Identifying points of vulnerability in the cell death map of patients’ tumors: towards precision cancer therapy

Targeted therapy of melanoma patients carrying the BRAFV600E driver mutation with vemurafenib provides a temporary remission, followed by relapses. Acquired drug resistance can develop from persister cells that survive prolonged drug treatment. Here we propose a functional approach to circumvent this problem by killing persister cells through identification and targeting soft-spots in the cell death machinery. To this end, we developed a personalized prescreening platform that maps the soft-spots in each tumor, prior to vemurafenib treatment. The platform is based on applying siRNA sub-libraries targeting apoptosis, autophagy and necroptosis genes, and identifying the hits that reduce the number of persister cells upon BRAF inhibition. We have demonstrated the feasibility of this approach in an analysis of a cohort of 12 metastatic melanoma early passage BRAFV600E cell cultures. We identified a large heterogeneity among patients’ tumors in terms of the number of soft-spots and their position within the Programmed Cell Death (PCD) map. In some tumors, the soft-spots were spread over the three PCD modules and in others the number of soft-spots was low. After validating the soft-spots, we were able to replace the siRNAs with small molecule inhibitors when available. Most importantly, we could reduce the number of drug resistant clones emerging after prolonged treatment with vemurafenib. This approach has the potential to dramatically change the state-of-the-art of rational combinatorial drug therapy in precision cancer treatment, by reducing the number of the persister cells surviving the initial treatment, thereby lessening the odds of developing drug resistance at later stages, and preventing tumor relapse.