Mechanisms of acquired resistance to rapalogs in metastatic renal cell carcinoma.

Lana Hamieh,Sabina Signoretti,David F Mcdermott,Daniel Rosebrock,Dimitri Livitz,Wenhua Gao,Jean-Christophe Pignon,Barbara Ogórek,Andre Fay,David J Kwiatkowski,Damir Khabibullin,Toni K Choueiri,Neeraj Agarwal,David Nanus

doi:10.1371/journal.pgen.1007679

Abstract

The mechanistic target of rapamycin (mTOR) is an established therapeutic target in renal cell carcinoma (RCC). Mechanisms of secondary resistance to rapalog therapy in RCC have not been studied previously. We identified six patients with metastatic RCC who initially responded to mTOR inhibitor therapy and then progressed, and had pre-treatment and post-treatment tumor samples available for analysis. We performed deep whole exome sequencing on the paired tumor samples and a blood sample. Sequence data was analyzed using Mutect, CapSeg, Absolute, and Phylogic to identify mutations, copy number changes, and their changes over time. We also performed in vitro functional assays on PBRM1 in RCC cell lines. Five patients had clear cell and one had chromophobe RCC. 434 somatic mutations in 416 genes were identified in the 12 tumor samples. 201 (46%) of mutations were clonal in both samples while 129 (30%) were acquired in the post-treatment samples. Tumor heterogeneity or sampling issues are likely to account for some mutations that were acquired in the post-treatment samples. Three samples had mutations in TSC1; one in PTEN; and none in MTOR. PBRM1 was the only gene in which mutations were acquired in more than one post-treatment sample. We examined the effect of PBRM1 loss in multiple RCC cell lines, and could not identify any effect on rapalog sensitivity in in vitro culture assays. We conclude that mTOR pathway gene mutations did not contribute to rapalog resistance development in these six patients with advanced RCC. Furthermore, mechanisms of resistance to rapalogs in RCC remain unclear and our results suggest that PBRM1 loss may contribute to sensitivity through complex transcriptional effects.

Highlights

Both everolimus and temsirolimus, analogs of rapamycin termed rapalogs, are FDA-approved and in common used for treatment of metastatic renal cell carcinoma (RCC) based on seminal randomized clinical trials [1,2,3]
We evaluated six metastatic renal cell carcinoma (mRCC) patients with available pre-treatment specimens who were treated with mechanistic target of rapamycin (mTOR) inhibitors and had a good clinical outcome, and had a second biopsy at the time of resistance
We conclude that mechanisms of resistance to rapalog therapy in RCC are not explained by gene mutations in most cases, and may depend on more subtle transcriptional and/or epigenetic changes

Summary

Introduction

Analogs of rapamycin termed rapalogs, are FDA-approved and in common used for treatment of metastatic RCC based on seminal randomized clinical trials [1,2,3]. The Phosphatidylinositol 3-kinase (PI3K)/AKT/mechanistic target of rapamycin It is frequently activated in a variety of cancer types [4], and new uses of rapalogs in combination with other therapies continue to be discovered [5,6]. MTORC1 is negatively regulated by the TSC protein complex which consists of TSC1, TSC2, and TBC1D7, which converts the small GTPase RHEB into its inactive GDP-bound form. Activating RHEB mutations which activate mTORC1 are quite rare and known to occur in cancer [13]

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Discussion

Conclusion