CDH1-mutated clinically advanced urothelial bladder cancer (UBC): A genomic landscape and real-world clinical outcome study (RWCOS).
Authors: Necchi Andrea , Li Roger , Rose Kyle M. , Davaro Facundo , Davaro Elizabeth , Spiess Philippe E. , Grivas Petros , Bratslavsky Gennady , Jacob Joseph M , Basnet Alina , Pavlick Dean C. , Huang Richard S.P. , Lin Douglas I. , Danziger Natalie , C. F. Quintanilha Julia C. F. , Ross Jeffrey S. , Graf Ryon 
Published: March 2023

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Background: CDH1 mutated UBCs are characterized by plasmacytoid histology and are associated with an aggressive clinical course at the time of diagnosis. Methods: Cohort 1: 6,676 clinically advanced UBC patients (pts) underwent comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GA), microsatellite instability (MSI), tumor mutational burden (TMB), and genomic loss of heterozygosity (gLOH, high ≥16%). Predominant genetic ancestry was determined using a SNP-based approach and classified as one of the 5 categories: African (AFR), European (EUR), Central and South American (AMR), South Asian (SAS), or East Asian (EAS). Cohort 2: 586 UBC pts underwent a RWCOS using the nationwide (US-based) de-identified Flatiron Health-Foundation Medicine urothelial clinico-genomic database (FH-FMI CGDB). The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care) Jan 2011-Apr 2022. Differences in real-world progression-free survival (rwPFS) and overall survival (rwOS) were evaluated by Cox proportional hazard models. Results: Cohort 1: 217 (3.3%) of UBC had a CDH1 short variant (SV) mutation with 65.2% featuring plasmacytoid histology. When compared with CDH1 wild-type (WT) UBC, the CDH1-mutated UBC had similar age, gender, and genetic ancestry. The CDH1-mutated UBC featured a higher frequency of MSI (2.7% vs 0.8%; p=.002), mean TMB (14.8 vs 9.9 mut/Mb p<.0001), RB1 GA (52.5% vs 20.3%; p<.0001), PTEN GA (9.2% vs 4.3%; p=.006) and PIK3CA GA (29.5% vs 21.8%; p=.02), but less gLOH high (6.8% vs 15.9%; p=.009), CDKN2A loss (12.4% vs 38.3%; p<.0001), MTAP loss (10.1% vs 25.1%; p<.0001) and FGFR3 GA (9.7% vs 18.1%; p=.002). TP53 GA were similar (62.3% vs 60.3%). Cohort 2: 22 (3.7%) featured CDH1 mutations. Compared with the CDH1 WT pts, the age, gender, ethnicity and ECOG status were similar. Evaluation of the RWCOS showed that CDH1 mutation was associated with less favorable outcomes for 270 UBC pts treated with immune checkpoint inhibitors (ICPI) including rwPFS (2.8 vs 3.5 months; p=.096) and rwOS (3.3 vs 9.5 months; p=.03). Similar comparisons for 316 UBC pts treated with chemotherapy showed no significant adverse impact of CDH1 mutation status on either rwPFS (7.9 vs 6.2 months) and rwOS (13.4 vs 13.4 months). Conclusions: In addition to its classic association with plasmacytoid histology, CDH1-mutated UBC features a unique CGP pattern including higher MSI and TMB status and activating GA in the MTOR pathway while harboring a lower FGFR3 GA frequency. RWCOS further supports that CDH1 mutation predicts resistance to ICPI-based treatments but does not impact responsiveness to chemotherapy. These results further support that CGP has the potential to customize the treatment and improve outcomes for UBC patients based on the determination of their genomic signatures.