Extended Data Fig. 3: Glioma progression associated with increasing proportions of NPC-like cells.
From: Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas
a. Box plots depict proportions of OPC-like and NPC-like cells in IDH-mutant gliomas, stratified by grade and subtype (n=7 for IDHO grade 2, n=2 for IDHO grade 3, n=5 for IDHA grade 2, n=11 for IDHA grade 3, n=5 for IDHA grade 4). Boxes depict 25th, 50th and 75th percentiles, and whiskers depict extreme values. One-tailed t-test P-value: 0.013 for NPC-like proportions. b. Box plots depict relative proportions of NPC-like versus OPC-like cells, inferred from bulk expression data for IDH-mutant gliomas (TCGA), stratified by grade and subtype (n=81 for IDHO grade 2, n=70 for IDHO grade 3, n=114 for IDHA grade 2, n=104 for IDHA grade 3, n=7 for IDHA grade 4). One-tailed t-test P-value: 0.039; *** defines p<0.001. c. Barplot depicts the ratio of NPC-like to OPC-like cells in scRNA-seq data for six matched pairs of primary and recurrent tumors. Data are presented as mean values +/- SEM. d. UMAP visualization of malignant cells projected onto normal brain cells, as in Figs. 1b and 3a, with heat depicting the proliferation scores of individual malignant cells. e. Trajectory analysis was performed on combined scRNA-seq data for malignant cells and normal OPCs, using the Monocle package. The pseudotime coloring and best-fit trajectory are consistent with progression from normal OPC to OPC-like and then NPC-like malignant cells. f. Plot depicts CNAs for loci subject to CNAs (rows) across single cells (columns) from a second IDH-mutant glioma (OPK438), as in Fig. 3g. Malignant cells are grouped into subclones based on CNAs, and compared to normal cells from the same resection (left). Malignant cell state assignments indicated.
