Single cell multiomic analysis of clonal and transcriptional programs of CD19 CAR T cells in the immunotherapy response

CD19-directed CAR T-cell therapy has shown high rates of complete response against relapsed/refractory B-ALL, but it is only maintained in 50% of patients after a year. The impact of CAR T-cells' phenotypic, clonal, and functional heterogeneity on clinical outcomes remains unclear. Thus, a deeper examination of how clonal kinetics and diversity of CAR T-cells translate into short-term effectiveness and long-term persistence is crucial to pinpoint. scTCR-seq and scRNA-seq were used to analyze samples from manufactured Infusion Product (IP) and peripheral blood during the CAR T-cell expansion peak (Peak) of five B-ALL patients. Our study revealed that patients with higher CD4 T-cell proportions at IP had a larger response, while patients with higher exhaustion scores had worse prognosis regardless of the presence of the CAR. At Peak, a significant increase in clonally expanding CD8+ T-cells was observed but impressive expansion of cytotoxic γδ T-cells correlated with patient outcome pointing out its importance. These findings provide insight into the interplay between the immune response and CAR-T-cell therapy and could contribute to the development of more effective treatments.