Abstract B07: Rho-mediated gene transcription promotes BRAFi resistance in de-differentiated melanoma cells

Abstract

The goal of this study is to identify pharmacologically tractable resistance mechanisms, and ultimately to prevent or reverse drug resistance in melanoma. We demonstrate that a subset of BRAFi-resistant melanoma cell lines showed diminished expression of melanocyte differentiation markers (e.g., Sox10). The transcriptional signature of 15% of treatment-naïve TCGA SKCM (skin cutaneous melanoma) tumors is similar to that of de-differentiated BRAFi-resistant cell lines. This transcriptional signature in BRAFi-resistant melanoma cells and human tumors is associated with increased Rho activation and increased expression of a RhoA/C gene signature. Using a machine learning approach, we predict that these tumors have decreased sensitivity to multiple BRAF/MEK inhibitors, consistent with our observations in multiple cell line models. De-differentiated tumors are predicted to have increased sensitivity to multiple ROCK inhibitors, and this prediction was validated in multiple BRAFi-resistant cell line models. Since ROCK is one of the canonical Rho effector proteins, these data suggest that melanoma cells and tumors with low differentiation characteristics activate the Rho pathway and are sensitive to Rho pathway inhibition. As a consequence of the effect of Rho on the actin cytoskeleton, Rho regulates gene transcription through modulating transcriptional co-activators such as MRTFA and YAP1. Both MRTFA and YAP1 are activated in de-differentiated BRAFi-resistant cells and are predicted to be activated in human tumors with a similar transcriptomic profile. Consistent with our predictions, melanoma cells with MRTFA activation are sensitive to an MRTFA pathway inhibitor and those with high YAP1 activity are sensitive to indirect blockade of YAP1 activation. In total, these results demonstrate that over the course of drug resistance a subset of cells and tumors lose melanocyte lineage characteristics and gain Rho activation. In summary, our work has used bioinformatics/ML approaches to identify Rho-mediated gene transcription as an important, targetable mechanism of BRAFi resistance in de-differentiated melanomas. We experimentally demonstrate the efficacy of this approach in multiple BRAFi-resistant models, highlighting the potential of targeting Rho-mediated transcription for treating drug-resistant melanomas. Citation Format: Sean A. Misek, Kate M. Appleton, Tom S. Dexheimer, Erika M. Lisabeth, Roger S. Lo, Scott D. Larsen, Kathleen A. Gallo, Richard R. Neubig. Rho-mediated gene transcription promotes BRAFi resistance in de-differentiated melanoma cells [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr B07.