Comprehensive DNA methylation and extensive mutation analyses reveal an association between the CpG island methylator phenotype and oncogenic mutations in gastric cancers.

Recent development of personal sequencers for extensive mutation analysis and bead array technology for comprehensive DNA methylation analysis have made it possible to obtain integrated pictures of genetic and epigenetic alterations on the same set of cancer samples. Here, we aimed to establish such pictures of gastric cancers (GCs). Comprehensive methylation analysis of 30 GCs revealed that the number of aberrantly methylated genes was highly variable among individual GCs. Extensive mutation analysis of 55 known cancer-related genes revealed that 19 of the 30 GCs had 24 somatic mutations of eight different genes (CDH1, CTNNB1, ERBB2, KRAS, MLH1, PIK3CA, SMARCB1, and TP53). Integration of information on the genetic and epigenetic alterations revealed that the GCs with the CpG island methylator phenotype (CIMP) tended to have mutations of oncogenes, CTNNB1, ERBB2, KRAS, and PIK3CA. This is one of the first studies in which both genetic and epigenetic alterations were extensively analyzed in the same set of samples. It was also demonstrated for the first time in GCs that the CIMP was associated with oncogene mutations.

[1]  D. Fang,et al.  Mutation and methylation of hMLH1 in gastric carcinomas with microsatellite instability. , 2003, World journal of gastroenterology.

[2]  A. Kaneda,et al.  Lysyl Oxidase Is a Tumor Suppressor Gene Inactivated by Methylation and Loss of Heterozygosity in Human Gastric Cancers , 2004, Cancer Research.

[3]  Brian Everitt,et al.  Cluster analysis , 1974 .

[4]  N. Matsubara,et al.  Oncogenic PIK3CA mutations in colorectal cancers and polyps , 2012, International journal of cancer.

[5]  A. Regev,et al.  An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors , 2008, Nature Genetics.

[6]  T. Ushijima,et al.  Methylation destiny: Moira takes account of histones and RNA polymerase II , 2010, Epigenetics.

[7]  P. Minoo,et al.  Role of BRAF‐V600E in the serrated pathway of colorectal tumourigenesis , 2007, The Journal of pathology.

[8]  M. Jackson,et al.  Genetic pathways and mutation profiles of human cancers: site- and exposure-specific patterns. , 2007, Carcinogenesis.

[9]  Hidemi Ito,et al.  Integrated analysis of genetic and epigenetic alterations reveals CpG island methylator phenotype associated with distinct clinical characters of lung adenocarcinoma. , 2012, Carcinogenesis.

[10]  T. Hirao,et al.  The prognostic significance of amplification and overexpression of c‐met and c‐erb B‐2 in human gastric carcinomas , 1999, Cancer.

[11]  Megan F. Cole,et al.  Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells , 2006, Cell.

[12]  Zohar Yakhini,et al.  Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer , 2007, Nature Genetics.

[13]  P. Laird,et al.  Epigenetic stem cell signature in cancer , 2007, Nature Genetics.

[14]  N. Cho,et al.  CpG island hypermethylator phenotype in gastric carcinoma and its clinicopathological features , 2010, Virchows Archiv.

[15]  M. Esteller,et al.  Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome , 2011, Epigenetics.

[16]  Kelly M. McGarvey,et al.  Polycomb CBX7 promotes initiation of heritable repression of genes frequently silenced with cancer-specific DNA hypermethylation. , 2009, Cancer research.

[17]  Kelly M. McGarvey,et al.  A stem cell–like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing , 2007, Nature Genetics.

[18]  H. Lee,et al.  Evaluation of HER-2 gene status in gastric carcinoma using immunohistochemistry, fluorescence in situ hybridization, and real-time quantitative polymerase chain reaction. , 2007, Human pathology.

[19]  T. Ushijima,et al.  Effects of genome architecture and epigenetic factors on susceptibility of promoter CpG islands to aberrant DNA methylation induction. , 2011, Genomics.

[20]  B. Teh,et al.  Methylation Subtypes and Large-Scale Epigenetic Alterations in Gastric Cancer , 2012, Science Translational Medicine.

[21]  T. Kinoshita,et al.  Development of a novel approach, the epigenome-based outlier approach, to identify tumor-suppressor genes silenced by aberrant DNA methylation. , 2012, Cancer letters.

[22]  S. H. Lee,et al.  Frequent somatic mutations of the beta-catenin gene in intestinal-type gastric cancer. , 1999, Cancer research.

[23]  Peter A. Jones,et al.  Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. , 2007, Cancer cell.

