Genetics supersedes epigenetics in colon cancer phenotype. Cancer Cell 4, 121-31

The Burnham Institute, La Jolla Cancer Center, Cancer Genetics and Epigenetics Program, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
Cancer Cell (Impact Factor: 23.52). 09/2003; 4(2):121-31. DOI: 10.1016/S1535-6108(03)00190-9
Source: PubMed


A CpG island DNA methylator phenotype has been postulated to explain silencing of the hMLH1 DNA mismatch repair gene in cancer of the microsatellite mutator phenotype. To evaluate this model, we analyzed methylation in CpG islands from six mutator and suppressor genes, and thirty random genomic sites, in a panel of colorectal cancers. Tumor-specific somatic hypermethylation was a widespread age-dependent process that followed a normal Gaussian distribution. Because there was no discontinuity in methylation rate, our results challenge the methylator phenotype hypothesis and its hypothetical pathological underlying defect. We also show that the mutator phenotype dominates over the gradual accumulation of DNA hypermethylation in determining the genotypic features that govern the phenotypic peculiarities of colon cancer of the mutator pathway.

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Available from: Kentaro Yamashita
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    • "Some investigators conferred distinctive phenotypic and biological properties to the tumors displaying a so-called CpG island methylator phenotype (CIMP), which was viewed as preceding the development of a subset of MSI colon cancers [18,19]. However, no apparent bimodal distribution was seen for the somatic hypermethylation alterations in gastrointestinal cancers [20,21] thus challenging the CIMP hypothesis. Nearly 15 years later, the CIMP concept, despite the publication of many CIMP papers (reviewed in [22]) still awaits for a clear definition, including a stable set of CIMP markers, as well as for identification of the underlying methylator gene(s) [22,23]. "
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    ABSTRACT: Background Recent work led to recognize sessile serrated adenomas (SSA) as precursor to many of the sporadic colorectal cancers with microsatellite instability (MSI). However, comprehensive analyses of DNA methylation in SSA and MSI cancer have not been conducted. Methods With an array-based methylation sensitive amplified fragment length polymorphism (MS-AFLP) method we analyzed 8 tubular (TA) and 19 serrated (SSA) adenomas, and 14 carcinomas with (MSI) and 12 without (MSS) microsatellite instability. MS-AFLP array can survey relative differences in methylation between normal and tumor tissues of 9,654 DNA fragments containing all NotI sequences in the human genome. Results Unsupervised clustering analysis of the genome-wide hypermethylation alterations revealed no major differences between or within these groups of benign and malignant tumors regardless of their location in intergenic, intragenic, promoter, or 3′ end regions. Hypomethylation was less frequent in SSAs compared with MSI or MSS carcinomas. Analysis of variance of DNA methylation between these four subgroups identified 56 probes differentially altered. The hierarchical tree of this subset of probes revealed two distinct clusters: Group 1, mostly composed by TAs and MSS cancers with KRAS mutations; and Group 2 with BRAF mutations, which consisted of cancers with MSI and MLH1 methylation (Group 2A), and SSAs without MLH1 methylation (Group 2B). AXIN2, which cooperates with APC and β-catenin in Wnt signaling, had more methylation alterations in Group 2, and its expression levels negatively correlated with methylation determined by bisulfite sequencing. Within group 2B, low and high AXIN2 expression levels correlated significantly with differences in size (P = 0.01) location (P = 0.05) and crypt architecture (P = 0.01). Conclusions Somatic methylation alterations of AXIN2, associated with changes in its expression, stratify SSAs according to some clinico-pathological differences. We conclude that hypermethylation of MLH1, when occurs in an adenoma cell with BRAF oncogenic mutational activation, drives the pathway for MSI cancer by providing the cells with a mutator phenotype. AXIN2 inactivation may contribute to this tumorigenic pathway either by mutator phenotype driven frameshift mutations or by epigenetic deregulation contemporary with the unfolding of the mutator phenotype.
    Full-text · Article · Jun 2014 · BMC Cancer
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    • "The notion of CpG island methylator phenotype (CIMP) arose from the initial observation that a subset of colorectal cancers has higher frequency of DNA hypermethylation at candidate tumor-suppressor promoters ( Toyota et al. 1999). Thus far, the hypermethylated sites used to characterize CIMP have not been standardized, leading to inconsistencies in whether a colon cancer is appropriately described as CIMP ( Yamashita et al. 2003; Issa 2004; Anacleto et al. 2005). Consequently, clinical studies attempting to correlate CIMP with prognosis and responsiveness to 5-fluorouracil chemotherapy have produced contradicting results ( Van Rijnsoever et al. 2003; Shen et al. 2007; Barault et al. 2008; Lee et al. 2008; Kim et al. 2009; Ogino et al. 2009). "
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    ABSTRACT: A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to be hypermethylated in CIMP tumors only; and importantly, 80% of these sites were located in CpG islands. These data demonstrate on a genome-wide level that the additional hypermethylation seen in CIMP tumors occurs almost exclusively at CpG islands and support definitively that these tumors were appropriately named. When these sites were examined more closely, we found that 25% were adjacent to sites that were also hypermethylated in non-CIMP tumors. Thus, CIMP is also characterized by more extensive methylation of sites that are already prone to be hypermethylated in colon cancer. These observations indicate that CIMP tumors have specific defects in controlling both DNA methylation seeding and spreading and serve as an important first step in delineating molecular mechanisms that control these processes.
    Full-text · Article · Feb 2012 · Genome Research
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    • "DNA methylation status was determined for TSHZ1, 2, and 3 gene promoters, using genomic DNA from the same cells/tissues analyzed for gene expression. We employed the sodium bisulfite modification method followed by PCR and DNA sequencing as previously described [53]. Briefly, DNA sequences surrounding the transcription initiation sites of the TSHZ genes were retrieved from the Ensembl Human Genome Database, and the CpG-rich regions were identified. "
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    ABSTRACT: Neoplastic cells harbor both hypomethylated and hypermethylated regions of DNA. Whereas hypomethylation is found mainly in repeat sequences, regional hypermethylation has been linked to the transcriptional silencing of certain tumor suppressor genes. We attempted to search for candidate genes involved in breast/prostate carcinogenesis, using the criteria that they should be expressed in primary cultures of normal breast/prostate epithelial cells but are frequently downregulated in breast/prostate cancer cell lines and that their promoters are hypermethylated. We identified several dozens of candidates among 194 homeobox and related genes using Systematic Multiplex RT-PCR and among 23,000 known genes and 23,000 other expressed sequences in the human genome by DNA microarray hybridization. An additional examination, by real-time qRT-PCR of clinical specimens of breast cancer, further narrowed the list of the candidates. Among them, the most frequently downregulated genes in tumors were NP_775756 and ZNF537, from the homeobox gene search and the genome-wide search, respectively. To our surprise, we later discovered that these genes belong to the same gene family, the 3-member Teashirt family, bearing the new names of TSHZ2 and TSHZ3. We subsequently determined the methylation status of their gene promoters. The TSHZ3 gene promoter was found to be methylated in all the breast/prostate cancer cell lines and some of the breast cancer clinical specimens analyzed. The TSHZ2 gene promoter, on the other hand, was unmethylated except for the MDA-MB-231 breast cancer cell line. The TSHZ1 gene was always expressed, and its promoter was unmethylated in all cases. TSHZ2 and TSHZ3 genes turned out to be the most interesting candidates for novel tumor suppressor genes. Expression of both genes is downregulated. However, differential promoter methylation suggests the existence of distinctive mechanisms of transcriptional inactivation for these genes.
    Full-text · Article · Mar 2011 · PLoS ONE
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