Fig. 6: BBB cells were reshaped in CNSm.

a UMAP visualization of other stromal cells. b Cell percentage of other stromal cells between BM and LM. Main cell differences highlighted with yellow transparent background. c Schematic diagram of the difference in other stromal cells between BM and LM. d Differential gene expression analysis between Endo1 and Endo2. e Representative GO Biological Processes gene sets enriched in Endo1 (upper panel) and Endo2 (lower panel). f mIHC staining of indicated genes to validate differential features of endothelial cells in BM and LM. g Inferred cell trajectory of endothelial cells, colored by endothelial cells (upper panel) and pseudotime (lower panel). h Correlation between the percentage of MKI67 positive cells in cancer cells and endothelial cell subsets (Endo1 and Endo2) in endothelial cells. Samples were colored by tissue types. i mIHC staining of indicated genes to show the spatial relationship between blood vessels with angiogenesis features in BM. j, k UMAP visualization of blood-brain barrier (BBB) associated cells from HBVA, panBM, and our LC-CNSm dataset, colored by cell annotation (j) and datasets (k). The lower legend depicts the data sources and cell types of each cell cluster. The colors of cell clusters indicated their data sources. HBVA, vascular cells from normal samples; panBM, vascular cells from pan-brain parenchymal metastasis patients, LC-CNSm, our dataset. EC endothelial cells, EC.Art arterial endothelial cells, EC.Cap capillary endothelial cells, EC.Ven venous endothelial cells, Fib fibroblasts, Fib.M matrix associated fibroblasts, Fib.P para-vascular fibroblasts, Peri pericytes, SMC smooth muscle cells. l The selective scores of endothelial cells, showing different functional patterns in normal and CNSm conditions, ION ion transporters, ABC ATP-binding cassette transporters, SLC solute carrier transporters, TJ tight junction. m Gene expression values of adhesion molecules and chemokines in endothelial cells of 3 datasets. n Heatmap of gene expression for differentially expressed transporters in BBB cells. o Expression patterns of ABCG2, ABCB1, and solute carriers, SLC3A2, SLC2A1, and SLC38A5 in endothelial cells among three BBB datasets.