Extended Data Fig. 4: Overlap of the IL-27-induced gene program with signatures from four states of T cell impairment, tolerance and dysfunction.

a, Pearson correlation between wild-type CD4⁺ and CD8⁺ T cells for the 1,201 genes that were differentially expressed between wild-type CD4⁺ T cells stimulated in the presence or absence of IL-27 (FDR < 0.05). b, Expression profile of 118 differentially expressed genes (from a) encoding cell-surface receptors and cytokines are shown as a heat map. c, The IL-27-induced gene program (1,201 genes) was compared to T cell signatures obtained from four states of T cell non-responsiveness. Number of overlapping genes between the IL-27 gene program and each signature is depicted. ***P < 0.001, hypergeometric test: nasal anti-CD3 4.7 × 10⁻²¹; cancer 1.2 × 10^−33; antigen-specific tolerance 4 × 10⁻¹⁴; and viral exhaustion 1.7 × 10⁻²⁶. d, P-value statistics for the significance of the overlap between the IL-27-induced gene program (1,201) and genes induced in other states of T cell non-responsiveness using WilcoxGST and camera. e, Gene signatures from c were sub-sampled and projected onto the CD8⁺ single-cell TIL data. Changes were quantified by randomly selecting decreasing subsets of genes from each signature and calculating the average silhouette width of cells that scored high for the different generated signatures based on Euclidian distance between the principal component values used to generate the t-SNE plot. The top and bottom hinges in the boxplot correspond to the first and third quartiles, and the horizontal line denotes the median (Methods). f, Panels I–V, t-SNE plots of the 588 CD8⁺ single-cell TILs (dots) obtained from wild-type mice bearing B16F10 melanoma tumour. Cells are coloured by their signature score. The score reflects the relative average expression of the genes in the overlap of the IL-27 gene signature with the signatures for each of the indicated states of T cell non-responsiveness. Panel VI is a projection of a signature of the differentially expressed genes between CD8⁺ TILs from wild-type and IL-27RA-knockout mice bearing B16F10 melanomas (Methods). The contour plot marks the region of highly scored cells by taking into account only those cells that have a signature score above the mean score. Cells that had a statistically significant score (adjusted P < 0.05) are marked by a plus symbol (Methods).