Translational profiling of neuronal subtypes reveals early vulnerability of somatostatin-expressing neurons in pre-symptomatic fatal familial insomnia

Selective neuronal vulnerability is a common, yet poorly understood characteristic of neurodegenerative diseases and is particularly prominent in familial prion diseases, such as Creutzfeldt-Jakob disease (CJD) and fatal familial insomnia (FFI), where different mutations in the prion protein manifest as neuropathologically distinct diseases. 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 CJD and FFI. Overall design: We analyzed four cell types (Gad2+, PV+, SST+, vGluT2+) in three genotypes (FFI, CJD and WT control). 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) 3-7 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 anaysis was performed for each sample set, comparing FFI vs. Control or CJD vs. Control.