Skip to main content
. Author manuscript; available in PMC: 2020 Mar 16.
Published in final edited form as: Nat Immunol. 2019 Sep 16;20(10):1335–1347. doi: 10.1038/s41590-019-0480-4

Figure 3: Ptpn2 deletion promotes effector-skewed Slamf6+ and Tim-3+ subpopulations during LCMV infection.

Figure 3:

(a) tSNE projection of single-cell RNA-seq profiles from 7,027 control or Ptpn2-deleted P14+ CD8+ T cells responding to day 30 LCMV Clone 13 infection. Clusters are distinct colors. Representative of one experiment, n = 4 pooled mice. (b) Enrichment of gene signatures in the clusters. Representative of one experiment, n = 4 pooled mice. (c) Plots depicting the inter-cluster density for control or Ptpn2-deleted cells. Representative of one experiment, n = 4 pooled mice. (d) Quantification of the proportion of control or Ptpn2-deleted cells in each cluster. Error bars represent the 95% confidence interval and the dotted line represents the proportion of Ptpn2-deleted cells among all cells projected. Representative of one experiment, n = 4 pooled mice. (e-f) Signature enrichments of co-transferred control and Ptpn2-deleted cells from the (e) progenitor or (f) terminally exhausted clusters. Representative of one experiment, n = 4 pooled mice. (g-h) GSEA curves for significantly enriched signatures in (g) Slamf6+ cells and (h) Tim-3+ cells for bulk RNA-seq 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. (i-j) Row-normalized heat map of effector-associated genes in (i) Slamf6+ cells and (j) Tim-3+ cells for bulk RNA-seq 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. (k) Quantification of frequency of tumor cells killed when co-cultured with control or Ptpn2-deleted CD8+ T cells (2:1 effector: target ratio) isolated from day 8 LCMV Clone 13 infection. Representative of two independent experiments, n = 5 mice. (l) Quantification of frequency of tumor cells killed when co-cultured with Tim-3+ control or Tim-3+ Ptpn2-deleted CD8+ T cells (2:1 effector: target ratio) isolated from day 8 LCMV Clone 13 infection. Representative of two independent experiments, n = 5 mice. Statistical significance was assessed by the two-sided Wilcoxon rank sum test (b, e, f), two-sided binomial test (d), two-sided Kolmogorov-Smirnov test (g-h), and two-sided Student’s paired t-test (k-l) (ns p>.05, * p≤.05, ** p≤.01, *** p≤.001, **** p≤.0001). See also Supplementary Figure 3.