RICTOR/mTORC2 downregulation in BRAFV600E melanoma cells promotes resistance to BRAF/MEK inhibition

The main drawback of BRAF/MEK inhibitors (BRAF/MEKi)-based targeted therapy in the management of BRAF-mutated cutaneous metastatic melanoma is the development of therapeutic resistance. Thus, identification of prognostic markers of targeted therapy resistance is of pivotal importance. We aimed to assess in this context the role of mTORC2, a signaling complex defined by the presence of the essential RICTOR subunit, regarded as an oncogenic driver in several tumor types, including melanoma. We interrogated The Cancer Genome Atlas (TCGA) melanoma patients’ database to explore both overall survival and molecular signatures as a function of intra-tumor RICTOR levels and found that low RICTOR levels in BRAF-mutated melanomas correlate with a worse clinical outcome. Gene Set Enrichment Analysis of low-RICTOR tumors display gene signatures suggestive of activation of the mitochondrial Electron Transport Chain (ETC) energy production. In vitro analysis showed that RICTOR-deficient BRAFV600E cells are intrinsically tolerant to BRAF/MEKi and anticipate the onset of resistance to BRAFi upon prolonged drug exposure. Moreover, in drug-naïve cells we observed a decline in RICTOR expression shortly after BRAFi exposure. Proteomic screening aimed to identify proteins modulated by changes in RICTOR expression identified alterations in several proteins involved in mitochondrial metabolism and NAD+ biosynthetic processes. We found that in RICTOR-depleted cells, both mitochondrial respiration and expression of nicotinamide phosphoribosyltransferase (NAMPT) are enhanced, and the combination of BRAFi with drugs targeting NAMPT or ETC restores the sensitivity of RICTOR-deficient cells in vitro and in a xenograft setting in vivo. Our work unveils an unforeseen tumor-suppressing role for mTORC2 in the early adaptation phase of BRAFV600E melanoma cells to targeted therapy and identifies the NAMPT-ETC axis as a potential therapeutic vulnerability of low RICTOR tumors. Importantly, our findings indicate that the evaluation of intra-tumor RICTOR levels has a prognostic value in metastatic melanoma and may help to guide therapeutic strategies in a personalized manner.