Examination of a CpG Island Methylator Phenotype and Implications of Methylation Profiles in Solid Tumors

Abstract

The CpG island methylator phenotype (CIMP), thoroughly described in colorectal cancer and to a lesser extent in other solid tumors, is important in understanding epigenetics in carcinogenesis and may be clinically useful for classification of neoplastic disease. Therefore, we investigated whether this putative phenotype exists in exposure-related solid tumors, where somatic gene alterations and enhanced clonal growth are selected for by carcinogens, and examined the ability of methylation profiles to classify malignant disease. We studied promoter hypermethylation of 16 tumor suppressor genes and 3 MINT loci (acknowledged classifiers of CIMP) in 344 bladder cancers, 346 head and neck squamous cell carcinomas (HNSCC), 146 non-small-cell lung cancer (NSCLC), and 71 malignant pleural mesotheliomas (MPM). We employed rigorous statistical methods to examine the distribution of promoter methylation and the usefulness of these profiles for disease classification. In bladder cancer, HNSCC, and NSCLC, there was a significant correlation (P < 0.0001) between methylation of the three MINT loci and methylation index, although the distribution of methylated loci varied significantly across these disease. Although there was a significant (P < 0.001) association between gene methylation profile and disease, rates of misclassification of each disease by their methylation profile ranged from 28% to 32%, depending on the classification scheme used. These data suggest that a form of CIMP exists in these solid tumors, although its etiology remains elusive. Whereas the gene profiles of hypermethylation among examined loci could not unequivocally distinguish disease type, the existence of CIMP and the relative preponderance of hypermethylation in these cancers suggest that methylation analysis may be clinically useful as a targeted screening tool.

DNA methylation profile of 28 potential marker loci in malignant mesothelioma

“…We generally find a higher methylation frequency compared to other investigators (e.g. [25,30]), which is likely due to our use of the quantitative and highly sensitive MethyLight technique. We have identified three loci (ESR1, SLC6A20 and SYK) that are significantly more methylated in MM than in non-tumor lung from lung cancer patients and several negative markers, of which APC is the strongest.…”

“…A three-marker methylation panel can distinguish between our MM and non-tumor lung tissues with considerable sensitivity but specificity needs to be strengthened through the identification of additional loci. The modest number of informative genes identified to date suggests that other types of loci might need to be examined [30]. An epigenomic approach, in which methylation of thousands of CpG islands can be quickly prescreened, followed by a detailed evaluation of selected markers by MethyLight, might prove more fruitful in rapidly identifying strong candidate genes that are highly MM-specific.…”

“…The power of DNA methylation as a marker derives not only from its ability to be detected in a wide variety of samples (from fresh specimens to bodily fluids and archival paraffin-embedded specimens) but also from the defined localization of the lesion (in promoter CpG islands of genes), allowing the design of gene-specific, targeted probes [22]. To date, findings regarding the role of DNA methylation in MM are still rather limited [23][24][25][26][27][28][29][30][31][32][33][34][35].…”

Clustering of Lynch syndrome malignancies with no evidence for a role of DNA mismatch repair

“…Methylation of this region has been previously shown to correlate with lack of MLH1 expression and thus been defined as the "critical region" within the MLH1 promoter (15). Two additional MLH1 COBRA assays (-751 to -573 and -26 to +113) were evaluated along with sequences corresponding to the MINT1,-2,-12,-25, and -31 loci (16,17). PCR primers, product sizes, and restriction sites evaluated are presented in supplemental Table 1.…”

“…The CpG island methylator phenotype (CIMP) has been thoroughly described in colorectal cancer and to a lesser extent in other solid tumors including endometrial cancer (16,17,18). This phenotype is often associated with distinctive clinical characteristics and prognosis.…”