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.

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