Publication of IMPRS-LS student Jonathan Swietlik


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Swietlik, J.J., Bärthel, S., Falcomatà, C., Fink, D., Sinha, A., Cheng, J., Ebner, S., Landgraf, P., Dieterich, D.C., Daub, H., Saur, D., and Meissner, F.
(IMPRS-LS students are in bold)
Nat Commun, 2023, 14, 2642.
doi: 10.1038/s41467-023-38171-8

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

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.