Proteomics-based characterization of matrix-bound nanovesicles from fibroblast-derived ECM

Abstract

Extracellular matrix (ECM) is a non-cellular tissue architecture containing biophysical and biochemical cues and functions as a reservoir of various biomolecules. Extracellular vesicles (EVs) are important mediators for intercellular communications containing biomolecules such as microRNAs, lipids, and proteins, and they have been considered to exist in a liquid phase. Recently, a new subpopulation of extracellular vesicles, matrix-bound nanovesicles (MBVs), was discovered and found to be bioactive. However, there is no broad proteomics-based analysis of MBVs although properties of microRNAs and lipids have been revealed. In this study, we isolated MBVs from fibroblast-derived ECM and performed LC-MS/MS-based global proteomic characterization to demonstrate how MBVs and soluble EVs differ in protein contents. We discovered that there were distinct proteomic properties of MBVs compared to soluble EVs in specific proteins, EV transport, and EV-ECM interactions. Therefore, this study is expected to provide a proteomics-basis for future studies on MBVs acting as unique microenvironment stimuli in the ECM.