Defining the genetic basis of everolimus sensitivity in metastatic bladder cancer (MBC) by whole-genome sequencing (WGS).

Abstract

4527 Background: MBC is rarely cured with standard chemotherapy and novel agents are clearly needed. A phase II trial of everolimus in MBC resulted in 1 near-complete response (CR), 1 partial response, and 3 minor responses. We used WGS and a Next Generation exon capture assay to identify the genetic aberrations underlying treatment response. Methods: In the near-CR case, tumor and peripheral blood DNA was subjected to WGS (Illumina) using 2x100 bp paired-end libraries for 40X haploid coverage. Raw sequence data was aligned to hg19 and somatic point mutation detection was performed. Tumor DNA from 13 additional patients on the trial was analyzed using an exon capture sequencing assay. Results: 184 exonic somatic mutations were identified in the everolimus complete responder by WGS, including a 2 bp frameshift truncation in TSC1 and a nonsense mutation in NF2. Sanger sequencing of an additional 96 high-grade bladder tumors found 5 (6.2%) tumors containing TSC1 alterations and no NF2 mutations. Of the 13 patients on the trial who underwent targeted exon sequencing, 3 (23%) possessed nonsense TSC1 mutations and 2 had minor treatment responses (17% and 24% tumor regression). 1 patient with a 7% tumor regression had a somatic missense TSC1 variant. 8 (89%) of 9 patients with tumor progression as best response were TSC1 wild-type. Patients with TSC1-mutant tumors remained on drug for longer duration (7.7 vs. 2 months, p=0.004, Wilcoxon rank sum test). Conclusions: Everolimus is an active agent in MBC in patients with TSC1 mutant tumors. The pattern of co-mutation in patients with TSC1 mutant tumors is complex and combination therapies will likely be required to achieve durable responses in most patients. Our results also highlight the potential utility of WGS in identifying novel predictors of response to targeted inhibitors.