DLBCL cells emerge post CD19 CAR-T with cross-antigen resistance and a gene signature predictive of clinical CAR-T response

Abstract Current understanding of lymphoma cell-intrinsic mechanisms of relapse following CAR-T cell treatment of diffuse large B-cell lymphoma (DLBCL) include antigen-loss and apoptosis resistance. Herein, CD19 CAR-T response and resistance were modeled and it was identified that treatment-naïve CD19 expression does not correlate with CAR-T sensitivity, but resistance is frequently accompanied by reversible downregulation of CD19, that once restored is not paralleled with restored sensitivity to CAR-T mediated killing. Profiling a suite of DLBCL cell lines to CD19 CAR-T sensitivity, reveals that DLBCL cells become non-responsive to CAR-T mediated killing, including to alternative antigen-targeting of CD20 or CD22. Leveraging these resistant models, we identified gene signatures present in the CAR-T resistant DLBCL cell lines that correlate with patient response to CTL019 in two independent clinical trials. Finally, we show that combination strategies to overcome this resistance, including upfront dual antigen-targeting and combined treatment with an Mcl-1 inhibitor, improve CAR-T responses.