Analysis of inactivating TSC1 and TSC2 alterations in advanced genitourinary (GU) cancers from a real-world patient population in the Foundation Medicine genomic database.

Abstract

704 Background: Identification of genetic alterations in cancer via genomic profiling may contribute to better outcomes for patients with advanced GU cancers. Patients with perivascular epithelioid cell tumors in AMPECT (NCT02494570), who had inactivating alterations in the tumor suppressor genes TSC1 or TSC2, critical negative regulators of mTOR activity, had confirmed responses (8/9 patients with inactivating TSC2 alterations and 1/5 patients with inactivating TSC1 alterations) to the mTOR inhibitor nab-sirolimus. PRECISION 1 (NCT05103358), an enrolling tumor-agnostic study, is assessing nab-sirolimus in patients with advanced cancers bearing inactivating TSC1 and/or TSC2 alterations. We used data from a real-world genomic database to enumerate frequencies of TSC1 and TSC2 inactivating alterations in patients with GU cancers. Methods: Next-generation sequencing data from Foundation Medicine’s database of 463,546 patients with advanced cancer (as of March 29, 2022) were analyzed using the FoundationInsights web-based platform to identify inactivating TSC1 or TSC2 alterations in patients with GU cancers. TSC1 or TSC2 alterations were categorized as short variants [base substitutions, insertions and deletions], rearrangements, and copy number deletions. Tumors with these alterations were also evaluated for mutations in other genes, tumor mutational burden (TMB), and microsatellite instability status. Results: Of patients in the database, 9.6% of those with bladder cancer, 5.2% of those with kidney cancer, and 0.7% of those with prostate cancer had inactivating TSC1 or TSC2 alterations. Overall, inactivating TSC1 or TSC2 alterations were present in 1518 of the 36,920 patients with GU cancers. A majority of these 1518 patients (74%) were male and most (78%) were 51–80 years of age at the time the sample was obtained. Of samples with inactivating TSC1 and TSC2 alterations (n=1518), 84.9% were in TSC1 and 15.7% were in TSC2; alterations included short variants (76.7% and 12.2 %), rearrangements (2.4% and 2%), and copy number deletions (5.6% and 1.3%), respectively. TMB was low (<6 mutations/megabase) in 52% of tumors and most (89%) were microsatellite stable. Other commonly mutated genes in this cohort with TSC1 or TSC2 inactivating alterations were TERT (64.4%), TP53 (44.1%), and CDKN2A (40%). Conclusions: Inactivating TSC1 and/or TSC2 alterations commonly occurred in GU cancers. A proportion of GU tumors have a low TMB and/or are microsatellite stable, suggesting that TSC1 and TSC2 inactivating alterations may be driver mutations rather than passenger mutations in those tumors. Therefore, patients with inactivating alterations in TSC1 or TSC2 may benefit from mTOR inhibition via nab-sirolimus. This hypothesis is being tested in the PRECISION 1 study which is open for enrollment of patients with TSC1 or TSC2 alterations.