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

Chimeric 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, CAR-T therapy ultimately fails for some patients. Notably, around half of relapsing patients develop CD19 negative (CD19(neg)) B-ALL allowing leukemic cells to evade CD19-targeted therapy. Herein, we investigate leukemic cells of a relapsing B-ALL patient, at two-time points: before (T1) and after (T2) anti-CD19 CAR-T treatment. We show that at T2, the B-ALL 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 CAR-T cell therapy and thus that the relapse results from the selection of these rare CD19(neg) B-ALL 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. CD19-negative relapses are observed in patients with B-cell acute lymphoblastic leukemia (B-ALL) treated with anti-CD19 CAR-T cells. Here, by single-cell RNA sequencing of leukemic cells in a patient with B-ALL, the authors show that pre-existing CD19 negative leukemic subclones are present before CAR-T cell therapy and can account for the relapse.

Automated summary

The study demonstrates that CD19-negative leukemic subclones may already exist before CAR-T cell therapy in patients with B-ALL, leading to potential relapse. By utilizing single-cell RNA sequencing, pre-existing CD19 negative subclones were identified, highlighting the possibility of assessing the risk of targeted therapy failure.