Actionable Genomic Landscapes From a Real-world Cohort of Localized Urothelial Carcinoma Patients

ASCO Genitourinary Cancers Symposium 2022, Tempus-authored Presentation
Authors Thomas Gerald, Vitaly Margulis, Xiaosong Meng, Suzanne Cole, Qian Qin, Greg Call, Elizabeth Mauer, Yair Lotan, Solomon L. Woldu

Background: Recent targeted therapies for advanced and metastatic urothelial cancer have generated enthusiasm, but the actionable genomic landscape of early-stage disease remains largely unknown. Here, we used real-world evidence to investigate differences between somatic and germline mutations in localized, early-stage urothelial cancers and advanced urothelial cancers.

Methods: We retrospectively analyzed de-identified NGS data from 1,146 bladder cancer patients (stages I-IV) with formalin-fixed, paraffin-embedded tumor biopsies sequenced using the Tempus|xT solid tumor assay (DNA-seq of 595-648 genes at 500x coverage; whole-exome capture RNA-seq). For the subset of patients with tumor-normal match sequencing (n=758), additional incidental germline alterations in 46 different genes were assessed.

Results: A total of 1,146 bladder cancer tumors were investigated: stage I-II (n=124), stage III (n=159), and stage IV (n=863)—summarized in Table. Tumor mutational burden (TMB) was calculated for 1,126 tumors, and TMB-high (TMB-H; ≥10 mutations per megabase) was similar across tumor stages. PD-L1 immunohistochemical staining was performed on 698 tumors, and no significant differences were observed. Microsatellite instability high (MSI-H) status was detected in only 2 (1.6%) stage I-II tumors and 8 (0.9%) stage IV tumors. Alterations—single nucleotide variants, insertions/deletions, and copy number variants—in FGFR2/3, homologous recombination repair genes (18 genes including BRCA1/2 and ATM), additional DNA repair gene mutations (ERCC2, RB1, FANCC) and NTRK fusions were detected at similar frequencies across disease stages. In 758 patients with tumor/normal matched sequencing, we identified a low rate of incidental germline mutations in MUTYH (stage III, 1%; stage IV, 1.9%), BRCA2 (stages I-II, 1.2%; stage III, 1%; stage IV, 0.5%), BRIP1 (stages I-II, 1.2%), ATM (stage III, 1%; stage IV, 0.7%), MSH6 (stage III, 1%; stage IV, 0.2%), and TP53 (stage III, 1%; stage IV, 0.2%).

Conclusions: Patients with bladder cancer have similar rates of potentially actionable mutations and genomic landscapes regardless of clinical disease stage. These findings provide a rationale for further investigating targeted therapies among early-stage bladder cancer patients.