Proteomic Tracking Extracellular Vesicle RNA Interactors in Recipient Immune Cells through Orthogonal Labelings.

Area of Science:

• Extracellular vesicle (EV) biology
• Proteomics
• RNA biology
• Immunology

Background:

• Extracellular vesicles (EVs) are crucial for intercellular communication, transporting RNA molecules.
• RNA-binding proteins (RBPs) in recipient cells interact with EV RNA cargos, mediating cellular responses.
• Understanding the dynamics of EV RNA-protein interactions is key to deciphering EV-mediated signaling.

Purpose of the Study:

• To introduce a novel chemical proteomic strategy, ERICOL, for profiling RNA-binding proteins (RBPs) interacting with extracellular vesicle (EV) RNA.
• To investigate the dynamic patterns of EV RNA uptake and RBP engagement in recipient cells.
• To explore how cancer-derived EVs, particularly those with IDH1 mutations, alter the RBP landscape in immune cells.

Main Methods:

• Developed Extracellular RNA Interactome Capture through Orthogonal Labelings (ERICOL), a targeted cross-linking and quantitative chemical proteomic strategy.
• Utilized metabolic labeling of RNAs and stable isotope labeling of proteins for systematic profiling.
• Performed time-resolved analysis of tumor-derived EVs in Jurkat T cells and primary human CD8+ T cells.

Main Results:

• ERICOL enabled systematic profiling of EV RBPs in recipient cells.
• Time-resolved analysis revealed dynamic patterns of EV RNA uptake and RBP engagement.
• IDH1 mutation in intrahepatic cholangiocarcinoma (ICC)-derived EVs induced specific alterations in the EV RBP landscape in CD8+ T cells.

Conclusions:

• ERICOL provides a powerful strategy for comprehensive profiling of EV RNA interactome dynamics.
• The study offers mechanistic insights into EV-mediated immune modulation.
• Cancer-derived EVs, influenced by mutations like IDH1, can significantly alter the RBP landscape and immune cell function.