Point mutations of the mTOR-RHEB pathway in renal cell carcinoma

Abstract

Aberrations in the mTOR (mechanistic target of rapamycin) axis are frequently reported in cancer. Using publicly available tumor genome sequencing data, we identified several point mutations in MTOR and its upstream regulator RHEB (Ras homolog enriched in brain) in patients with clear cell renal cell carcinoma (ccRCC), the most common histology of kidney cancer. Interestingly, we found a prominent cluster of hyperactivating mutations in the FAT (FRAP-ATM-TTRAP) domain of mTOR in renal cell carcinoma that led to an increase in both mTORC1 and mTORC2 activities and led to an increased proliferation of cells. Several of the FAT domain mutants demonstrated a decreased binding of DEPTOR (DEP domain containing mTOR-interacting protein), while a subset of these mutations showed altered binding of the negative regulator PRAS40 (proline rich AKT substrate 40). We also identified a recurrent mutation in RHEB in ccRCC patients that leads to an increase in mTORC1 activity. In vitro characterization of this RHEB mutation revealed that this mutant showed considerable resistance to TSC2 (Tuberous Sclerosis 2) GAP (GTPase activating protein) activity, though its interaction with TSC2 remained unaltered. Mutations in the FAT domain of MTOR and in RHEB remained sensitive to rapamycin, though several of these mutations demonstrated residual mTOR kinase activity after treatment with rapamycin at clinically relevant doses. Overall, our data suggests that point mutations in the mTOR pathway may lead to downstream mTOR hyperactivation through multiple different mechanisms to confer a proliferative advantage to a tumor cell.

Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin

“…On the other hand, we found these mutations have little effect on mTORC2 activities. One study suggested mTOR mutations could increase mTORC2 activities, but the effects were very subtle (83), which is largely in line with our findings. Importantly, all activating mutations are sensitive to rapamycin treatment.…”

“…As a central player in the PI3K/AKT/mTOR pathway, mTOR functions as an integrator of intracellular and extracellular signals in HEAT domains are nonactivating mutations, which is consistent with previous reports (64,83,96,97). Of note, mutations from different clusters could show different activities toward S6K in vitro, which is also reflected by the different tumor growth rates in vivo.…”

“…We showed that mTORC1 activities of L1460P (F1) and C1483F (F1) mutants were reduced when DEP-TOR was overexpressed (Supplemental Figure 8), which suggests that DEPTOR may directly bind and thereby inhibit mTOR near the F1 cluster. Reduced binding to DEPTOR was also observed in 1 mTOR mutant in the K3 cluster (R2505P) ( Figure 4D), which is consistent with other reports (64,83). However, overexpression of DEPTOR did not inhibit the activity of the mTOR R2505P mutant (Supplemental Figure 8), implicating an indirect mechanism.…”

Genetic landscape of T- and NK-cell post-transplant lymphoproliferative disorders

“…Similar mutations, which have been shown to activate both mTORC1 and 2 signaling in other neoplasms, may contribute to T-cell growth, survival and proliferation, in part by metabolic reprogramming of lymphocytes. [48] Activation of the mTOR pathway has been reported in T-cell lymphomas, but the presence of mTOR mutations has not been systematically investigated in these malignancies. Of interest, rapamycin analogues, which disrupt the mTORC signaling cascade have shown promise in early phase clinical trials of PTCL patients.…”

Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues

“…Moreover, DEPTOR binding weakened for both mTOR complexes when mutations in the FRAP-ATM-TTRAP (FAT) domain in clear cell renal cell carcinoma. Consequently, point mutations in the FAT domain promoted mTORC1 and mTORC2 activity, as well as increased cancer cell proliferation, thereby decreasing DEPTOR binding and indicating poor patient prognosis46. Abnormally high DEPTOR expression activated the PI3K-AKT pathway and was regarded as a poor prognostic biomarker, which has been found in various types of solid neoplasms such as esophageal squamous cell carcinoma47, breast cancer4849, and HCC50.…”