DNA methylation in the promoter region of the p16 (CDKN2/MTS-1/INK4A) gene in human breast tumours

Abstract

SummaryThe p16 (CDKN2/MTS-1/INK4A) gene is one of several tumour-suppressor genes that have been shown to be inactivated by DNA methylation in various human cancers including breast tumours. We have used bisulphite genomic sequencing to examine the detailed sequence specificity of DNA methylation in the CpG island promoter/exon 1 region in the p16 gene in DNA from a series of human breast cancer specimens and normal human breast tissue (from reductive mammaplasty). The p16 region examined was unmethylated in the four normal human breast specimens and in four out of nine breast tumours. In the other five independent breast tumour specimens, a uniform pattern of DNA methylation was observed. Of the nine major sites of DNA methylation in the amplified region from these tumour DNAs, four were in non-CG sequences. This unusual concentration of non-CG methylation sites was not a general phenomenon present throughout the genome of these tumour cells because the methylated CpG island regions of interspersed L1 repeats had a pattern of (almost exclusively) CG methylation similar to that found in normal breast tissue DNA and in DNA from tumours with unmethylated p16 genes. These data suggest that DNA methylation of the p16 gene in some breast tumours could be the result of an active process that generates a discrete methylation pattern and, hence, could ultimately be amenable to theraputic manipulation.

Breast Cancer Intra-Tumor Heterogeneity: One Tumor, Different Entities

“…The question that now remains to be answered is whether breast cancer Given that BRCA1 is recognized as an important susceptibility gene, it can be assumed that both epigenetic modifications and mutations participate in the initiation of an oncogenic phenotype 85 . Other tumor-suppressor genes, such as CDKN2A and PTEN, undergo CpG island promoter methylation, but in normal cells, the promoter region is unmethylated 86,87 . Epigenetic studies have revealed that breast cancer subtypes display different methylation profiles and are epigenetically distinct 88 .…”

The evidence for functional non-CpG methylation in mammalian cells

“…Four independent studies analyzing breast cancer, prostate cancer, and brain lymphoma have reported methylation of non-CpG sites (mostly CpNpG sites, where N indicates A, C, T, or G) in the CDKN2A promoter. [20][21][22][23] NonCpG methylation has been reported at other important cancerrelated genes, such as GSTP1 24 and TP53 25 in endometrial and lung cancer specimens, respectively. Whether non-CpG methylation is a contributing factor or a consequence of these diseases is currently unclear.…”

Mechanisms of inactivation of E-cadherin in breast carcinoma: modification of the two-hit hypothesis of tumor suppressor gene

“…A high proportion (37.3%) of hypermethylated alleles were present in our breast carcinomas and all three islands were simultaneously hypermethylated in all hypermethylated tumors. To further explore whether there was variation in methylation status at dierent CpG sites in the same CpG island (as seen in hypermethylated p16, Gonzalgo et al, 1997;Woodcock et al, 1999), the methylation pattern of individual CpG sites was examined in greater detail by bisul®te-modi®ed genomic sequencing (Figure 4) in selected tumor tissues, and a uniform pattern of methylation of entire CpG sites was Figure 2 Transcriptional mechanisms suggested to be implicated in reduced/negative E-cadherin (E-cad) expression. (a) Schematic diagram of the E-cad promoter showing the 7160 polymorphic site, the E-boxes for Snail binding, and three CpG islands implicated in hypermethylation.…”