Extended Data Fig. 11: CREM modulates NK cell function through its transcriptional and epigenetic activities.
From: CREM is a regulatory checkpoint of CAR and IL-15 signalling in NK cells
(a) UpSet plots of CREM binding sites in NT, IL-15, and CAR70 NK cells from one representative donor (same donor used to generate CAR70/IL-15 NK cells in Fig. 5b) as analyzed by CREM ChIP-seq; (b) Hallmark gene sets enriched in the CREM targets in NT, IL-15, and CAR70 NK cells and the proportion of genes in each set that was recovered among the targets (n = 3 donors per group); (c) Gene set enrichment analysis (GSEA) enrichment plot of upregulated and downregulated direct targets of CREM (based on CREM ChIP-seq data from CAR70/IL-15 NK cells) in CREM KO vs. CREM WT CAR70/IL-15 NK cells as assessed by bulk RNA-seq (n = 2 donors); (d) Venn diagram of the overlap between 2 donors in CREM ChIP-seq targets in CAR70/IL-15 NK cells that are downregulated (top) or upregulated (bottom) in CREM KO CAR70/IL-15 NK cells; (e) GSEA bar plots of downregulated (top) and upregulated (bottom) pathways (only direct targets of CREM from CREM ChIP-seq in CAR70/IL-15 NK cells were considered in each pathway) in CREM KO CAR70/IL-15 NK cells as assessed by bulk RNA-seq (n = 2 donors); (f) GSEA enrichment plots of upregulated and downregulated pathways (only direct targets of CREM from CREM ChIP-seq in CAR70/IL-15 NK cells were considered in each pathway) in CREM KO vs. CREM WT CAR70/IL-15 NK cells as assessed by bulk RNA-seq (n = 2 donors); (g) Hallmark gene sets reflecting enriched pathways in gained and lost accessible chromatin peaks in CREM KO CAR70/IL-15 NK cells in coculture with UMRC3 tumor cells as analyzed by ATAC-seq (n = 2 donors); GSEA was used for pathway enrichment between gained and lost accessible chromatin peaks; (h) GSEA analyses reflecting enriched Hallmark gene sets in accessible peaks in CREM KO vs. WT CAR70/IL-15 NK cells in coculture with tumor cells; (i) Chromatin accessibility tracks for select genes in CREM WT (top) vs. CREM KO (bottom) CAR70/IL-15 NK cells in coculture with UMRC3 cells from one representative donor; (j) Heatmap and hierarchical clustering of differentially accessible transcription factor motifs in CREM WT and CREM KO CAR70/IL-15 NK cells with UMRC3 tumor cell coculture. Heatmap was generated by merging data from two donors; NES: normalized enrichment score. Statistical comparisons were performed using one-sided hypergeometric test with FDR correction (b), and GSEA modeling one-sided Kolmogorov-Smirnov test with FDR correction (c,e-h).
