Abstract 2786: Methylation profiling of endometrial cancers from a population-based case control study

Abstract

Background: Analysis of DNA methylation profiles may be useful for developing novel tumor classifications and identifying potential early detection markers. Several studies have measured methylation of CpG islands in endometrial cancer but analyses were mainly limited to small sets of candidate genes. Methods: We conducted methylation profiling on 166 representative paraffin embedded endometrial cancer tissues from the Polish endometrial cancer study, a population-based case-control study conducted in Warsaw and Lodz, 2000-2003. Tissue cores of microscopically confirmed regions of well-preserved cancer were removed from formalin fixed paraffin embedded blocks using a 1.0 mm diameter needle, followed by DNA extraction and bisulfite treatment. We used the Illumina Golden Gate platform to assess CpG methylation at 1505 sites representing 807 genes from various classes, including tumor suppressor genes, oncogenes, DNA repair genes, and cell cycle control genes. After normalization and restricting the analysis to genes that showed a standard deviation of >0.15, we conducted unsupervised hierarchical clustering analysis. In addition, we analyzed candidate methylation targets in relation to histologic subtype, grade, and endometrial cancer risk factors. Replicate samples included on the arrays showed a high reproducibility of the assay. Results: DNA extracted from tissue blocks had excellent quantity and quality for methylation profiling. A third of the target genes showed consistently high methylation in all endometrial cancers, while another third had consistently low methylation levels. In total, 482 methylation targets showed a standard deviation of >0.15 across all samples. Unsupervised hierarchical clustering based on the informative subset generated four clusters with distinct methylation profiles. Preliminarily, histologic subtypes were differentially distributed across the four clusters (p=0.03). Tumor grade and endometrial cancer risk factors were unrelated to cluster membership. Of the 166 endometrial cancers tested, 36 (21%) showed strong methylation of MLH1, which encodes for a mismatch repair protein. In addition, we analyzed ten markers previously suggested as indicative of a “methylator phenotype” in colorectal cancers (CIMP), but did not find a similar entity in endometrial cancers. Conclusions: Our data indicate that there are many consistently methylated genes in endometrial cancers that might provide targets for novel early detection assays. A subset of methylation markers showed heterogeneity between cancers and was associated with different distribution of histologic subtypes. Preliminarily, methylation patterns were unrelated to age and body mass; further analyses of endometrial cancer risk factor associations are ongoing. In addition, we have preliminarily estimated that MLH1 methylation occurs in 21% of endometrial cancers in a population-based study. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2786.