Extended Data Fig. 4: PGE₂ rewires metabolism of TILs.

a-b, Gene set enrichment analysis (GSEA) enrichment plot for a, mitochondrial gene expression and b, fatty acid metabolic process in repeatedly activated CD8⁺ T cells after 24 h of PGE₂. The y-axis represents enrichment score and the x-axis shows genes (vertical black lines) represented in the pathways. The coloured band at the bottom represents the degree of correlation of the expression of these genes (red for a high gene expression and blue for a low gene expression). c, Schematic representation of the systems biology approach used to reconstruct metabolic models and infer fluxes and metabolic states consistent with the gene expression profile of repeatedly activated CD8⁺ T cells and TILs treated with PGE₂ for 24 h (created with BioRender.com). d, Heatmap representation of deregulation of metabolic fluxes (row) inferred from the generated metabolic model upon PGE₂ treatment in repeatedly activated CD8⁺ T cells (n = 3). e, Violin plot representation of reaction rate fold changes associated by metabolic subsystems upon PGE₂ treatment in repeatedly activated CD8⁺ T cells (n = 3). f, Representative map of tricarboxylic acid cycle and electron transport chain (ETC) reactions, coloured by flux deregulation (blue for downregulated and red for upregulated inferred state). g-h, Violin plot representation of metabolic task (MT) derived for g, cell growth and h, energy and reactive oxygen species enrichment analysis using gene expression data (blue) or the inferred fluxes (red) in repeatedly activated CD8⁺ T cells upon PGE₂ treatment (n = 3). i, Mitochondrial ROS levels in CD8⁺ TILs in response to PGE₂ (n = 6). Data are presented as the mean ± S.D. Statistical comparisons were performed using paired two-tailed t test. Independent biological samples were used with exact numbers of biological replicates listed in each panel.