Microdissected pancreatic cancer proteomes reveal tumor heterogeneity and therapeutic targets

• DOI: 10.1172/jci.insight.138290
• Publication Date: 2020-07-07T16:11:00Z
• Authors: Tessa Y.S. Le Large; Giulia Mantini; Laura L. Meijer; Thang V. Pham; Niccola Funel; Nicole C.T. van G...; Bart Kok; Jaco Knol; Hanneke W.M. van ...; Sander R. Piersma; Connie R. Jimenez; G. Kazemier; Elisa Giovannetti; Maarten F. Bijlsma
• Keywords: Aged, 80 and over; Male; 0301 basic medicine; 0303 health sciences; Proteome; Middle Aged; Prognosis; Xenograft Model Antitumor Assays; Extracellular Matrix; 3. Good health; Gene Expression Regulation, Neoplastic; Pancreatic Neoplasms; Survival Rate; Mice; 03 medical and health sciences; Biomarkers, Tumor; Tumor Cells, Cultured; Animals; Humans; Female; Stromal Cells; Aged; Carcinoma, Pancreatic Ductal

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a relative paucity of cancer cells that are surrounded by an abundance of nontumor cells and extracellular matrix, known as stroma. The interaction between stroma and cancer cells contributes to poor outcome, but how proteins from these individual compartments drive aggressive tumor behavior is not known. Here, we report the proteomic analysis of laser-capture microdissected (LCM) PDAC samples. We isolated stroma, tumor, and bulk samples from a cohort with long- and short-term survivors. Compartment-specific proteins were measured by mass spectrometry, yielding what we believe to be the largest PDAC proteome landscape to date. These analyses revealed that, in bulk analysis, tumor-derived proteins were typically masked and that LCM was required to reveal biology and prognostic markers. We validated tumor CALB2 and stromal COL11A1 expression as compartment-specific prognostic markers. We identified and functionally addressed the contributions of the tumor cell receptor EPHA2 to tumor cell viability and motility, underscoring the value of compartment-specific protein analysis in PDAC.