CD19-CAR T Cells Develop Exhaustion Epigenetic Programs during a Clinical Response

Background:

CD19-CAR T-cell therapy has emerged as a curative approach for patients with relapsed/refractory B-cell malignancies, including lymphoma and acute lymphoblastic leukemia (ALL). However, many patients develop recurrent disease after initial responses. Therapeutic failure is most likely due to T cell extrinsic and intrinsic mechanisms. While CD19-negative relapse has emerged as a major extrinsic mechanism, T cell intrinsic mechanisms remain elusive. T-cell exhaustion is driven by epigenetic programs, however epigenetic changes in CAR T cells pre and post infusion have not been determined longitudinally. Thus, the goal of this study was to determine the epigenetic landscape of CD19-CAR T cells pre and post infusion as an initial step to elucidate intrinsic mechanisms that limit CAR T-cell effector functions in humans.

Methods/Results:

A longitudinal analysis of CD8+ CD19-CAR T cell epigenetic changes was performed by whole-genome DNA methylation profiling of CAR T cells during manufacturing and from peripheral blood mononuclear cells (PBMCs) of infused patients. DNA methylation profiling was performed on samples from 15 patients enrolled on our institutional, autologous CD19-CAR T cell therapy study (NCT03573700). CAR T cell expansion and persistence was determined by measuring vector copy numbers in the PBMCs of treated patients. B cell aplasia was tracked by monitoring B cell reconstitution as an additional measure of CD19-CAR T cell function. We had previously established novel exhaustion DNA methylation datasets that delineate between progenitor and fully exhausted T cells. These datasets served as a guide for stratifying our post-infusion CAR T cells along the exhaustion developmental trajectory. Lastly, publicly available single-cell transcriptional profiles of CD19-CAR T cells from patients were mined to validate expression of the transitory exhaustion signature.

Our data show that CD19-CAR T cells lose repressive DNA methylation at effector loci (e.g. PRF1, TBET) while gaining methylation at genes (e.g. LEF1, TCF7) associated with memory potential. We confirmed that these epigenetic changes are coupled to endogenous human T cell effector and memory differentiation by cross-referencing our epigenetic data with publicly available transcriptional profiles for antigen-specific effector and long-lived memory CD8 T cells from individuals vaccinated for yellow fever. Furthermore, we show that CAR T cells were unable to mount an in vivo recall response after recovery of antigen-positive B cells or disease relapse. This observation, coupled to the fact that these patients' CAR T cells developed exhaustion-associated DNA methylation programs, further supports the broader conclusion that CAR T cells acquire stable epigenetic exhaustion programs that limit their protective capacity.

Conclusion:

Our data demonstrate for the first time that CAR T cell expansion during a clinical response is coupled to progressive restriction of gene regulatory programs that control T cell fate potential. Furthermore, we show that CD19-CAR T cells undergo exhaustion epigenetic programs that are coupled to an inability to mount a recall response in the presence of antigen-positive normal and malignant B cells. This work lays the foundation for future efforts aimed at improving the efficacy of cellular therapy by reversing epigenetic programs that are coupled to CAR T-cell exhaustion.