Bone marrow single cell transcriptome profile 3 months after transplantation in blood cancer patients who received hematopoietic stem cell transplantation

Relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains the leading cause of treatment failure in patients with hematologic malignancies. To better understand the mechanisms underlying relapse, we comprehensively explored the expression of inhibitory receptors (IRs) in bone marrow T cell at differentiation stage and examined transcriptional differences. Among the evaluated IRs, TIM3 was significantly upregulated in CD3+ T cells of patients with early relapse (ER) compared to patients with complete remission (CR). Notably, double-negative T (DNT) cells, a unique subset with MHC-independent cytotoxic potential, constituted a high proportion of BM T cells and expressed increased TIM3 expression in ER patients. Moreover, regulatory T cells (Tregs) showed elevated TIM3 levels, contributing to an immunosuppressive microenvironment after allo-HSCT. Transcriptional analysis revealed downregulation of interferon-gamma signaling, oxidative phosphorylation, and T-cell receptor genes in ER patients , indicative of impaired cytotoxic function. Functional assays demonstrated that TIM3 blockade with sabatolimab restored T cell cytotoxicity, leading to enhanced leukemia cell apoptosis in ER patients. These findings highlight TIM3 as a key regulator of immune dysfunction in post-transplant relapse and support its potential as a therapeutic target. Three month samples were collected from bone marrow after chemotherapy and HSCT for leukaemia and subjected to Ficoll gradient isolation. The dataset includes scRNAseq data from two complete remission (CR), two early relapse (ER) and one late relapse (LR) patients.