We identified thousands of genes differentially expressed in a range of cell types and characterized the accompanying differences in chromatin accessibility. The differentially expressed genes and differentially accessible regions were highly correlated between D1- and D2-type medium spiny neurons, which are components of the direct and indirect pathways, respectively, of the basal ganglia. Pathways enriched in individuals with AUD related to RNA processing (‘RNA Metabolism’, ‘Processing of Capped Intron-Containing pre-mRNA’) and immune response (‘Innate Immune System’, complement-related pathways). Recent studies have also found dysregulation of neuroimmune genes in neurons in several brain regions in mice.60, Gene regulatory network analysis allowed us to identify transcription factors possibly regulating these differences. For example, FOXO1 was shown to have significantly lower activity in D2 medium spiny neurons from individuals with AUD, based on the chromatin openness of its target genes. FoxO1 in mice has been linked to regulation of energy homeostasis in neurons,49 and a lack of FoxO1 in the brain caused a depressive-like phenotype.50,51 This could represent a novel regulatory gene in neurons in AUD, as AUD and major depression frequently co-occur.61
