Extended Data Fig. 4: Validation of IFN signature in malignant cells and glioma organoids.
From: Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas
a. Boxplot depicts IFN signature scores (RNA-seq) for grade 2 IDH mutant and WT gliomas (n=35 for IDH mutant and n=5 for IDH WT) with high purity estimates (>80%). Boxes depict 25th, 50th and 75th percentiles, and whiskers depict extreme values. One-tailed t-test P-values: *** defines p<0.001. b. Heatmap shows DNA methylation levels, proliferation scores, and IFN scores (rows) in grade 2 IDH-mutant and grade 2 IDH WT TCGA gliomas (columns) based on the 2016 WHO classification. c. Heatmap depicts the expression of IFN pathway genes (columns) clustered by their expression across malignant cells, immune cell lineages, and oligodendrocytes (rows). This analysis distinguished malignant cell-specific IFN-related genes. d. UMAP visualization of scRNA-seq data compares cells from a glioma organoid (red) and the primary tumor from which it was derived (blue). e. Heatmaps depict the expression of variable genes associated with different cell states (rows) in single cells (columns) grouped by nominal cell identity. The glioma organoids recapitulate cell types and transcriptional programs as seen in the primary tumors.
