Comparative high-dimensional profiling reveals distinct immune reconstitution dynamics between CD19 and CD7 CAR-T therapies in acute leukemia

Abstract

Abstract Background: Chimeric antigen receptor T-cell (CAR-T) therapies targeting distinct lineage antigens such as CD19 (B-cell) or CD7 (T-cell) have demonstrated potent anti-leukemic activity, yet their in vivo dynamics and immune reconstitution profiles remain underexplored. Given the fundamentally different immunologic niches occupied by these targets, we hypothesized that CD19 and CD7 CAR-T cells would drive divergent immune remodeling patterns, with implications for efficacy, persistence, and toxicity. Aims: This study aimed to: 1) Decipher differential immune reconstitution patterns post-CD19 vs. CD7 CAR-T infusion; 2) Correlate these dynamics with durability of response and complication rates. Methods: We performed the first in-depth, comparative and prospective biomonitoring of 28 patients with relapsed/refractory B-ALL (n=18) or T-ALL/LBL (n=10) treated with CD19- or CD7-directed CAR-T cells, respectively. A total of 209 paired bone marrow and peripheral blood samples were collected at 5 timepoints (pre-infusion, D14, D28, 2 months, 3 months). High-dimensional profiling with a 40-marker CyTOF analysis was performed to assess CAR-T cell dynamics, endogenous immune reconstitution, and associations with clinical endpoints. Results: Both therapies achieved comparable initial response rates, however, CD7 CAR-T recipients experienced higher relapse (40% vs. 16.7%) and severe infection rates (40% vs. 16.7%). Mechanistically, CD7 CAR-T cells exhibited rapid early activation with high IFN-γ, Granzyme B, and Perforin expression at Day 14, followed by early exhaustion (PD-1, TIGIT, TIM-3 upregulation) and loss of functional persistence beyond Day 60. Conversely, CD19 CAR-Ts maintained a sustained activation state with memory-associated phenotypes. Distinct target cell clearance kinetics were also observed: CD19 CAR-Ts induced rapid and durable B-cell aplasia, while CD7 CAR-Ts mediated delayed CD7+ T-cell depletion accompanied by expansion of CD7– T-cells. By Month 3, CD19 CAR-T recipients exhibited superior endogenous cytotoxic T-cell recovery and polyfunctionality, suggesting improved long-term immunosurveillance. Conclusion: This first comparative profiling of CD19 and CD7 CAR-T therapies reveals target-specific immunologic trade-offs. CD19 CAR-Ts offer prolonged persistence and immune surveillance but at the cost of B-cell aplasia. In contrast, CD7 CAR-T cells achieve rapid tumor debulking but are limited by early exhaustion, delayed target clearance, and impaired immune reconstitution, increasing relapse and infection risk. These findings underscore the necessity for antigen-specific CAR-T design and tailored post-infusion management strategies to optimize long-term outcomes.