(600b) Computational Model Predicts the Mechanism of CD28 Co-Stimulation in CAR-Engineered T Cells

Background. Chimeric antigen receptors (CARs) are engineered receptors that mediate T cell activation. To do so, CARs are comprised of a variety of different activating domains (such as CD3ζ) and co-stimulatory domains (such as CD28) derived from endogenous T cells. These intracellular domains initiate signaling required for T cell activation, including ERK activation through the MAPK pathway. Although in vitro and preclinical studies show that the addition of co-stimulatory domains on CARs enhances T cell activity, the mechanisms by which this happens are not clear. Therefore, we have constructed a computational mechanistic model of CAR-mediated activation of ERK in T cells. We apply mathematical modeling to improve our understanding of how CAR structure influences downstream T cell signaling and to develop new hypotheses for the optimal design of CAR-engineered T cell systems. We are particularly interested in activation of the MAPK signaling pathway, leading to ERK phosphorylation, as this pathway mediates T cell proliferation.

Methods. In this work, we model anti-CD19 CARs bearing the CD3ζ domain alone or in combination with CD28. The model simulates CAR T cell activation based on our previous modeling work, as well as other models and experimentally measured kinetic data and parameters in the literature. The full model includes modules for LCK autoregulation (Rohrs, et al., 2016), site-specific phosphorylation of CD3ζ and CD28 (Rohrs, et al., 2018), LAT signalosome formation, CD45 phosphatase activity, Ras activation (Das et al., 2009), MAPK pathway activation (Birtwistle et al., 2012), and SHP1 negative feedback (Altan-Bonnet and Germain, 2005). Overall, the model includes signaling initiated by antigen binding to the CAR and culminates in phosphorylation of ERK. We first confirmed that the model qualitatively reproduces experimental data showing the effects of modifications to various proteins in the signaling pathway on the ERK response time. We then used an ensemble modeling approach to explore a variety of mechanisms to investigate how CD28 co-stimulation enhances the predicted ERK response time.

Results and Conclusion. The model predicts that CD28 primarily influences ERK activation by modifying the phosphorylation kinetics of CD3ζ. Importantly, we were able to validate this novel prediction using experimental measurements of ERK activation in Jurkat T cells engineered with anti-CD19 CARs. The model also generates new hypotheses involving the influence of negative feedback by the phosphatase SHP1 on the effect of CD28 co-stimulation. Overall, this novel systems biology study combining experimental measurements with robust mathematical modeling enriches our understanding of CAR T cell co-stimulatory activation and allows for the improved development of CAR- engineered T cells.