Abstract A100: Large-scale cell line profiling of small molecule MAPK pathway inhibitors identifies important differences between therapeutics acting on the same biochemical target
Authors: Kooijman Jeffrey J. , Koerdi Awan Al , van Riel Wilhelmina E. , Bossche Esmee van den , Dylus Jelle , de Roos Jeroen A.D.M. , Melis Janneke J.T.M. , Zaman Guido J.R. 
Published: December 2023

The mitogen-activated protein kinase (MAPK) pathway is frequently dysregulated in cancer, leading to unrestricted cell growth. Inhibitors that specifically target key components of the pathway, such as B-RAF and MEK inhibitors, have been approved for treatment of V600E-mutant melanoma, while inhibitors of G12C-mutant K-RAS, have been approved for lung cancer. Several dimer-selective pan-RAF inhibitors, and inhibitors of other components in the pathway, such as ERK and G12D-mutant K-RAS, are currently in clinical development. Cancer cell panel profiling, in combination with genomics, proteomics and bioinformatics, was performed to get more insight into mechanistic differences of small molecules acting on the same primary target, and to study the role of cell-type specific factors. Approximately twenty inhibitors of either RAF, MEK, ERK, or RAS were profiled in nine-point duplicate dose ranges in cell viability assays of more than hundred human cancer cell lines that have been derived from diverse tumor tissues (the Oncolines® panel). The half-maximal inhibitory concentration (IC50) calculated from the dose-response curves in the cell viability assays was used to relate drug response to genetic, genomic and (phospho-)proteomic features in the cancer cell lines. Oncogenic alterations in MAPK components, including BRAF, KRAS, NRAS, and MAP2K1 mutations, were represented in multiple cell lines of the panel, and were related to drug response. Additionally, to identify cell-intrinsic transcriptomic or proteomic factors that predict response to the inhibitors, the relationship between drug response and basal gene and protein expression levels (as reported in the DepMap database) was analyzed. Lastly, cell line responses to the different inhibitors were correlated with the DepMap cell line CRISPR knockout dataset, enabling the identification of genes whose dependency most closely resembles the response to inhibitors of the MAPK pathway. Our approaches unveiled subtle but important differences in cell line targeting between inhibitors acting on the same biochemical target, such as the relative preference of belvarafenib to target B-RAF-mutant cell lines, which was not seen for naporafenib. Our results may help guiding the development and application of precision medicine strategies in the context of MAPK pathway-targeted therapies.

Citation Format: Jeffrey J. Kooijman, Awan Al Koerdi, Wilhelmina E. van Riel, Esmee van den Bossche, Jelle Dylus, Jeroen A.D.M. de Roos, Janneke J.T.M. Melis, Guido J.R. Zaman. Large-scale cell line profiling of small molecule MAPK pathway inhibitors identifies important differences between therapeutics acting on the same biochemical target [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A100.