title: Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array.
abstract: BACKGROUND
  DNA methylation is a potential tumor marker for several cancers, including colorectal cancer (CRC), because of its heritable and stable characteristics.
  
  
  METHODS
  Using a high-resolution, genome-wide approach, we epigenotyped >450,000 CpG sites in tumor and adjacent non-tumor tissues from 23 microsatellite instability (MSI)/microsatellite stability (MSS) CRC cases. Using matrix-assisted laser desorption ionization-time of flight mass spectrometry, the methylation status of five frequently hypermethylated genes were confirmed in 75 independent CRC series and 353 CRC patients with available plasma.
  
  
  RESULTS
  Compared with non-tumor tissues, 13 MSI tumors had 34,836 (7 %) aberrant methylation sites, 87 % of which were hypermethylated. In contrast, only 9,806 (2 %) differentially methylated sites were identified in ten MSS cases (62 % hypermethylated). In both MSI and MSS, 228 promoter-associated CpG islands were hypermethylated, with AGBL4, ZNF625, MDFI, TWIST1, and FLI1 being most frequently hypermethylated. In an independent set of 35 MSI and 40 MSS cases, the methylation status of these five genes significantly differed between tumor and adjacent non-tumor tissues. Of 353 CRC patients, 230 (65.2 %), 232 (65.7 %), and 247 (70.0 %) had AGBL4, FLI1, and TWIST1 promoter hypermethylation in circulating cell-free DNA, respectively. In patients without metastasis, the sensitivity of any two or three hypermethylation markers was 52.8-57.8 and 27.9-38.9 %, respectively. The sensitivity of any two or three markers was significantly high in patients with stage IV disease (73.0 and 55.6 %, respectively). The prognostic value of these epimarkers was inconclusive.
  
  
  CONCLUSIONS
  DNA methylation patterns differed in CRC subtypes. The identified hypermethylation markers in CRC patients may have good sensitivity in different CRC stages.
authors.affiliation: Department of Clinical Pathology, Yang-Ming Branch, Taipei City Hospital, Taipei, Taiwan.
authors.forename: Pei-Ching
authors.initials: PC
authors.lastname: Lin
authors.affiliation: Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.|Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Jen-Kou
authors.initials: JK
authors.lastname: Lin
authors.affiliation: Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan.
authors.forename: Chien-Hsing
authors.initials: CH
authors.lastname: Lin
authors.affiliation: Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.|Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Hung-Hsin
authors.initials: HH
authors.lastname: Lin
authors.affiliation: Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.|Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Shung-Haur
authors.initials: SH
authors.lastname: Yang
authors.affiliation: Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.|Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Jeng-Kai
authors.initials: JK
authors.lastname: Jiang
authors.affiliation: Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.|Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Wei-Shone
authors.initials: WS
authors.lastname: Chen
authors.affiliation: Department of Life Sciences and Genome Research Center and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Chih-Chi
authors.initials: CC
authors.lastname: Chou
authors.affiliation: Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan. petsai@nhri.org.tw.|Department of Life Sciences and Genome Research Center and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan. petsai@nhri.org.tw.
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Tsai
authors.affiliation: Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan. changsc@vghtpe.gov.tw.|Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan. changsc@vghtpe.gov.tw.
authors.forename: Shih-Ching
authors.initials: SC
authors.lastname: Chang
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D015179:Colorectal Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D005500:Follow-Up Studies; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D053842:Microsatellite Instability; D018895:Microsatellite Repeats / Q000235:genetics; D008875:Middle Aged; D009362:Neoplasm Metastasis; D009367:Neoplasm Staging; D011379:Prognosis; D011401:Promoter Regions, Genetic / Q000235:genetics; D015996:Survival Rate
chemical_list: D014408:Biomarkers, Tumor