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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.

SUBMITTER: Swietlik JJ

PROVIDER: S-EPMC10167354 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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

Swietlik Jonathan J JJ Bärthel Stefanie S Falcomatà Chiara C Fink Diana D Sinha Ankit A Cheng Jingyuan J Ebner Stefan S Landgraf Peter P Dieterich Daniela C DC Daub Henrik H Saur Dieter D Meissner Felix F

Nature communications 20230508 1

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-de ...[more]

PMID: 37156840

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Project description:Human pancreatic stellate cells (HPSCs) are an essential stromal component and mediators of pancreatic ductal adenocarcinoma (PDAC) progression. Small extracellular vesicles (sEVs) are membrane-enclosed nanoparticles involved in cell-to-cell communications and are released from stromal cells within PDAC. A detailed comparison of sEVs from normal pancreatic stellate cells (HPaStec) and from PDAC-associated stellate cells (HPSCs) remains a gap in our current knowledge regarding stellate cells and PDAC. We hypothesized there would be differences in sEVs secretion and protein expression that might contribute to PDAC biology. To test this hypothesis, we isolated sEVs using ultracentrifugation followed by characterization by electron microscopy and Nanoparticle Tracking Analysis. We report here our initial observations. First, HPSC cells derived from PDAC tumors secrete a higher volume of sEVs when compared to normal pancreatic stellate cells (HPaStec). Although our data revealed that both normal and tumor-derived sEVs demonstrated no significant biological effect on cancer cells, we observed efficient uptake of sEVs by both normal and cancer epithelial cells. Additionally, intact membrane-associated proteins on sEVs were essential for efficient uptake. We then compared sEV proteins isolated from HPSCs and HPaStecs cells using liquid chromatography-tandem mass spectrometry. Most of the 1481 protein groups identified were shared with the exosome database, ExoCarta. Eighty-seven protein groups were differentially expressed (selected by 2-fold difference and adjusted p value ≤0.05) between HPSC and HPaStec sEVs. Of note, HPSC sEVs contained dramatically more CSE1L (chromosome segregation 1-like protein), a described marker of poor prognosis in patients with pancreatic cancer. Based on our results, we have demonstrated unique populations of sEVs originating from stromal cells with PDAC and suggest that these are significant to cancer biology. Further studies should be undertaken to gain a deeper understanding that could drive novel therapy.

Project description:Rationale: The current understanding on manipulating signaling pathways to generate mature human islet organoids with all major hormone-secreting endocrine cell types (i.e., α, β, δ, and γ cells) from induced pluripotent stem cells (iPSCs) is insufficient. However, donor islet shortage necessitates that we produce functional islets in vitro. In this study, we aimed to find decellularized pancreatic extracellular matrix (dpECM) proteins that leverage signaling pathways and promote functional iPSC islet organogenesis. Methods: We performed proteomic analysis to identify key islet promoting factors from porcine and rat dpECM. With this, we identified collagen type II (COL2) as a potential biomaterial cue that endorses islet development from iPSCs. Using global transcriptome profiling, gene set enrichment analysis, immunofluorescence microscopy, flow cytometry, Western blot, and glucose-stimulated hormonal secretion analysis, we examined COL2's role in regulating iPSC pancreatic lineage specification and signaling pathways, critical to islet organogenesis and morphogenesis. Results: We discovered COL2 acts as a functional biomaterial that augments islet development from iPSCs, similar to collagen type V (COL5) as reported in our earlier study. COL2 substantially stimulates the formation of endocrine progenitors and subsequent islet organoids with significantly elevated expressions of pancreatic signature genes and proteins. Furthermore, it enhances islets' glucose sensitivity for hormonal secretion. A cluster of gene expressions associated with various signaling pathways, including but not limited to oxidative phosphorylation, insulin secretion, cell cycle, the canonical WNT, hypoxia, and interferon-γ response, were considerably affected by COL2 and COL5 cues. Conclusion: We demonstrated dpECM's crucial role in refining stem cell differentiation microenvironments for organoid development and maturation. Our findings on biomaterial-stimulated signaling for stem cell specification, organogenesis, and maturation open up a new way to increase the differentiation efficacy of endocrine tissues that can contribute to the production of biologically functional islets.

Dataset Information

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

Publications

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

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