Extended Data Fig. 10: Gene set enrichment in tumours with high CD39⁺ CD8⁺ TIL count.

We investigated transcriptomic profiles of whole tumours using bulk RNA sequencing in conjunction with the percentage CD39 expression in CD8⁺ TILs as measured by mass cytometry. Among the 25% most varying genes, we identified ten gene modules by performing hierarchical clustering on the Pearson correlation matrix of the genes. Notably, a cluster whose expression correlated with the frequency of CD39⁺ TILs was enriched in genes related to ‘adaptive immune response’, ‘T cell receptor signalling pathway’ and ‘interferon-gamma mediated signalling pathway’ (see also Supplementary Table 4). Pathways related to peptide presentation by MHC molecules were also overrepresented in this cluster, which contained genes such as class I MHC molecules, TAP1 and TAP2 molecules and proteasome-related genes. n = 46 patients. Data are from at least five independent experiments. Two-sided hypergeometric test.