StarTrace: a multiplex organoid avatar drug testing platform for personalized medicine

The goal of precision medicine is to improve clinical outcomes of cancer patients by choosing treatments most likely to work. One idea is to match tumor response to cancer-causing somatic mutations, but this strategy still faces limitations in colorectal cancer due to poorly understood genetic influences on drug resistance. We describe here a simple, direct drug-sensitivity assay platform applied to mixtures of patient-derived organoid avatars as a practical solution for choosing therapy, sidestepping the need for exhaustive knowledge of drug-genetic interactions. The platform multiplexes organoids using a clonal barcoding method, called StarTrace, which simultaneously tests pools of multiple patients’ organoid avatars for sensitivity or resistance to small molecule inhibitors. We utilized both quantitative real-time PCR-based and single-molecule sequencing assays to track the relative Darwinian fitness of each barcoded organoid within the pool. This approach compares different patients’ organoid avatars’ responses to various drugs based on relative changes in barcode abundance, which may inform treatment selection in future applications. StarTrace provides a quantitative platform that enables streamlined and scalable assessment of drug responses, with potential applications in preclinical drug development and future personalized therapy strategies.