Abstract A026: Defining the epigenetic drug landscape and rational combinations for pediatric cancer using the PRISM screening assay

Abstract Cancer remains a leading cause of death for children and adolescents, underscoring the need for therapeutic advances. The PRISM assay enables rapid profiling of emerging anti-cancer agents by barcoding and pooling >900 genetically and functionally characterized cancer cell lines. The PRISM assay reveals not only drug potency and selectivity, but also genomic correlates of sensitivity and predictive biomarkers. To better represent pediatric, hematopoietic, and rare cancers in our cell collection, we expanded the PRISM panel in collaboration with the Pediatric Cancer Dependencies Accelerator project by adding 109 new cell lines, including 21 pediatric models, 60 hematopoietic lines, and 14 previously unrepresented subtypes. In many pediatric cancers, epigenetic proteins are frequently altered and are promising therapeutic targets; therefore, we screened clinically relevant compounds targeting epigenetic proteins at 8 concentrations for 5 days. The SMARCA2/4 inhibitor, BRM/BRG1 ATP Inhibitor-1, and the BRD9 degrader, CFT8634, showed strong activity in atypical teratoid rhabdoid tumor (ATRT) models. In contrast, the SMARCA2-selective degrader, ACBI2, was less active in ATRT, despite similar potency. Further work will investigate the mechanistic basis of this differential activity. As some small molecules developed against epigenetic targets may require a longer incubation period to enact their cytotoxic effects, we developed a 10-day PRISM assay, twice as long as our standard 5-day assay. We tested the EZH2 inhibitor, mevrometostat, in both the 5-day and 10-day assay and observed greater potency, selectivity, and stronger correlations with EZH2 dependency in the 10-day assay. Finally, given the prevalence and utility of combination treatments for pediatric cancers, we also wanted to probe the drug combination landscape. We screened a collection of combinations in a 5x5 dose matrix format, focusing on inhibitors targeting DNA repair proteins (ATR, ATM, WEE1, CHEK1, PolTheta, USP1, DNA-PK, Topo1) in combination with talazoparib or gemcitabine. We observed synergy in pediatric subtypes for many but not all of the combinations tested. We identified selective synergies in pediatric subtypes, including Ewing sarcoma with talazoparib-based combinations and B-ALL with low-dose talazoparib + ATM inhibitor AZD1390. Further analysis of this combination dataset will refine our understanding of specific contexts in which we observe synergy and reveal biomarkers of synergistic effects. Together, these advances position PRISM to accelerate pediatric cancer research by expanding disease-relevant models and enabling long-duration single-agent screening and matrix combination screening at scale. All data will eventually be made publicly available on depmap.org, providing a resource for the pediatric cancer research community to explore novel therapeutic opportunities. Citation Format: Colleen T. Harrington, Antonella Masciotti, Ursula Widocki, Ashish Bino George, Blanche Ip, Tenzin Sangpo, Li Wang, Laura Doherty, Aydin Golabi, Rachael Barry, Emily Reeves, John Davis, Melissa Ronan, Matthew G. Rees, Jennifer A. Roth. Defining the epigenetic drug landscape and rational combinations for pediatric cancer using the PRISM screening assay [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr A026.