BACKGROUND: Alcohol use disorder (AUD) is a significant public health problem. Gene expression studies offer promising opportunities to better understand the pathogenic processes. METHODS: As cell-types differ in their function, gene expression profiles will typically vary across cell-types. When studying bulk tissue, failure to account for this cellular diversity has a detrimental impact on the ability to detect disease associations. We therefore assayed the transcriptomes of 32,531 individual nuclei extracted from the nucleus accumbens (NAc) of 9 donors with AUD and 9 controls. RESULTS: Our study identified 17 clearly delineated cell-types. We detected 26 transcriptome-wide significant association signals that mainly involved medium spiny neurons (MSN) with both D1-type and D2-type dopamine receptors, microglia and oligodendrocytes. A significantly higher number of findings than expected by chance replicated in an existing single nucleus gene expression study of alcohol dependence in the pre-frontal cortex. For the MSN we observed genes and pathways related to neurodegeneration, disruption of circadian rhythms, alterations in glucose metabolism, and changes in synaptic plasticity. For microglia we found neuroinflammation and immune-related processes and for oligodendrocytes disruptions in myelination. Some findings were particularly robust. For example, the altered CD53 expression in microglia replicated in the same cell-type in pre-frontal cortex and was previously implicated by expression studies in rodents and studies of DNA sequence variants and methylation in humans. CONCLUSIONS: This identification of the specific cell-types from which the association signals originate is key for designing proper follow-up experiments and, eventually, for developing new and targeted clinical interventions.

The authors have declared no competing interest.

This work was supported by grant 5R01AA026057 (PI Clark) and a NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation (PI Clark).

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Texas A&M University IRB, Reference number 097974, Date November 04 2019: Ruling "The Institution determined that the proposed activity is not research involving human subjects as defined by DHHS and FDA regulations." Virginia Commonwealth University IRB, Reference number HM20019402, Date May 18 2020 Ruling "VCU IRB review or approval is not required before you proceed with your involvement this project". As this research involves deceased individuals is not human subjects research according to 45 CFR 46.102(f).

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