title: Genome-wide identification of RNA editing in hepatocellular carcinoma.
abstract: We did whole-transcriptome sequencing and whole-genome sequencing on nine pairs of Hepatocellular carcinoma (HCC) tumors and matched adjacent tissues to identify RNA editing events. We identified mean 26,982 editing sites with mean 89.5% canonical A→G edits in each sample using an improved bioinformatics pipeline. The editing rate was significantly higher in tumors than adjacent normal tissues. Comparing the difference between tumor and normal tissues of each patient, we found 7 non-synonymous tissue specific editing events including 4 tumor-specific edits and 3 normal-specific edits in the coding region, as well as 292 edits varying in editing degree. The significant expression changes of 150 genes associated with RNA editing were found in tumors, with 3 of the 4 most significant genes being cancer related. Our results show that editing might be related to higher gene expression. These findings indicate that RNA editing modification may play an important role in the development of HCC.
authors.affiliation: BGI-Shenzhen, Shenzhen, China. Electronic address: kanglinxm@gmail.com.
authors.forename: Lin
authors.initials: L
authors.lastname: Kang
authors.affiliation: Scientific Informatics, MSD R&D (China), Beijing, China. Electronic address: xiao.qiao.liu@merck.com.
authors.forename: Xiaoqiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, China; BGI-Tech, BGI-Shenzhen, Shenzhen, China. Electronic address: gongzhuolin@bgitechsolutions.com.
authors.forename: Zhoulin
authors.initials: Z
authors.lastname: Gong
authors.affiliation: BGI-Shenzhen, Shenzhen, China; BGI-Tech, BGI-Shenzhen, Shenzhen, China. Electronic address: zhenghch@genomics.cn.
authors.forename: Hancheng
authors.initials: H
authors.lastname: Zheng
authors.affiliation: BGI-Shenzhen, Shenzhen, China; King Abdulaziz University Jeddah, Saudi Arabia; Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address: wangj@genomics.org.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China; BGI-Tech, BGI-Shenzhen, Shenzhen, China. Electronic address: liyr@genomics.org.cn.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, China; King Abdulaziz University Jeddah, Saudi Arabia; James D. Watson Institute of Genome Science, Hangzhou, China. Electronic address: yanghm@genomics.cn.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: Merck Research Laboratories, Merck & Co., Inc., Boston, MA, USA. Electronic address: james_hardwick@merck.com.
authors.forename: James
authors.initials: J
authors.lastname: Hardwick
authors.affiliation: Merck Research Laboratories, Merck & Co., Inc., Boston, MA, USA. Electronic address: hongyue_dai@merck.com.
authors.forename: Hongyue
authors.initials: H
authors.lastname: Dai
authors.affiliation: Department of Surgery, The University of Hong Kong, Hong Kong. Electronic address: poontp@hkucc.hku.hk.
authors.forename: Ronnie T P
authors.initials: RT
authors.lastname: Poon
authors.affiliation: Department of Surgery, The University of Hong Kong, Hong Kong. Electronic address: nikkilee@hku.hk.
authors.forename: Nikki P
authors.initials: NP
authors.lastname: Lee
authors.affiliation: Pfizer Oncology, San Diego, CA, USA; Asian Cancer Research Group, Inc., Wilmington, DE, USA. Electronic address: mao_m@yahoo.com.
authors.forename: Mao
authors.initials: M
authors.lastname: Mao
authors.affiliation: BGI-Shenzhen, Shenzhen, China; Guangzhou Key Laboratory of Cancer Trans-Omics Research, BGI-Guangzhou, Guangzhou, China. Electronic address: pengzhiyu@genomics.cn.
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Peng
authors.affiliation: Scientific Informatics, MSD R&D (China), Beijing, China; Scientific Informatics, Merck & Co., Inc., Boston, MA, USA. Electronic address: ronghua_chen@merck.com.
authors.forename: Ronghua
authors.initials: R
authors.lastname: Chen
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D016678:Genome; D055106:Genome-Wide Association Study; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D017393:RNA Editing; D017423:Sequence Analysis, RNA; D059467:Transcriptome
keywords: Hepatocellular carcinoma; RNA-Seq; RNA-editing