Rational drug combinations to selectively target 9p21-deleted bladder cancer

Precision medicine for cancer therapy has the potential to offer personalized genotype-targeted treatments that exploit the selective dependencies of tumor cells. While several tumor types benefit from the use of targeted therapy, current precision medicine approaches for bladder cancer (BLCA) are limited. Furthermore, despite the recent therapeutic opportunities offered by immunotherapy, many BLCA patients do not respond to immunotherapy, and recurrence remains a major problem, pointing to the need for new effective therapies. In this project we investigated the synthetic lethal vulnerabilities exposed by 9p21 loss in BLCA, the most common copy-number alteration in this tumor. Previous studies have investigated 9p21 loss across several cancer types and identified PRMT5 and MAT2A as synthetic lethal interactions in this context. Consequently, PRMT5 (MRTX1719) and MAT2A (AG270) inhibitors have been developed and are currently being tested in clinical trials to treat MTAP-deleted tumors. Here, we performed a multi-parametric drug screening using 9p21 isogenic BLCA cells to uncover drugs with a 9p21-selective activity on cell morphology and viability. Two drugs resulted significantly more effective in cells with 9p21 loss, cytarabine and methotrexate, however with limited therapeutic index. Therefore, we propose different drug combinations to reduce toxicity and increase treatment efficacy by exploiting the dependencies of 9p21 loss. First, we demonstrated synergy between cytarabine and MRTX1719 or AG270, specifically in 9p21-deleted cells. Second, the study of cytarabine, MRTX1719, and AG270 activity showed induction of replication stress selectively in 9p21-deleted cells, suggesting rational drug combination with ATR inhibitors. Finally, we demonstrate the efficacy of these combinations in pancreatic adenocarcinoma and pleural mesothelioma cells with 9p21 loss, suggesting that other tumor types may benefit from these treatments. We recognize that while this study is limited by the lack of validation in more complex cancer models the implications of drugs with current clinical application could favor the translational potential of our findings.