Identification of predictive biomarkers of response for mTOR pathway inhibitors in renal cell carcinomaTowards a molecular rationale for treatment selection in patients

Resum

Renal cell carcinoma (RCC) is a heterogeneous group of tumors with at least 10 compounds approved for the treatment of metastatic disease. Unfortunately, there is a large interindividual variability in the response to these drugs, and no molecular criteria exist to guide treatment. In the case of mTOR inhibitors, these drugs are effective in a subgroup of patients, but the molecular mechanisms causing the different sensitivity are unknown. The main objective of this thesis was the discovery of RCC molecular alterations able to predict sensitivity to mTOR inhibitors, helping to personalize the treatment of patients with renal cancer. For this purpose, cases with extraordinary responses and large series of metastatic patients treated with mTOR inhibitors were studied. In addition, we explored whether the alteration of mTOR pathway could be proposed as a potential therapeutic target in chromophobe RCC. First, we studied two RCC patients with exceptional temsirolimus responses. Whole exome sequencing of the primary tumors and metastatic lesions unveiled clonal mutations in MTOR and TSC2, able to activate of mTOR pathway, and which could explain the extreme sensitivity of these tumors to therapy. Second, we characterized a series of more than 100 RCC patients treated with mTOR inhibitors, by sequencing MTOR, TSC1 and TSC2 and by performing immunohistochemistry (IHC) of PTEN, p-S6K1 and p-S6. This study showed that mutations in these genes and negative staining of PTEN were associated with better response to mTOR inhibitors. Third, we carried out a molecular characterization of 92 RCC chromophobe patients by next generation sequencing and IHC. Among other results, we showed that mutations in mTOR pathway are common in this tumor and that they are associated with a poor survival, suggesting that these patients with aggressive tumors may benefit from mTOR inhibitor therapy. Fourth, sequencing the whole exome of three chromophobe RCC cases highly sensitive to mTOR inhibitors, uncovered USP9X as the only mutated gene shared among the tumors. USP9X silencing in cellular models recapitulated mTOR inhibitor sensitivity in the patients and an unbiased ubiquitylome analysis revealed p62 as a direct USP9X substrate able to alter autophagy regulation and that synergized with mTOR pathway inhibition