Simultaneous profiling of native-state proteomes and transcriptomes of brain cell types using proximity labeling
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ABSTRACT: Phenotyping cells at transcriptomic and proteomic levels is an essential step to understanding cellular contributions to development, aging, injury, and disease. Since proteome and transcrip-tome level abundances modestly correlate, complementary profiling of both is needed. We report a method called simultaneous protein and RNA -omics (SPARO) to capture the cell type-specific transcriptome and proteome simultaneously in vitro and in vivo. SPARO leverages TurboID to biotinylate RNA-interacting cytosolic proteins, enabling enrichment of proteins for proteomics and protein-associated RNA for transcriptomics. We validate SPARO first using well-controlled in vitro systems to verify that the proteomes and transcriptomes obtained reflect the global proteo-mes and transcriptomes. The effect of neuroinflammatory activation by lipopolysaccharide is al-so faithfully captured. We apply SPARO to obtain native-state proteomes and transcriptomes from astrocytes and neurons, thereby validating the approach in vivo. We interrogate mRNA-protein concordance and discordance, providing insights into molecular processes that exhibit uniform or cell type-specific patterns.
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE287770 | GEO | 2026/02/16
REPOSITORIES: GEO
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