A Long-Term Neuroepigenomic Profile of Prenatal Alcohol Exposure

Fetal Alcohol Spectrum Disorders (FASD) represent the largest preventable cause of cognitive deficits in the western world. The mechanism(s) of how prenatal alcohol exposure (PAE) results in FASD remain unknown. Towards this end, mouse models of PAE have successfully recreated endophenotypes that are characteristic of FASD. This doctoral thesis examines the long-term epigenomic alterations associated with PAE. I have examined both mice with PAE and human patients with FASD.In the first set of experiments, mice with PAE and matched controls were raised to adulthood and then their whole brains were examined for alterations to gene expression, non-coding RNA (ncRNA) expression, and DNA methylation. Long-term alterations were observed in genes related to neurodevelopment, cellular signaling, and immune processes. Furthermore, there was an enrichment for alterations to genomically imprinted clusters of ncRNA and genes related to PTEN/PI3K/AKT/mTOR signaling.In the second set of experiments, buccal epithelial swabs were collected from young children with FASD and matched controls. Children from a discovery cohort were examined for alterations to DNA methylation, which revealed changes to genes involved in neurodevelopment and synaptic signaling as well as hippo signaling. Select candidates (COLEC11 and HTT) were confirmed by sodium bisulfite pyrosequencing. Examination of a replication cohort revealed that while similar pathways are altered, the effect is not identical and that sex and age may alter the methylation profile. A larger group of children, representative of the general population, were then analyzed using a targeted sodium bisulfite next-generation sequencing panel and pyrosequencing. No single gene examined was found to be consistently affected in all FASD children.Finally, the mouse and human results were compared to identify alterations to shared loci, ontologies, and pathways. The clustered protocadherins, which are involved in generating individual neuronal identity, showed increased DNA methylation in both species. Together, the results suggest that a shared DNA methylation profile related to neurodevelopment is present in both the brains of adult mice and the buccal epithelial swabs of young children with PAE. These results may be used in future functional studies of candidate loci as well as towards the development of much needed diagnostics and precision medicine.