Fig. 6

The cytokine stimulation controls ETO2::GLIS2 leukemia cellular and molecular features. A Experimental design: Fetal or CB CD34⁺ EG transduced or CRISPR-edited cells were either cultured for 7 days in the LT-LC medium (± IL3/SCF) or injected into sublethally irradiated NSG or NSGS mice. After 7 days of culture or at disease development in vivo, EG cells were collected and live hCD45⁺(GFP⁺) cells were sorted prior to single cell and bulk transcriptome analysis. Patient cells (n = 4) were also analysed by scRNAseq. B UMAP representation of the integration of cells from all conditions and cluster identification. Clusters were defined using the Louvain algorithm. C Score of enrichment of the gene signature [8] upregulated in ETO2::GLIS2 patients projected on the UMAP of the integration (red: cells presenting an enrichment of the signature; blue: cells with a depletion of the signature; grey: lack of significance). D Cells from each condition are highlighted in red on the UMAP of the integration. E Percentage of cells in clusters 0 + 3 + 5 + 14 + 15 for each condition. F Projection of the level of expression of NCAM1 on cells of the integration. G Left panel: score of enrichment of a megakaryocyte progenitor gene signature (MSigDB, Hay et al., [63]) on the integration. Middle panel: percentage of cells presenting enrichment of the signature (red). Right panel: projection of the level of expression of ITGA2B on cells of the integration. H Percentage of cells in clusters 2 + 6 + 7 + 8 + 9 for each condition. I Projection of the level of expression of AIF1 on cells of the integration. J eft panel: score of enrichment of a HSC gene signature (MSigDB, Hay et al., [63]) on the integration. Middle panel: percentage of cells presenting enrichment of the signature (red). Right panel: projection of the level of expression of CD44 on cells of the integration. K Projection of the level of expression of KIT and IL3RA on cells of the integration. L Upper panel: experimental design of the ATACseq approach. Lower panel: histogram representation of the intensity at loci that present gained accessibility in + IL3 + SCF vs –IL3-SCF cells. M Peaks differentially gained in (L) were annotated to the closest gene. The corresponding gene list was used to compared bulk RNAseq data from leukemic cells in CB NSGS vs FL NSG using GSEA. N Score of enrichment of the gene list used in (M) projected on the integration