Proteomic analyses of ECM during pancreatic ductal adenocarcinoma progression reveal different contributions by tumor and stromal cells

Abstract

Significance We describe here the most comprehensive analyses of extracellular matrix (ECM) of pancreatic ductal adenocarcinoma (PDAC) yet available, which detected previously unknown molecular changes during PDAC progression in both mouse models and human patients. These data distinguish ECM proteins produced by tumor cells from those produced by stromal cells and show that it is the diverse set of tumor cell-derived proteins that correlate best with poor patient survival. In contrast, the stroma-derived ECM proteins, which comprise the bulk of the microenvironmental ECM, include both proteins correlating with good survival and proteins correlating with poor survival. These data may help explain why prior nonselective depletion of the stroma led to poorer patient outcomes and suggest more precise ECM manipulations as PDAC treatments. Pancreatic ductal adenocarcinoma (PDAC) has prominent extracellular matrix (ECM) that compromises treatments yet cannot be nonselectively disrupted without adverse consequences. ECM of PDAC, despite the recognition of its importance, has not been comprehensively studied in patients. In this study, we used quantitative mass spectrometry (MS)-based proteomics to characterize ECM proteins in normal pancreas and pancreatic intraepithelial neoplasia (PanIN)- and PDAC-bearing pancreas from both human patients and mouse genetic models, as well as chronic pancreatitis patient samples. We describe detailed changes in both abundance and complexity of matrisome proteins in the course of PDAC progression. We reveal an early up-regulated group of matrisome proteins in PanIN, which are further up-regulated in PDAC, and we uncover notable similarities in matrix changes between pancreatitis and PDAC. We further assigned cellular origins to matrisome proteins by performing MS on multiple lines of human-to-mouse xenograft tumors. We found that, although stromal cells produce over 90% of the ECM mass, elevated levels of ECM proteins derived from the tumor cells, but not those produced exclusively by stromal cells, tend to correlate with poor patient survival. Furthermore, distinct pathways were implicated in regulating expression of matrisome proteins in cancer cells and stromal cells. We suggest that, rather than global suppression of ECM production, more precise ECM manipulations, such as targeting tumor-promoting ECM proteins and their regulators in cancer cells, could be more effective therapeutically.