Fig. 2

scRNA-seq reveals the transcriptional heterogeneity and dynamic evolution of patient with Ph-like ALL. A Schematic representation of the isolation, sequencing, and analysis of the single cells. B Six broad immune cell types assigned to all profiled single cells via cell type identification analysis. C Expression levels of lineage-specific genes overlaid on the tSNE representation. D Marker-based cell type identification analysis defined six B-cell subtypes. E tSNE plots showing the three cell cycle phases in the patient with Ph-like B-ALL (left panel). The expression of S and G2 genes highlights the proliferating cells. Dot plot showing the average expression levels and cell expression proportions of CD34 and selected cell cycle genes in the indicated clusters (right panel). The colors represent the average expression levels, and dot sizes represent the expression percentage of selected genes in the indicated clusters. F Trajectory analysis of B-cell clusters classified into six subtypes (n = 9,393 cells), colored by pseudotime. Solid and dotted lines represent distinct cell trajectories defined by single-cell transcriptomes. G Cell clusters overlaid on the tSNE representation and split by samples. H Violin plots show the expression of well-known B-cell marker genes. I A volcano plot of DEGs up-regulated (red) or down-regulated (blue) in the relapse-specific clusters (clusters 2 and 14); the top 10 up-regulated genes are labeled. The p-value is derived using the Wilcoxon rank-sum test. J Pathways up-regulated in the relapse-specific clusters (clusters 2 and 14). The p-value is derived using a hypergeometric test. K Expression levels of the relapse-specific gene ACSM3 overlaid on the tSNE representation (left panel). Boxplot (right panel) showing significantly higher expression levels of ACSM3 in relapsed patients with CNS-L