Single-Cell Multi-Omics Analysis Reveals the Role of CX3CR1+ GNLY+ CD8+ T Cells in Improving Survival of Patients with Relapse/Refractory Hematologic Malignancies after Haplo+Cord HSCT

Background Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative treatment for hematological malignancies. Previous works have shown superior survival outcomes of sequential transplantation of haploidentical stem cell and unrelated cord blood (haplo+cord HSCT) among recipients with relapsed/refractory leukemia, compared with single cord HSCT. However, the underlying mechanisms of immune reconstitution remain largely unexplored. Methods we first performed scRNA-seq and scATAC-seq on bone marrow mononuclear cells (BMMCs) from nine patients with relapsed/refractory leukemia underwent haplo+cord or single cord HSCT to profile the immune landscapes at single cell resolution. Second, we compared the differences of gene expression and chromatin accessibility between the subsets of immune cells. Finally, by integrating multi-omics data, we explored the gene expression regulation mechanism behind the differences between two transplant group. Results We observed distinct composition and function of global immune landscapes (T, B, natural killer cells and monocytes) between two transplant strategies, where immune cells from haplo+cord HSCT involved in interferon signaling pathway and response to virus. Analysis on T cells revealed two cytotoxic CD8+ T cells populations, enriched in haplo+cord HSCT (expressing GNLY, GZMB and PRF1) and enriched in single cord HSCT (expressing CXCR4 and GZMK) respectively. Interestingly, the augmented expression of GNLY and CX3CR1 suggested a dual property of effector and memory of haplo+cord HSCT enriched CD8+ T cells that potentially offers long-term protection for patients post-transplantation. The transcription factor IRF7, IRF9 and TBX21 played the key role on regulating immune signal transduction of CD8+ T cell subsets after haplo+cord HSCT, which might be the mechanism of transcriptional regulation for cytotoxic CD8+T cell function. Finally, single cell multi-omics analysis delineate regulatory network controlling lineage-specific gene expression after HSCT, illustrated by the example of GNLY expression in CD8+ T cells regulated by an enhancer cluster within CTCF-mediated chromatin loop. Conclusions These data collectively constitute the transcriptomic and epigenetic landscape of bone marrow post-transplantation in hematopoietic malignancies at single-cell resolution, demonstrating that a CX3CR1+ GNLY+ CD8+ T cells characterized by effector and memory property served the improved survival of patients receiving haplo+cord HSCT. keywords Single cell multi-omics, CX3CR1+ GNLY+ CD8+T cells, haplo+cord HSCT, single cord HSCT, relapsed/refractory leukemia