Single-cell characterization of BM HSPCs and T cells from patients with REL and those with CR. (A) Overview of the experimental setup. (B) Uniform manifold approximation and projection (UMAP) of 8492 post-QC cells representing BM HSPCs and T cells from 6 patients with AML on day 100 after allo-HCT. Cells are colored according to cell type. HSPCs included myeloid/lymphoid progenitors (MLP), B-cell precursors (preB), T-cell precursors (pre/proT), megakaryocyte-erythroid progenitors (MEP), neutrophil progenitors (NP), monocyte-dendritic progenitors (MDP), late monocytic precursors/monocytes (MP/mono), and dendritic cells (pDCs, cDCs). (C-D) Scaled expression (C) of marker genes and TF activity (D) are shown for each cell type cluster in panel B as heat maps. Values are averaged across all cells in the cluster. TF activity is obtained from SCENIC (“Methods”). (E-G) UMAP as shown in panel B indicating the normalized gene expression of selected genes, with the range of normalized gene expression indicated in the parenthesis of each UMAP. QC, quality control. The BM biopsy illustration in the lower part of panel A was adapted from the original work of Cancer Research UK under a CC BY-SA 4.0 license.