Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues

Abstract

Background: Prenatal alcohol exposure (PAE) can alter the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE resulted in blood alcohol levels of ~80–150 mg/dl throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal days (P) 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing.Results: PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental period at a false-discovery rate (FDR) < 0.05. In addition, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR < 0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses.Conclusions: Persistent DNA methylation changes in the hypothalamus may be associated with the long-term physiological and neurobehavioral alterations in observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology of neurodevelopmental and mental health disorders, as they share numerous phenotypes and comorbidities.

Murine Models for the Study of Fetal Alcohol Spectrum Disorders: An Overview

“…Ethanol and ROS can modify the activity of methyltransferases and demethylases, directly affecting the global DNA methylation pattern during development. A recent study performed in mice after PAE found 118 differentially methylated regions (DMRs) related to transcription factor binding sites (223). The pathways affected by these DMRs were epigenetic remodeling, hormonal signaling, metabolism, and immune response, revealing persistent occurrence of these alterations in all developmental stages (223).…”

“…A recent study performed in mice after PAE found 118 differentially methylated regions (DMRs) related to transcription factor binding sites (223). The pathways affected by these DMRs were epigenetic remodeling, hormonal signaling, metabolism, and immune response, revealing persistent occurrence of these alterations in all developmental stages (223). Demethylation following ethanol exposure causes a decrease in IGF-2 levels in utero, generating an important delay in growth and leading to skeletal malformations (224).…”

Alteration of the brain methylation landscape following postnatal inflammatory injury in rat pups

“…Individual values are represented by square (Sham) and dots (LPS) for each gene and box plot represent minimal to maximal value with line at median many neurodevelopmental and neurodegenerative diseases including autism spectrum disorder, Down syndrome, Alzheimer disease, and schizophrenia. 62,63 It was suggested that methylation in intergenic and introns could target regulatory sequences that play a role in gene expression. In accordance to our results, animal studies showed that adverse events during the perinatal period can lead to sustained alteration of the brain methylome up to 1 year after the initial insult.…”

“…In our study, neonatal inflammation-induced WMI resulted in DNA methylation alteration that persisted up to 21 days post-injury. [63][64][65][66] One major group of pathways that emerged from our methylome analysis following neonatal inflammation-induced WMI was related to the axon. 61,62 For example, exposure to maternal maltreatment during the first days of life in rats induced a global alteration of DNA methylation in the amygdala and hippocampus at adolescence (P30).…”

Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects

“…Mouse and rat studies showed the association between prenatal ethanol exposure and gene expression changes in postnatal and adult stages [34][35][36][37] . This study examined ethanol-induced gene expression changes during embryogenesis before gastrulation.…”