Fig. 1

Comparative analysis of mixed phenotype acute leukemia (MPAL) samples single-cell landscape with healthy bone marrow (BM). A UMAP showing the profile of MPAL and healthy samples (n = 67,024 cells), colored based on the individual sample. B Dot plot showing expression of canonical cell markers used to annotate clusters on the X-axis and final cell type labels on the Y-axis. C Split UMAP based on clinical groups (i.e., B/My MPAL, T/My MPAL, Healthy) to visualize cellular clusters associated with specific clinical groups. Dotted lassos highlight the locations of the immune cell populations. D UMAP highlighting the heterogenous blast populations from selected patients. The cell types from M2 (T/My MPAL) and M3 (B/My MPAL) are highlighted on the UMAP. The major blast populations are shown (lassoed) for each sample: M2-My and M2-T, and M3-My and M3-B. E Table and bar plot with cell type distributions, disease subtype, MRD status after treatment, and clinical outcomes. F Heatmap showing top 20 overexpressed genes in B/My MPAL and T/My MPAL blast cells. DEGs were identified by comparing the profile of B/My or T/My MPAL blast cells and healthy immune cells based on fold change and adjusted P-values (i.e., average log2FC > 0.25 and adjusted p-value < 0.05). The top 20 genes were selected based on the highest fold change. G Gene ontology enrichment results for the overexpressed genes (average log2FC > 0.25 and adjusted p-value < 0.05) in MPAL blasts compared to progenitor cells in healthy BM samples. The gene ontology analysis was performed using clusterProfiler package from R/Bioconductor using Biological Process GO categories. The Biological Process with Benjamini–Hochberg p-value < 0.05 is considered significant. The X-axis represents the GeneRatio, which indicates the fraction of MPAL significantly overexpressed genes that can be found in biological gene sets (specifically, GO categories). The size of each dot corresponds to the count of input genes that are present in a particular GO biological category. The color of the dot reflects the adjusted p-value obtained from the enrichment analysis. Specifically, pink and blue colors are used to represent the most and least significantly enriched GO terms associated with MPAL significantly overexpressed genes, respectively. H Macrophage migration inhibitory factor (MIF) signaling in T/My and B/My MPAL cell types. Signaling was inferred using cellular communication analysis, showing the estimated interactions between cell types in MPAL samples via the ligand (MIF) and receptors (CD74, CXCR4, CD44) expression