System level study of the cell death functional signature in metastatic melanoma cell lines

Targeted drug therapy for melanoma patients carrying the BRAFV600E driver mutation provides a temporary remission, followed by severe relapses due to the dominance of drug-resistant tumors. Acquired drug resistance can develop from persister tumor cells that maintain their cell viability during prolonged drug treatment. Here we propose a functional approach to circumvent this problem, by identifying the soft-spots in the cell death machinery of patients’ metastases, the targeting of which strongly reduces the number of persister cells. This challenge requires a smart solution, as there exists huge heterogeneity in the composition of the cell death map among patients’ tumors. To this end, we developed a personalized prescreening platform that maps the soft-spots in each tumor carrying the BRAF mutation, before patients are treated with the drug. The platform is based on applying siRNA libraries targeting 81 genes of apoptosis, autophagy and necroptosis pathways, one at a time, and identifying the hits that dramatically reduce the number of persister cells upon BRAF inhibitor treatment. We have demonstrated the feasibility of this approach in an analysis of the first cohort of 12 metastatic melanomas carrying BRAF mutation supplied by the Sheba Medical Center. It proved a large heterogeneity in the number and position of the soft spots among patients. By superimposing the soft-spots on the integrated map of programmed cell death that we have delineated in our lab, possible synergy through double hits can be rationally designed. This approach has the potential to dramatically change the state-of-the-art of combinatorial drug therapy in precision cancer treatment, by reducing the number of the persister cells surviving the initial treatment by several orders of magnitude, thereby lessening the odds of developing drug resistance at later stages, and preventing tumor relapses.