Single-cell profiling identifies pre-existing CD19-negative subclones in a B-ALL patient with CD19-negative relapse after CAR-T therapy

International audienceChimeric antigen receptor T cell (CAR-T) targeting the CD19 antigen represents an innovative therapeutic approach to improve the outcome of relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL). Yet, despite a high initial remission rate, CART therapy ultimately fails for some patients. Notably, around half of relapsing patients develop CD19 negative (CD19 neg) BALL allowing leukemic cells to evade CD19-targeted therapy. Herein, we investigate leukemic cells of a relapsing BALL patient, at two-time points: before (T1) and after (T2) anti-CD19 CART treatment. We show that at T2, the BALL relapse is CD19 negative due to the expression of a non-functional CD19 transcript retaining intron 2. Then, using single-cell RNA sequencing (scRNAseq) approach, we demonstrate that CD19 neg leukemic cells were present before CART cell therapy and thus that the relapse results from the selection of these rare CD19 neg BALL clones. In conclusion, our study shows that scRNAseq profiling can reveal pre-existing CD19 neg subclones, raising the possibility to assess the risk of targeted therapy failure