The changes in DNA methylation status in cancer cells are characterized by 
hypermethylation of promoter CpG islands and diffuse genomic hypomethylation. 
Alu and long interspersed nucleotide element-1 (LINE-1) 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 Alu and LINE-1 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 Alu and LINE-1 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. Alu 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, LINE-1 methylation significantly 
decreased from normal to ADH/FEA, while it was similar in ADH/FEA, DCIS and IBC. 
In IBC, Alu hypomethylation correlated with negative estrogen receptor (ER) 
status, and LINE-1 hypomethylation was associated with negative ER status, ERBB2 
(HER2) amplification and p53 overexpression. Alu and LINE-1 methylation status 
was significantly different between breast cancer subtypes, and the HER2 
enriched subtype had lowest methylation levels. In survival analyses, low Alu 
methylation status tended to be associated with poor disease-free survival of 
the patients. Our findings suggest that LINE-1 hypomethylation is an early event 
and Alu hypomethylation is probably a late event during breast cancer 
progression, and prominent hypomethylation of Alu and LINE-1 in HER2 enriched 
subtype may be related to chromosomal instability of this specific subtype.