A Multiscale Protein Abundance Structured Population Kinetic Model Systematically Explores the Design Space of Constitutive and Inducible CAR-T cells

Engineered chimeric antigen receptor (CAR)-T cells are designed to bind to antigens overexpressed on the surface of tumor cells and induce tumor cell lysis. However, healthy cells can express these antigens at lower abundances and can get lysed by CAR-T cells. A wide variety of CAR-T cells have been designed that increase tumor cell elimination while decreasing destruction of healthy cells. However, given the cost and labor-intensive nature of such efforts, a systematic exploration of potential hypotheses becomes limited. To this end, we develop a framework (PASCAR) by combining multiscale population dynamic models and multi-objective optimization approaches with data obtained from published cytometry and cytotoxicity assays to systematically explore design space of constitutive and tunable CAR-T cells. We demonstrate PASCAR can quantitatively describe in vitro and in vivo results for constitutive and inducible CAR-T cells and can successfully predict experiments outside the training data. Our exploration of the CAR design space reveals that CAR affinities in an intermediate range of dissociation constants (KD) in constitutive and tunable CAR-T cells can dramatically decrease healthy cell lysis but sustain a high rate of tumor cell killing. In addition, our modeling provides guidance towards optimal tuning of CAR expressions in synNotch CAR T cells. The proposed framework can be extended for other CAR immune cells.