Bulk and Single-cell Transcriptomic Brain Data Identify Overlapping Processes and Cell-types with Human AUD and Mammalian Models of Alcohol Use

Abstract

This study explores the neurobiological underpinnings of alcohol use disorder (AUD) by integrating bulk and single-cell transcriptomic data from humans, primates, and mice across three brain regions associated with addiction (i.e., prefrontal cortex (PFC), nucleus accumbens (NAc), and central amygdala (CeA)). We compared AUD RNA expression and cell-type abundance from 92 human brain to data from 53 primates and 90 mice engaged in diverse alcohol use paradigms. The findings revealed significant and reproducible correlations between human AUD and mammalian models of alcohol use that vary by tissue, species, and behavioral paradigm. The strongest correlations occurred between primate and mouse models of binge drinking (i.e., high drinking in the dark). Certain primate models demonstrated that the brain RNA correlations with human alcohol use disorder (AUD) were approximately 40% as strong as the correlations observed within human samples themselves. By integrating single-cell transcriptomic data, this study observed decreased oligodendrocyte proportions in the PFC and NAc of human AUD with similar trends in animal models. Gene co-expression network analyses revealed conserved systems associated with human AUD and animal models of heavy/binge alcohol consumption. Gene co-expression networks were enriched for pathways related to inflammation, myelination, and synaptic plasticity and the genes within them accounted for ~20% of the heritability in human alcohol consumption. Identified hub genes were associated with relevant traits (e.g., impulsivity, motivation) in humans and mice. This study sheds light on conserved biological entities underlying AUD and chronic alcohol use, providing insights into the cellular, genetic, and neuromolecular basis across species.

Figure 1. AUD Brain RNA Signature Robustly Correlated with Animal Models of Alcohol Use

Transcriptome-wide correlations of differentially expressed genes across traits, brain regions and species. A) Heatmap of AUD RNA correlations with mouse and primate models of alcohol use; **** p < 0.001; blank = p > 0.05; NA = not applicable B) Scatterplot showing reproducibility of brain RNA correlations using an independent sample of AUD; R = Pearson correlation coefficient. Self Admin = ethanol self-administration; CIE = chronic intermittent ethanol exposure; HDID = high drinking in the dark; PFC = pre-frontal cortex, NAc = nucleus accumbens; CeA = central nucleus of amygdala.

Figure 2. Single-cell Deconvolution of AUD and Alcohol Use Brain Signatures Across Animal Models and Brain Regions

In silico cytometry of human AUD and preclinical alcohol use across traits, brain regions, and species. A-C shows clustering of cell-types by brain region and species. D-F shows the proportion of each cell type by group across species, brain regions and pre-clinical models. HDID = high drinking in the dark; Oligo = oligodendrocytes, Excit = excitatory neuron; Inhib = inhibitory neuron; NascIntN = nascent interneuron; MSN_D2 = dopamine D2 receptor medium spiny neuron; OPC = oligodendrocyte progenitor cell; PFC = pre-frontal cortex, NAc = nucleus accumbens; CeA = central nucleus of amygdala; **** p < 0.001; * p < 0.05; # p < 0.1

Figure 3. Conserved Gene Co-expression Networks Associated with Human AUD and Animal Models of Alcohol Use

Gene co-expression networks associated with alcohol use across samples and species. X-axis shows the WGCNA gene co-expression network and the y-axis shows the mean differential expression test statistic by brain region and trait. All gene networks in this plot were significant via permutation analyses (padj < 0.05). WGCNA = weighted gene co-expression network analysis; CIE = chronic intermittent alcohol exposure; HDID = high drinking in the dark. Note color for WGCNA networks are arbitrary and the magenta gene network in the PFC is distinct from the magenta gene network in the CeA.

Figure 4. Conserved Gene Co-expression Networks Associated with Human AUD and Animal Models of Alcohol use

Image created via Biorender.com. Note enriched cell-types are displayed next to WGCNA networks and dashed lines between genes are for visual purposes only and not derived from gene-gene connectivity metrics. Bottom right two gene networks are in the CeA, the top left is in the PFC and the rest are in the NAc.

Figure 5. Conserved AUD & Alcohol Use Networks Enriched for GWAS Associations of Alcohol Use

Results from partitioned heritability analyses. DNA variants within 100kb of the genes from conserved WGCNA networks that were associated with human AUD and mammalian models of alcohol use were included in these analyses. * P < 0.05; NS = P > 0.05.