Immunophenotype of CAR T cells and apheresis products predicts response in CD22 CAR T cell trial for B cell acute lymphoblastic leukemia

Although CAR T cell therapy is increasingly used to treat relapsed B cell acute lymphoblastic leukemia (ALL), 20%-30% of patients do not respond, and few clinical predictors of response have been established, especially in the pediatric population. A deeper analysis of CAR T cell infusion products, along with the apheresis product used as the starting material for CAR T cell manufacturing, provides valuable insights for predicting clinical outcomes. We analyzed infusion products and CD4/8-selected T cell starting materials from pediatric and young adult patients on a single-center study with relapsed/refractory B cell ALL who were undergoing treatment with CD22 CAR T cells and evaluated differences between T cells from responders and non-responders (NCT023215612). We found that CAR T cells from non-responders had a more differentiated T cell phenotype and overexpressed genes associated with cytotoxicity and exhaustion compared with those of responders. Furthermore, we found that these differences could be tracked back to the apheresis materials prior to CAR T cell manufacturing. Using flow cytometry-based immunophenotypic markers, we developed a scoring system that distinguished non-responders based on T cell phenotype at the time of apheresis. These findings can help inform outcomes for patients and providers as well as provide insights into targeted manufacturing changes to optimize CAR T cell efficacy.