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Misek SA, Appleton KM, Dexheimer TS, Lisabeth EM, Lo RS, Larsen SD, Gallo KA, Neubig RR. Abstract B07: Rho-mediated gene transcription promotes BRAFi resistance in de-differentiated melanoma cells. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-b07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
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.
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Affiliation(s)
| | | | | | | | - Roger S. Lo
- 2University of California, Los Angeles, Los Angeles, CA,
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Misek SA, Appleton KM, Dexheimer TS, Lisabeth EM, Lo RS, Larsen SD, Gallo KA, Neubig RR. Rho-mediated signaling promotes BRAF inhibitor resistance in de-differentiated melanoma cells. Oncogene 2019; 39:1466-1483. [PMID: 31659259 PMCID: PMC7024013 DOI: 10.1038/s41388-019-1074-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/25/2019] [Accepted: 10/14/2019] [Indexed: 01/04/2023]
Abstract
Over half of cutaneous melanoma tumors have BRAFV600E/K mutations. Acquired resistance to BRAF inhibitors (BRAFi) remains a major hurdle in attaining durable therapeutic responses. In this study we demonstrate that approximately 50–60% of melanoma cell lines with vemurafenib resistance acquired in vitro show activation of RhoA family GTPases. In BRAFi-resistant melanoma cell lines and tumors, activation of RhoA is correlated with decreased expression of melanocyte lineage genes. Using a machine learning approach, we built gene expression-based models to predict drug sensitivity for 265 common anti-cancer compounds. We then projected these signatures onto the collection of TCGA cutaneous melanoma and found that poorly differentiated tumors were predicted to have increased sensitivity to multiple Rho kinase (ROCK) inhibitors. Two transcriptional effectors downstream of Rho, MRTF and YAP1, are activated in the RhoHigh BRAFi-resistant cell lines, and resistant cells are more sensitive to inhibition of these transcriptional mechanisms. Taken together, these results support the concept of targeting Rho-regulated gene transcription pathways as a promising therapeutic approach to restore sensitivity to BRAFi-resistant tumors or as a combination therapy to prevent the onset of drug resistance.
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Affiliation(s)
- S A Misek
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - K M Appleton
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - T S Dexheimer
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - E M Lisabeth
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - R S Lo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, CA, 90095, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA.,David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - S D Larsen
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.,Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI, 48109, USA
| | - K A Gallo
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - R R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA. .,Nicholas V. Perricone, M.D., Division of Dermatology, Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, 48824, MI, USA.
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