Figure 6.

Preexisting lymphomyeloid primed progenitor and myeloid blasts in treatment-naive patients as indicators of lineage switch. (A) Frequencies of CD19⁺ blasts that were projected to the myeloid lineage (GMPs, monocytes, and dendritic cells) in all 18 infant KMT2A-r patients based on scRNA-Seq and scATAC-Seq data. (B) Projection of patient PAYZLC data onto normal hematopoietic trajectory. Top panel, projection of scRNA-Seq data. Bottom panel, projection of scATAC-Seq data. Gray dots, cells from healthy donors; colored dots, patient cells. (C) Volcano plot for differentially expressed genes between M-lineage blasts and B-lineage blasts. Analysis was based on projected blasts from all 18 patients. DEGs were identified with the cutoff of abs(log₂FC) >0.5 and FDR <0.01. Those with abs(log₂FC) >1 are highlighted in blue. (D) Violin plots for representative signature genes in M-lineage blasts and B-lineage blasts. (E) Heatmap of differential TF motif accessibility in B-lineage and myeloid-lineage blasts. Analysis was based on projected blasts from 18 patients. Values are z-score normalized deviation scores calculated using chromVAR. TFs with differential accessibility between B-lineage and myeloid-lineage blasts were identified using Wilcoxon test of the normalized deviation scores between the 2 groups with an FDR cutoff <0.05. (F-G) UMAP of scRNA-Seq (F) and scATAC-Seq (G) data for a pediatric KMT2A-r patient with paired samples before and after lineage switch. Left panel, UMAP of paired samples, colored by assigned cell populations. Total numbers of sequenced cells are indicated. Right panel, projection of patient cells to the normal hematopoietic trajectory. Gray dots, cells from healthy donors; colored dots, patient cells. (H) Fraction of B-, myeloid-lineage, and LMPP blasts before and after lineage switch. Top panel, fraction based on scRNA-Seq data; bottom panel, fraction based on scATAC-Seq data. (I) Violin plots of gene expression of B-lineage and myeloid-lineage marker genes before and after lineage switch. (J) Enriched pathways among differentially expressed genes between normal LMPP from healthy donors and LMPP-like blasts in patient samples before lineage switch.