Single-cell profiling reveals immune circuit disruption preceding CAR-T relapse in B-ALL

Chimeric antigen receptor T (CAR-T) cell therapy has transformed treatment outcomes for B-cell acute lymphoblastic leukemia (B-ALL), yet disease relapse remains a major clinical challenge. To elucidate mechanisms underlying relapse, we analyzed longitudinal single-cell RNA-seq profiles from peripheral blood mononuclear cells (PBMCs) of five B-ALL patients treated with CAR-T cells. Within total T cells, MHCII⁺ CD8⁺T cells were markedly reduced at relapse, whereas naive-like CD8⁺ T cells were enriched. Trajectory reconstruction revealed that antigen-processing and antigen-presentation pathways are critical for the transition from naive-like to MHCII⁺ CD8⁺ T cells. In relapsed patients, MHCII⁺ CD8⁺ T cells exhibited impaired progression along this trajectory and remained transcriptionally similar to the naive-like state. Within the monocyte lineage, antigen-presenting monocytes in relapsed patients skewed toward a non-classical phenotype, characterized by enhanced chemotaxis, taxis, and oxidative phosphorylation, whereas a patient who maintained remission to day 360 displayed antigen-processing, antigen-presentation, and type I interferon activation signatures. Analysis of B-ALL cells revealed that relapsed leukemic cells exhibit increased stemness, “don't-eat-me” signaling, and immaturity scores, along with reduced mature B-cell differentiation signatures. Together, our multi-patient single-cell analysis reveals a coordinated dysregulation of monocytes, CD8⁺ T-cell antigen presentation, and intrinsic leukemic cell states during CAR-T relapse, highlighting a potential B-ALL-monocyte-T-cell axis that may drive immune evasion and inform strategies to prevent or treat CAR-T failure.