Fig. 6: Gene re-expression representative of photoreceptor-rich retinoblastoma in MYCN-knockdown cell models.
From: A MYCN-driven de-differentiation profile identifies a subgroup of aggressive retinoblastoma
a Volcano plot shows the MYCN-RB signature of 244 genes derived from the overlap of previously identified MYCN targets and sleuth-modeled MYCN-knockdown expression pattern (Supplementary Data 25). Red dots correspond to significantly regulated MYCN targets (Storey-Tibshirani adjusted p ≤ 0.1). Orange dots correspond to other MYCN targets (Storey-Tibshirani adjusted p > 0.1). Black dots represent non-MYCN targets significantly downregulated in sleuth-modeled MYCN-knockdown expression pattern. b GSEA showing genes overexpressed in cluster A, genes representative of photoreceptor-rich retinoblastoma12,13 and the cluster B signature in the sleuth-modeled MYCN-knockdown expression pattern. Y-axis indicates enrichment score (ES). X-axis shows pathway genes. The dual-colored band represents the degree of correlation in the expression of these genes with MYCN-knockdown (red, MYCN-knockdown; blue, control). c Box plot (left) showing aggregated log1p-transformed transcript tpm values for OPTN expression and combined Storey-Tibshirani-adjusted p in 52 retinoblastomas. OPTN protein expression (right) in MYCN-knockdown retinoblastoma cell lines 48 h after doxycycline treatment. Dot plots show ratios of median fluorescence intensity (MFI) for OPTN in shNTC-expressing (doxycycline-treated cells vs non-treated cells) and shMYCN-expressing (doxycycline-treated cells vs non-treated cells) retinoblastoma from three independent experiments. Data are from 3 independent experiments, with average values (blue bots) indicated and p-values calculated with Welch t-test reported. Representative plots of flow cytometry for OPTN are shown in Supplementary Fig. S7c. Venn diagrams showing the pathways (FDR adjusted p ≤ 0.05) associated with downregulated genes (d) and upregulated genes (e) in MYCN-knockdown retinoblastoma cell lines. The 9 pathways depleted in all 4 cell lines are listed. f List of genes upregulated in both RB1−/− cell lines. Box plots showing the expression scores of the MYCN-RB signatures (g), and upregulated genes (h) after MYCN-knockdown in each of the 3 retinoblastoma clusters. Boxes show upper and lower quantile and median. Whiskers extend from the hinge to ±1.5 times the interquartile range.
