<i>Alu</i> and <i>LINE-1</i> Hypomethylation Is Associated with HER2 Enriched Subtype of Breast Cancer

<div><p>The changes in DNA methylation status in cancer cells are characterized by hypermethylation of promoter CpG islands and diffuse genomic hypomethylation. <i>Alu</i> and long interspersed nucleotide element-1 (<i>LINE-1</i>) are non-coding genomic repetitive sequences and methylation of these elements can be used as a surrogate marker for genome-wide methylation status. This study was designed to evaluate the changes of <i>Alu</i> and <i>LINE-1</i> hypomethylation during breast cancer progression from normal to pre-invasive lesions and invasive breast cancer (IBC), and their relationship with characteristics of IBC. We analyzed the methylation status of <i>Alu</i> and <i>LINE-1</i> in 145 cases of breast samples including normal breast tissue, atypical ductal hyperplasia/flat epithelial atypia (ADH/FEA), ductal carcinoma in situ (DCIS) and IBC, and another set of 129 cases of IBC by pyrosequencing. <i>Alu</i> methylation showed no significant changes during multistep progression of breast cancer, although it tended to decrease during the transition from DCIS to IBC. In contrast, <i>LINE-1</i> methylation significantly decreased from normal to ADH/FEA, while it was similar in ADH/FEA, DCIS and IBC. In IBC, <i>Alu</i> hypomethylation correlated with negative estrogen receptor (ER) status, and <i>LINE-1</i> hypomethylation was associated with negative ER status, <i>ERBB2 (HER2)</i> amplification and p53 overexpression. <i>Alu</i> and <i>LINE-1</i> methylation status was significantly different between breast cancer subtypes, and the HER2 enriched subtype had lowest methylation levels. In survival analyses, low <i>Alu</i> methylation status tended to be associated with poor disease-free survival of the patients. Our findings suggest that <i>LINE-1</i> hypomethylation is an early event and <i>Alu</i> hypomethylation is probably a late event during breast cancer progression, and prominent hypomethylation of <i>Alu</i> and <i>LINE-1</i> in HER2 enriched subtype may be related to chromosomal instability of this specific subtype.</p>