Fig. 3: Tet2-KO HSCs exhibit transcriptional signatures for self-renewal capacity under inflammatory stress. | Nature Communications

Fig. 3: Tet2-KO HSCs exhibit transcriptional signatures for self-renewal capacity under inflammatory stress.

From: Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells

Fig. 3

a WT and Tet2-KO mice were treated for 5 weeks with and without IL1β (n = 4 mice/group). BM cells were harvested and lineage-negative cells were enriched by magnetic selection. This enrichment increases the representation of progenitors but reduces the percentage of differentiated cells. Cells were analyzed by 10X single-cell RNA (scRNA) sequencing. b UMAP of 54,984 cells representing 17 clusters and bar graph representing their proportions including hematopoietic stem cell (HSC), progenitor (Prog), immature myeloid progenitor (IMP), granulocyte or monocyte progenitor (Gran/Mono Prog), monocyte (Mono), macrophage (Mac), neutrophil (Neut), basophil (Baso), megakaryocyte progenitor (MegP), common lymphoid progenitor (CLP), T cell (T-cell), plasmacytoid dendritic cells and B cell (pDc/B-cell), eosinophil (Eo), megakaryocyte-erythroid progenitor (MEP), colony-forming unit erythroid (CFU-E), erythroblast CD45- EryB (EryB_CD45-) and erythroblast CD45+ EryB (EryB_CD45 + ). c Venn diagram of differentially expressed genes (DEGs) in Tet2-KO HSCs relative to WT treated with vehicle or IL1β. d Volcano plot of DEGs in Tet2-KO relative to WT HSCs with or without IL1β stimulation. Selected genes based on enriched pathways are labeled. q values were determined using DESeq2. e Gene-set enrichment analysis (GSEA) from HSCs in Tet2-KO relative to WT showing selected significantly enriched gene sets (FDR < 0.05), with IL1β (red) or vehicle (black) or pathways not significantly enriched in the vehicle (grey). q values were determined by GSEA v4.2.1 using an empirical phenotype-based permutation test procedure. f Heatmap of upregulated DEGs in Tet2-KO relative to WT HSCs with and without IL1β stimulation for HSCs, Prog, IMPs, and GMPs. The genes shown are the lead genes for enriched pathways by GSEA analysis within HSCs, categorized into “Inflammation only”, “Inflammation and Self-renewal”, or “Self-renewal only” using the GSEA subcategories assigned in Fig. 3e. q values were determined by DESeq2. g Enrichment score plots for the gene signature of the top 100 upregulated genes in Tet2-KO relative to WT with IL1β (top) or vehicle (bottom) using DEGs from human TET2 mutant (left) versus TET2 WT (right) acute myeloid leukemia with p values determined by GSEA v4.2.1. For q values: *q < 0.05, **q < 0.01, ***q < 0.001, ****q < 0.0001.

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