Longitudinal immune reconstitution dynamics in refractory T-ALL treated with CD7 CAR-T cells bridging to allogeneic stem cell transplantation

Abstract Introduction T-cell acute lymphoblastic leukemia (T-ALL) is associated with a poor prognosis, with 20–30% of adults refractory to induction chemotherapy and <50% 5-year survival despite intensive therapies. Persistent MRD poses a major challenge. The first-in-human trial of donor-derived CD7 CAR-T cells for T-ALL, corroborated by multicenter evidence, demonstrated 87.5–100% complete remission in relapsed/refractory patients. However, this approach concomitantly eliminates malignant CD7⁺ and healthy T/NK cells, triggering compensatory expansion of CD7⁻ T cells and immune imbalance. The interplay between therapeutic efficacy, toxicity, and immune reconstitution remains elusive, necessitating detailed longitudinal investigations. Methods To address this, we performed integrated multiomic analysis of a primary refractory T-ALL patient who achieved sustained remission. Treatment involved sequential CD7 CAR-T-cell infusions (5×10⁶/kg on day 0 and 3×10⁶/kg on day 62 post- infusion) followed by matched-sibling allo-HSCT on day 96. We analyzed peripheral blood at four key points using single-cell RNA sequencing (67,000 cells), TCRβ tracking, pseudotime trajectory analysis, and cell‒cell communication modeling (CellChat). Results The patient received two infusions of CD7 CAR-T cells and achieved deep remission with minimal residual disease (MRD) negativity one week after the second CAR-T-cell therapy; moreover, more CD7+ T cells were killed. Compared with the first infusion, the second infusion caused milder toxicity (grade 1 cytokine release syndrome [CRS], IL-6 peak 402 pg/mL), while the first infusion caused grade 2 CRS (IL-6 883 pg/mL), and the tumor was completely cleared. Disease-free survival was maintained for more than 1,183 days after allogeneic hematopoietic stem cell transplantation (HSCT). No neurotoxicity occurred throughout the process, and cytopenia was repaired after engraftment. Single-cell data revealed a triphasic immune remodeling process. In phase 1 (after the first CAR-T-cell treatment, D14), cytotoxic CD8+ effector cells expanded massively and expressed functional activity markers. CD4+ T cells differentiated into regulatory and effector lineages, forming a Th1-type environment. Intercellular communication surged (1,798 pathways), driven by antigen presentation, costimulation, and adhesion signals. In phase 2 (after the second CAR-T-cell treatment, D70), residual cancer cells were effectively eliminated, while CD7+ lymphocytes were nearly completely depleted. CD7-CD8+ T cells dominated the expansion (96.4%). Importantly, strong intercellular communication persisted (892 pathways), indicating active coordination within the CD7- cell compartment. In phase 3 (after HSCT, D121), myeloablative conditioning (before HSCT) led to a dramatic collapse of the signaling network (359 pathways), resulting in nonselective depletion of hematopoietic cells, including CD7- T cells. This reset resulted in the loss of stimulatory signals and the emergence of immunosuppressive pathways. Pseudotime analysis confirmed that conditioning eliminated CAR-T-cell-driven immunity, allowing naive-like T cells to regenerate through a thymus-dependent pathway. The immune balance was eventually restored, and CD7+ T cells recovered quantitatively on day 250. However, functional maturation lagged, manifesting as metabolic disorders and signaling defects, which explains the susceptibility to infections in the early stage after HSCT. The CD7- T-cell pool provided the necessary transitional immune function until HSCT-mediated reconstitution. The transition to CD7+ immunity marked the recovery of function. Conclusions This work establishes the “triphasic remodeling model” (clonal burst, compensatory adaptation, and myeloablation-enabled reset) as a paradigm for cellular immunotherapy, explaining stage-specific needs. Our integrated analytical approach distinguishes therapeutic from iatrogenic effects, and this framework provides a blueprint for managing refractory T-ALL by orchestrating transitions between distinct immune states.