Abstract 4517: Epigenome landscape of human normal purified hepatocytes: analysis by the International Human Epigenome Consortium (IHEC)
Authors: Arai Eri , Miura Fumihito , Totoki Yasushi , Yamashita Satoshi , Tian Ying , Gotoh Masahiro , Ojima Hidenori , Nakagawa Hiroyuki , Takahashi Yoriko , Nakamura Hiromi , Hama Natsuko , Kato Mamoru , Kimura Hiroshi , Suzuki Yutaka , Ito Takashi , Shibata Tatsuhiro , Kanai Yae 
Published: July 2016

As a research group participating in the International Human Epigenome Consortium, we have performed whole-genome bisulfite sequencing (WGBS) using post-bisulfite adaptor tagging, chromatin immunoprecipitation (ChIP)-sequencing (seq), RNA-seq and whole-genome sequencing (WGS) using normal hepatocytes purified from partial hepatectomy specimens of 6 Japanese patients without hepatitis virus infection, chronic liver disease or hepatocellular carcinoma.

DNA methylation profiles such as low CpG methylation levels in the region 200 bp upstream from the transcription start site (TSS200), the first coding exon and CpG island were obtained. CHH methylation was observed more frequently on the anti-sense strands than on the sense strands in the 5’ untranslated region (UTR), first intron, gene body and 3’ UTR. non-CpG methylation was inversely correlated with gene expression levels.

Personal differentially methylated regions (pDMRs) were observed less frequently in TSS200, the first coding exon, TSS1500, and CpG island where CpG methylation levels were low, indicating that the regions important for expression regulation may be protected from personal variations of CpG methylation. Histone modification profiles of pDMRs differed considerably among samples. pDMRs were observed around the TSSs of genes whose expression levels are reportedly regulated by CpG methylation, such as LRP1B, RASGRF2 and TFF1. pDMRs were located more frequently in the vicinity of loci showing genetic variation (single-nucleotide variations [SNVs] and/or insertions/deletions [indels]) than on all autosomes. Although further study is needed to clarify the molecular background of such genome-epigenome interaction, we speculate that SNVs and indels may affect the binding of non-coding RNAs and/or protein complexes that induce histone modification or CpG methylation alterations around the SNV and indel loci. MetaCore pathway analysis revealed that genes showing both genetic (SNVs and indels) and epigenetic (pDMRs) variations in multiple samples were significantly accumulated in signaling pathways participating in hepatocyte function and disease susceptibility.

Our data suggest that genetic variations may induce epigenetic variations and generate individual differences in the phenotypes of normal hepatocytes and/or determine disease susceptibility through variations in expression. After accumulation of numerous reference epigenome profile data in the IHEC database, comparison between IHEC data for normal cells and cancer cells may facilitate the accurate identification of cancer-specific epigenome profiles, which would be indispensable to the development of biomarkers and molecular targeted therapies.

Citation Format: Eri Arai, Fumihito Miura, Yasushi Totoki, Satoshi Yamashita, Ying Tian, Masahiro Gotoh, Hidenori Ojima, Hiroyuki Nakagawa, Yoriko Takahashi, Hiromi Nakamura, Natsuko Hama, Mamoru Kato, Hiroshi Kimura, Yutaka Suzuki, Takashi Ito, Tatsuhiro Shibata, Yae Kanai. Epigenome landscape of human normal purified hepatocytes: analysis by the International Human Epigenome Consortium (IHEC). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4517.