Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling

Deep molecular phenotyping of cells at transcriptomic and proteomic levels is an essential first step to understanding cellular contributions to development, aging, injury, and disease. Since proteome and transcriptome level abundances only modestly correlate with each other, complementary profiling of both levels of abundances are needed. We report a novel method to capture the cell type-specific transcriptome and proteome simultaneously from both in vitro and in vivo experimental model systems. This method leverages the ability of biotin ligase, TurboID, to biotinylate cytosolic proteins including ribosomal and RNA-binding proteins, which allows enrichment of biotinylated proteins for proteomics as well as protein-associated mRNA for transcriptomics. We validated this approach first using well-controlled in vitro systems to verify that the proteomes and transcriptomes obtained reflect the ground truth, bulk proteomes and transcriptomes. We also show that the effect of a biological stimuli (e.g., neuroinflammatory activation by LPS) can be faithfully captured. We also applied this approach to obtain native-state proteomes and transcriptomes from two key brain cell types (Aldh1l1-expressing astrocytes and Camk2a-expressing neurons), thereby validating the in vivo application of this approach. We also used these data to interrogate protein mRNA concordance and discordance across two brain cell types, providing insights into shared and unique molecular processes such as cytoskeletal and mitochondrial-related functions.