Fig. 3: HP1α translates Treg-dependent suppressive signals at the chromatin level. | Nature Communications

Fig. 3: HP1α translates Treg-dependent suppressive signals at the chromatin level.

From: Heterochromatic gene silencing controls CD4+ T cell susceptibility to regulatory T cell-mediated suppression in a murine allograft model

Fig. 3

a Differentially-expressed genes (DEG) between WT and HP1α-deficient T cells. b GSEA of KEGG pathways performed using transcriptomes of HP1α-deficient and WT Tconv exposed to Treg. c GO enrichment analyses of genes more highly expressed in WT Tconv than in HP1α KO Tconv exposed to Treg. d GSEA of exhaustion signature genes performed using transcriptomes of HP1α-deficient and WT Tconv exposed to Treg. e Number of differentially-accessible peaks (DAP) between WT and HP1α-deficient T cells. f Relationship between the genes more highly expressed and the genes associated with peaks more open in HP1α KO Tconv than in WT Tconv exposed to Treg. g Expression levels of the 54 genes selected from the intersection in f. Horizontal bars represent the median, and the top and bottom of the boxes the upper and lower quartiles, respectively. The whiskers go from the minimum to the lower quartile and from the upper quartile to the maximum. Statistical significance was calculated using the Pairwise Wilcoxon Rank Sum Test (two-tailed). h GO enrichment analyses of the 54 genes selected from the intersection in f. i Th1 signature enrichment analyses of the 54 genes selected from the intersection in f. j ATAC–seq and RNA-seq tracks at the Il2 locus. k UMAP plot of tumor-infiltrating CD4+ T lymphocytes from melanoma patients28. Cells are colored based on 6 clusters defined using the SNN algorithm. l Relative proportions of CD4+ T cell subsets in patients who responded (R) or not (NR) to immunotherapy. m Teff:Tex ratio in R and NR patients. Statistical significance was calculated using Wilcoxon rank sum Test (two-tailed). Horizontal bars represent the median, and the top and bottom of the boxes the upper and lower quartiles, respectively. The whiskers go from the minimum to the lower quartile and from the upper quartile to the maximum. n GSEA of genes downregulated in HP1α-deficient vs control Tconv performed using transcriptomes of human Teff and Tex. Significance was estimated using rank-based gene permutations. Source data are provided in the Source data file.

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