Fig. 3

Mapping the single-cell landscape of early T-cell precursor acute lymphoblastic leukemia (ETP-ALL). A UMAP clusters of 50,907 cells colored based samples and different ALL (left) including T/myeloid mixed phenotype acute leukemia (T/My MPAL), near-ETP/ETP-ALL, and non-ETP T-ALL. The right side is the UMAP colored by clusters obtained based on K-mean clustering using the Seurat package. B Cell type annotations for the three T-Lineage subtypes shown on UMAPs. Clusters with the overlap of cells and transcriptome profiles among different T-ALL subtypes have been lassoed and labeled. C Venn diagram analysis to visualize commonly overexpressed genes (average log2FC > 0.25, adjusted p-value < 0.05) in T/My MPAL compared to non-ETP T-ALL blast cells, and near-ETP/ETP-ALL compared to non-ETP T-ALL blast cells. D Feature map of selected T/My MPAL, non-ETP T-ALL, and near-ETP/ETP-ALL blast cells overexpressed genes. Low and high expressions are shown with gray and purple colors respectively. E Gene network plot for enriched GO categories associated with overexpressed near-ETP/ETP-ALL genes. The network nodes have been colored based on fold change in near-ETP/ETP-ALL, and the size of the central dots represents the size of the selected GO category. F Density plot showing stemness index distribution of blast cells T/My MPAL, near-ETP/ETP-ALL, non-ETP T-ALL, and non-blast immune cells. The stemness index was calculated as the first principal component value of each cell after performing principal component analysis with the expression of the genes in a stem cell gene set as the features (Additional file 1: Table S3)