GSE111420
The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes
Background: C3H mice have been frequently used in cancer studies as animal models  of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC).  Epigenetic modifications, including DNA methylation, are among pivotal control  mechanisms of gene expression leading to carcinogenesis. Although information on  somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet  to be clarified. Methods: We performed next generation sequencing-based analysis of DNA  methylation and microarray analysis of gene expression to explore genes regulated by  DNA methylation. Overlaying these data, we selected cancer-related genes whose  expressions are inversely correlated with DNA methylation levels in the associated  differentially methylated regions (DMRs) located around transcription start sites (TSSs)  (promoter DMRs). We further assessed mutuality of the selected genes for expression  and DNA methylation in human HCC using the Cancer Genome Atlas (TCGA)  database. Results: We obtained data on genome-wide DNA methylation profiles in the normal  and tumor livers of C3H mice. We identified promoter DMRs of genes which are  reported to be related to cancer and whose expressions are inversely correlated with  the DNA methylation, including Mst1r, Slpi and Extl1. The association between DNA  methylation and gene expression was confirmed using a DNA methylation inhibitor 5-  aza-2'-deoxycytidine (5-aza-dC) in Hepa1c1c7 cells and Hepa1-6 cells.  Overexpression of Mst1r in Hepa1c1c7 cells illuminated a novel downstream pathway  via IL-33 upregulation. Database search indicated that gene expressions of Mstr1 and  Slpi are upregulated and the TSS upstream regions are hypomethylated also in human  HCC. These results suggest that DMRs, including those of Mst1r and Slpi, are  involved in liver tumorigenesis in C3H mice, and also possibly in human HCC. Conclusions: Our study clarified genome wide DNA methylation landscape of C3H  mice. The data provide useful information for further epigenetic studies of mice models  of HCC. The present study particularly proposed novel DNA methylation-regulated  pathways for Mst1r and Slpi, which may be applied not only to mouse HCC but also to  human HCC. Overall design: Examination of 6 mice liver DNA methylation modifications (normal liver tissue 3 samples vs liver tumor tissue 3 samples)