Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations.

Colorectal cancer (CRC) is a complex and heterogeneous disease in which genomic instability and DNA promoter methylation play important roles. The aim of this study was to investigate the relationship between chromosomal instability (CIN), microsatellite instability (MSI) and promoter methylation of CRC-associated genes. Therefore, 71 CRCs were analysed for CIN and MSI by comparative genomic hybridization and the mononucleotide marker BAT-26, respectively. Promoter methylation of the tumour suppressor and DNA repair genes hMLH1, O(6)-MGMT, APC, p14(ARF), p16(INK4A), RASSF1A, GATA-4, GATA-5 and CHFR was analysed using methylation-specific polymerase chain reaction. These integrative analyses showed that in CIN+ CRCs, promoter methylation of GATA-4 and p16(INK4A) was inversely related to chromosomal loss at 15q11-q21 and gain at 20q13, respectively (P values: 3.8 x 10(-2) and 4.5 x 10(-2), respectively). Interestingly, promoter methylation of RASSF1A, GATA-4, GATA-5 and CHFR, as well as a high methylation index (MI), was positively related to chromosomal gain at 8q23-qter (P values: 1.5 x 10(-2), 3.8 x 10(-2), 3.9 x 10(-2), 4.9 x 10(-2) and 8.2 x 10(-3), respectively). MSI was associated with BRAF mutation, promoter methylation of hMLH1, APC and p16(INK4A) and a high MI (total number of methylated genes) (P values: 2.4 x 10(-2), 2.5 x 10(-3), 1.8 x 10(-2), 4.6 x 10(-2) and 1.0 x 10(-2), respectively). Therefore, we conclude that promoter methylation of pivotal tumour suppressor and DNA repair genes is associated with specific patterns of chromosomal changes in CRC, which are different from methylation patterns in MSI tumours.

[1]  S. Ogino,et al.  18q loss of heterozygosity in microsatellite stable colorectal cancer is correlated with CpG island methylator phenotype-negative (CIMP-0) and inversely with CIMP-low and CIMP-high , 2007, BMC Cancer.

[2]  J. Meyerhardt,et al.  Molecular correlates with MGMT promoter methylation and silencing support CpG island methylator phenotype-low (CIMP-low) in colorectal cancer , 2007, Gut.

[3]  R. Wolff,et al.  APC Mutations and Other Genetic and Epigenetic Changes in Colon Cancer , 2007, Molecular Cancer Research.

[4]  J. Herman,et al.  Promoter Methylation Precedes Chromosomal Alterations in Colorectal Cancer Development , 2006, Cellular oncology : the official journal of the International Society for Cellular Oncology.

[5]  M. van Engeland,et al.  Clonal analysis favours a monoclonal origin for serous borderline tumours with peritoneal implants , 2006, The Journal of pathology.

[6]  G. Watanabe,et al.  APC gene methylation is inversely correlated with features of the CpG island methylator phenotype in colorectal cancer , 2006, International journal of cancer.

[7]  Jane Fridlyand,et al.  Chromosomal Instability in Microsatellite-Unstable and Stable Colon Cancer , 2006, Clinical Cancer Research.

[8]  R. Ward,et al.  Colorectal cancer: a model for epigenetic tumorigenesis , 2006, Gut.

[9]  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.

[10]  S. Baylin,et al.  Epigenetic gene silencing in cancer – a mechanism for early oncogenic pathway addiction? , 2006, Nature Reviews Cancer.

[11]  M. Nowak,et al.  Dynamics of colorectal cancer. , 2005, Seminars in cancer biology.

[12]  M. Toyota,et al.  CIMP, at last. , 2005, Gastroenterology.

[13]  J. Herman,et al.  CHFR promoter hypermethylation in colon cancer correlates with the microsatellite instability phenotype. , 2005, Carcinogenesis.

[14]  G. Thomas,et al.  Frequency of BRAF T1796A mutation in papillary thyroid carcinoma relates to age of patient at diagnosis and not to radiation exposure , 2005, The Journal of pathology.

[15]  J. Schouten,et al.  Chromosomal instability in flat adenomas and carcinomas of the colon , 2005, The Journal of pathology.

[16]  Martin A Nowak,et al.  Can chromosomal instability initiate tumorigenesis? , 2005, Seminars in cancer biology.

[17]  T. Motoyama,et al.  Hypermethylation of Chfr and hMLH1 in gastric noninvasive and early invasive neoplasias , 2005, Virchows Archiv.

[18]  T. Kouzarides,et al.  Myc represses transcription through recruitment of DNA methyltransferase corepressor , 2005, The EMBO journal.

[19]  W. Giaretti,et al.  Chromosomal Instability, Aneuploidy, and Gene Mutations in Human Sporadic Colorectal Adenomas , 2004, Cellular oncology : the official journal of the International Society for Cellular Oncology.

[20]  J. Herman,et al.  Methylation-Specific PCR Unraveled , 2004, Cellular oncology : the official journal of the International Society for Cellular Oncology.

