Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma

Surbhi Jain, Sitong Chen, Kung Chao Chang, Yih Jyh Lin, Chi Tan Hu, Batbold Boldbaatar, James P. Hamilton, Selena Y. Lin, Ting Tsung Chang, Shun Hua Chen, Wei Song, Stephen J. Meltzer, Timothy M. Block, Ying Hsiu Su

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Hypermethylation of the glutathione S-transferase π 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100% to 0%. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite-PCR sequencing. We found that the 5′ region of the position -48 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 3′ region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 3′ region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 5′ region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 3′ region, we found that the methylation of the 5′-end of the GSTP1 promoter was significantly more specific than that of the 3′-end (97.1% vs. 60%, p<0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8% of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC.

Original languageEnglish
Article numbere35789
JournalPloS one
Volume7
Issue number4
DOIs
Publication statusPublished - 2012 Apr 20

Fingerprint

Methylation
hepatoma
Genetic Markers
Liver
methylation
Hepatocellular Carcinoma
Genes
genetic markers
DNA
Genetic Promoter Regions
liver
Tissue
promoter regions
genes
bisulfites
hepatitis
Assays
Polymerase Chain Reaction
Hepatitis
Liver Diseases

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Jain, Surbhi ; Chen, Sitong ; Chang, Kung Chao ; Lin, Yih Jyh ; Hu, Chi Tan ; Boldbaatar, Batbold ; Hamilton, James P. ; Lin, Selena Y. ; Chang, Ting Tsung ; Chen, Shun Hua ; Song, Wei ; Meltzer, Stephen J. ; Block, Timothy M. ; Su, Ying Hsiu. / Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma. In: PloS one. 2012 ; Vol. 7, No. 4.
@article{82ce2a7e87c34940a2ce2bfebfb09219,
title = "Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma",
abstract = "Hypermethylation of the glutathione S-transferase π 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100{\%} to 0{\%}. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite-PCR sequencing. We found that the 5′ region of the position -48 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 3′ region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 3′ region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 5′ region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 3′ region, we found that the methylation of the 5′-end of the GSTP1 promoter was significantly more specific than that of the 3′-end (97.1{\%} vs. 60{\%}, p<0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8{\%} of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC.",
author = "Surbhi Jain and Sitong Chen and Chang, {Kung Chao} and Lin, {Yih Jyh} and Hu, {Chi Tan} and Batbold Boldbaatar and Hamilton, {James P.} and Lin, {Selena Y.} and Chang, {Ting Tsung} and Chen, {Shun Hua} and Wei Song and Meltzer, {Stephen J.} and Block, {Timothy M.} and Su, {Ying Hsiu}",
year = "2012",
month = "4",
day = "20",
doi = "10.1371/journal.pone.0035789",
language = "English",
volume = "7",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "4",

}

Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma. / Jain, Surbhi; Chen, Sitong; Chang, Kung Chao; Lin, Yih Jyh; Hu, Chi Tan; Boldbaatar, Batbold; Hamilton, James P.; Lin, Selena Y.; Chang, Ting Tsung; Chen, Shun Hua; Song, Wei; Meltzer, Stephen J.; Block, Timothy M.; Su, Ying Hsiu.

In: PloS one, Vol. 7, No. 4, e35789, 20.04.2012.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma

AU - Jain, Surbhi

AU - Chen, Sitong

AU - Chang, Kung Chao

AU - Lin, Yih Jyh

AU - Hu, Chi Tan

AU - Boldbaatar, Batbold

AU - Hamilton, James P.

AU - Lin, Selena Y.

AU - Chang, Ting Tsung

AU - Chen, Shun Hua

AU - Song, Wei

AU - Meltzer, Stephen J.

AU - Block, Timothy M.

AU - Su, Ying Hsiu

PY - 2012/4/20

Y1 - 2012/4/20

N2 - Hypermethylation of the glutathione S-transferase π 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100% to 0%. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite-PCR sequencing. We found that the 5′ region of the position -48 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 3′ region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 3′ region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 5′ region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 3′ region, we found that the methylation of the 5′-end of the GSTP1 promoter was significantly more specific than that of the 3′-end (97.1% vs. 60%, p<0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8% of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC.

AB - Hypermethylation of the glutathione S-transferase π 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100% to 0%. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite-PCR sequencing. We found that the 5′ region of the position -48 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 3′ region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 3′ region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 5′ region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 3′ region, we found that the methylation of the 5′-end of the GSTP1 promoter was significantly more specific than that of the 3′-end (97.1% vs. 60%, p<0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8% of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC.

UR - http://www.scopus.com/inward/record.url?scp=84859942963&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84859942963&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0035789

DO - 10.1371/journal.pone.0035789

M3 - Article

C2 - 22536438

AN - SCOPUS:84859942963

VL - 7

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 4

M1 - e35789

ER -