The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer

Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction of patients respond to the treatment. To better understand which factors drive clinical benefit, we have generated whole exome and RNA sequencing data from 27 advanced urothelial carcinoma patients treated with anti-PD-(L)1 monoclonal antibodies. We assessed the influence on the response of non-synonymous mutations (tumor mutational burden or TMB), clonal and subclonal mutations, neoantigen load and various gene expression markers. We found that although TMB is significantly associated with response, this effect can be mostly explained by clonal mutations, present in all cancer cells. Our findings were validated in an additional cohort. Thus, using clonal TMB over total TMB could increase prediction accuracy. They also show that responders with few clonal mutations had abnormally high levels of T and B cell immune markers, suggesting a high immune cell infiltration signature could be an added predictive biomarker for this subset of patients. Our results support the idea that highly clonal cancers are more likely to respond to ICI and suggest that non-additive effects of different immune signatures should be considered for predictive models.