GBMs display at least two distinct SE states. (a) Similarity of 30 GSC samples by consensus clustering of 10% most variable regions by H3K27ac signal (n = 14,621). The GSCs clustered into four groups, group 1 GSCs (n = 15), group 2 GSCs (n = 9), group 3 GSCs (n = 2), and group 4 GSCs (n = 4). (b) H3K27ac occupancy around the significantly different SE (FDR-adjusted P < 0.01) between group 1 GSCs and group 2 GSCs (group 1 SEs, n = 597; group 2 SEs, n = 651). (c) H3K27ac activity at the BCAN, HMGA2, and MSRB3 SEs for group 1 GSCs (n = 15) and group 2 GSCs (n = 9). Gene expression from RNA-seq (FPKM, log₂FPKM) of BCAN, HMGA2, and MSRB3 shown on the right (group 1 GSCs, n = 14; group 2 GSCs, n = 9). (d) Change in H3K27ac activity at group 1 and group 2 SEs (FDR-adjusted P < 0.01, left) and change in expression of SE-associated genes (FDR-adjusted P < 0.1, right). (e) Effect of in vitro shRNA knockdown of BCAN, HMGA2, and MSRB3 on growth of group 1 and group 2 GSCs. Cell proliferation experiments were performed in biological replicates with more than four technical replicates per time point. Error bars indicated as standard deviation of four technical replicates. (f) Effect of in vivo shRNA knockdown of BCAN and HMGA2 on survival of mice. A log-rank test was used to calculate significance of survival differences with P values indicated as **, P ≤ 0.001 and ***, P ≤ 0.0001.