Single-cell RNA sequencing profiling of T-cell subpopulations in mice cured of or relapsed with BCR-ABL1 B-ALL after dasatinib therapy. (A,B) Uniform manifold approximation and projection (UMAP) visualization of 14 836 individual peripheral blood leukocytes collected from cured (7578 single cells) (A) and relapsed mice (7258 single cells) (B). (C) Each cell was classified into 1 of 5 immune cell types based on the expression of marker genes. (D) The difference in immune cell composition is shown as the percentage of peripheral blood leukocytes in cured mice relative to relapsed mice. (E,F) Flow cytometry of peripheral blood cells showed a higher proportion of CD3 (E) and CD4 (F) T cells in cured mice compared with relapsed animals. (G) Single-cell expression of marker genes of the T-cell population. Memory T-cell markers: Tcf7, Sell, Ccf7, and Il7r. Effector T-cell markers: Ifng, Gzma, Gzmb, and Pdcd1. NK T-cell markers: Klra1 and Xcl1. (H-J) UMAP visualization of T cells collected from cured and relapsed mice. Each cell was classified into 1 of 4 subpopulations based on the expression of marker genes; 4 subpopulations (H); distribution of cells from cured mice (green) and relapsed mice (brown) (I); T-cell distribution of 4 subpopulation in cured (left) or relapsed (right) groups, respectively (J). (K,L) To identify genes related to ALL cure, we compared gene expression profiles of T cells from cured mice vs relapsed mice and specifically focused on CD8 T1 cells (memory like) (K) and CD8 T2 cells (effector like) (L). Differentially expressed genes were analyzed for pathway enrichment using GSEA. The bar plot shows the normalized enrichment scores of gene sets.