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

Area of Science:

• Molecular Biology
• Genomics
• Proteomics

Background:

• Deep molecular phenotyping is crucial for understanding cellular roles in health and disease.
• Transcriptome and proteome abundances show only modest correlation, necessitating complementary profiling.

Purpose of the Study:

• To introduce a novel method for simultaneous, cell type-specific capture of both transcriptome and proteome.
• To validate the method's accuracy and applicability in both in vitro and in vivo systems.

Main Methods:

• Simultaneous Protein and RNA-omics (SPARO) utilizes TurboID biotin ligase to label cytosolic proteins.
• Labeled proteins and associated RNA are enriched for parallel proteomic and transcriptomic analysis.
• Validation performed in vitro using controlled systems and in vivo using neural cell types (astrocytes, neurons).

Main Results:

• SPARO accurately reflects ground truth bulk proteomes and transcriptomes in vitro.
• The method successfully captures responses to biological stimuli like lipopolysaccharide.
• SPARO effectively profiles native-state proteomes and transcriptomes from distinct in vivo cell types.

Conclusions:

• SPARO provides a powerful tool for simultaneous transcriptomic and proteomic profiling.
• The method enables interrogation of protein-mRNA concordance and discordance across cell types.
• This approach offers new insights into cell type-specific molecular regulation in development, aging, and disease.