Abstract 6572: Integrative network propagation to uncover potential drug resistance mechanisms in FGFR2 fusion-positive cholangiocarcinoma
Authors: Hwang Yeonjoo , Swaney Danielle L. , Bardeesy Nabeel , Gordan John D. 
Published: September 2020

Abstract
Drug resistance emerges in response to most targeted therapies and is a common mechanism of treatment failure in patients with advanced cancer. We have studied resistance in intrahepatic cholangiocarcinoma (ICC) with oncogenic FGFR2 fusions. FGFR2 fusions are seen in 10-15% of ICC patients, and FGFR inhibition (FGFRi) is associated with relatively rapid emergence of resistance. While some FGFRi resistance results from mutations that block drug from binding, previous analysis has revealed polyclonal mechanisms relying on multiple pathways. Given this complexity of treatment-emergent resistance, we have employed computational strategies to integrate the phenotypic response to FGFRi with essential growth mechanisms in FGFR2 fusion-driven ICC. We applied network propagation approaches to the results of multiple -omics platforms to develop an integrated network map of the response of a patient-derived FGFR2 fusion-positive ICC line to the FGFR inhibitor TAS-120. For this analysis, multiple distinct -omics datasets (RNASEQ, global phosphoproteomics) were propagated across the ReactomeFI network, based on experimentally proven physical interactions. We propagated each dataset across the network separately and multiplied the propagation scores for each gene to generate a combined p-value, allowing us to uncover significant pathways in the network that may not have been apparent in the individual datasets. We have identified numerous groups of nodes of functional importance, including a large cluster of proteins involved in Rho family GTPase signaling. To pursue a potentially druggable target, we evaluated the Rho effector Protein Kinase N2 (PKN2). Follow-up biochemical analysis suggests that PKN2 modulates signaling feedback to AKT following FGFRi and results in altered phosphorylation of the apoptotic regulator BAD. Consistent with this, we have found that PKN2 is required for sensitivity to FGFRi in the patient-derived line using a cell viability assay. Furthermore, synergy assays with TAS-120 and the AKT inhibitor MK2206, SGK inhibitor GSK650934, and Bcl-2 inhibitor ABT-263 each resulted in significant synergistic activity, suggesting that AKT is a key effector in PKN2-mediated FGFRi resistance. We are in the process of validating these results in different cell lines and further characterizing the mechanism by which PKN2 is contributing to the FGFR/AKT signaling. In addition to identifying PKN2 as a key mediator of pathway feedback, multiple other candidate resistance mechanisms have emerged, including well established and relatively understudied pathways. These results allow multiple further avenues of investigation, and demonstrate the value of systems approaches in identifying new targets to counter drug resistance.
Citation Format: Yeonjoo Hwang, Danielle L. Swaney, Nabeel Bardeesy, John D. Gordan. Integrative network propagation to uncover potential drug resistance mechanisms in FGFR2 fusion-positive cholangiocarcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6572.