Fig. 4: Following allo-HSCT, blood cells from patients have decreased CA at sites of accessibility associated with ILC2 cells at the time of the diagnosis of aGVHD. | Nature Communications

Fig. 4: Following allo-HSCT, blood cells from patients have decreased CA at sites of accessibility associated with ILC2 cells at the time of the diagnosis of aGVHD.

From: Type II innate lymphoid cell plasticity contributes to impaired reconstitution after allogeneic hematopoietic stem cell transplantation

Fig. 4

a Isolation of human ILC2s (hILC2s) from peripheral blood of healthy donors. Enrichment of ILC2s is followed by expansion of ILC2s and transdifferentiation for 14–21 days with IL-7 and IL-2 and IL-4, IL-33, IL-25 for hILC2s or IL-12, IL-18, IL-1β for proinflammatory cytokine human ILC2s (pc-hILC2s). b ATAC heatmap of z-score normalized ATAC signal of differential regions (two-sided Wald Test DESeq2), p adj < 0.05) of chromatin accessibility. R1 and R2 indicate replicate numbers. c Enriched motifs identified at differential sites of CA in hILC2 and pc-hILC2s (HOMER). d Average normalized ATAC signal was calculated at differential regions of chromatin accessibility that contain the GATA3 (left) or Tbet (right) binding motif. Dashed lines represent a second replicate. Rep 2 indicates replicate 2 (e) Blood was collected from patients 2–28 days prior to allogeneic HSCT. Post-transplant samples were collected at the time of aGVHD diagnosis (disease) or during a scheduled three-month follow-up (stable). Frozen buffy coats were thawed, and live cells were isolated by magnetic separation prior to snATAC-seq. f Differential analysis of aggregate ATAC signal over gene bodies +/− 2 kb for all genes. Volcano plot depicting log2FoldChange between pre- and post- samples for each gene score and − log10(p adj). Blue dots indicate p adj < 0.05 (two-sided Wald Test (DESeq2), p < 0.05). g Gene ontology (GO) analysis was performed for genes with differential ATAC signals for both the pre- and post-transplant cells. Bar plots indicate enrichment (− log10(p adj)) for the top 5 terms (One-sided Fisher’s Test). h Average normalized ATAC signal at hILC2-associated sites of CAs (Fig. 4b) was calculated per nucleus for each patient sample. Violin plots show the top 90% of the signal. Black dots indicate the mean of each distribution. i Average normalized ATAC signal at pc-hILC2-associated sites of CAs (Fig. 4b) per nucleus for each patient sample. Violin plots show the top 90% of the signal. Black dots indicate the mean of each distribution (***p < 0.001, two-sided t test).

Back to article page