[24]  R. Wolff,et al.  Poor survival associated with the BRAF V600E mutation in microsatellite-stable colon cancers. , 2005, Cancer research.

[25]  T. Tsukamoto,et al.  Lack of association between CpG island methylator phenotype in human gastric cancers and methylation in their background non‐cancerous gastric mucosae , 2007, Cancer science.

[26]  Zhengyan Kan,et al.  Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer , 2011, Nature Genetics.

[27]  Puay Hoon Tan,et al.  Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. , 2012, The Journal of molecular diagnostics : JMD.

[28]  Shuji Fujita,et al.  Frequent loss of Brm expression in gastric cancer correlates with histologic features and differentiation state. , 2007, Cancer research.

[29]  M. Toyota,et al.  Genetic, epigenetic, and clinicopathologic features of gastric carcinomas with the CpG island methylator phenotype and an association with Epstein–Barr virus , 2006, Cancer.

[30]  A. Kaneda,et al.  CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas. , 2005, Cancer research.

[31]  T. Yano,et al.  Comparison of HER2 gene amplification assessed by fluorescence in situ hybridization and HER2 protein expression assessed by immunohistochemistry in gastric cancer. , 2006, Oncology reports.

[32]  C. Fenoglio-Preiser,et al.  beta-Catenin mutation is a frequent cause of Wnt pathway activation in gastric cancer. , 2002, Cancer research.

[33]  N. Sasaki,et al.  Helicobacter pylori infection and the development of gastric cancer. , 2001, The New England journal of medicine.

[34]  T. Dallman,et al.  Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[35]  P. Laird,et al.  Analysis of the Association between CIMP and BRAFV600E in Colorectal Cancer by DNA Methylation Profiling , 2009, PloS one.

[36]  A. Kaneda,et al.  High Levels of Aberrant DNA Methylation in Helicobacter pylori–Infected Gastric Mucosae and its Possible Association with Gastric Cancer Risk , 2006, Clinical Cancer Research.

[37]  Mitsuru Sasako,et al.  Focus on gastric cancer. , 2004, Cancer cell.

[38]  M. Toyota,et al.  Frequent epigenetic inactivation of SFRP genes and constitutive activation of Wnt signaling in gastric cancer , 2007, Oncogene.

[39]  S. Ogino,et al.  PIK3CA mutation in colorectal cancer: relationship with genetic and epigenetic alterations. , 2008, Neoplasia.

[40]  J. Herman,et al.  CpG island methylator phenotype in colorectal cancer. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  T. Tsukamoto,et al.  FHL1 on chromosome X is a single-hit gastrointestinal tumor-suppressor gene and contributes to the formation of an epigenetic field defect , 2013, Oncogene.

[42]  Bin Tean Teh,et al.  Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes , 2012, Nature Genetics.

[43]  P. Laird,et al.  CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer , 2006, Nature Genetics.

[44]  T. Ushijima,et al.  The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. , 2009, Genome research.

[45]  M. Fraga,et al.  The Polycomb group protein EZH2 directly controls DNA methylation , 2006, Nature.

[46]  Yi Ding,et al.  Methylation and mutation analysis of p16 gene in gastric cancer. , 2003, World journal of gastroenterology.

[47]  Wei Zhao,et al.  Mutations of PIK3CA in gastric adenocarcinoma , 2005, BMC Cancer.

[48]  N. Ahuja,et al.  Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[49]  T. Tsukamoto,et al.  Identification of a DNA methylation marker that detects the presence of lymph node metastases of gastric cancers. , 2012, Oncology letters.

[50]  H. Tsuda,et al.  Association between frequent CpG island methylation and HER2 amplification in human breast cancers. , 2009, Carcinogenesis.

[51]  C. Caldas,et al.  E-cadherin gene (CDH1) promoter methylation as the second hit in sporadic diffuse gastric carcinoma , 2001, Oncogene.

[52]  C. Roberts,et al.  SWI/SNF nucleosome remodellers and cancer , 2011, Nature Reviews Cancer.

[53]  S. Schwartz,et al.  The prevalence of PIK3CA mutations in gastric and colon cancer. , 2005, European journal of cancer.

[54]  Takeshi Toyoda,et al.  Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. , 2010, Cancer research.

[55]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[56]  Hiroyuki Yamamoto,et al.  IGFBP7 is a p53-responsive gene specifically silenced in colorectal cancer with CpG island methylator phenotype. , 2010, Carcinogenesis.

[57]  M. Esteller.  CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future , 2002, Oncogene.

[58]  H. Masoudi,et al.  β‐Catenin (CTNNB1) gene amplification: A new mechanism of protein overexpression in cancer , 2005, Genes, chromosomes & cancer.