Abstract 1071: Age-dependent DNA methylation in normal breast epithelium and breast cancer

Abstract

Abstract Breast cancer risk factors include age, genetic alterations, weight, diet and others. More recently accumulating evidence suggests that epigenetic alterations are frequent and play important role in breast cancer development and progression. Epigenetic alterations include changes in DNA methylation, histone modifications and miRNA expression in the absence of changes in DNA sequence. The epigenetic changes in cancer include global loss of DNA methylation that might lead to genomic instability and gain of methylation at many promoters of tumor suppressor genes that leads to gene silencing. Interestingly, work from our own laboratory and others have established that in many different tissues, DNA methylation changes due to age have similar patterns as to changes that occur in cancer. Therefore, the goal of this study is to identify and characterize age-dependent DNA methylation changes in normal breast epithelium and their contribution to breast cancer development. To differentiate between age-dependent and independent DNA methylation changes, we utilized DNA extracted from 27 primary human mammary epithelial cells (age range 33-82 years old) derived from adjacent or contralateral normal mammary tissue of breast cancer patients. We measured DNA methylation using a highly sensitive methodology developed in our laboratory called Digital Restriction Enzyme Analysis of Methylation (DREAM). We also studied DNA methylation in six different breast cancer cell lines by DREAM. We also used publically available 450K TCGA data for 685 breast tumor and 98 normal samples. Using bioinformatic approach, we have defined age dependent (Spearman R > |0.38|, p <0.05) and independent (Spearman R < |0.37|, p>0.05) sites that exhibit DNA methylation changes in normal breast epithelium. Interestingly, we found that the age-related genes are more seeded (exhibit low level of methylation) in their promoter CpG islands and are enriched for polycomb group target genes compared to the non-age related genes (p value = 0.032). Furthermore, these age-related genes (for example HOXD9, TDRD10, MYOD1, DPYS, GDA, GIPC2, FAM162B, LAMA1, PKDREJ, etc) have increased DNA methylation in tumors compared to the normal samples in TCGA with a methylation difference of up to 50%. These changes are significantly different compared to not-age related genes or random genes (p<0.0001). The age-related genes that gained DNA methylation in tumors in TCGA dataset, were also hypermethylated in breast cancer cell lines compared to immortalized human mammary epithelial cells. Thirty one percent of the common genes between TCGA data set and breast cancer cell lines, showed decreased mRNA expression in RNA-seq data available through the TCGA data portal. Therefore, in this study we have characterized age-dependent epigenetic changes in normal breast epithelium as potential breast cancer risk associated alterations. Citation Format: Shoghag B. Panjarian, Carolyn Slater, Jozef Madzo, Jaroslav Jelinek, Xiaowei Chen, Jean-Pierre Issa. Age-dependent DNA methylation in normal breast epithelium and breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1071. doi:10.1158/1538-7445.AM2015-1071