Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

Tatsuro Tajiri,Toshiyuki Maeda,Hidenobu Soejima,Yoshinao Oda,Kenichi Nishioka,Ryoko Harada,Kenichiro Hata,Kenichi Kohashi,Kazumasa Mitsui,Shigehisa Aoki,Kazuhiko Nakabayashi,Janette Mareska Rumbajan,Ken Higashimoto,Ryota Souzaki,Keiichiro Joh,Tomoaki Taguchi,Hitomi Yatsuki,Tsutomu Saji

doi:10.1186/1471-2407-13-608

Abstract

BackgroundAberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors.MethodsThe methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms.ResultsAmong 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations.ConclusionsOur analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma.

Highlights

Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma
Aberrant methylation of a CpG unit was defined as when the difference of methylation indexes between two samples exceeded 0.15, which was based on the fact that we have previously found that the differences of H19-DMR hypermethylation or KvDMR1 hypomethylation in Beckwith-Wiedemann syndrome (BWS) patients were at least more than 0.15
One possible explanation is that the occurrence of the aberrant hypomethylation at certain DMRs may be a very early and specific event prior to tumor development, there is another possibility that the tumor may induce methylation changes in the adjacent tissues

Summary

Introduction

Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. Hepatoblastoma is the most common primary liver tumor in children, accounting for just over 1% of pediatric cancers and 79% of liver cancers in children under the age of 15 [1]. Most of these tumors are purely derived from epithelium composed exclusively of immature hepatocytic elements, muscle in addition to the elements mentioned above. Mutations or upregulation of the genes involved in embryonic development have been reported. Several imprinted genes, including IGF2, DLK1, PEG3, PEG10, MEG3, and NDN, have been reported to be overexpressed in hepatoblastoma [2]

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