Fig. 2: High-resolution map of immune infiltration of brain metastases.
a UMAP projection of tumor-infiltrating cells colored according to cell lineages (n = 9 patients, n = 9 tumor samples, n = 15,415 cells). On top right, a diagram representation of the sample cohort considered for all figure panels is shown. A detailed UMAP projection is shown for T cell and NK and proliferating leukocyte cell clusters. Cytotoxic lymphocyte (CLym), cancer-associated fibroblast (CAF), tumor-associated macrophage (TAM), T cell regulatory (Treg), dendritic (DC), natural killer (NK). b Heatmap showing the relative abundance of tumor-infiltrating cell type, measured as the proportion of cells of the cell type vs. the total of sequenced cells, across tumor samples in the UMAP projection. Some cell types have been aggregated: B cells 1 and 2 into B cells and CLym [T cell + NK], [» T cell] and [»NK] into CLym. Rows represent cell types, sorted by variance (represented on the left, standard deviation from low to high). Columns represent patients, sorted according to the relative abundance of CLym; the primary tumor of origin is shown below. The last column represents all patients together (pancancer, PAN). Top panel shows a stacked bar plot representing the relative abundance of each cell type. Color legend is shown in the cell type labels of the heatmap. c Boxplot representing G1/S and G2/M scores across cell clusters in a. Each boxplot represents a cell distribution, the total of cells represented in each boxplot is found in b PAN column. Statistically significant differences where fold change is >0.1 are shown with an asterisk (P value < 0.05, Mann–Whitney U test). All boxplots indicate median (center line), 25th and 75th percentiles (bounds of box), and minimum and maximum (whiskers). Proliferating (Prolif).
