Abstract 5213: A systems biology approach to understanding differential phenotypic outcome of BRAF(V600E) inhibition in melanoma cells.
Authors: Mohammad Fallahi-Sichani, Nathan J. Moerke, Anahita Dastur, Cyril H. Benes, Peter K. Sorger
Journal: Cancer Research (2013)

Abstract Melanoma is the deadliest form of skin cancer and the leading cause of death from skin disease. The BRAF(V600E) mutation is found in approximately 60% of melanomas. It causes constitutive activation of the RAF/MEK/ERK signaling pathway in these tumors leading to uncontrolled cell growth. Inhibition of BRAF(V600E) induces apoptosis in melanoma cells which has been used as the basis for molecular targeted therapy of melanoma. Small-molecule compounds such as Vemurafenib, Dabrafenib and other selective BRAF(V600E) inhibitors specifically bind BRAF(V600E), and have been shown to cause dramatic, but transient, tumor regression in vivo. The precise mechanisms of cell death following BRAF inhibition remain obscure; the literature posits a diversity of ways in which apoptosis is induced. However, it is unclear whether a single but complex network is involved or whether mechanisms differ from one cell type to the next. This is an important issue because use of BRAF(V600E) inhibitors in the treatment of melanoma is seriously challenged by the absence of durable responses; even in initially responsive patients tumors usually re-emerge within months and are observed to be drug resistant. An important challenge is thus to understand determinants of initial sensitivity to BRAF inhibition beyond V600E mutation and to determine which of these are involved in resistance. Using high throughput measurement of the abundance and state of modification of multiple proteins representing diverse signaling pathways at the basal level and over time in multiple melanoma cell lines exposed to different doses of BRAF inhibitors and data-driven mathematical modeling, we determine how the complex dynamics of signaling pathways are controlled in different cell lines and how drugs targeting BRAF(V600E) alter this signaling. Our analysis shows that the basal level of some proteins such as PTEN, pERK, pS6, pAkt, and β-catenin vary up to 100-fold among different lines prior drug treatment. Further, these cell lines show different degrees of oncogene addiction and remarkable diversity with respect to the level of ERK inhibition and apoptosis as well as activation or inhibition of other signaling cascades following BRAF inhibition. We use mathematical modeling to relate basal levels of signaling proteins and their dynamics following BRAF inhibition to pharmacological descriptors of sensitivity to multiple BRAF drugs. Thus, we identify key signaling nodes within the signaling networks of the melanoma cells which determine the differential phenotypic consequences of BRAF inhibition. This approach will be critical for predicting and ultimately improving drug sensitivity in resistant tumors (e.g. via co-treatment strategies). Citation Format: Mohammad Fallahi-Sichani, Nathan J. Moerke, Anahita Dastur, Cyril H. Benes, Peter K. Sorger. A systems biology approach to understanding differential phenotypic outcome of BRAF(V600E) inhibition in melanoma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5213. doi:10.1158/1538-7445.AM2013-5213