Fig. 2: Characterization of intratumoral heterogeneity in APL blasts reveals a complex trajectory with multiple branches and a small subpopulation of APL stem-like cells.

a UMAP plot of APL blasts (upper panel; n = 126,802 cells). Eighteen clusters are labeled in different colors and numbers (lower panel). GMP granulocyte-monocyte progenitors, EOS eosinophils, Prog progenitors, MDP monocyte-DC progenitors, PrecDC pre-conventional dendritic cells, Promono promonocytes. b The left heatmap shows Spearman’s correlation between the 18 APL clusters, calculated using the average expression profiles of the clusters. The right heatmap illustrates the expression levels of cell type-specific genes in each cluster. c Visualization of RNA velocity-based cell-state transitions of APL blasts. d UMAP plot of APL blasts with six branches, i.e., stem-like, Prog-like, S100^hiGMP-like, GMP-like, cycling GMP-like, and MDP-like branches. e Pseudotime-ordered analysis of four major branches in APL blasts, including stem-like, Prog-like, S100^hiGMP-like, and GMP-like branches. f Heatmap showing the dynamic changes in gene expression (n = 116 genes) along the pseudotime. Cell branches are labeled by colors (upper panel), including stem-like cells (center), S100^hiGMP-like cells (left), and GMP-like (right). Characteristic transcription factors (TFs) are listed on the right. g UMAP plots of the targeted scRNA-seq (scTarget) data from two APL patients, with color coding for sample types (left panel) and branches (right panel). On the right panel, cells detected more than three PML/RARα fusion reads were illustrated. h The expression levels of PML/RARα in six branches of APL blasts. i Branch-specific expression patterns for PML/RARα targets across the APL trajectory. The left heatmap visualizes the single-cell expression of PML/RARα-regulated branch-specific marker genes across branches, with rows representing genes and columns for cells. To offer a clear and representative depiction of the branch-specific expression patterns for PML/RARα targets, we selected 1000 cells from each branch for interpretation. The right heatmap displays the mean gene expression (n = 1758 genes) across branches, accompanied by the annotations of representative marker genes on the right side. Cor. correlation, Exp. expression.