Multi-omics reveals evolution from CD7-negative T cell dysregulation to EBV-positive LPD after CD7 CAR-T therapy

EBV activation specifically occurs in a subset of patients following CD7 CAR-T therapy, subsequently leading to EBV-positive lymphoproliferative disorder (EBV+ LPD), descriptively referred to as post-CD7 CAR-T lymphoproliferative disorder (PCLD) in this study. To comprehensively characterize PCLD, we employed single-nucleus RNA sequencing, ATAC sequencing, and Stereo-seq to perform multi-omic spatial profiling of PCLD, and compared it with classical post-transplant lymphoproliferative disorder (PTLD), EBV-negative diffuse large B-cell lymphoma (EBV- DLBCL) and normal lymph nodes. Infiltrating T cells in PCLD are uniquely characterized by CD7 negativity, exhibiting limited proliferation upon infection stimulation and impaired antiviral activity against EBV. Macrophages are recruited in an attempt to sustain viral clearance; however, the Macro_IDO1 subset emerges as the dominant macrophage population, exhibiting an immunosuppressive phenotype marked by elevated IDO1 expression. Spatially, macrophages, predominantly Macro_IDO1, aggregate to form an immunosuppressive niche that restricts T-cell infiltration and is enriched for inhibitory ligand-receptor interactions, including the PD-1/PD-L1 axis. T-cell function is further compromised, enabling sustained EBV infection of B cells and driving malignant transformation. EBV-driven B cells undergo plasmacytic differentiation and sustained proliferation, actively remodeling the microenvironment. This study provides a comprehensive molecular characterization of lymphoproliferative disorder following CD7 CAR-T therapy, elucidates spatial tumor-immune interactions, mechanisms of EBV-driven B-cell transformation and potential intervention strategies.