Quantitative single-cell characterization of CAR+ T cell effector functions

Adoptive cell therapy (ACT) utilizing chimeric antigen receptor (CAR) T cells rendered specific for CD19 have demonstrated significant anti-tumor effects in patients with CD19+ chronic lymphocytic leukemia (CLL). In spite of the clinical promise of ACT in achieving complete responses, their efficacy remains unpredictable and new approaches are needed to address a priori define the therapeutic potential of T-cell based therapies. In our current work, we characterize the in vitro functionality of CD19-specific (CD19RCD28) CAR+ T cells propagated using artificial antigen presenting cells expressing membrane bound IL-21, by employing a novel methodology single-cell nanowell screening that determines their cytotoxic ability and cytokine secretion capability at single-cell resolution. We show that CAR+ T cells exert specific cytotoxicity against NALM6 cells (31 ± 8 %) when co-incubated at a 1:1 ratio in nanowell containers. Furthermore, single CAR+ T cells were capable of engaging and killing multiple targets; 17 ± 8% of T cells killed two target cells and 9 ± 3% killed three target cells within the 6 hour window of observation. In parallel, microengraving was used to determine the cytokine secretion profile of these same cells. Hierarchical clustering of the two functions indicated that interferongamma (IFNg) secretion is not correlated to cytotoxicity or the ability of T cells to kill multiple target cells. Simultaneously, monitoring apoptosis on CAR+ T cells allowed us to quantify their activation-induced cell death (AICD). CAR+ T cells that secreted IFNg upon target ligation did not undergo AICD whereas T cells that engaged in repeated killing showed an increased propensity to undergo AICD (p = 0.04). Dynamic time-lapse imaging of the interactions between CAR+ T cells and tumor cells indicated that the majority of CAR+ T cells have high basal motility, form long-lived interactions with tumor cells (50 100 min) that lead to motility arrest and subsequent tumor-cell apoptosis. However, contact lifetimes or overall contact duration were not reliable predictors of subsequent tumor-cell apoptosis. Finally, kinetics of serial killing suggest that motile CAR+ T cells that form short-lived contacts exhibit rapid killing with very little motility arrest in vitro. In summary, our SNS based methodology allows the deep functional characterization of clinical grade CAR+ T cells and can be used to: (1) determine in vitro functions of CAR+ T cells that correlate with clinical efficacy and (2) inform CAR design to maximize effector functionality while minimizing AICD.