Figure 4. Group-specific TFs define... | Rockefeller University Press

Figure 4.

$Figure 4. Group-specific TFs define group identity. (a) Schematic representation of the methodology used for identification of group-specific TFs. (b) Consensus TFs and group-specific TFs (P < 0.05), with fraction-of-target genes for which the TF potentially plays an important role in regulation (left), fraction of group 1 and group 2 GSC samples that had an SE associated with the TF (middle), and median expression of TFs for both the groups (right). (c) Comparative traces for H3K27ac ChIP-seq and mRNA levels from GSCs in groups 1 and 2 are displayed (two-sided Wilcoxon rank-sum test, P < 6.37 × 10−05, P < 3.05 × 10−06, P < 5.5405 × 10−03 for OLIG1, OLIG2, and RUNX2, respectively). (d) GSCs from group 1 and group 2 were transduced with either a control shRNA sequence that does not target a sequence in the mammalian genome (shCONT) or one of two shRNAs targeting OLIG2 and RUNX2 (shOLIG2 and shRUNX2). Cellular proliferation was measured over a time course using CellTiter-Glo. Cell proliferation experiments were performed in biological replicates with more than four technical replicates per time point. Error bars indicated as standard deviation of four technical replicates. (e) GSCs from group 2 were transduced with either a control shRNA sequence that does not target a sequence in the mammalian genome (shCONT) or one of two shRNAs targeting RUNX2 (shRUNX2) then xenotransplanted into the right frontal lobes of immunocompromised NSG mice. Survival of tumor-bearing mice is displayed by the Kaplan–Meier method. A log-rank test was used to calculate significance of survival differences with P values indicated as **, P ≤ 0.001 and ***, P ≤ 0.0001.$

Group-specific TFs define group identity. (a) Schematic representation of the methodology used for identification of group-specific TFs. (b) Consensus TFs and group-specific TFs (P < 0.05), with fraction-of-target genes for which the TF potentially plays an important role in regulation (left), fraction of group 1 and group 2 GSC samples that had an SE associated with the TF (middle), and median expression of TFs for both the groups (right). (c) Comparative traces for H3K27ac ChIP-seq and mRNA levels from GSCs in groups 1 and 2 are displayed (two-sided Wilcoxon rank-sum test, P < 6.37 × 10⁻⁰⁵, P < 3.05 × 10⁻⁰⁶, P < 5.5405 × 10⁻⁰³ for OLIG1, OLIG2, and RUNX2, respectively). (d) GSCs from group 1 and group 2 were transduced with either a control shRNA sequence that does not target a sequence in the mammalian genome (shCONT) or one of two shRNAs targeting OLIG2 and RUNX2 (shOLIG2 and shRUNX2). Cellular proliferation was measured over a time course using CellTiter-Glo. 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. (e) GSCs from group 2 were transduced with either a control shRNA sequence that does not target a sequence in the mammalian genome (shCONT) or one of two shRNAs targeting RUNX2 (shRUNX2) then xenotransplanted into the right frontal lobes of immunocompromised NSG mice. Survival of tumor-bearing mice is displayed by the Kaplan–Meier method. A log-rank test was used to calculate significance of survival differences with P values indicated as **, P ≤ 0.001 and ***, P ≤ 0.0001.