Fig. 3: Mass cytometry reveals an accumulation of ETV6-RUNX1 expressing progenitor cells in S phase. | Nature Communications

Fig. 3: Mass cytometry reveals an accumulation of ETV6-RUNX1 expressing progenitor cells in S phase.

From: Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability

Fig. 3: Mass cytometry reveals an accumulation of ETV6-RUNX1 expressing progenitor cells in S phase.

a Dotplots of UMAP dimensionality reduction for cell surface markers CD45, CD45RA, CD34, and CD19 in IPSC B-cell differentiations, 10,000 cells each of wild-type and ETV6-RUNX1 knockin are displayed. b Heatmap showing median scaled expression of the indicated markers in manually annotated annotated clusters. See also Supplementary Fig. 3a. c Barplot showing proportion of cells in each population annotated in (a) for parental (MIFF3, 195473 cells), ETV6-RUNX1 knock-in (ER2.1, 415891 cells; ER2.8, 379947 cells) and reverted (D5, 64072 cells) cell lines. d Dotplot for UMAP dimensionality reduction based on cell cycle markers pRb, IdU, CycB1 and pHisH3. Colors represent manually annotated SOM clusters, assigning cells to a cell cycle phase. e Heatmap showing median scaled expression of the indicated markers in the indicated clusters. See also Supplementary Fig. 3b. f Barplots showing proportion of cells in each phase of the cell cycle for each of the cell populations indicated in (a). g Heatmap of Pearson’s Chi-squared standardized residuals showing the relative contribution of the cell cycle phases to the Chi-squared calculation for each population in (f). Pearson’s Chi-squared test revealed that the distribution of cells across populations differed significantly between ETV6-RUNX1 (ER2.1/ER2.8) and wild-type (MIFF3/D5) (Chi-squared = 177910, df = 4, p value < 2.2e−16) (c). Pearson’s Chi-squared test revealed that the distribution of cells across cell cycle phases differed significantly between ETV6-RUNX1 (ER2.1/ER2.8) and wild-type (MIFF3/D5) in each of the populations (CD45: Chi-squared = 10707, df = 4, p value < 2.2e−16; CD45RA: Chi-squared = 700.4, df = 4, p value < 2.2e−16; HSPC: Chi-squared = 68112, df = 4, p value < 2.2e−16; CD19lo: Chi-squared = 14807, df = 4, p value < 2.2e−16; PreB: Chi-squared = 98.129, df = 4, p value < 2.2e−16) (f). Source data are provided as a Source Data file.

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