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bioRxiv · 10.1101/2021.05.04.442611

Modeling the Pancreatic Cancer Microenvironment in Search of Control Targets

Plaugher, D. R.·Murrugarra, D.
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Abstract

Pancreatic Ductal Adenocarcinoma is among the leading causes of cancer related deaths globally due to its extreme difficulty to detect and treat. Recently, research focus has shifted to analyzing the microenvironment of pancreatic cancer to better understand its key molecular mechanisms. This microenvironment can be represented with a multi-scale model consisting of pancreatic cancer cells (PCCs), pancreatic stellate cells (PSCs), as well as cytokines and growth factors which are responsible for intercellular communication between the PCCs and PSCs. We have built a stochastic Boolean network (BN) model, validated by literature and clinical data, in which we probed for intervention strategies that force this gene regulatory network (GRN) from a diseased state to a healthy state. To do so, we implemented methods from phenotype control theory to determine a procedure for regulating specific genes within the microenvironment. We identify target genes and molecules such that the application of their control drives the GRN to the desired state by suppression (or expression) and disruption of specific signaling pathways that will eventually lead to the eradication of the cancer cells. After applying well studied control methods such as stable motifs, feedback vertex set, and computational algebra, we discovered that each produces a different set of control targets that are not necessarily minimal nor unique. Yet, we were able to gain more insight about the performance of each process and the overlap of targets discovered. Nearly every control set contains cytokines, KRas, and HER2/neu which suggests they are key players in the systems dynamics. To that end, this model can be used to produce further insight into the complex biological system of pancreatic cancer with hopes of finding new potential targets.

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Plaugher, D. R., Murrugarra, D.. 2021-05-04. Modeling the Pancreatic Cancer Microenvironment in Search of Control Targets. https://doi.org/10.1101/2021.05.04.442611

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