Neurexin 3 is differentially methylated and downregulated following chronic ethanol use.

Background : Increasing evidence confirms the value of unbiased epigenomic and transcriptomic profiling in the identification of neuroadaptations in alcohol use disorder (AUD). Through this integrated omics analysis, we identified neurexin3 ( NRXN3 ) as a critical player in mediating alcohol’s effects on the cortex in primates and mice. Neurexins are presynaptic cell adhesion molecules critical in synaptic adaptations. Although neurexin3 has been linked to substance use disorders, the specific regulatory mechanisms that enable NRXN3 ’s transcript/isoform diversity and the downstream effects on synaptic dynamics contributing to AUD remain unknown. Methods : We conducted unbiased genome-wide DNA methylation (DNAm) and RNAseq analyses of the dorsolateral prefrontal cortex (dlPFC) of rhesus macaques that remained alcohol-naïve (controls) or self-administered ethanol for 12 months. qPCR and immunohistochemistry were used to measure the levels of Nrxn3 transcripts and isoforms in parvalbumin interneurons in the prelimbic cortex (PLC) of mice following chronic ethanol exposure. Results : Our unbiased omics analyses identified sex-specific differences in DNAm and gene expression. However, there was a shared enrichment in signaling pathways mediating synaptic neurotransmission and plasticity. Specifically, we found differential DNAm mapping to NRXN3 , and a specific downregulation of transcript NRXN3b . We further showed this downregulation was conserved in mice following chronic ethanol use, and occurred in parvalbumin interneurons of the PLC. Conclusions: Our research provides significant insights into the complex mechanisms by which ethanol affects the expression of NRXN3 within the PFC/PLC and how this might be modulating synaptic plasticity in a cell type and sex-specific manner.