Antigen experience history directs distinct functional states of CD8+ CAR T cells during the anti-leukemia response [RNA-seq]
Adoptive transfer of immune cells expressing chimeric antigen receptors (CARs) is an effective therapy for B-lineage malignancies. However, most patients will relapse and this therapeutic has yet to show strong efficacy in other hematologic or solid tumors. One opportunity for improvement lies in the ability to select or generate T cells that have the highest potential for potent anti-tumor responses and T cell persistence. Here, we dissect the biology of CD8+ CAR T cells by controlling whether the T cell has encountered cognate TCR antigen prior to CAR generation. We find that prior antigen experience influences multiple aspects of in vitro and in vivo CAR T cell functionality, boosting effector function and leukemia clearance in the setting of limiting target antigen density. However, this comes at the expense of proliferative capacity, resistance to dysfunction, and clearance of wildtype leukemia in the setting of limiting CAR+ cell dose. Epigenetic and transcriptomic comparisons of these cell populations uncover that modulation of the Runx2 transcription factor differentially impacts CAR T cell functionality depending on prior cell state. Collectively, our data demonstrate that prior antigen experience status determines functional attributes of a CAR T cell, as well as amenability to functional enhancement by transcription factor modulation. Overall design: To investigate the role of prior T cell antigen experience in responses of CD8+ chimeric antigen receptor (CAR) T cells to leukemia, we adoptively transferred C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells into C57BL/6-background CD45.1+ hosts, followed by vaccination with ovalbumin, anti-mouse CD40, and PolyI:C to generate memory CD8+ T cells ("memory-derived"), or used naïve C57BL/6-background Rag2-/- OT-I TCR transgenic CD8+ T cells from naïve hosts ("naïve-derived"). We then transduced both populations with an anti-mouse CD19 CAR containing CD28 costimulatory domain and CD3zeta domain. Memory or naive-derived T cells were compared by RNAseq at three timepoints, Pre-CAR Transduction ("PreCAR", Day -5, ex vivo), Post-CAR Transduction ("PostCAR", Day 0, in vitro), and 4 days after infusion into C57BL/6-background Rag1-/- mice bearing the mouse CD19+ murine B-cell acute lymphoblastic leukemia cell line, E2A-PBX1 ("Tumor", Day +4, Ex Vivo).