Proteomics of extracellular vesicles derived from primary cells of pancreatic ductal adenocarcinoma patients identifies ribosomal proteins associated with survival

Pancreatic ductal adenocarcinoma remains a formidable clinical challenge, with a very poor survival rate. It is highly metastatic and quickly exhibits chemoresistance, both of which are mediated by interactions of the tumor cells with their microenvironment. Extracellular vesicles are key mediators by which tumor cells interact with their microenvironment. Here, we utilized a data-independent acquisition proteomics workflow tocharacterize the protein cargo of extracellular vesicles isolated from patient-derived primary cells and cell lines of varying aggressiveness. Mapping 1432 unique proteins with high reproducibility, we identified protein signatures that robustly discriminated between short-term and long-term survival phenotypes. While the data set was highly enriched for established exosomal markers, differential expression and PLS-DA modeling revealed that the most significant indicators of short survival (high aggressiveness) were ribosomal proteins. STRING analysis confirmed these as highly connected interactome hubs. These findings suggest that the differential loading of translational machinery into the extracellular space likely via microvesicles or coisolated nonvesicular particles contributes to poor prognosis, offering new insights into the systemic secretome of aggressive tumors.