AACR 2026 Poster #6415

Large-scale functional drug screening has been limited by low throughput reliance on simple 2D systems and a lack of high-resolution mechanistic readouts. To address these challenges, we implemented Chem-Seq and Functional-Seq, scalable transcriptomic profiling platforms that enable high-content screening of both chemical and genetic perturbations in clinically relevant cancer models. Methods Experiments were conducted across six tumor models, including cell lines and four patient-derived xenograft organoids from Champions Oncology’s proprietary Patient-Derived Xenograft Organoid (PDXO) bank, which preserves tumor heterogeneity and 3D architecture. We applied Chem-Seq to 44 standard-of-care (SOC) oncology therapeutics spanning diverse pathways, including MAPK, PI3K/AKT/mTOR, CDK, EGFR/HER2, MET, AMPK, proteasome, and topoisomerase inhibition. Compounds were tested at various concentrations to capture dose-dependent transcriptional changes and pathway-specific effects. Functional-Seq was performed in parallel using siRNA-mediated knockdown of selected drug targets to generate loss-of-function signatures that anchor interpretation of Chem-seq profiles. This also serves as a proof-of-concept for using a predefined siRNA signature bank to match unknown compounds in larger screens.