title: Large-scale characterization of DNA methylation changes in human gastric carcinomas with and without metastasis.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  Methylation changes of GFRA1, SRF, and ZNF382 may be a potential biomarker set for prediction of gastric carcinoma metastasis.
authors.affiliation: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Zhaojun
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China. Shihezi University School of Medicine, Shihezi, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Gao
authors.affiliation: GRU Cancer Center, Georgia Regents University, Augusta, Georgia.
authors.forename: Lirong
authors.initials: L
authors.lastname: Pei
authors.affiliation: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Liankun
authors.initials: L
authors.lastname: Gu
authors.affiliation: Department of Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Lianhai
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Oncology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Budong
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Division of Epigenetics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.
authors.forename: Naoko
authors.initials: N
authors.lastname: Hattori
authors.affiliation: Department of Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China.
authors.forename: Jiafu
authors.initials: J
authors.lastname: Ji
authors.affiliation: Department of Molecular Oncology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan.
authors.forename: Yasuhito
authors.initials: Y
authors.lastname: Yuasa
authors.affiliation: Department of Pathology, Seoul National University College of Medicine, Jongno-gu, Seoul, Korea.
authors.forename: Wooho
authors.initials: W
authors.lastname: Kim
authors.affiliation: Division of Epigenetics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Ushijima
authors.affiliation: GRU Cancer Center, Georgia Regents University, Augusta, Georgia. dengdajun@bjmu.edu.cn hshi@gru.edu.
authors.forename: Huidong
authors.initials: H
authors.lastname: Shi
authors.affiliation: Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, Beijing, China. dengdajun@bjmu.edu.cn hshi@gru.edu.
authors.forename: Dajun
authors.initials: D
authors.lastname: Deng
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor; D002277:Carcinoma / Q000235:genetics*; D002681:China; D019175:DNA Methylation / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D051097:Glial Cell Line-Derived Neurotrophic Factor Receptors / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009362:Neoplasm Metastasis; D011401:Promoter Regions, Genetic; D026362:Serum Response Factor / Q000235:genetics*; D013274:Stomach Neoplasms / Q000235:genetics* / Q000473:pathology; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D004268:DNA-Binding Proteins; C494987:GFRA1 protein, human; D051097:Glial Cell Line-Derived Neurotrophic Factor Receptors; C476858:SRF protein, human; D026362:Serum Response Factor; D014157:Transcription Factors; C116326:ZNF382 protein, human