psychological / metabolism


  • GRIN1 protein, human
  • Inhibitor of Differentiation Proteins
  • Neoplasm Proteins
  • Nerve Tissue Proteins
  • Receptors, N-Methyl-D-Aspartate
  • TPPP protein, human
  • ID3 protein, human