[21]  Elena Marchiori,et al.  Breakpoint identification and smoothing of array comparative genomic hybridization data , 2004, Bioinform..

[22]  J. Issa.  CpG island methylator phenotype in cancer , 2004, Nature Reviews Cancer.

[23]  N. Matsubara,et al.  Colorectal cancer with mutation in BRAF, KRAS, and wild-type with respect to both oncogenes showing different patterns of DNA methylation. , 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[24]  N. Matsubara,et al.  BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum , 2004, Gut.

[25]  B. Ylstra,et al.  High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides , 2004, Journal of Clinical Pathology.

[26]  B. Leggett,et al.  Identification of Genes Uniquely Involved in Frequent Microsatellite Instability Colon Carcinogenesis by Expression Profiling Combined with Epigenetic Scanning , 2004, Cancer Research.

[27]  J. Saurin,et al.  Chfr inactivation is not associated to chromosomal instability in colon cancers , 2003, Oncogene.

[28]  J. Herman,et al.  GATA-4 and GATA-5 Transcription Factor Genes and Potential Downstream Antitumor Target Genes Are Epigenetically Silenced in Colorectal and Gastric Cancer , 2003, Molecular and Cellular Biology.

[29]  Hoguen Kim,et al.  Chromosomal imbalances in the colorectal carcinomas with microsatellite instability. , 2003, The American journal of pathology.

[30]  O. Sieber,et al.  Genomic instability — the engine of tumorigenesis? , 2003, Nature Reviews Cancer.

[31]  M. Perucho,et al.  Genetics supersedes epigenetics in colon cancer phenotype. , 2003, Cancer cell.

[32]  R Alexandra Goldbohm,et al.  Effects of dietary folate and alcohol intake on promoter methylation in sporadic colorectal cancer: the Netherlands cohort study on diet and cancer. , 2003, Cancer research.

[33]  C. Compton,et al.  Characterization of sporadic colon cancer by patterns of genomic instability. , 2003, Cancer research.

[34]  A. Duval,et al.  Evaluation of tumor microsatellite instability using five quasimonomorphic mononucleotide repeats and pentaplex PCR. , 2002, Gastroenterology.

[35]  J. Arends,et al.  Colorectal adenoma to carcinoma progression follows multiple pathways of chromosomal instability. , 2002, Gastroenterology.

[36]  Stella Pelengaris,et al.  c-MYC: more than just a matter of life and death , 2002, Nature Reviews Cancer.

[37]  H. Nagai,et al.  Extensive methylation of hMLH1 promoter region predominates in proximal colon cancer with microsatellite instability. , 2001, Gastroenterology.

[38]  Ajay N. Jain,et al.  Assembly of microarrays for genome-wide measurement of DNA copy number , 2001, Nature Genetics.

[39]  J. Herman,et al.  Analysis of adenomatous polyposis coli promoter hypermethylation in human cancer. , 2000, Cancer research.

[40]  A. de la Chapelle,et al.  Genetic and epigenetic modification of MLH1 accounts for a major share of microsatellite-unstable colorectal cancers. , 2000, The American journal of pathology.

[41]  B. Iacopetta,et al.  Routine detection of the replication error phenotype in clinical tumor specimens using fluorescence-SSCP. , 2000, BioTechniques.

[42]  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.

[43]  K. Kinzler,et al.  Genetic instabilities in human cancers , 1998, Nature.

[44]  S N Thibodeau,et al.  Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability. , 1998, Cancer research.

[45]  J. Herman,et al.  Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[46]  K. Hoang-Xuan,et al.  Determination of the replication error phenotype in human tumors without the requirement for matching normal DNA by analysis of mononucleotide repeat microsatellites , 1998, Genes, chromosomes & cancer.

[47]  J C Reed,et al.  Somatic Frameshift Mutations in the BAX Gene in Colon Cancers of the Microsatellite Mutator Phenotype , 1997, Science.

[48]  J. Herman,et al.  Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Hiroyuki Yamamoto,et al.  Frameshift mutator mutations , 1996, Nature.

[50]  K. Kinzler,et al.  Analysis of mismatch repair genes in hereditary non–polyposis colorectal cancer patients , 1996, Nature Medicine.

[51]  K. Kinzler,et al.  Microsatellite instability and mutations of the transforming growth factor beta type II receptor gene in colorectal cancer. , 1995, Cancer research.

[52]  B. Vogelstein,et al.  A genetic model for colorectal tumorigenesis , 1990, Cell.

[53]  Y. Nakamura,et al.  Genetic alterations during colorectal-tumor development. , 1988, The New England journal of medicine.

[54]  C. Compton,et al.  The CpG island methylator phenotype and chromosomal instability are inversely correlated in sporadic colorectal cancer. , 2007, Gastroenterology.

[55]  J. Issa,et al.  Epigenetics in colorectal cancer. , 2002, Current opinion in gastroenterology.

[56]  B. Leggett,et al.  Microsatellite instability in the insulin–like growth factor II receptor gene in gastrointestinal tumours , 1996, Nature Genetics.