Fig. 3: An overview of cell types observed in bone marrow of healthy and leukemic individuals.
See also Supplementary Figs. 2 and 7. a Data from the five individuals (Fig. 1a) were integrated using scanorama60 and visualized in two dimensions using uMAP62,63. Clusters are color-coded. N = 5228 cells. b Fraction of CD34+ cells in total bone marrow from the five individuals. CD34+ cells were enriched during FACS sorting for a higher representation in the single-cell RNA-seq data (Supplementary Fig. 2). c CD34+ cells from a healthy individual22 highlighted on the uMAP. Black dots correspond to cells from the HSC/MPP cluster. d Cells from each patient were highlighted separately on the uMAP. Black dots correspond to cells from the HSC/MPP cluster. e Logicle-transformed expression of key FACS markers highlighted on the uMAP (Supplementary Fig. 7a). f Data from n = 667 cells from the HSC/MPP cluster were integrated across individuals using MNN64. The smoothened expression of several marker genes of healthy HSC/MPP subsets22 is plotted over the first dimension of variability identified by MNN (Supplementary Fig. 7f). g Volcano plot of the log10 expression change (Log FC) in n = 569 AP1-high CD34+ blasts vs. n = 667 HSC/MPP-like cells, plotted against corrected p-values from MAST, using a model that accounts for differences in library quality and patient identity/batch (see the Methods section Single-cell gene expression data analysis). AP1-high CD34 + blasts were chosen for this comparison since AP1-low blasts, in terms of all marker genes, appear to constitute an intermediate state between Healthy-like HSC/MPPs and AP1-high blasts. h Log-normalized expression of FOS and JUN on the uMAP from panel a. See panel e for a color scale. i Venn diagram displaying genes with significant overexpression in AP1-high CD34+ blasts and CD34− blasts, compared to all other cells from the data set.
