Methylation Profile of Single Hepatocytes Derived from Hepatitis B Virus-Related Hepatocellular Carcinoma

Ran Tao,Lanjuan Li,Zhe Yang,Jian Wu,Longyan Jiang,Jiaojiao Xin,Liyuan Zhang,Jing Guo,Wu Zhang,Jun Li,Rakesh K Srivastava

doi:10.1371/journal.pone.0019862

Abstract

BackgroundWith the development of high-throughput screening, a variety of genetic alterations has been found in hepatocellular carcinoma (HCC). Although previous studies on HCC methylation profiles have focused on liver tissue, studies using isolated hepatocytes are rare. The heterogeneity of liver composition may impact the genuine methylation status of HCC; therefore, it is important to clarify the methylation profile of hepatocytes to aid in understanding the process of tumorigenesis.Methods and FindingsThe global methylation profile of single hepatocytes isolated from liver tissue of hepatitis B virus (HBV) related HCC (HBHC) was analyzed using Illumina Infinium Human Methylation27 BeadChips, and combined bisulfite restriction analysis (COBRA) and bisulfite sequencing were used to validate the 20 significant hypermethylated genes identified. In this study, we found many noteworthy differences in the genome-wide methylation profiles of single hepatocytes of HBHC. Unsupervised hierarchical clustering analysis showed that hepatocyte methylation profiles could be classified according to three cell types: hepatocytes of HCC, adjacent hepatocytes and normal hepatocytes. Among the 20 most hypermethylated genes in the hepatocytes of HBHC, 7 novel genes (WNK2, EMILIN2, TLX3, TM6SF1, TRIM58, HIST1H4Fand GRASP) were found to be hypermethylated in HBHC and hypomethylated in paired adjacent liver tissues; these findings have not been reported in previous studies on tissue samples.ConclusionThe genome-wide methylation profile of purified single hepatocytes of HBHC was aided in understanding the process of tumorigenesis, and a series of novel methylated genes found in this study have the potential to be biomarkers for the diagnosis and prognosis of HBHC.

Highlights

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world and is commonly developed from liver cirrhosis that are secondary to viral infection [1]
The genome-wide methylation profile of purified single hepatocytes of HBV related HCC (HBHC) was aided in understanding the process of tumorigenesis, and a series of novel methylated genes found in this study have the potential to be biomarkers for the diagnosis and prognosis of HBHC
To eliminate the effect of different clinical backgrounds, we focused on hepatitis B virus (HBV) related hepatocellular carcinoma (HCC) (HBHC)

Summary

Introduction

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world and is commonly developed from liver cirrhosis that are secondary to viral infection [1]. Epigenetic changes have been reported recently as one of the mechanisms of tumorigenesis, and DNA methylation, which is one of the major epigenetic alterations, has been reported in HCC. In HCC, DNA hypermethylation of candidate genes, including. With the development of high-throughput screening, a variety of genetic alterations has been found in hepatocellular carcinoma (HCC). Previous studies on HCC methylation profiles have focused on liver tissue, studies using isolated hepatocytes are rare. The heterogeneity of liver composition may impact the genuine methylation status of HCC; it is important to clarify the methylation profile of hepatocytes to aid in understanding the process of tumorigenesis

Methods

Results

Discussion

Conclusion