Abstract 3776: Identification of gene regulatory networks mediating melanoma cell resistance to temozolomide
Authors: Tongwu Zhang, Mai Xu, Donald Chow, Chris Sereduk, Jeffrey M. Trent, Hongwei Yin, Kevin M. Brown
Journal: Cancer Research (2014)

Abstract Melanoma is the most dangerous type of skin cancer and the leading cause of death from skin cancer. While there are multiple promising new immunotherapeutic and targeted approaches for treating melanoma, not all patients are eligible for these therapies and most of those that are ultimately relapse, highlighting a critical need for improved chemotherapeutics. Temozolomide (TMZ) is an orally administered DNA-alkylating agent used in the treatment of advanced cancers including melanoma. TMZ has shown some advantage in the clinic in terms of preventing central nervous system relapse and patient quality of life. In order to find novel vulnerabilities that may be exploited to sensitize melanoma cells to TMZ, we utilized mRNA expression and TMZ-sensitivity profiling in a panel of 18 melanoma cell lines to develop a classifier of TMZ-sensitivity using the support vector machine (SVM) method. We subsequently applied this classifier to predict the TMZ-sensitivity in 47 independent melanoma cell lines. TMZ sensitivity profiling in smaller set of 22 of these lines resulted in a prediction accuracy of approximately 80%. We analyzed the genes differentiating TMZ-sensitive and -resistant melanoma cells using both microarray data in 40 cell lines, and more recently RNA-sequencing from the original 18 cell line training set. We found no correlation between TMZ sensitivity and expression of the DNA repair gene (MGMT), base excision repair gene (PARP1, PARG, etc.), and DNA mismatch repair gene (MLH1, MSH2, etc.). Instead, analysis using the Ingenuity IPA pathway analysis tool found that upregulation of MITF and a large set of MITF target genes, as well as downregulation TGFB1 and TGFB1 targets were strongly associated with TMZ resistance in melanoma cell line (p = 2.82E-67 and p = 1.17E-52, respectively in the microarray analysis; similar results observed in RNA sequencing data). E-cadherin (CDH1), which is know to play a key role in invasion and transition from radial to vertical growth in melanoma, was found to be one of the genes most significantly correlated with TMZ resistance. Finally, we also analyzed exome-sequencing data from these cell lines (n=55) and found that TMZ-sensitivity did not significantly correlate with the presence or absence of mutations to genes commonly mutated in melanoma. In conclusion, our gene expression data suggest that TMZ resistance in melanoma cells in vitro is likely mediated by large gene regulatory networks governed by MITF and TGFB1. Citation Format: Tongwu Zhang, Mai Xu, Donald Chow, Chris Sereduk, Jeffrey M. Trent, Hongwei Yin, Kevin M. Brown. Identification of gene regulatory networks mediating melanoma cell resistance to temozolomide. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3776. doi:10.1158/1538-7445.AM2014-3776