The mutational profile of muscle-invasive urothelial carcinoma and its association with the course of the disease

Study aim: The primary aim of the study was to evaluate the mutational profile of muscle-invasive urothelial car¬cinoma (MIUC) using next generation sequencing (NGS). A secondary aim was to identify mutations that provide potential targets for anticancer therapy, while an exploratory aim was to identify the associations between the mutational profile and the course of the disease. Materials: The study used tumor tissue and medical data from 50 patients with MIUC of the bladder (48 (96.0 %)) or renal pelvis (2 (4.0 %)). DNA and RNA alterations were studied in cells isolated from tumors with histologically confirmed invasive UC using NGS with a panel of 523 genes. Results: The median age was 72 (51-87) years; the study sample included 43 men (86.0 %). MIUC was confirmed in all patients, either de novo (T2-T4a in 32 (64.0 %) patients, including 2 (4.0 %) patients with renal pelvis cancer) or as a result of progression of non-muscle-invasive bladder cancer (Tis-Tl in 18 (36.0 %) patients). Regional metastases were diagnosed in 8 (16.0 %) subjects, and distant metastases in 5 (10.0 %) patients. High grade UC was confirmed for 44 (88.0 %) samples (including concomitant carcinoma in situ in 4 (8.0 %) cases). The median tumor mutational burden (TMB) was 10.9 (0.0-49.6) muts / Mb (high TMB (> 10 muts / Mb) in 30 (60.0 %) out of 50 cases). The level of microsatellite instability was low in all samples; 244 therapeutically significant and oncogenic mutations in 84 genes were detected in 50 samples (median: 5 (1-11) mutations per sample). Level 1-2 pathogenic mutations were detected in 13 genes of 29 (58.0 %) samples (in > 1 gene in 13 cases (26.0 %)), with a frequency of>10% in the FGFR3 (9 (18.0 %)), TSC1 (9 (18.0 %)), PIK3CA (7 (14.0 %)), ERBB2 (6 (12.0 %)) genes. Level 3-4 mutations were identified in 12 genes of 33 (66.0 %) samples (in > 1 gene in 15 (10.0 %) cases), with a frequency of>10% in the KDM6A (19 (38.0 %)), ARID1A (12 (24.0%)) and MDM2 (7 (14.0%)) genes. Oncogenic mutations were detected in 63 genes of 46 (92.0%) samples (in > 1 gene in 37 (74.0 %) cases), with a frequency of >10% in the TP53 (25 (50.0 %)), FGF4 (5 (10.0 %)), RBI (6 (12.0 %)), CDKN1A, STAG2, FGF3, CCND1 genes (5 (10.0 %) samples with mutations for each). Invasive de novo UC is associated with a higher incidence of high TMB compared with recurrent UC (71.9 % vs. 38.9 %,p = 0.024) and a higher frequency of mutations in the PI3K signaling pathway genes (46.8 % vs. 16.7 %,p = 0.031). Conclusion: MIUC is characterized by high TMB and low frequency of microsatellite instability. The most common mutations providing potential therapeutic targets are alterations of the FGFR3, TSC1, PIK3CA, and ERBB2 genes. De novo MIUC is associated with a higher frequency of high TMB and an increased frequency of mutations in the PI3K signaling pathway genes compared with invasive recurrence of non-muscle-invasive UC.