Supplementary Figure 4 from Definition of the Landscape of Promoter DNA Hypomethylation in Liver Cancer
PDF file - 1468K, Methylation and expression of MMP2, NUPR1, S100A5, and PLAU in NorHep treated with 5-azaCdR at 1.0 �M concentration. (A) Global methylation level estimated using luminometric methylation assay (LUMA) in NorHep treated with 5-azaCdR for 5 or 20 days. LUMA assay and treatment with 5-azaCdR were performed as described in the Supplementary Methods. (B) Fold change in relative gene expression as measured by QPCR in cells treated with 5-azaCdR for 5 days except for NUPR1 where an increase in expression was observed after 20 days of treatment compared to the control cells cultured in the absence of the drug. (C) State of methylation as determined by pyrosequencing in the promoter region of MMP2, NUPR1, S100A5, and PLAU in NorHep treated with 5-azaCdR for 5 days or 20 days (NUPR1). Methylation level was estimated in the same CpGs as in the experiment with HepG2 cells after MBD2 depletion. All results represent mean � S.D. of two or three independent experiments, measured in triplicate ***P < 0.001, **P <0.01, *P <0.05. (D) Correlation between the extent of promoter demethylation and gene induction for 230 genes epigenetically induced in HCC patients. Each point in the scatter plot represents a differential methylation and differential expression for every gene in each HCC patient. For both differential methylation and differential expression, we used the log-fold change of the microarray probe that the most significantly differentiated between cancer and normal for the given gene. The correlation is negative with Pearson's correlation coefficient -0.1 (P <0.0019).