Fig. 6: Interactions between effectorness and cytokine condition regulate gene expression.

a Schematic representation of the gene expression interaction model. Effectorness and cytokine conditions were incorporated into a linear model with an interaction term (Methods). Genes were assigned to four groups: genes induced by cytokine-stimulation regardless of effectorness (left panel), genes which correlate with effectorness regardless of cytokine-stimulation (central left panel), and genes which correlate with both effectorness and cytokine-stimulation either independently (central right panel) or through an interaction (right panel). b Plots of gene expression (y axis) as a function of effectorness (x axis), with cells stratified by cytokine condition. Two example genes significantly associated with effectorness regardless of cytokine conditions (top panels) and two example genes with a strong interaction between effectorness and Th17 or iTreg-stimulation (bottom panels). Each dot represents a single-cell. c Protein expression levels for 18 genes associated with effectorness in activated T_N, T_CM, and T_EM and T_EMRA cells regardless of cytokines condition (genes used in the analysis: ACTB, CCL3, CCL5, CTSW, GNLY, GZMA, GZMB, HLA-DPB1, HLA-DQA1, HLA-DRA, HLA-DRB1, HOPX, IFNG, LGMN, LMNA, NFKBIA, TMEM173, TNFRSF18)). Expression values were obtained from a publicly available quantitative proteomics data set (Methods). Significance was calculated using one-way ANOVA (p = 3.42 × 10⁻¹²) and group means were compared using Tukey’s Honest Significant Difference test. Only significant p-values are shown (p < 0.05). Each dot represents an individual gene (n = 18). d Levels of IFNγ and IL-9 protein in Th0 and Th17-stimulated T_N, T_CM, and T_EM cells as assessed by flow cytometry. Representative cytometry histograms of IFNγ and IL-9 expression (left panels) and mean fluorescence intensity (MFI) of cytokine-expressing cells (right panels). P-values were calculated using one-way ANOVA. Each dot represents a biologically independent sample. Number of samples: 6 (IFNγ) and 4 (IL-9). Boxplot centers represent median values, while the boxplot bounds represent the 25% and 75% quantiles. Boxplot whiskers represent the 25% quantile − 1.5 × interquartile range (IQR) and the 75% quantile + 1.5 × IQR, respectively. Source data are provided as a Source Data file.