Fig. 2: SnRNA-seq reveals a subset of MBEN-cells with similarity to astrocytes.

a UMAP-projection of the integrated dataset (10X snRNA-seq + SMARTseq V2.5 snRNA-seq) shows intratumoral heterogeneity in MBEN (nine samples, n = 29,658 cells). b Heatmap depicting marker genes for indicated cell types of all nine clusters. The first five clusters represent malignant MBEN cells. Clusters 6–9 are identified as perivascular fibroblasts/ pericytes, astrocytic cells, oligodendrocytes/ oligodendroglial precursors and a mixture of microglia and endothelial cells. c InferCNV-analysis using non-malignant cells as a control confirms malignant origin for the vast majority of cells as well as a CNV signature of malignant cells in the astrocytic cluster. d IGV-representation of case MB266 showing pathogenic SNVs within the gene SMO. Three cells with an astrocytic phenotype harbour the same SNV as detected using bulk sequencing. e UMAP projection of the SMARTseq V2.5-dataset without correction for patient batch effects (six samples, n = 1526 cells). Cells were mapped to a reference dataset (Sepp et al., bioRxiv 2021) to identify cells with an astrocytic phenotype. As shown, these clustered close to malignant cells. The zoom-in highlights three cells with an astrocytic phenotype and SMO-mutations. f UMAP projection as in d (six samples, n = 1526 cells). Cells in which the same SNVs as in bulk sequencing were detected are highlighted in red. As shown, three cells within the astrocytic population harbor SNVs. g UMAP projection of the 10X snRNA-seq dataset which was not corrected for patient-associated batch effects (nine samples, n = 28,132 cells). Whereas the majority of cells are clustering according to patient, significant mixing of cells occurs in two clusters (encircled), representing non-malignant cells. Source data are provided as a Source Data file.