Extended Data Fig. 4: GBM stem-like states exhibit PRC2 target hypomethylation compared with more differentiated-like cell states.
From: Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states
a, Differentially methylated TSS (±1Kb) between stem-like (NPC-like, n = 175 vs. OPC-like, n = 51; left) and differentiated GBM cellular states (MES-like, n = 201; AC-like, n = 168; right). b, Differential gene expression between AC-like (n = 205) and MES-like cells (n = 232). Genes with an absolute log2(fold-change) > 1 and BH-FDR < 0.05 were defined as differentially expressed (DE). DE genes belonging to immune response pathways are highlighted. c, Q-Q plot comparing the observed -log10P values of all genes used in the differential methylation analysis between GBM cellular states (Fig. 2c) to expected -log10P values. d, Distribution of mean promoter DNAme values in stem-like and differentiated cells for representative differentially methylated PRC2 target genes (Fig. 2c). e, Normalized enrichment scores for gene sets (MSigDB C2) enriched at hypomethylated promoters in NPC/OPC-like (turquoise) or MES-/AC-like (orange) cells (Fig. 2c; n = 15,218 genes). f, Enrichment score plot for SUZ12 targets46 gene set enriched at hypomethylated promoters in NPC-/OPC-like cells (Fig. 2c; n = 15,218 genes). g, Same as (a) for a representative GBM sample (MGH105; NPC-/OPC-like, n = 50 cells; MES-/AC-like, n = 138 cells). Genes belonging to PRC2 targets46 are labelled. h, Mean CpG methylation at promoters of PRC2 targets46 between cell states for each of the 7 GBM samples. Difference in median promoter DNAme at PRC2 targets46 between cell states is indicated. i, Median promoter DNAme at PRC2 targets46 of MES-/AC-like and NPC-/OPC-like cells for each of the 7 GBM samples. j, Mean CpG methylation at ChIP-seq maps50 of EZH2 and SUZ12 between GBM cell states (n = 706 cells). P values were determined by generalized linear model (a, c, g), weighted F-test (b), permutation test (f), two-sided Mann-Whitney U test (i, j). Boxplots represent the median, bottom and upper quartiles, whiskers correspond to 1.5 times the interquartile range.
