title: DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach.
abstract: BACKGROUND
  Methylation-induced silencing of promoter CpG islands in tumor suppressor genes plays an important role in human carcinogenesis. In colorectal cancer, the CpG island methylator phenotype (CIMP) is defined as widespread and elevated levels of DNA methylation and CIMP+ tumors have distinctive clinicopathological and molecular features. In contrast, the existence of a comparable CIMP subtype in gastric cancer (GC) has not been clearly established. To further investigate this issue, in the present study we performed comprehensive DNA methylation profiling of a well-characterised series of primary GC.
  
  
  METHODS
  The methylation status of 1,421 autosomal CpG sites located within 768 cancer-related genes was investigated using the Illumina GoldenGate Methylation Panel I assay on DNA extracted from 60 gastric tumors and matched tumor-adjacent gastric tissue pairs. Methylation data was analysed using a recursively partitioned mixture model and investigated for associations with clinicopathological and molecular features including age, Helicobacter pylori status, tumor site, patient survival, microsatellite instability and BRAF and KRAS mutations.
  
  
  RESULTS
  A total of 147 genes were differentially methylated between tumor and matched tumor-adjacent gastric tissue, with HOXA5 and hedgehog signalling being the top-ranked gene and signalling pathway, respectively. Unsupervised clustering of methylation data revealed the existence of 6 subgroups under two main clusters, referred to as L (low methylation; 28% of cases) and H (high methylation; 72%). Female patients were over-represented in the H tumor group compared to L group (36% vs 6%; P = 0.024), however no other significant differences in clinicopathological or molecular features were apparent. CpG sites that were hypermethylated in group H were more frequently located in CpG islands and marked for polycomb occupancy.
  
  
  CONCLUSIONS
  High-throughput methylation analysis implicates genes involved in embryonic development and hedgehog signaling in gastric tumorigenesis. GC is comprised of two major methylation subtypes, with the highly methylated group showing some features consistent with a CpG island methylator phenotype.
authors.forename: Marie
authors.initials: M
authors.lastname: Loh
authors.forename: Natalia
authors.initials: N
authors.lastname: Liem
authors.forename: Aparna
authors.initials: A
authors.lastname: Vaithilingam
authors.forename: Pei Li
authors.initials: PL
authors.lastname: Lim
authors.forename: Nur Sabrina
authors.initials: NS
authors.lastname: Sapari
authors.forename: Eiram
authors.initials: E
authors.lastname: Elahi
authors.forename: Zuan Yu
authors.initials: ZY
authors.lastname: Mok
authors.forename: Chee Leong
authors.initials: CL
authors.lastname: Cheng
authors.forename: Benedict
authors.initials: B
authors.lastname: Yan
authors.forename: Brendan
authors.initials: B
authors.lastname: Pang
authors.forename: Manuel
authors.initials: M
authors.lastname: Salto-Tellez
authors.forename: Wei Peng
authors.initials: WP
authors.lastname: Yong
authors.forename: Barry
authors.initials: B
authors.lastname: Iacopetta
authors.affiliation: Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. Richie_Soong@nus.edu.sg.
authors.forename: Richie
authors.initials: R
authors.lastname: Soong
mesh_terms: D000230:Adenocarcinoma / Q000150:complications / Q000235:genetics* / Q000378:metabolism; D000367:Age Factors; D000368:Aged; D016022:Case-Control Studies; D018899:CpG Islands; D056750:Cyclin A1 / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D016481:Helicobacter Infections / Q000150:complications; D016480:Helicobacter pylori; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D053842:Microsatellite Instability; D008875:Middle Aged; D010641:Phenotype; D011518:Proto-Oncogene Proteins / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D012737:Sex Factors; D015398:Signal Transduction; D013274:Stomach Neoplasms / Q000150:complications / Q000235:genetics* / Q000378:metabolism; D018631:ras Proteins / Q000235:genetics; D000094742:Secreted Frizzled-Related Proteins
chemical_list: D056750:Cyclin A1; D018398:Homeodomain Proteins; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D011518:Proto-Oncogene Proteins; D048493:Proto-Oncogene Proteins B-raf; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins; C503745:CCNA1 protein, human; C489213:HOXA5 protein, human; C117307:KRAS protein, human; C117636:SFRP1 protein, human; D000094742:Secreted Frizzled-Related Proteins; C482119:BRAF protein, human