title: Three DNA methylation epigenotypes in human colorectal cancer.
abstract: OBJECTIVE
  Whereas the CpG island methylator phenotype (CIMP) in colorectal cancer associates with microsatellite instability (MSI)-high and BRAF-mutation(+), the existence of an intermediate-methylation subgroup associated with KRAS-mutation(+) is controversial, and suitable markers for the subgroup have yet to be developed. Our aim is to clarify DNA methylation epigenotypes of colorectal cancer more comprehensively.
  
  
  METHODS
  To select new methylation markers on a genome-wide scale, we did methylated DNA immunoprecipitation-on-chip analysis of colorectal cancer cell lines and re-expression array analysis by 5-aza-2'-deoxycytidine/Trichostatin A treatment. Methylation levels were analyzed quantitatively in 149 colorectal cancer samples using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Colorectal cancer was epigenotyped by unsupervised two-way hierarchical clustering method.
  
  
  RESULTS
  Among 1,311 candidate silencing genes, 44 new markers were selected and underwent quantitative methylation analysis in colorectal cancer samples together with 16 previously reported markers. Colorectal cancer was clustered into high-, intermediate-, and low-methylation epigenotypes. Methylation markers were clustered into two major groups: group 1 showing methylation in high-methylation epigenotype, and group 2 showing methylation in high- and intermediate-methylation epigenotypes. A two-step marker panel deciding epigenotypes was developed with 95% accuracy: the 1st panel consisting of three group-1 markers (CACNA1G, LOX, SLC30A10) to extract high-methylation epigenotype, and the 2nd panel consisting of four group-2 markers (ELMO1, FBN2, THBD, HAND1) and SLC30A10 again to divide the remains into intermediate- and low-methylation epigenotypes. The high-methylation epigenotype correlated significantly with MSI-high and BRAF-mutation(+) in concordance with reported CIMP. Intermediate-epigenotype significantly correlated with KRAS-mutation(+). KRAS-mutation(+) colorectal cancer with intermediate-methylation epigenotype showed significantly worse prognosis.
  
  
  CONCLUSIONS
  Three methylation epigenotypes exist in colorectal cancer, and suitable classification markers have been developed. Intermediate-methylation epigenotype with KRAS-mutation(+) correlated with worse prognosis.
authors.affiliation: Genome Science Division, Department of Gastrointestinal Surgery, Research Center for Advanced Science and Technology, Translational Systems Biology and Medicine Initiative, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Yagi
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Akagi
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Hayashi
authors.forename: Genta
authors.initials: G
authors.lastname: Nagae
authors.forename: Shingo
authors.initials: S
authors.lastname: Tsuji
authors.forename: Takayuki
authors.initials: T
authors.lastname: Isagawa
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Midorikawa
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nishimura
authors.forename: Hirohiko
authors.initials: H
authors.lastname: Sakamoto
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Seto
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Aburatani
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kaneda
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D011905:Genes, ras; D005838:Genotype; D006801:Humans; D010641:Phenotype
chemical_list: D014408:Biomarkers, Tumor