Fig. 2: OTX-2002 increases epigenetic modification and reduces MYC expression. | Nature Communications

Fig. 2: OTX-2002 increases epigenetic modification and reduces MYC expression.

From: Targeted transcriptional downregulation of MYC using epigenomic controllers demonstrates antitumor activity in hepatocellular carcinoma models

Fig. 2

A Western blot quantification of HA-MYC-EC-E1 and HA-MYC-EC-E2 proteins. Results are from one independent experiment (n = 2 technical replicates) and were repeated once. B DNA methylation at the MYC-EC-E1 target site. Results are from one independent experiment (n = 6 technical replicates) and were repeated once. C ChIP-qPCR analysis at the MYC-EC-E2 target site (24 h). Results are from one independent experiment (n = 2 technical replicates) and were repeated once. D Time course results from one independent experiment (n = 6 technical replicates for untreated MYC mRNA and cell viability, n = 5 technical replicates for untreated MYC protein, n = 3 technical replicates for NC mRNA and OTX-2002 treated MYC mRNA and cell viability, n = 2 technical replicates for untreated MYC methylation, NC mRNA and OTX-2002 treated MYC protein and methylation) and were repeated once. E Time course results from one independent experiment (n = 6 technical replicates for untreated MYC mRNA and cell viability, n = 4 technical replicates for untreated MYC protein, n = 3 technical replicates for NC mRNA and OTX-2002 treated MYC mRNA and cell viability, n = 2 technical replicates for untreated MYC promoter methylation, NC mRNA and OTX-2002 treated MYC protein and promoter methylation) and were repeated once. F Evaluation of single treatment over 15 days. Results are from one independent experiment (n = 3 technical replicates) and were repeated once. G GSEA results when tested against all Hallmark gene sets in PHH and Hep 3B cells after 24-h treatment. NES indicates directional association between RNA-seq data and gene set (negative=inhibition); −log10(padj) indicates significance of association with a threshold of padj < 0.01. DESeq2 identified differentially expressed genes using Wald test statistics and the Benjamini-Hochberg (BH) method to correct for multiple testing. The sorted test statistics were input to fGSEA with the Hallmark gene set (MSigDB). A permutation test of the input list estimated significant enrichment and the BH method accounted for multiple testing with a significant adjusted p < 0.05. Results are from one independent experiment and were repeated once. For all relevant panels error bars represent mean ± standard error of the mean (SEM). Source data are provided as a Source Data file.

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