Functional T Cell Assays Are Predictive of Pre-Clinical Potency to Generate Allogeneic, Hypoimmune CD19 CAR T Cells (2022)

Introduction: Allogeneic, hypoimmune (HIP) T cells may provide universal CAR T cells that persist in patients and deliver therapeutic efficacy without the need for immunosuppression to limit graft rejection. Healthy donor T cells possess a spectrum of biological activities that contribute to final CAR T cell functionality. Thus, identifying characteristics that are predictive of CAR T cell potency is essential for generating high-quality, allogeneic, HIP CAR T cells for clinical studies. Here, we define a series of T cell functional assays that differentiate T cell potency that may be used to select high-quality CAR T cell donors for clinical trials. Methods: Human T cells from healthy donors were obtained by leukapheresis and used to generate allogeneic HIP CD19 CAR T cells by disrupting B2M, CIITA, and TCRa using Cas12b gene editing, and lentiviral transduction to overexpress CD47 and to express the CD19 CAR. Generated CAR T cells were evaluated in vitro by repetitive tumor challenge (3x) performed over a 14-day period using the IncuCyte platform. Bulk cytokine analysis and single-cell cytokine levels were evaluated for polyfunctionality (Isoplexis IsoLight). For bulk cytokine profiling, 10 cytokines were measured (GM-CSF, GzmA, GzmB, IFN-g, TNF-a, IL-2, IL-6, IL-17A, IL-1b, IL-1RA). Gene expression profiling was assessed on pre-production, post-CAR manufacturing, and post-serial tumor challenge CD4+ and CD8+ T cells using the nCounter CAR T panel. In vivo efficacy was evaluated using a systemic NALM-6 challenge in immune-deficient NSG mice at HIP CD19 CAR T cell doses of 5e5 and 5e6 cells per animal. Results: We have defined assays that produce single, quantitative indices to enable the classification of CAR T cells as exceptional, good, or poor based on functional performance. To do this, we assessed differences in CAR T cell performance when placed under 'stress' (i.e., low effector to target (E:T) ratios or repetitive tumor challenge) and defined indices that exceed (exceptional), meet (good), or trail (poor) a described median value. For serial tumor challenge, median CAR T cell expansion was 4-fold during each restimulation cycle, with exceptional donors exceeding this value (expansion index >10% above median). Bulk cytokine values produced from CAR T cells ranged from 1.08-2.08 pg/CAR T cell with exceptional donors ascending 10% above the median; while donors scored as exceptional produced a polyfunctionality index >15% via Isoplexis analysis. During in vivo challenge, we observed a median area under the curve (AUC) value of 29 at the high (5e6) CAR T dose, and an AUC value of 10548 at the low (5e5) CAR T dose. Metrics from the serial tumor challenge, bulk cytokine quantification, Isoplexis analysis, and in vivo challenge were compared in an unbiased way to collectively rank CAR T cell donors as exceptional, good, or poor. In addition, gene expression profiling of ranked donors identified that exceptional donors are less activated and have a reduced NK-like signature at the pre-production state. Additionally, exceptional donors have an activated phenotype at a resting CAR T (post-CAR manufacturing) state. CAR T cells skew towards Th1/Tc1 and Th17/Tc17 states at resting (post-CAR manufacturing) and activated (tumor challenge) stages for exceptional donors. Exceptional donors showed a higher amount of mucosal-associated invariant T (MAIT) cells at the pre-production, resting (post-CAR manufacturing), and early activation (tumor challenge) steps. Summary: We have evaluated four assays that could identify CAR T cell variability and segregate CAR T cells into exceptional, good, or poor-performing donors. These assays provide single, quantitative readouts on T cell quality when CAR T cells are placed under 'stress' and may be used to predictively measure T cell quality differences between healthy donors. The information collected across these CAR T productions will be potentially useful for allogeneic donor selection for HIP CAR T manufacturing.