Genome-wide identification of RNA editing in hepatocellular carcinoma

Lin Kang; Xiaoqiao Liu; Zhoulin Gong; Hancheng Zheng; Jun Wang; Yingrui Li; Huanming Yang; James Hardwick; Hongyue Dai; Ronnie T P Poon; Nikki P Lee; Mao Mao; Zhiyu Peng; Ronghua Chen

doi:10.1016/j.ygeno.2014.11.005

Genome-wide identification of RNA editing in hepatocellular carcinoma

Genomics. 2015 Feb;105(2):76-82. doi: 10.1016/j.ygeno.2014.11.005. Epub 2014 Nov 25.

Authors

Lin Kang¹, Xiaoqiao Liu², Zhoulin Gong³, Hancheng Zheng⁴, Jun Wang⁵, Yingrui Li⁶, Huanming Yang⁷, James Hardwick⁸, Hongyue Dai⁹, Ronnie T P Poon¹⁰, Nikki P Lee¹¹, Mao Mao¹², Zhiyu Peng¹³, Ronghua Chen¹⁴

Affiliations

¹ BGI-Shenzhen, Shenzhen, China. Electronic address: kanglinxm@gmail.com.
² Scientific Informatics, MSD R&D (China), Beijing, China. Electronic address: xiao.qiao.liu@merck.com.
³ BGI-Shenzhen, Shenzhen, China; BGI-Tech, BGI-Shenzhen, Shenzhen, China. Electronic address: gongzhuolin@bgitechsolutions.com.
⁴ BGI-Shenzhen, Shenzhen, China; BGI-Tech, BGI-Shenzhen, Shenzhen, China. Electronic address: zhenghch@genomics.cn.
⁵ BGI-Shenzhen, Shenzhen, China; King Abdulaziz University Jeddah, Saudi Arabia; Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address: wangj@genomics.org.cn.
⁶ BGI-Shenzhen, Shenzhen, China; BGI-Tech, BGI-Shenzhen, Shenzhen, China. Electronic address: liyr@genomics.org.cn.
⁷ BGI-Shenzhen, Shenzhen, China; King Abdulaziz University Jeddah, Saudi Arabia; James D. Watson Institute of Genome Science, Hangzhou, China. Electronic address: yanghm@genomics.cn.
⁸ Merck Research Laboratories, Merck & Co., Inc., Boston, MA, USA. Electronic address: james_hardwick@merck.com.
⁹ Merck Research Laboratories, Merck & Co., Inc., Boston, MA, USA. Electronic address: hongyue_dai@merck.com.
¹⁰ Department of Surgery, The University of Hong Kong, Hong Kong. Electronic address: poontp@hkucc.hku.hk.
¹¹ Department of Surgery, The University of Hong Kong, Hong Kong. Electronic address: nikkilee@hku.hk.
¹² Pfizer Oncology, San Diego, CA, USA; Asian Cancer Research Group, Inc., Wilmington, DE, USA. Electronic address: mao_m@yahoo.com.
¹³ BGI-Shenzhen, Shenzhen, China; Guangzhou Key Laboratory of Cancer Trans-Omics Research, BGI-Guangzhou, Guangzhou, China. Electronic address: pengzhiyu@genomics.cn.
¹⁴ Scientific Informatics, MSD R&D (China), Beijing, China; Scientific Informatics, Merck & Co., Inc., Boston, MA, USA. Electronic address: ronghua_chen@merck.com.

PMID: 25462863
DOI: 10.1016/j.ygeno.2014.11.005

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.

Keywords: Hepatocellular carcinoma; RNA-Seq; RNA-editing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Carcinoma, Hepatocellular / genetics*
Computational Biology / methods
Genome*
Genome-Wide Association Study
Humans
Liver Neoplasms / genetics*
RNA Editing*
Sequence Analysis, RNA
Transcriptome*

Associated data

SRA/SRA074279