Aberrant methylations in cancer cells: Where do they come from?

Abstract

Cancer epigenetics is rapidly moving into a translational phase, and knowledge on how aberrant DNA methylation is induced is becoming important. Aging, chronic inflammation, and viral infections are known to promote methylation of non-core regions of promoter CpG islands (CGI). The non-core methylation and 'seeds of methylation', scattered methylation in a CGI, are considered to serve as triggers for dense methylation of a promoter CGI, which permanently represses expression of its downstream gene. Decreased gene transcription is an important factor that promotes induction of dense methylation. The presence of the CGI methylator phenotype (CIMP), in which methylation of multiple CGI was observed, is under dispute. Some gastric cancer cell lines have increased rates of de novo methylation, and neuroblastoma cases with CIMP show qualitatively different prognosis from those without. This strongly supports the presence of CIMP, but it seems to contain multiple entities. Limited knowledge is available for epimutagens, the chemicals that induce DNA demethylation or methylation. We have developed an assay system to detect demethylating agents, and an assay system for methylating agents is necessary. Efforts in the field on how aberrant methylation is induced will lead to new cancer prevention, diagnostics, and therapeutics. (1) The first example was identified for the RB gene in sporadic retinoblastomas in 1993 (2,3) followed by VHL, (4) CDKN2A ( p16 ), (5,6) CDH1 (E-cadherin), (7,8) and hMLH1.(9) Now, many tumorsuppressor genes are known to be inactivated by methylation of their promoter CGI in a wide variety of cancers.(1) Methylation of a promoter CGI excludes some methylation-sensitive transcription factors, such as CTCF, and recruits methyl-CpG binding proteins, such as MeCP2 and MBD1-MBD3.(10) These methyl-CpG binding proteins further recruit histone deacetylases, histone methyltransferases, and heterochromatin proteins.(11) It is believed that changes in chromatin structure will block the access of transcription complex to DNA, and repress transcription.In parallel with the mechanistic studies on how DNA methylation leads to gene silencing, the search for genomic regions aberrantly methylated in cancers has also made a lot of progress. (12) In the late 1990s, before the human genome sequence was available, several genome-wide screening methods were developed, such as restriction landmark genomic scanning-methylation, methylation-sensitive-representational difference analysis (MS-RDA), methylation-sensitive-arbitrarily primed PCR, and methylated CpG island amplification-RDA.(13 -17) These methods revealed that cancers harbor many aberrantly methylated genomic regions. Now, owing to completion of the sequencing of the human genome, it has become evident that, even if limited to CGI in promoter regions or putative promoter regions (5′ regions) of genes, most cancers have multiple aberrant methylations. (18)(19)(20)(21) These aberrant methylations are considered to provide a good source of tumor markers,and targets ...

DNA methylation of microRNA genes in gastric mucosae of gastric cancer patients: Its possible involvement in the formation of epigenetic field defect

“…33,34 Also, males have twice as high an incidence of gastric cancers as females. 1 In H. pylori-negative healthy volunteers, methylation levels of miR-124a-1, miR-124a-2 and miR-124a-3 were not correlated with age (Spearman correlation test: r 5 0.…”

Silencing of tissue factor pathway inhibitor‐2 gene in malignant melanomas

“…It is generally difficult to distinguish genes that are functional in a tissue, even with low expression levels, such as Rb, BRCA1 and HIF-1, [33][34][35] from genes that are not functional in a tissue and have little expression. 36 To make the distinction, it was considered informative to examine whether or not TFPI-2 expression can be induced in response to cellular stress. Therefore, HEMs were irradiated with increasing doses of UVB.…”

ABF-1 is frequently silenced by promoter methylation in follicular lymphoma, diffuse large B-cell lymphoma and Burkitt's lymphoma

“…The cloned plasmids were purified with Quiaprep Spin Miniprep Kit (Qiagen) and sequenced using BigDye Terminator v1.1 Cycle Sequencing Kit and ABI Prism 310 Genetic Analyzer (both from Applied Biosystems, Warrington, UK). Clones (5)(6)(7)(8) were sequenced from each sample. The methylation intensity was expressed as percent of methylated CpGs and shown by color coding.…”

“…Methylation of promoter CpG islands generally results in gene silencing. 7 We investigated the methylation status of the ABF-1 promoter CpG island using two commonly accepted methods: bisulfite sequencing and pyrosequencing. We first compared ABF-1 promoter methylation in BL and cHL cell lines (Figure 2b).…”

“…Along with genomic mutations robust and stable gene inactivation has been shown to be achieved by epigenetic gene silencing. 7 We therefore determined whether this mechanism contributes to the regulation of ABF-1 expression in distinct types of B-NHLs. Figure 1 Activated B-cell factor 1 (ABF-1) expression can be reactivated by 5-aza-dC in follicular lymphoma (FL) and Burkitt's lymphoma (BL) cell lines.…”