Differential neuronal loss across brain regions in neurodegenerative diseases is known as selective vulnerability. Synucleinopathies are a group of disorders involving α-synuclein (α-Syn), a neuronal protein that participates in aggregate formation and is linked to neurodegeneration. To investigate the molecular basis of selective vulnerability, we used a mouse model to assess the in vivo effects of a pathogenic human α-Syn mutant (A53T) on neuronal subpopulations of the Substantia Nigra and Locus Coeruleus—two regions with distinct sensitivities—at early and late disease stages. Single-nucleus RNA sequencing, combined with a gene regulatory network built from public data, enabled inference of differential transcriptional regulator activity in response to α-Syn A53T. We identified similar activity changes in dopaminergic and noradrenergic cells, but with temporal shifts; specifically, protective regulators were enriched at an early stage in noradrenergic, in contrast to dopaminergic cells. Validation with public data from Parkinson’s Disease supports these findings, and ongoing analyses aim to attribute part of the temporal shift to intrinsic basal expression differences between these neuronal populations.