swMATH ID: 42849
Software Authors: Plaugher, Daniel; Aguilar, Boris; Murrugarra, David
Description: Uncovering potential interventions for pancreatic cancer patients via mathematical modeling. Pancreatic ductal adenocarcinoma (PDAC) is widely known for its poor prognosis because it is often diagnosed when the cancer is in a later stage. We built a Boolean model to analyze the microenvironment of pancreatic cancer in order to better understand the interplay between pancreatic cancer, stellate cells, and their signaling cytokines. Specifically, we have used our model to study the impact of inducing four common mutations: KRAS, TP53, SMAD4, and CDKN2A. After implementing the various mutation combinations, we used our stochastic simulator to derive aggressiveness scores based on simulated attractor probabilities and long-term trajectory approximations. These aggression scores were then corroborated with clinical data. Moreover, we found sets of control targets that are effective among common mutations. These control sets contain nodes within both the pancreatic cancer cell and the pancreatic stellate cell, including PIP3, RAF, PIK3 and BAX in pancreatic cancer cell as well as ERK and PIK3 in the pancreatic stellate cell. Many of these nodes were found to be differentially expressed among pancreatic cancer patients in the TCGA database. Furthermore, literature suggests that many of these nodes can be targeted by drugs currently in circulation. The results herein help provide a proof of concept in the path towards personalized medicine through a means of mathematical systems biology. All data and code used for running simulations, statistical analysis, and plotting is available on a GitHub repository at https://github.com/drplaugher/PCC_Mutations.
Homepage: https://www.sciencedirect.com/science/article/abs/pii/S0022519322001953
Source Code:  https://github.com/drplaugher/PCC_Mutations
Dependencies: Macaulay2
Keywords: pancreatic cancer; phenotype control; cytokines; pancreatic stellate cells; Boolean networks
Related Software: Macaulay2
Cited in: 1 Document

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