Extended Data Fig. 8: Validation of control vs GBM-associated immune cells assessed by single-cell RNA-Seq and mass cytometry.
From: Multiomic spatial landscape of innate immune cells at human central nervous system borders
a. UMAP color-coded for the expression of the indicated modules scores. Module scores are based on the Mann-Whitney U statistic. The cell cycle module genes are published27. b. UMAP color-coded for DAM and myeloid cell homing module expression28,29. Module scores are based on the Mann-Whitney U statistic. c. Marimekko chart showing the integration results of the present dataset with published data43. Cluster assignments of the present data were transferred on the Antunes et al dataset. Asterisks indicate statistical significance from one-sided hypergeometric tests with Benjamini–Hochberg adjustment for multiple testing. *p < 0.05; **p < 0.01; ***p < 0.001. d. Single-cell heatmap showing the expression of the top 20 cluster markers with selected genes shown on the left. Cluster colors are consistent with panel b. The color scale represents Pearson’s residuals from a regularized negative-binomial regression. e. Spatial plot of hypoxia (red) and adjacent necrosis (orange) analyzed with Nanostring CosMX. The white arrow indicates a spatial trajectory shown in panel f. The shown data is representative of 8 analyzed fields from 2 glioblastoma samples. f. Spatial trajectory heatmap showing the smoothed gene expression along the trajectory from figure panel e with representative genes on the right. g. Spider visualization of mass cytometry data from 2,439 CD45+ glioblastoma-derived cells color-coded for clusters. Cell type assignment is based on published cell type marker expression. CD45- cells are labeled as ‘others’. h. Spider presentation (top) and Marimekko chart (bottom) showing the distribution of diagnoses per cluster. i. Protein expression single-cell heatmap of the cells in panel e. The color scale represents Pearson’s residuals from a regularized negative-binomial regression. j. Dot-line plot depicting the expression of selected proteins between tumor-associated and control CAMs in C7 from panel e (top) and microglia from C1 (bottom). The indicated p values were calculated using unpaired two-sided t-tests with Benjamini–Hochberg multiple testing adjustment. Each symbol represents one cell. Medians are indicated.
