CELL-TYPE SPECIFIC TRANSCRIPTOMIC DYSREGULATION IN THE STRIATUM ARE A FEATURE OF SUBSTANCE USE AND NEURODEGENERATION THAT CAN BE USED TO EVALUATE PRECLINICAL GENE THERAPY

Abstract

Alcohol use disorder (AUD) and Huntington Disease (HD) are neuropsychological diseases with an impact on the striatum. AUD is characterized by inflexible drinking, which is thought to be mediated by effects of chronic intermittent ethanol exposure on the dorsal striatum, the input nucleus of the basal ganglia. In our study of AUD, we used single-nuclei RNA-sequencing (snRNA-seq; n = 86,715 cells) to examine the impact of chronic intermittent ethanol exposure on the dorsal striatum in C57BL/6 male and female mice. We detected 462 differentially expressed genes at FDR < 0.05, the majority of which were mapped to spiny projection neurons (SPNs), the most prominent cell type in the striatum. Gene co-expression network analysis and functional annotation of differentially expressed genes revealed down-regulation of postsynaptic intracellular signaling cascades specifically in canonical SPNs. Inflammation-related genes were down-regulated across many striatal cell types. Gene set enrichment analyses also pointed to altered states of rare cell types, including the induction of angiogenesis-related genes in vascular cells. These data provide important clues as to the impact of ethanol on striatal biology and provide a key resource for future investigation.

As a monogenic disorder, Huntington’s disease (HD) is at the forefront for gene-therapy innovation in neurodegeneration. One challenge to clinical innovation is our ability to discern detailed information about how HD and its potential therapeutics impact the brain. Single-nucleus RNA sequencing is a cutting-edge technology capable of providing this level of detail. Here, we studied cell type-specific transcriptomic effects of HD mutations in the striatum of a knock-in mouse model, HttQ111/+. Further, we examined the cellular impacts of a non-allele specific Htt-lowering antisense oligonucleotide (ASO). We characterized substantial transcriptional effects of the HD mutation in spiny projection neurons, the cell type most vulnerable to HD neurodegeneration. Surprisingly, Htt-lowering ASO treatment exacerbated many of these transcriptional changes. Understanding these cell type-specific effects of ASO treatment could aid in the interpretation of Htt-lowering toxicity that has recently been observed in human patients.