Abstract 412: DNA methylation in ductal carcinoma in situ and its relation with disease progression
Authors: Kevin C. Johnson, Panpan Chen, Devin Koestler, Julia E. Weiss, Erik G. Jenson, Jonathan D. Marotti, Tracy Onega, Brock C. Christensen
Journal: Cancer Research (2014)

Abstract Ductal carcinoma in situ (DCIS) of the breast is a non-invasive lesion associated with a ten-fold increased relative risk for future invasive ductal cancer (IDC). DNA methylation is recognized as an important epigenetic regulator of gene expression and DNA methylation alterations are widespread in breast cancer. In addition, not all patients with DCIS will later present with invasive disease and epigenetic alterations in DCIS associated with disease progression are not clear. To investigate the relation of methylation with progression from DCIS to IDC we first identified patients with DCIS and a subsequent diagnosis of IDC through the New Hampshire Mammography Network (n=13). Next, we identified age-matched subjects with DCIS who did not have a subsequent diagnosis of IDC over a similar follow up period (n=27). Slides from all 40 patients underwent central pathology review by a breast pathologist, and 2 or 3 mm tissue cores were taken from archived FFPE blocks from selected areas of DCIS and adjacent normal tissue for DNA extraction and bisulfite modification. We measured DNA methylation genome-wide using the Illumina HumanMethylation450 BeadChip and processed the data using the ChAMP pipeline for quality control and normalization, after which 380,000 CpG sites remained in the data set. To investigate the relation of methylation with progression from DCIS to IDC, locus-specific differences in DNA methylation of 40 DCIS samples were examined using linear regression models fit to each of 380,000 CpG sites, modeling the logit-transformed methylation beta-values and adjusting for subject age and DCIS grade. Over 1,000 CpG sites exhibited large differences in DNA methylation levels (probes with a median Δβ &amp;gt; 0.2), and had a nominal P-value &amp;lt; 0.05, between patients with and without a subsequent diagnosis of IDC. Among the 1,007 CpG loci with significant and sizable changes in methylation, the majority (87.1%) exhibited increased methylation in women with a subsequent diagnosis of IDC compared to those without. We also sought to determine the relation of DNA methylation with DCIS grade among CpG loci that track to genes previously associated with DCIS grade, modeling the methylation as the dependent variable and DCIS grade (low/intermediate or high) as the independent variable. Comparing DCIS samples of low/intermediate grade with high grade we found that 15 CpG loci located near the transcriptional start site of the APC gene demonstrated significant (P &amp;lt; 0.05) hypermethylation in high grade DCIS compared to low/intermediate grade DCIS. Ongoing analyses are highlighting profound differences between DCIS and available matched adjacent-normal samples (n=15) and examining the enrichment of regulatory features among differentially methylated loci. This work contributes to the understanding of epigenetic alterations that occur in earlier stages of disease and illustrates the potential of DNA methylation as a predictive marker in DCIS. Citation Format: Kevin C. Johnson, Panpan Chen, Devin Koestler, Julia E. Weiss, Erik G. Jenson, Jonathan D. Marotti, Tracy Onega, Brock C. Christensen. DNA methylation in ductal carcinoma in situ and its relation with disease progression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 412. doi:10.1158/1538-7445.AM2014-412