Fig. 6: Functional modeling of T cell response in human brain slices.

a, b Illustration of the workflow using neocortical slice cultures. c Density plots to quantify the spatial distance between HMOX⁺ and HMOX⁻ IBA1⁺ myeloid cells and tumor (upper plot) and T cells (bottom). P values are determined by non-paired t-test statistics after proving the normal distribution. d Immunostainings of IBA1 (Macrophages and Microglia) in magenta and HMOX1 in cyan, tumor cells are depicted in gray. In the upper panel, the control set with no myeloid cell depletion (M+) is shown, the bottom panel contains the myeloid cell-depleted sections. The experiments and stainings were repeated at least six times for each condition. e Two examples of the reconstruction of cellular relationships. Each point represents a cell as indicated by the legend at the bottom. Lines in orange represent a myeloid-T cell connection (with a distance lower than 100 µm). Tumor-myeloid relationships are illustrated in purple (with a distance lower than 100 µm). The dots of the connected myeloid cells show the expression of HMOX1 by the inner color filling. f ELISA measurements of IL-10 and IL-2. P values are determined by one-way ANOVA (c, e, f, j) adjusted by Benjamini–Hochberg (c, e, f, j) for multiple testing. Data were given as mean ± standard deviation. g Scatterplot of GZMB (y-axis) versus TIM3 protein level (x-axis). Each dot represents a segmented T cell from different experimental conditions as indicated by the legend at the right. Right part: A quantification of the data. P values are determined by one-way ANOVA. h Immunostainings of T cells (CSFE-Tagged, in red) and GZMB, a marker of T cell activation (green). The experiments and stainings were repeated at least six times for each condition.