Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis

Zhaojun Liu, Jun Zhang, Yanhong Gao, Lirong Pei, Jing Zhou, Liankun Gu, Lianhai Zhang, Budong Zhu, Naoko Hattori, Jiafu Ji, Yasuhito Yuasa, Wooho Kim, Toshikazu Ushijima, Huidong Shi, Dajun Deng

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Abstract

PURPOSE: Metastasis is the leading cause of death for gastric carcinoma. An epigenetic biomarker panel for predicting gastric carcinoma metastasis could have significant clinical impact on the care of patients with gastric carcinoma. The main purpose of this study is to characterize the methylation differences between gastric carcinomas with and without metastasis.

EXPERIMENTAL DESIGN: Genome-wide DNA methylation profiles between 4 metastatic and 4 nonmetastatic gastric carcinomas and their surgical margins (SM) were analyzed using methylated-CpG island amplification with microarray. The methylation states of 73 candidate genes were further analyzed in patients with gastric carcinoma in a discovery cohort (n=108) using denatured high performance liquid chromatography, bisulfite-sequencing, and MethyLight. The predictive values of potential metastasis-methylation biomarkers were validated in cohorts of patients with gastric carcinoma in China (n=330), Japan (n=129), and Korea (n=153).

RESULTS: The gastric carcinoma genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared with SMs. Significant differential methylation was validated in the CpG islands of 15 genes (P<0.05) and confirmed using bisulfite sequencing. These genes included BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Methylation changes of GFRA1, SRF, and ZNF382 resulted in up- or downregulation of their transcription. Most importantly, the prevalence of GFRA1, SRF, and ZNF382 methylation alterations was consistently and coordinately associated with gastric carcinoma metastasis and the patients' overall survival throughout discovery and validation cohorts in China, Japan, and Korea.

CONCLUSION: Methylation changes of GFRA1, SRF, and ZNF382 may be a potential biomarker set for prediction of gastric carcinoma metastasis.

Original languageEnglish (US)
Pages (from-to)4598-4612
Number of pages15
JournalClinical cancer research : an official journal of the American Association for Cancer Research
Volume20
Issue number17
DOIs
StatePublished - Sep 1 2014

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DNA Methylation
Stomach
Neoplasm Metastasis
Carcinoma
Methylation
CpG Islands
Biomarkers
Korea
China
Japan
Genome
Genes
Epigenomics
Cause of Death
Exons
Patient Care
Up-Regulation
Down-Regulation
High Pressure Liquid Chromatography
Survival

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis. / Liu, Zhaojun; Zhang, Jun; Gao, Yanhong; Pei, Lirong; Zhou, Jing; Gu, Liankun; Zhang, Lianhai; Zhu, Budong; Hattori, Naoko; Ji, Jiafu; Yuasa, Yasuhito; Kim, Wooho; Ushijima, Toshikazu; Shi, Huidong; Deng, Dajun.

In: Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 20, No. 17, 01.09.2014, p. 4598-4612.

Research output: Contribution to journalArticle

Liu, Zhaojun ; Zhang, Jun ; Gao, Yanhong ; Pei, Lirong ; Zhou, Jing ; Gu, Liankun ; Zhang, Lianhai ; Zhu, Budong ; Hattori, Naoko ; Ji, Jiafu ; Yuasa, Yasuhito ; Kim, Wooho ; Ushijima, Toshikazu ; Shi, Huidong ; Deng, Dajun. / Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis. In: Clinical cancer research : an official journal of the American Association for Cancer Research. 2014 ; Vol. 20, No. 17. pp. 4598-4612.
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T1 - Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis

AU - Liu, Zhaojun

AU - Zhang, Jun

AU - Gao, Yanhong

AU - Pei, Lirong

AU - Zhou, Jing

AU - Gu, Liankun

AU - Zhang, Lianhai

AU - Zhu, Budong

AU - Hattori, Naoko

AU - Ji, Jiafu

AU - Yuasa, Yasuhito

AU - Kim, Wooho

AU - Ushijima, Toshikazu

AU - Shi, Huidong

AU - Deng, Dajun

PY - 2014/9/1

Y1 - 2014/9/1

N2 - PURPOSE: Metastasis is the leading cause of death for gastric carcinoma. An epigenetic biomarker panel for predicting gastric carcinoma metastasis could have significant clinical impact on the care of patients with gastric carcinoma. The main purpose of this study is to characterize the methylation differences between gastric carcinomas with and without metastasis.EXPERIMENTAL DESIGN: Genome-wide DNA methylation profiles between 4 metastatic and 4 nonmetastatic gastric carcinomas and their surgical margins (SM) were analyzed using methylated-CpG island amplification with microarray. The methylation states of 73 candidate genes were further analyzed in patients with gastric carcinoma in a discovery cohort (n=108) using denatured high performance liquid chromatography, bisulfite-sequencing, and MethyLight. The predictive values of potential metastasis-methylation biomarkers were validated in cohorts of patients with gastric carcinoma in China (n=330), Japan (n=129), and Korea (n=153).RESULTS: The gastric carcinoma genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared with SMs. Significant differential methylation was validated in the CpG islands of 15 genes (P<0.05) and confirmed using bisulfite sequencing. These genes included BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Methylation changes of GFRA1, SRF, and ZNF382 resulted in up- or downregulation of their transcription. Most importantly, the prevalence of GFRA1, SRF, and ZNF382 methylation alterations was consistently and coordinately associated with gastric carcinoma metastasis and the patients' overall survival throughout discovery and validation cohorts in China, Japan, and Korea.CONCLUSION: Methylation changes of GFRA1, SRF, and ZNF382 may be a potential biomarker set for prediction of gastric carcinoma metastasis.

AB - PURPOSE: Metastasis is the leading cause of death for gastric carcinoma. An epigenetic biomarker panel for predicting gastric carcinoma metastasis could have significant clinical impact on the care of patients with gastric carcinoma. The main purpose of this study is to characterize the methylation differences between gastric carcinomas with and without metastasis.EXPERIMENTAL DESIGN: Genome-wide DNA methylation profiles between 4 metastatic and 4 nonmetastatic gastric carcinomas and their surgical margins (SM) were analyzed using methylated-CpG island amplification with microarray. The methylation states of 73 candidate genes were further analyzed in patients with gastric carcinoma in a discovery cohort (n=108) using denatured high performance liquid chromatography, bisulfite-sequencing, and MethyLight. The predictive values of potential metastasis-methylation biomarkers were validated in cohorts of patients with gastric carcinoma in China (n=330), Japan (n=129), and Korea (n=153).RESULTS: The gastric carcinoma genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared with SMs. Significant differential methylation was validated in the CpG islands of 15 genes (P<0.05) and confirmed using bisulfite sequencing. These genes included BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Methylation changes of GFRA1, SRF, and ZNF382 resulted in up- or downregulation of their transcription. Most importantly, the prevalence of GFRA1, SRF, and ZNF382 methylation alterations was consistently and coordinately associated with gastric carcinoma metastasis and the patients' overall survival throughout discovery and validation cohorts in China, Japan, and Korea.CONCLUSION: Methylation changes of GFRA1, SRF, and ZNF382 may be a potential biomarker set for prediction of gastric carcinoma metastasis.

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