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Melanoma is a deadly form of cancer characterized by remarkable therapy resistance. Analyzing the transcriptome of MAPK inhibitor sensitive- and resistant-melanoma, we discovered that APAF-1 is negatively regulated by MITF in resistant tumors. This study identifies the MITF/APAF-1 axis as a molecular driver of MAPK inhibitor resistance. A drug-repositioning screen identified quinacrine and methylbenzethonium as potent activators of apoptosis in a context that mimics drug resistance mediated by APAF-1 inactivation. The compounds showed anti-tumor activity in invitro and invivo models, linked to suppression of MITF function. Both drugs profoundly sensitize melanoma cells to MAPK inhibitors, regulating key signaling networks in melanoma, including the MITF/APAF-1 axis. Significant activity of the two compounds in inhibiting specific epigenetic modulators of MITF/APAF-1 expression, such as histone deacetylases, was observed. In summary, we demonstrate that targeting the MITF/APAF-1 axis may overcome resistance and could be exploited as a potential therapeutic approach to treat resistant melanoma.

Melanoma is a deadly form of cancer characterized by high aggressiveness and remarkable therapy-resistance. The inactivation of apoptosis constitutes a common strategy adopted by cancer cells to survive death-stimulating drugs. We examined the transcriptome of human melanoma samples responders and resistant to MAPK inhibitors and discovered that APAF-1, the main component of apoptosome, is downregulated in resistant tumors. The decreased expression of APAF-1 was correlated with high levels of the melanoma survival oncogene MITF . We therefore demonstrated that the MITF/APAF-1 axis could be relevant in driving resistance to MAPK inhibitor treatments. A drug-repositioning screen identified Quinacrine and Methylbenzethonium as potent activators of apoptosis in a context that mimics drug resistance mediated by APAF-1 inactivation. Our findings demonstrated the pro-apoptotic and tumor-suppressor activity of the compounds in a large panel of melanoma cells, including patient-derived cells and in vivo models, where the two drugs showed remarkable suppression of MITF function. Quinacrine and Methylbenzethonium profoundly sensitize BRAF and NRAS mutant melanoma cells to MAPK-pathway inhibitors, thus indicating their pharmacological relevance in melanoma. Transcriptomic profiles of melanoma cells revealed that both compounds regulate key-signaling networks in melanoma, including the MITF gene network. In summary, we demonstrate that inhibiting a driver of MAPK inhibitor resistance could improve current approaches of targeted melanoma therapy.

MicroRNAs (miRNAs) are attractive therapeutic targets and promising candidates as molecular biomarkers for various therapy-resistant tumors. However, the association between miRNAs and drug resistance in melanoma remains to be elucidated. We used an integrative genomic analysis to comprehensively study the miRNA expression profiles of drug-resistant melanoma patients and cell lines. MicroRNA-181a and -181b (miR181a/b) were identified as the most significantly down-regulated miRNAs in resistant melanoma patients and cell lines. Re-establishment of miR-181a/b expression reverses the resistance of melanoma cells to the BRAF inhibitor dabrafenib. Introduction of miR-181 mimics markedly decreases the expression of TFAM in A375 melanoma cells resistant to BRAF inhibitors. Furthermore, melanoma growth was inhibited in A375 and M14 resistant melanoma cells transfected with miR-181a/b mimics, while miR-181a/b depletion enhanced resistance in sensitive cell lines. Collectively, our study demonstrated that miR-181a/b could reverse the resistance to BRAF inhibitors in dabrafenib resistant melanoma cell lines. In addition, miR-181a and -181b are strongly down-regulated in tumor samples from patients before and after the development of resistance to targeted therapies. Finally, melanoma tissues with high miR-181a and -181b expression presented favorable outcomes in terms of Progression Free Survival, suggesting that miR-181 is a clinically relevant candidate for therapeutic development or biomarker-based therapy selection.