Single-cell characteristics of leukemia-infiltrating nonleukemic T lymphocytes in T-ALL. (A) UMAP plot showing 11 distinct clusters of nonleukemic T cells combining CD7⁺ BMMCs from 5 relapsed T-ALL patients at diagnosis (R-Dx-T) or relapse (R-Rel-T), 3 patients with nonrelapsed T-ALL, at diagnosis (NR-Dx-T), and CD3⁺ BMMCs from 2 HDs (HD-T). (B) Heat map hierarchically displays top 5 gene signatures featuring each of the 11 subclusters of nonleukemic T cells in panel A. (C) Bar plot comparing the proportion of each subcluster across 4 groups: R-Dx-T, R-Rel-T, NR-Dx-T, and HD-T. Wilcoxon rank sum test is used for statistical analysis; ∗P < .05. (D) UMAP plot of nonleukemic T-cell identities colored according to TCR clonal abundance of the 15 T-ALL samples and HDs. The gray color indicates a lack of TCR. (E-F) Stacked bar plots depicting frequency of the 3 TCR clonality categories across the 4 groups: R-Dx-T, R-Rel-T, NR-Dx-T, and HD-T for all the nonleukemic T cells (E), and for each of the 11 functional T subclusters, respectively (F). The 3 TCR clonal expansion groups were denoted with colors: in which category “>10” in blue indicates that there were at least 10 cells that express the identical TCR clonotype; category “5-10” in purple indicating that 5 to 10 T cells express an identical TCR clonotype; and category “1-5” in salmon indicates that only 1 to 5 cells express a specific TCR clonotype. (G-H) Heat maps hierarchically display the top 20 group-specific genes and pathways that are enriched in CD8_GNLY_effector T subcluster (G) or CD8_GZMK_exhausted T subcluster (H) across the 4 patient groups (R-Dx-T, R-Rel-T, NR-Dx-T, and HD-T) by gene set enrichment analysis (GSEA). FDR, false discovery rate.