A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma. Issue 7 (22nd July 2020)

• Record Type: Journal Article
• Authors: Aguilar, Boris; Gibbs, David L; Reiss, David J; McConnell, Mark; Danziger, Samuel A; Dervan, Andrew; Trotter, Matthew; Bassett, Douglas; Hershberg, Robert; Ratushny, Alexander V; Shmulevich, Ilya
• Is Part Of: GigaScience. Volume 9:Issue 7(2020)
• Publication Date: 2020-07-22
• Subjects: cancer modeling -- data-driven model -- pancreatic ductal adenocarcinoma -- multicellular model; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giaa075
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: Mechanistic models, when combined with pertinent data, can improve our knowledge regarding important molecular and cellular mechanisms found in cancer. These models make the prediction of tissue-level response to drug treatment possible, which can lead to new therapies and improved patient outcomes. Here we present a data-driven multiscale modeling framework to study molecular interactions between cancer, stromal, and immune cells found in the tumor microenvironment. We also develop methods to use molecular data available in The Cancer Genome Atlas to generate sample-specific models of cancer. Results: By combining published models of different cells relevant to pancreatic ductal adenocarcinoma (PDAC), we built an agent-based model of the multicellular pancreatic tumor microenvironment, formally describing cell type–specific molecular interactions and cytokine-mediated cell-cell communications. We used an ensemble-based modeling approach to systematically explore how variations in the tumor microenvironment affect the viability of cancer cells. The results suggest that the autocrine loop involving EGF signaling is a key interaction modulator between pancreatic cancer and stellate cells. EGF is also found to be associated with previously described subtypes of PDAC. Moreover, the model allows a systematic exploration of the effect of possible therapeutic perturbations; our simulations suggest that reducing bFGF secretion by stellate cells will have, on average, a positive impact on cancer apoptosis. Conclusions: The developed framework allows model-driven hypotheses to be generated regarding therapeutically relevant PDAC states with potential molecular and cellular drivers indicating specific intervention strategies.