title: Prognostic CpG methylation biomarkers identified by methylation array in esophageal squamous cell carcinoma patients.
abstract: BACKGROUND
  Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with poor prognosis. We aimed to identify a panel of CpG methylation biomarkers for prognosis prediction of ESCC patients.
  
  
  METHODS
  Illumina's GoldenGate methylation array, supervised principal components, Kaplan-Meier survival analyses and Cox regression model were conducted on dissected tumor tissues from a training cohort of 40 ESCC patients to identify potential CpG methylation biomarkers. Pyrosequencing quantitative methylation assay were performed to validate prognostic CpG methylation biomarkers in 61 ESCC patients. The correlation between DNA methylation and RNA expression of a validated marker, SOX17, was examined in a validation cohort of 61 ESCC patients.
  
  
  RESULTS
  We identified a panel of nine CpG methylation probes located at promoter or exon1 region of eight genes including DDIT3, FES, FLT3, NTRK3, SEPT5, SEPT9, SOX1, and SOX17, for prognosis prediction in ESCC patients. Risk score calculated using the eight-gene panel statistically predicted poor outcome for patients with high risk score. These eight-gene also showed a significantly higher methylation level in tumor tissues than their corresponding normal samples in all patients analyzed. In addition, we also detected an inverse correlation between CpG hypermethylation and the mRNA expression level of SOX17 gene in ESCC patients, indicating that DNA hypermethylation was responsible for decreased expression of SOX17.
  
  
  CONCLUSIONS
  This study established a proof-of-concept CpG methylation biomarker panel for ESCC prognosis that can be further validated by multiple cohort studies. Functional characterization of the eight prognostic methylation genes in our biomarker panel could help to dissect the mechanism of ESCC tumorigenesis.
authors.affiliation: 1. Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan;
authors.forename: I-Ying
authors.initials: IY
authors.lastname: Kuo
authors.affiliation: 2. Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan; ; 3. Department of Surgery, Chia-Yi Christian Hospital, Chiayi, Taiwan;
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Chang
authors.affiliation: 4. National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan;
authors.forename: Shih-Sheng
authors.initials: SS
authors.lastname: Jiang
authors.affiliation: 4. National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan;
authors.forename: Chung-Hsin
authors.initials: CH
authors.lastname: Chen
authors.affiliation: 4. National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan;
authors.forename: I-Shou
authors.initials: IS
authors.lastname: Chang
authors.affiliation: 5. Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan;
authors.forename: Bor-Shyang
authors.initials: BS
authors.lastname: Sheu
authors.affiliation: 2. Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan;
authors.forename: Pei-Jung
authors.initials: PJ
authors.lastname: Lu
authors.affiliation: 5. Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan;
authors.forename: Wei-Lun
authors.initials: WL
authors.lastname: Chang
authors.affiliation: 6. Department of Surgery, National Cheng Kung University Hospital, Tainan, Taiwan;
authors.forename: Wu-Wei
authors.initials: WW
authors.lastname: Lai
authors.affiliation: 1. Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan; ; 2. Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan; ; 7. Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Yi-Ching
authors.initials: YC
authors.lastname: Wang
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics; D063646:Carcinogenesis; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D000077277:Esophageal Squamous Cell Carcinoma; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000096:biosynthesis* / Q000235:genetics; D011379:Prognosis; D011401:Promoter Regions, Genetic
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: CpG methylation; DNA methylation array; esophageal squamous cell carcinoma; prognosis.; pyrosequencing