Fig. 2: Transcriptional activation of RCOR2 by neo-TADs in RELA ependymoma. | Nature Communications

Fig. 2: Transcriptional activation of RCOR2 by neo-TADs in RELA ependymoma.

From: 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Fig. 2: Transcriptional activation of RCOR2 by neo-TADs in RELA ependymoma.The alternative text for this image may have been generated using AI.

a Chromatin contacts in a reconstructed ZFTA tumor genome (sample 4EP53) including the tandem duplication that leads to the ZFTA-RELA fusion (chr1:63532174-65429788, green boxes). Solid black boxes show TADs identified by applying TopDom to the Hi-C data mapped on to the reconstructed tumor genome, including a neo-TAD that spans the DNA breakpoint. b, c Reconstructed genomic locus containing the ZFTA-RELA fusion gene in the ZFTA ependymoma sample 4EP53 (b) and 11EP22 (c). The black boxes/ triangles indicate TADs reported by TopDom when applied to the reconstructed tumor genome. A neo-TAD is identified that spans the DNA breakpoint and places RCOR2 into a new regulatory environment. d Boxplot of RCOR2 gene expression across ependymoma groups using Affymetrix gene expression data (n = 393). RCOR2 is significantly upregulated in ZFTA tumors (ZFTA vs all other tumor classes limma p-val.: 7.62e−27). The center line, box limits, whiskers, and points indicate the median, upper/lower quartiles, 1.5× interquartile range and outliers, respectively. e Correlation between RCOR2 and ZFTA in ZFTA (left side, n = 76, cor = 0.663, p-val = 6.93e−11) and PFA ependymoma samples (right side, n = 200, cor=0.336 p-val = 1.13e−06). f–i shRNA time-course knock-down experiments in ZFTA (EP1NS) and PFA (EPD210FH) ependymoma cell lines using a scrambled control and two shRNA constructs each targeting either RCOR2 in EP1NS (f), RCOR2 in EPD210FH (g), LSD1 in EP1NS (h) and LSD1 in EPD210FH (i). All constructs are GFP tagged and GFP positive cells are sorted by FACS. For panel (f), error bars represent mean ± SD for n = 3 independent experiments (two-tailed paired t test p-val = 0.0018 and 0,0046; shRCOR#1 and shRCOR2#2, respectively). For panels (g–i), normalized data represent mean from n = 2 independent experiments per cell line. j, k Dose–response curves of single-compound treatment with ORY-1001 (j) or Entinostat (k) of ZFTA (EP1NS, BT165 and ST-1) and PFA (EPD210FH, BT214) ependymoma spheroids over a 72-h time-course using Celltiter-Glo cell viability assays. For each sample the results are presented as percentage of the Luminescence signal from control condition (i.e. water for ORY-1001 and DMSO for Entinostat). Error bars represent mean ± SD for n = 3 independent experiments (one-way ANOVA test p-val < 0,0001).

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