Fig. 7: Nr4a-deficient thymocytes escaping deletion acquire an Ag-dependent anergic program in the thymus. | Nature Communications

Fig. 7: Nr4a-deficient thymocytes escaping deletion acquire an Ag-dependent anergic program in the thymus.

From: Nr4a1 and Nr4a3 redundantly control clonal deletion and contribute to an anergy-like transcriptome in auto-reactive thymocytes to impose tolerance in mice

Fig. 7

a-d Panels depict Ikzf(a, b) and Nt5e/CD73 (c, d) expression in our RNAseq data (a, c) and VISION CITEseq (b, d) data as described earlier. RPKM graphs a, c show transcript abundance in CD69hi Va2 + SP4 thymocytes of either WT OT-II or DKO OT-II donor genotypes from chimeras depicted in 3a. (Supplementary Data 1a depicts p value and fdr for all pairwise comparisons across sample types, GSE235101). UMAP data (b, d) from publicly available VISION thymus CITEseq interface. e–g Representative plots (e) depict gating to identify HELIOS+ cells among SP4 Foxp3- OT-II thymocytes of each genotype from RIPmOVA and WT host chimeras (see 3a schematic). Graphs depict % (f) and absolute number (g) of HELIOS+ cells as gated in (e) +/- SEM. h. Representative plots depict gating to identify CD73+ cells among SP4 Foxp3- OT-II thymocytes of each genotype from RIPmOVA and WT host chimeras (see 3a schematic). Quantification is shown in Supp Fig 9a, b. i–n Representative plots depict gating among SP4 (i), and SP8 (l) subsets to identify HELIOS + CD73+ cells of each donor genotype from experimental DKO:WT polyclonal chimeras and from control WT:WT polyclonal chimeras (see 1c schematic). j, m Quantification of % CD73/HELIOS gates from each donor genotype as shown in (i, l). Lines connect donors in the same chimera. k, n Quantification of ratio of donor genotypes CD45.2/CD45.1 from each chimera among CD73/HELIOS in panels i, l Statistical tests: f one way ANOVA with pre-specified comparisons corrected for by Sidak test. g one way ANOVA with Tukey’s multiple hypothesis test. j, k, m, n, unpaired, parametric, two-tailed t-test, assume equal SD. Graphs in f, g, depict N = 7 WT host and N = 6 RIPmOVA host chimeras – biological replicates. Graphs in j, k, m, n depict N = 3 WT:WT control chimeras and N = 4 DKO:WT chimeras – biological replicates and are representative of 3 independent sets of chimeras. Source data are provided as a Source Data file.

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