FCCC LOGO Faculty Publications
Ursu O , Gosline SJC , Beeharry N , Fink L , Bhattacharjee V , Huang SC , Zhou Y , Yen T , Fraenkel E
Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens
PLoS One. 2017 Oct;12(10) :e0185650
PMID: 29023490    PMCID: PMC5638242   
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Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these molecules is challenging, since the compounds are often promiscuous. We present a network strategy that takes into account the polypharmacology of small molecules in order to generate hypotheses for their broader mode of action. We report a screen for kinase inhibitors that increase the efficacy of gemcitabine, the first-line chemotherapy for pancreatic cancer. Eight kinase inhibitors emerge that are known to affect 201 kinases, of which only three kinases have been previously identified as modifiers of gemcitabine toxicity. In this work, we use the SAMNet algorithm to identify pathways linking these kinases and genetic modifiers of gemcitabine toxicity with transcriptional and epigenetic changes induced by gemcitabine that we measure using DNaseI-seq and RNA-seq. SAMNet uses a constrained optimization algorithm to connect genes from these complementary datasets through a small set of protein-protein and protein-DNA interactions. The resulting network recapitulates known pathways including DNA repair, cell proliferation and the epithelial-to-mesenchymal transition. We use the network to predict genes with important roles in the gemcitabine response, including six that have already been shown to modify gemcitabine efficacy in pancreatic cancer and ten novel candidates. Our work reveals the important role of polypharmacology in the activity of these chemosensitizing agents.
1932-6203 Ursu, Oana Gosline, Sara J C Beeharry, Neil Fink, Lauren Bhattacharjee, Vikram Huang, Shao-Shan Carol Zhou, Yan Yen, Tim Fraenkel, Ernest R21 CA182651/CA/NCI NIH HHS/United States Journal Article United States PLoS One. 2017 Oct 12;12(10):e0185650. doi: 10.1371/journal.pone.0185650. eCollection 2017.