February 15, 2024
Journal Article

A proteomic meta-analysis refinement of plasma extracellular vesicles


Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were enriched with EV markers with independently validated 71% true-positive rate and depleted of known contaminants. These clusters had 133 clusters of differentiation antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of ß cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.

Published: February 15, 2024


Vallejo M.C., S. Sarkar, E.C. Elliott, H.R. Henry, S.M. Powell, I. Diaz Ludovico, and Y. You, et al. 2023. A proteomic meta-analysis refinement of plasma extracellular vesicles. Scientific Data 10. PNNL-SA-178237. doi:10.1038/s41597-023-02748-1

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