Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain

Proteomic profiling of brain cell types using isolation-based strategies pose limitations in resolving cellular phenotypes representative of their native state. We generated a novel mouse line for cell type-specific expression of biotin ligase TurboID, leading to in vivo biotinylation of proteins. Using adenoviral and transgenic approaches to label neurons, we show striking protein biotinylation in neuronal soma and axons throughout the brain and quantified over 2,000 neuron-derived proteins spanning synaptic proteins, transporters, ion channels and disease-relevant druggable targets. Next, we compared Camk2a-neuron and Aldh1l1-astrocyte proteomes and resolved brain region-specific proteomic differences within both cell types, some of which may underlie selective vulnerability to neurological diseases. Leveraging the cellular specificity of proteomic labeling, we used an antibody-based approach to uncover differences in neuron and astrocyte-derived signaling phospho-proteins and cytokines. This approach will facilitate the characterization of cell-type specific proteomes in a diverse number of tissues under both physiological and pathological states.