Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study

Hum Mol Genet. 2019 Aug 15;28(16):2659-2674. doi: 10.1093/hmg/ddz084.


DNA methylation acts at the interface of genetic and environmental factors relevant for autism spectrum disorder (ASD). Placenta, normally discarded at birth, is a potentially rich source of DNA methylation patterns predictive of ASD in the child. Here, we performed whole methylome analyses of placentas from a prospective study MARBLES (Markers of Autism Risk in Babies-Learning Early Signs) of high-risk pregnancies. A total of 400 differentially methylated regions (DMRs) discriminated placentas stored from children later diagnosed with ASD compared to typically developing controls. These ASD DMRs were significantly enriched at promoters, mapped to 596 genes functionally enriched in neuronal development, and overlapped genetic ASD risk. ASD DMRs at CYP2E1 and IRS2 reached genome-wide significance, replicated by pyrosequencing and correlated with expression differences in brain. Methylation at CYP2E1 associated with both ASD diagnosis and genotype within the DMR. In contrast, methylation at IRS2 was unaffected by within DMR genotype but modified by preconceptional maternal prenatal vitamin use. This study therefore identified two potentially useful early epigenetic markers for ASD in placenta.

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

  • Autism Spectrum Disorder / etiology
  • Autistic Disorder / etiology*
  • Autistic Disorder / metabolism
  • Biomarkers
  • Cadherins / metabolism
  • Case-Control Studies
  • Child
  • Cytochrome P-450 CYP2E1 / genetics*
  • DNA Methylation*
  • Disease Susceptibility
  • Epigenesis, Genetic
  • Female
  • Gene Expression Profiling
  • Genome-Wide Association Study
  • Humans
  • Insulin Receptor Substrate Proteins / genetics*
  • Male
  • Maternal Exposure*
  • Placenta / metabolism*
  • Pregnancy
  • Prenatal Exposure Delayed Effects*
  • Risk
  • Signal Transduction
  • Wnt Proteins / metabolism


  • Biomarkers
  • Cadherins
  • IRS2 protein, human
  • Insulin Receptor Substrate Proteins
  • Wnt Proteins
  • Cytochrome P-450 CYP2E1