Abstract B011: Network propagation of the kinase activity signatures of therapy-resistant tumors reveals novel druggable targets in BRAF(V600E)-mutated colorectal cancer


 Despite combination therapies targeting BRAF and EGFR, metastatic colorectal cancer (mCRC) with a BRAF(V600E) mutation confers poor prognosis with early development of drug resistance in a majority of patients. Treatment with a current standard of care (encorafenib plus panitumumab) temporarily suppresses tumor growth, but fails to promote regression and leads to eventual disease progression. Consequently, there is a need to better characterize the compensatory resistance pathways that are activated in response to treatment. To identify these parallel resistance mechanisms and novel druggable targets, we analyzed the effects of combination treatment with encorafenib (a BRAF-inhibitor) and panitumumab (an anti-EGFR antibody) in BRAF(V600E) mCRC patient-derived xenograft (PDX) tumor samples via a high throughput kinase activity mapping (HT-KAM) platform and advanced computational tools. HT-KAM uses libraries of peptides as combinatorial sensors that identify and measure the activity of >160 kinases involved in oncogenic pathways (Coppé et al 2019). As these key kinases provide an informative yet filtered view of proteome-wide signaling effects, we developed a network-based workflow to further analyze our HT-KAM results. Network propagation methods were applied to integrate this data into ReactomeFI, a well-validated gene/protein interaction network. Significant genes from the network propagation results were clustered and enriched for pathway analysis using additional scripts, and results were visualized using Cytoscape. Based on HT-KAM results comparing the kinase signatures of PDX tumors treated with encorafenib + panitumumab versus vehicle, EGFR was confirmed to be downregulated. Moreover, several kinases previously identified as (re-)activated upon treatment and progression were significantly upregulated, including kinases in the RAF–MEK–ERK cascade as well as AKTs and downstream effectors. In addition, STK11, a tumor suppressor also known as LKB1, was significantly downregulated, while the activity of several kinases involved in cell surface signaling were upregulated, including PKA and PKCs. Network propagation of this data and enrichment of network subclusters resulted in a broad range of pathways implicated in persistent cell survival. Among top hits, signaling networks orchestrated by GPCRs, MTOR, WNT and beta-catenin were significantly enriched, suggesting that multiple interacting pathways coordinate the response and resistance to BRAF/EGFR joint inhibition. Our workflow implementing network propagation and enrichment analysis of HT-KAM data pinpoints essential pathways that contain druggable targets. We are in the process of validating these dependencies in PDX models and translating these mechanisms into novel combinatorial targeted therapy interventions designed to overcome drug resistance in BRAF(V600E) mCRC.
 Citation Format: Yeonjoo Hwang, Mehdi Bouhaddou, Christina Moelders, Denise P. Muñoz, Chloe E. Atreya, Jean-Philippe Coppé. Network propagation of the kinase activity signatures of therapy-resistant tumors reveals novel druggable targets in BRAF(V600E)-mutated colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B011.