Clonal expansion of T memory stem cells determines early anti-leukaemic responses and long-term CAR T cell persistence in patients

Low-affinity CD19 CAR T cells display enhanced expansion and persistence, enabling fate tracking through integration site (IS) analysis. Here we show that IS from early (1 month) and late (>3 years) time-points cluster separately, suggesting different clonal contribution to early responses and prolonged anti-leukemic surveillance. CAR+ T central and effector memory in patients with long-term persistence remained highly polyclonal, whereas diversity dropped rapidly in patients with limited CAR T persistence. Analysis of shared integrants between the CAR T cell product and post-infusion demonstrated that, despite their low frequency, T memory stem cells (TSCM) clones in the product contributed substantially to the circulating CAR T cell pools, both during early expansion and long-term persistence. Our data may help identify patients at risk of early loss of CAR T cells and highlights the critical role of TSCM in both mediating early anti-leukemic responses and long-term surveillance by CAR T cells.