Extended Data Fig. 3: RNA-seq and ATAC-seq analysis of CD8+ T cells expanded with IL-2, H9 or H9T. | Nature

Extended Data Fig. 3: RNA-seq and ATAC-seq analysis of CD8+ T cells expanded with IL-2, H9 or H9T.

From: An engineered IL-2 partial agonist promotes CD8+ T cell stemness

Extended Data Fig. 3

a, Volcano plots of RNA-seq data from pre-activated mouse CD8+ T cells that were expanded for 6 days with IL-2, H9, or H9T. Shown are gene expression differences between cells expanded with IL-2 versus H9T (a) or H9 versus H9T (b). Data are representative of two independent experiments. c, Differentially expressed genes for CD8+ T cells expanded for 6 days with H9 versus H9T. Data are representative of two independent experiments. d, GSEA analysis of RNA-seq data compared with endogenous memory versus exhausted populations of cells, with Kolmogorov–Smirnov test. Data are representative of two independent experiments. eg, Pre-activated CD8+ T cells were expanded for 8 days with IL-2, H9, or H9T and then either permeabilized for intracellular staining of TCF-1 (e) and BLIMP-1 (f) or analysed for surface expression of CXCR3 (g). Data are representative of three independent experiments. h, i, Expression of CD62L and TIM-3 in control or Tcf7-deficient CD8+ T cells. CD8+ T cells were isolated from Tcf7 conditional knock-out mice (Tcf7 −/−)) or control littermates (Tcf7fl/fl) and activated for 2 days, rested overnight, followed with expansion in IL-2- or H9T-containing medium. Surface staining of CD62L (h) and TIM-3 (i) is shown. Data are mean ± SEM, n = 3 mice, two-sided t-test. Data are representative of two independent experiments. j, Differentially expressed genes from RNA-seq were aligned to ATAC-seq plots. Data are representative of two independent experiments. k, l, ATAC-seq data from CD8+ T cells expanded for 6 days were aligned with in vivo generated effector, exhausted, and memory populations; the ATAC-seq parts of k are also shown in Fig. 2j with ChIP–seq data. Shown is chromatin accessibility at the Havcr2 (k) and Il10 (l) loci. Data are representative of two independent experiments

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