Cell type specific gene expression analysis in pre-symptomatic huntington's disease.

Selective neuronal vulnerability is a common, yet poorly understood characteristic of neurodegenerative diseases and is particularly prominent in Huntington's disease (HD). To determine how presence of mutant prion protein influences gene expression at pre-symptomatic stages, we used RiboTag to isolate cell type-specific, translating RNA from GABAergic, glutamatergic, somatostatin- (SST) and parvalbumin-expressing neurons of 9-month-old knock-in mice of heterozygous for a Q185 expansion in the endogenous Hdh gene or littermate controls. We analyzed four cell types (Gad2+, PV+, SST+, vGluT2+) in HD mice and littermate controls. Cell type-specific RNA was obtained from in two brain regions (cerebrum sans olfactory bulb, and cerebellum). For cerebellum, only Gad2+ and vGluT2+ were analyzed. For each analyzed RiboTag sample set (genotype_celltype_region) 5-7 biological replicates were prepared and sequenced. Cell type-specific RNA was obtained using the RiboTag Immunoprecipitation method from brain tissue homogenates (details below). For a subset of samples, total RNA was isolated from brian homogenates as input control. Differential expression analysis was performed for each sample set, comparing HD vs. Control.