Fig. 3

Comparison of E/R+ cells to normal pro-B cells. a Six diagnostic and two post-treatment bone marrow samples analyzed with scRNA-seq are shown on the UMAP representation. b Expression level of the DNTT marker gene is shown in color on the ALL BM UMAP. c Gene set scoring of differentiation stage is shown as a heatmap, comparing ALL cells to normal bone marrow lymphoid cells. d Computationally predicted cell cycle stage of leukemic cells is colored separately for each donor on a UMAP. For ALL10 and ALL12, the sample origin (diagnostic or day 15 post-treatment) is indicated in the bottom panel. e Eight clusters (clu) formed from genes that distinguish ALL cells from normal pro-B cells are shown in the heatmap. The data corresponds to cluster centroids, and the colors indicate the mRNA detection metric ZP (zero proportion), with dark blue tones indicating low expression (high ZP) and light tones corresponding to a larger proportion of cells expressing the genes in each cluster. The number of genes in each cluster is indicated on the right. Cell cycle stage C: S/G2/M, G1: G1. f Genes modulating NK cell activity (TGFB1, TERF2, LY6E, and HLA-E) plotted as density plots that compare the gene expression distribution of E/R+ cells to pro-B cells (both in G1 cell cycle state)