Identification of proteins released by pancreatic cancer cells by multidimensional protein identification technology: a strategy for identification of novel cancer markers

Purpose. To identify novel proteins released by cancer cells that are involved in extracellular matrix (ECM) remodelling using small volume samples and automated technology. Procedure. We applied multidimensional protein identification technology (MudPIT), that incorporates two-dimensional capillary chromatography coupled to tandem mass spectrometry, to small quantities of serum-free supernatants of resting or phorbol ester-activated Suit-2 pancreatic cancer cells. Selected markers were validated in additional pancreatic cancer cell lines, primary cancers and xenografted cancer cells. Results. MudPIT analysis of 10 µl of supernatants identified 46 proteins, 21 of which are classified as secreted, and ten have never been associated with pancreatic cancer. These include CSPG2/versican, Mac25/angiomodulin, IGFBP-1, HSPG2/perlecan, syndecan 4, FAM3C, APLP2, cyclophilin B, beta2 microglobulin and ICA69. Evidence that cancer cells release these proteins in vivo was obtained for CSPG2/versican and Mac25/angiomodulin by immunohistochemistry on both primary pancreatic cancers and in a model consisting of Suit-2 cells embedded in an amorphous matrix and implanted in athymic mice. Conclusions. MudPIT allowed efficient and rapid identification of proteins released by cancer cells, including molecules previously undescribed in the type of cancer analyzed. Our finding that pancreatic cancer cells secrete a series of proteoglycans, including versican, perlecan, syndecan 1 and 4, challenges the common view that fibroblasts of tumor stroma are the sole source of these molecules.