Fig. 7: Partial restoration of wild-type signaling upon stimulation of JAK-STAT mutant T cells.

a, Outline of IFN-β stimulation experiments and analyses in JAK-STAT knockout cells cultured ex vivo. This figure focuses on T cells, while corresponding results for macrophages are shown in Extended Data Fig. 10. b, Grouping of genes based on the observed IFN-β stimulation effects in wild-type and mutant cells. Lines correspond to the mean transcriptional change across all genes in each group. c, Prevalence of the five gene groups from b in each JAK-STAT mutant. Genes with significant but minor differences of stimulation effects between wild-type and mutant cells were not assigned to any group (marked in black). d, Differential gene expression heatmap for IRF9 knockout and wild-type T cells upon IFN-β stimulation, annotated with the grouping of differentially expressed genes (rows). e, Share of genes for which the JAK-STAT mutant effect reverts the IFN-β stimulation effect. This is calculated as the percentage of all genes with an IFN-β stimulation effect in wild-type cells, the total number of which is shown in brackets. f, Mean differential gene expression (log₂FC) upon IFN-β stimulation across 80 core ISGs. Box plots show the full data range, with the box indicating interquartile range and median. g, Share of genes for which the IFN-β stimulation reverts the JAK-STAT mutant effect, relative to all genes with a JAK-STAT mutant effect in unstimulated cells (shown in brackets). MUT, mutant; WT, wild type.