Fig. 2: IFNG⁺CD8⁺ T cells, IFNG expression and tumor-reactive signaling.

a Proportion of total CD8⁺ T cells positive for IFNG expression per patient. 1958 CD8⁺ T cells in normal tissue adjacent to MSI (green), 7867 CD8⁺ T cells in normal tissue adjacent to MSS CRC (light blue), 11,420 tumoral MSI CD8⁺ T cells (orange) and 17,353 tumoral CD8⁺ T cells (blue) were analyzed. Median (line) quartile 2 and 3 (box), as well as quartiles 1 and 4 (whiskers) are indicated. Pairwise contrasts were calculated with Welch’s two-sided t-test (P < 0.05). b Density plot indicating the distribution of CD8⁺ T cells over the expression level of IFNG in CD8⁺ T cells present in MSI (11,420 cells) and MSS (17,353 cells) tumors. c, d Genetic signaling of co-expression correlation matrices, visualized as unrooted hierarchical distance for MSI (c) and MSS (d), highlighting the different modules characterizing IFNG⁺CD8⁺ T cells. e, f Activation map (binarized expression) for tumor-reactive signaling modules (Supplementary Table S2) for each sub-population of IFNG⁺CD8⁺ T cells in MSI (e) and MSS (f). g Dot plot of IFNG⁺ MAIT cells in MSI and MSS. These cells are a source of TCR-dependent and independent, activation, tissue residency and inflammation genetic signal. h Bar charts of average local alignment identity of TCR alpha and beta chains as well as binarized count of IL17⁺ cells and binarized counts of IFNG⁺ cells (statistical significance calculated using two-sample independent t-test, P value threshold < 0.05). i Joint topographical density plot between TCR activation signaling (y axis) and bystander activation signaling (x axis) for IFNG⁺CD8⁺ T cells including normal MSI (orange left), tumor MSI (orange right), normal MSS (blue left), and tumor MSS (blue right) with arrows indicating the population drifts from normal tissue mean population center (x). Quadrants defined as vertical and horizontal lines were used to calculate Welch test statistical cell quantification differences between MSI and MSS tumor samples (P value threshold < 0.05).