Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation

Abstract

Cell-selective proteomics is a powerful emerging concept to study heterocellular processes in tissues. However, its high potential to identify non-cell-autonomous disease mechanisms and biomarkers has been hindered by low proteome coverage. Here, we address this limitation and devise a comprehensive azidonorleucine labeling, click chemistry enrichment, and mass spectrometry-based proteomics and secretomics strategy to dissect aberrant signals in pancreatic ductal adenocarcinoma (PDAC). Our in-depth co-culture and in vivo analyses cover more than 10,000 cancer cell-derived proteins and reveal systematic differences between molecular PDAC subtypes. Secreted proteins, such as chemokines and EMT-promoting matrisome proteins, associated with distinct macrophage polarization and tumor stromal composition, differentiate classical and mesenchymal PDAC. Intriguingly, more than 1,600 cancer cell-derived proteins including cytokines and pre-metastatic niche formation-associated factors in mouse serum reflect tumor activity in circulation. Our findings highlight how cell-selective proteomics can accelerate the discovery of diagnostic markers and therapeutic targets in cancer.

Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication

“…The recent demonstration that cell-selective ANL labeling can also be performed in orthotopic cancer models in mice further broadens this perspective to investigate protein synthesis and secretion in cancer cells in the context of their microenvironment in vivo ( 72 , 73 ). This may be applicable to many cell line–derived xenograft models that have been developed in the past or even to patient-derived xenografts if the primary cells are amenable to lentiviral infection.…”

“…This may be applicable to many cell line–derived xenograft models that have been developed in the past or even to patient-derived xenografts if the primary cells are amenable to lentiviral infection. Alternatively, ANL labeling in mouse cancer cells has the advantage that grafting of cells can be performed in immunocompetent mice, thereby encapsulating interactions with infiltrating immune cells that may affect the tumor secretome and ECM composition ( 73 ).…”