Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells

Abstract

E-cadherin (E-cad) is a transmembrane adhesion glycoprotein, the expression of which is often reduced in invasive or metastatic tumors. To assess E-cad's distribution among different types of cancer cells, we used bisulfitesequencing for detailed, base-by-base measurement of CpG methylation in E-cad's promoter region in the NCI-60 cell lines. The mean methylation levels of the cell lines were distributed bimodally, with values pushed toward either the high or low end of the methylation scale. The 38 epithelial cell lines showed substantially lower (28%) mean methylation levels compared with the nonepithelial cell lines (58%). The CpG site at -143 with respect to the transcriptional start was commonly methylated at intermediate levels, even in cell lines with low overall DNA methylation. We also profiled the NCI-60 cell lines using Affymetrix U133 microarrays and found E-cad expression to be correlated with E-cad methylation at highly statistically significant levels. Above a threshold of f20% to 30% mean methylation, the expression of E-cad was effectively silenced. Overall, this study provides a type of detailed analysis of methylation that can also be applied to other cancer-related genes. As has been shown

The 3D tissue microenvironment modulates DNA methylation and E-cadherin expression in squamous cell carcinoma

“…While some E-cadherin promoter methylation data has shown much higher percentages of DNA methylation, our data are consistent with previous findings showing that a threshold of 20-30% is sufficient for E-cadherin gene silencing. 34 This supports evidence that, while histone modifications may prime a gene for silencing and cause low expression, the addition of DNA methylation is necessary to induce complete silencing. 38,39,52 Therefore, a gradient of epigenetic gene silencing may exist during the progression of cancer that dictates which genes are irreversibly silenced and which remain in a transient linked to their cellular microenvironment, as methylation-mediated gene silencing of the E-cadherin promoter is dynamically influenced by induction of complex cell-cell and cell-matrix interactions in the context of a 3D tissue.…”

“…Previous data examining CpG methylation within the E-cadherin promoter has shown that above a threshold of 20-30% methylation, E-cadherin gene expression is silenced. 34 Significantly, this same study showed consistent methylation at one specific CpG, which stromal compartment maintained loss of E-cadherin expression (Fig. 4B, thick arrow).…”

Comprehensive high-throughput arrays for relative methylation (CHARM)

“…This is critical for biological analysis, since epigenetic information is often chromosome-specific, e.g., imprinted genes. Furthermore, DNA methylation may have a threshold effect for regulating gene expression, e.g., ∼25% for E-cadherin in a broad range of cell types (Reinhold et al 2007). Note that transforming M directly into estimates of absolute methylation is not straightforward.…”

Efficacy of MS-275, a selective inhibitor of class I histone deacetylases, in human colon cancer models

“…In the HT29 and HCT116 models many integrins and tetraspanins, such as ß1-integrin, CD9 or CD81, were up-regulated, whereas these genes were down-regulated in Co5841, Co5776 and LoVo. Besides that, E-cadherin, an important suppressor of epithelial tumor cell invasiveness and metastasis which is epigenetically silenced through promoter methylation in many carcinomas (47), was downregulated in the non-responder models Co5841 and Co5776 upon MS-275 treatment. This implies that MS-275 did not induce the re-expression of E-cadherin, but rather promoted the hypermethylated status of the primary non-responder models.…”

“…This implies that MS-275 did not induce the re-expression of E-cadherin, but rather promoted the hypermethylated status of the primary non-responder models. E-Cadherin as well as claudin 4 (CLDN4), which were down-regulated in Co5776, are decreased in diffuse type and poorly differentiated tumors (47,48). Dysfunction of these proteins may therefore play a role in disruption of cellcell adhesion.…”