Novel Genetic Subtypes of Urothelial Carcinoma With Differential Outcomes on Immune Checkpoint Blockade.

Immune checkpoint blockade (ICB) therapy has significantly improved clinical outcomes in bladder cancer. Identification of correlates of benefit is critical to select appropriate therapy for individual patients.

To reveal genetic variables associated with benefit from ICB, we performed whole-exome sequencing on tumor specimens from 88 patients with advanced bladder cancer treated with ICB.

We identified several genetic factors that correlated with progression-free and overall survival after ICB therapy including ARID1A mutation, tumor mutational burden, intratumoral heterogeneity, the ratio of nonsynonymous to synonymous mutations in the immunopeptidome (immune dN/dS), and tumor cell purity. In addition, we noted that neutrophil-to-lymphocyte ratio and smoking history were negatively associated with overall survival. These genetic characteristics define four molecular subtypes demonstrating differential sensitivity to ICB. We validated the association of these four subtypes with clinical benefit from ICB in an independent cohort (IMvigor210). Finally, we showed that these molecular subtypes also correlate with outcome, although with distinct relationships, among patients not treated with ICB using The Cancer Genome Atlas (TCGA) bladder cancer cohort. Using parallel RNA sequencing data, the subtypes were also shown to correlate with immune infiltration and inflammation, respectively, in the IMvigor210 and TCGA cohorts.

Together, our study defines molecular subgroups of bladder cancer that influence benefit from ICB.

Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2023 Mar 16 [Epub ahead of print]

Michal Sarfaty, Mahdi Golkaram, Samuel A Funt, Hikmat Al-Ahmadie, Shannon Kaplan, Fan Song, Ashley Regazzi, Vladimir Makarov, Fengshen Kuo, Irina Ostrovnaya, Venkatraman Seshan, Chen Zhao, Benjamin Greenbaum, Li Liu, Jonathan E Rosenberg, Timothy A Chan

Genitourinary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY., Illumina, Inc, San Diego, CA., Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY., Center for Immunotherapy and Precision-Immuno-Oncology, Cleveland Clinic, Cleveland, OH., Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY., Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY.

Read an Expert Commentary by Bishoy Faltas, MD