Fig. 5: CREM drives NK cell dysfunction through transcriptional and epigenetic reprogramming.
From: CREM is a regulatory checkpoint of CAR and IL-15 signalling in NK cells
a, CREM-binding motif enrichment in CREM ChIP–seq in NT, IL-15, CAR70–IL-15 and CAR70 NK cells (n = 3 donors for NT, IL-15 and CAR70 and one donor for CAR70–IL-15 NK cells; Methods). b, UpSet plot of CREM-binding sites in CAR70–IL-15 NK cells from one representative donor. c, Venn diagram of CREM target genes (within 1 kb vicinity of the transcription start site (TSS) of a gene) in NT, IL-15, CAR70–IL-15 and CAR70 NK cells, with colours referring to the number of targets (blue, lowest to yellow, highest count). d, Hallmark gene sets enriched among the CREM targets in CAR70–IL-15 NK cells and proportion of genes in each set that were recovered among the targets. e, GSEA enrichment plots of upregulated and downregulated Hallmark pathways (only direct targets of CREM from ChIP–seq were considered in each Hallmark pathway) in CREM KO versus WT CAR70–IL-15 NK cells by RNA-seq (n = 2 donors); the red dashed lines indicate the top and bottom of the enrichment score. f, Averaged line graphs and heatmaps showing the ATAC–seq signal intensities surrounding the TSS of all genes in CREM KO and WT CAR70–IL-15 NK cells cultured with or without UMRC3 cells for 24 h (1:1 E/T ratio; n = 2 donors). g, Chromatin accessibility tracks for select genes in CREM WT and KO CAR70–IL-15 NK cells in culture with UMRC3 cells from one representative donor. h, GSEA of transcription factor motif families differentially accessible in CREM KO versus WT CAR70–IL-15 NK cells cultured with UMRC3 cells. i, Motif analyses of top open and closed peaks in CREM KO CAR70–IL-15 NK cells cultured with UMRC3 cells. Motif activities were quantified using ChromVar. j, Schematic of CREM-induction pathways in CAR–IL-15 NK cells, and its mechanism as an activation checkpoint. Created in BioRender. Rafei, H. (2025) https://BioRender.com/9ifmaz6. Statistical comparisons were performed using one-sided Fisher’s method with false-discovery rate (FDR) correction (a), one-sided hypergeometric test with FDR correction (d) or GSEA modelling one-sided Kolmogorov–Smirnov test with FDR correction (e,h).
