Fig. 1: Characterization of APL blasts through an integrative analysis of scRNA-seq data from APL and normal bone marrow (BM) cells.
a Overview of the experimental strategy. b UMAP plots of APL and normal BM cells (nā=ā239,332 cells), with color-coding indicating sample types (left panel), inferred cell populations (middle panel), and PML/RARĪ±-positive cells detected by scTarget in two APL samples (right panel). Cells detected with more than three PML/RARĪ± fusion reads are illustrated. HSPCs hematopoietic stem/progenitor cells, GMPs granulocyte-monocyte progenitors, NK Natural Killer, Ery erythroid. c UMAP plots with each cell (nā=ā239,332 cells) colored according to their normalized expression of MPO, CD14, CD3E, CD79A, and CA1, respectively. d Normalized expression level and expression percentage of cell type-specific genes in eight cell populations in APL and normal BM cells. e, f Gene Ontology (GO) enrichment analysis showing significantly enriched biological process terms for upregulated genes (e) and downregulated genes (f) in APL blasts compared with GMPs. g Inferred activated (red) and repressed (blue) TFs in APL blasts compared to normal GMPs. The central two-row graph illustrates the distribution of activated targets (depicted in red) and repressed targets (depicted in blue) of different TFs, with positions ranked according to the differential expression between APL blasts and normal GMPs (leftmost: most downregulated in APL blasts, rightmost: most upregulated in APL blasts). The regulatory model was based on the ARACNe-inferred interactome, provided in the build-in function of the VIPER R package. The P-value is shown on the left of the column, and the inferred differential activity level is shown on the right. The P-values were calculated using the msviper function in the VIPER R package. Two-sided P-values were calculated. APP antigen processing and presentation; MHC major histocompatibility complex.
