Fig. 6: Loss of IKZF2 hyperinteracting hub coincides with decrease in chromatin activity, gene expression, and architectural stripe in GSI-resistant T-ALL.
From: Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance
a Scatter plot showing log2 fold change of hub interactivity in GSI-resistant DND41 vs. hub interaction counts in GSI-sensitive cells. Dotted lines mark hubs with ≥ 2-fold decrease (“less interacting in GSI resistance”) or increase (“more interacting in GSI resistance”) in interaction counts in GSI-resistant vs. GSI-sensitive DND41 cells. Selected hubs are labeled. b Box-and-whisker plots comparing ATAC-seq (left), H3K27ac ChIP-seq (center), and RNA-seq (right) in hubs that lost interactivity in GSI-resistant cells. Box-and-whisker plots: center line, median; box limits, upper (75th) and lower (25th) percentiles; whiskers, 1.53 interquartile range (n = 118). P-value: two-tailed Wilcoxon rank sum test. c Box-and-whisker plots comparing ATAC-seq (left), H3K27ac ChIP-seq (center), and RNA-seq (right) in hubs that gained interactivity in GSI-resistant cells. Box-and-whisker plots: center line, median; box limits, upper (75th) and lower (25th) percentiles; whiskers, 1.53 interquartile range (n = 99). P-value: two-tailed Wilcoxon rank sum test. d Concordant changes in ATAC-seq, H3K27ac ChIP-seq, H3K27me3 CUT&RUN, and Hi-C over the IKZF2 hub between GSI-sensitive and GSI-resistant DND41 cells. Oligopaint DNA FISH probes are marked with pseudo-color magenta (IKZF2 3’), yellow (gray box-marked IKZF2 promoter), and cyan (IKZF2 5’) below the Ensembl gene track. e IKZF2 normalized RNA-seq reads in GSI-sensitive and GSI-resistant DND41 cells. Each dot represents a biological replicate (n = 3). P-value: two-sided t-test; error bars: ± SEM. f Center and right: cumulative distribution plots of the closest distance between the noted elements in the same cell between 1548 GSI-sensitive and 533 GSI-resistant allelic interactions (Kolmogorov–Smirnov p-value). Inserts show magnified curves at the gray boxes (not drawn to scale). Center: mean (± S.D.) distance in GSI-sensitive and GSI-resistant cells is 0.642 ( ± 0.50) µm, and 0.704 ( ± 0.52) µm, respectively. Right: mean (± S.D.) in GSI-sensitive and GSI-resistant cells is 2.26 ( ± 1.31) µm, and 2.41 ( ± 1.27) µm, respectively. Left: representative cells. g Normalized Hi-C contact maps in GSI-resistant (upper triangle) and GSI-sensitive (lower triangle) DND41 cells at the IKZF2 locus.
