title: Global analysis of DNA methylation in hepatocellular carcinoma by a liquid hybridization capture-based bisulfite sequencing approach.
abstract: BACKGROUND
  Epigenetic alterations, such as aberrant DNA methylation of promoter and enhancer regions, which lead to atypical gene expression, have been associated with carcinogenesis. In hepatocellular carcinoma (HCC), genome-wide analysis of methylation has only recently been used. For a better understanding of hepatocarcinogenesis, we applied an even higher resolution analysis of the promoter methylome to identify previously unknown regions and genes differentially methylated in HCC.
  
  
  RESULTS
  Optimized liquid hybridization capture-based bisulfite sequencing (LHC-BS) was developed to quantitatively analyze 1.86 million CpG sites in individual samples from eight pairs of HCC and adjacent tissues. By linking the differentially methylated regions (DMRs) in promoters to the differentially expressed genes (DEGs), we identified 12 DMR-associated genes. We further utilized Illumina MiSeq combining the bisulfite sequencing PCR approach to validate the 12 candidate genes. Analysis of an additional 78 HCC pairs on the Illumina MiSeq platform confirmed that 7 genes showed either promoter hyper-methylation (SMAD6, IFITM1, LRRC4, CHST4, and TBX15) or hypo-methylation (CCL20 and NQO1) in HCC.
  
  
  CONCLUSIONS
  Novel methylome profiling provides a cost-efficient approach to identifying candidate genes in human HCC that may contribute to hepatocarcinogenesis. Our work provides further information critical for understanding the epigenetic processes underlying tumorigenesis and development of HCC.
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Fei
authors: F
authors: Gao
authors: Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Huifang
authors: H
authors: Liang
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Hanlin
authors: H
authors: Lu
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Junwen
authors: J
authors: Wang
authors: Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Meng
authors: M
authors: Xia
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Zhimei
authors: Z
authors: Yuan
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Yu
authors: Y
authors: Yao
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Tong
authors: T
authors: Wang
authors: Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Xiaolong
authors: X
authors: Tan
authors: The Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Freeman Road, High Heaton, Newcastle upon Tyne, NE7 7DN UK.
authors: Arian
authors: A
authors: Laurence
authors: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Hua
authors: H
authors: Xu
authors: Translational Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Jingjing
authors: J
authors: Yu
authors: Translational Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Wei
authors: W
authors: Xiao
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Wei
authors: W
authors: Chen
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Ming
authors: M
authors: Zhou
authors: Science & Technology Department, BGI-Shenzhen, Shenzhen, 518083 Guangdong China.
authors: Xiuqing
authors: X
authors: Zhang
authors: Division of Gastroenterology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Qian
authors: Q
authors: Chen
authors: Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China.
authors: Xiaoping
authors: X
authors: Chen
keywords: DNA methylation; Hepatocellular carcinoma; Liquid hybridization capture-based bisulfite sequencing