High throughput CAR-T potency assay based on functional and transcriptional measurements on single cell co-cultures

ABSTRACT Over the last decade, cell based “living medicines” like chimeric antigen receptor (CAR)-T cell immunotherapies have led to miraculous cures in advanced and aggressive leukemias and lymphomas in children and adults. Prior to their introduction, these cancers were thought to be virtually untreatable, yet multiple clinical trials have now shown that administering CAR-T therapy can be even more effective than chemotherapy, the standard of care. Despite its great promise, many barriers continue to limit the potency of CAR-T therapies in treating solid and liquid tumors, and it is still not clear which biomarkers have the most clinical relevance. Unlike molecular therapies, such as small molecule drugs and biologics, which can be homogenously produced from batch to batch, cell-based therapies are inherently heterogeneous, and there are still many unknowns about which specific subpopulations contained in these “living medicines” contribute to overall therapeutic potency. Clinical data has consistently shown that the overall immune response is often dominated by relatively few CAR-T clones that both kill the target and rapidly proliferate after infusion. However, to date it has not been possible to further quantify these killer, proliferative subpopulations, due to our inability to measure these diverse functions simultaneously at the level of each single cell. To provide a more comprehensive solution for analyzing CAR-T potency, Celldom is commercializing a platform that can measure the functional properties of >100,000 CAR-T effector cells in co-culture format in a single experiment, and then use these functional measurements to make real time decisions about which cells to retrieve for genomic characterization. Our platform uses proprietary microwell plates to isolate discrete single cell co-cultures using simple workflows involving only liquid handling tools and centrifugation. We have built an imager that can maintain the viability of co-cultures over many days, while continuously monitoring multiple phenotypic parameters, such as cytotoxicity activity, and growth rate. With support from this proposal, we aim to include additional measurements of cytokine secretions, cell surface markers, and gene expression. In order to achieve this goal, we need to realize a combination of technical engineering milestones and immunological assay development milestones. Our engineering objectives are to apply video action recognition models to improve the accuracy of cytolysis measurements and coculture detection, and to establish a real-time image acquisition and computer vision data analysis pipeline that allows clones to be picked immediately at the end of the experiment. Our assay development objectives are to assess the range and limits of detection for 3 cytokines and 3 surface markers, to add these selection criteria for clone isolation. We further aim to retrieve high priority clones from specific microwells to analyze the transcriptional states and clonality of different sub-populations. Once all of these capabilities are in place, Celldom will have the most comprehensive platform on the market for measuring functional and molecular properties of individual T cells, which can help identify and further study the subpopulations that dominate the in vivo response.