In-Depth Proteome Profiling of Small Extracellular Vesicles Isolated from Cancer Cell Lines and Patient Serum

Extracellular vesicle (EV) secretion has been observed
in many
types of both normal and tumor cells. EVs contain a variety of distinctive
cargoes, allowing tumor-derived serum proteins in EVs to act as a
minimally invasive method for clinical monitoring. We have undertaken
a comprehensive study of the protein content of the EVs from several
cancer cell lines using direct data-independent analysis. Several
thousand proteins were detected, including many classic EV markers
such as CD9, CD81, CD63, TSG101, and Syndecan-1, among others. We
detected many distinctive cancer-specific proteins, including several
known markers used in cancer detection and monitoring. We further
studied the protein content of EVs from patient serum for both normal
controls and pancreatic cancer and hepatocellular carcinoma. The EVs
for these studies have been isolated by various methods for comparison,
including ultracentrifugation and CD9 immunoaffinity column. Typically,
500–1000 proteins were identified, where most of them overlapped
with the EV proteins identified from the cell lines studied. We were
able to identify many of the cell-line EV protein markers in the serum
EVs, in addition to the large numbers of proteins specific to pancreatic
and HCC cancers.