Abstract 4724: Optimizing 500 pooled PRISM cell lines for a 10-day assay to elucidate viability effects and mechanism of action for slower-acting therapeutics

Abstract PRISM (Profiling Relative Inhibition Simultaneously in Mixtures), using DNA-barcoded cell lines cultured as ~25 cell line pools, has been an effective drug discovery screening platform to rapidly test large numbers of potential therapeutics on over 900 different cancer cell lines. However, the conventional 5-day assay may be too short to offer the resolution needed to identify the full cellular response for slower-acting therapeutics such as those directed against epigenetic pathways. Here, we describe development of the PRISM 10-day extended assay with ~500 adherent solid tumor cancer cell lines to overcome this challenge. We found that the ranges of cell line growth rates within the standard PRISM pools were too large and not amenable for a long-term assay beyond 6 days—after 10 days of growth, slower cell lines dropped below the limit of barcode detection as faster cell lines overtook the pools. We therefore regenerated pools to reduce the range of growth rates within a pool. We show that this re-pooling, coupled with seeding density optimization, enables recovery of 98% of cell lines at day 10 in vehicle-treated wells, with acceptable data variability. The average estimated number of cell doublings across our cell lines, 7, is significantly greater than the number of doublings in the PRISM standard 5-day assay (~3 doublings). Importantly, we observe greater drug effects on day 10 versus day 6 when cells are treated with slow-acting DNA methyltransferase inhibitors such as decitabine; this also results in increased sensitivity to identify cellular biomarkers underlying differential response. In summary, we have successfully engineered a PRISM 10-day assay in ~500 adherent cell lines, where the extended duration can be beneficial in elucidating the effects and mechanism of action for epigenetic drug candidates. Citation Format: Melissa Ronan, Blanche C. Ip, Ellen Nguyen, Ursula Widocki, Tenzin Sangpo, Alvin Kalathungal, Nashielli Diaz-Gallegos, Anthony Fazio, Aydin Golabi, Maha Naim, Ashish Bino George, YuhJong Liu, Mustafa Kocak, Rishi Puram, Matthew G. Rees, Jennifer Roth. Optimizing 500 pooled PRISM cell lines for a 10-day assay to elucidate viability effects and mechanism of action for slower-acting therapeutics abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 4724.