Supplementary Figure 3: Ptpn2 deletion does not change the overall transcriptional or epigenetic states of the exhausted subpopulations.
From: PTPN2 regulates the generation of exhausted CD8+ T cell subpopulations and restrains tumor immunity
(a) Heat map of the tSNE clusters in Fig. 3a with representative genes highlighted. Representative of one experiment, n = 4 pooled mice. (b) Expression of indicated genes in individual cells overlaid on the defined clusters. Representative of one experiment, n = 4 pooled mice. (c) Quantification of Slamf6 and Tim-3 expression assessed by flow cytometry on co-transferred control and Ptpn2-deleted cells analyzed by single-cell RNA-seq. Representative of one experiment, n = 4 pooled mice. (d) Plots depicting the intra-cluster density for control or Ptpn2-deleted cells. Representative of one experiment, n = 4 pooled mice. (e) Principal components analysis of transcriptional profiles of co-transferred control and Ptpn2-deleted cells day 8 post LCMV Clone 13 infection. Representative of one experiment, n = 2 mice with n = 2 technical replicates per mouse. (f) Representative GSEA curves for bulk RNA-seq of control and Ptpn2-deleted co-transferred cells day 8 post LCMV Clone 13 infection. LCMV Slamf6 vs. Tim-3 Up top 50 and LCMV Slamf6 vs. Tim-3 Down top 50 signatures are depicted. Representative of one experiment, n = 2 mice with n = 2 technical replicates per mouse. (g) Venn diagrams of ATAC-seq peak overlaps of Tim-3+ and Slamf6+ co-transferred control and Ptpn2-deleted cells day 8 post LCMV Clone 13 infection. Representative of one experiment, n = 2 mice. (h-i) Representative ATAC-seq tracks for (h) Tcf7 and (i) Tox for Tim-3+ and Slamf6+ populations in co-transferred control and Ptpn2-deleted cells day 8 post LCMV Clone 13 infection. For comparison green depicts ATAC-seq tracks from CD8+ T cells day 30 post LCMV Armstrong infection10. Representative of one experiment, n = 2 mice. Statistical significance was assessed by two-sided Student’s paired t-test (c), two-sided Kolmogorov–Smirnov test (f), or hypergeometric test (g) (ns p>.05, * p≤.05, ** p≤.01, *** p≤.001, **** p≤.0001).
