DNA methyltransferase 3B plays a protective role against hepatocarcinogenesis caused by chronic inflammation via maintaining mitochondrial homeostasis

Eriko Iguchi,Haruhiko Takeda,Yoshihide Ueda,Ken Kumagai,Hiroyuki Marusawa,Hiroshi Seno,Yuji Eso,Soichi Arasawa,Atsushi Takai,Takahiro Shimizu

doi:10.1038/s41598-020-78151-2

Eriko Iguchi, Haruhiko Takeda + Show 8 more

Open Access

https://doi.org/10.1038/s41598-020-78151-2

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Abstract

Most hepatocellular carcinomas (HCCs) develop on the basis of chronic hepatitis, but the mechanism of epigenetic regulation in inflammatory hepatocarcinogenesis has yet to be elucidated. Among de novo DNA methyltransferases (DNMTs), DNMT3B has lately been reported to act specifically on actively transcribed genes, suggesting the possibility that it plays a role in the pathogenesis of cancer. We confirmed that DNMT3B isoforms lacking its catalytic domain were highly expressed in HCCs compared with non-tumorous liver tissue. To elucidate the role of DNMT3B in hepatocarcinogenesis, we generated a genetically engineered mouse model with hepatocyte-specific Dnmt3b deletion. The liver of the Dnmt3b-deficient mice exhibited an exacerbation of thioacetamide-induced hepatitis, progression of liver fibrosis and a higher incidence of HCC compared with the liver of the control mice. Whole-genome bisulfite sequencing verified a lower CG methylation level in the Dnmt3b-deficient liver, demonstrating differentially methylated regions throughout the genome. Transcriptome analysis revealed decreased expression of genes related to oxidative phosphorylation in the Dnmt3b-deficient liver. Moreover, primary hepatocytes isolated from the Dnmt3b-deficient mice showed reduced mitochondrial respiratory capacity, leading to the enhancement of oxidative stress in the liver tissue. Our findings suggest the protective role of DNMT3B against chronic inflammation and HCC development via maintaining mitochondrial homeostasis.

Highlights

reactive oxygen species (ROS) Reactive oxygen species RT-qPCR Quantitative real-time polymerase chain reaction TAA Thioacetamide whole-genome bisulfite sequencing (WGBS) Whole-genome bisulfite sequencing
Further analysis of these RNA sequencing (RNAseq) data showed that a large proportion of the expressed DNMT3B in hepatocellular carcinomas (HCCs) tissues did not have exons 21 and/or 22, which encode a C-terminal catalytic domain (Fig. 1B,C)[12,25,26]
We first demonstrated that DNMT3B was highly expressed in the HCC tissue than in the non-tumorous liver tissue but majority was the isoforms lacking catalytic activity, consistent with a previous r eport[19,20,26]

Summary

Introduction

ROS Reactive oxygen species RT-qPCR Quantitative real-time polymerase chain reaction TAA Thioacetamide WGBS Whole-genome bisulfite sequencing. While DNMT1 plays an important role in the maintenance of methylation after DNA replication, DNMT3A and DNMT3B contribute to de novo DNA m ethylation[12,13]. The PWWP domain in DNMTs is important for localizing these enzymes at the heterochromatin region While both DNMT3A and DNMT3B preferentially target CpG-rich sequences, DNMT3A exhibits a higher DNA methylation activity in naked DNA compared with DNMT3B; only DNMT3B can methylate DNA in the nucleosome core region[21]. We focused on the role of DNMT3B in regulating the DNA methylation pattern on the development of chronic hepatitis and HCC. We have generated a novel mouse model in which the Dnmt3b gene is deleted in hepatocytes and have revealed that DNMT3B plays an important role in protecting the liver tissue from the exacerbation of hepatitis and hepatocarcinogenesis

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