Hypermethylation of CpG islands is more prevalent than hypomethylation across the entire genome in breast carcinogenesis

This study aimed to establish a high-throughput, genome-wide and non-gene-specific approach to assess the methylation status of multiple CpG islands in parallel and employ it to detect the CpG island methylation profiling alterations in breast carcinogenesis. We used methylation-sensitive restriction fingerprint (MSRF) to screen the permutations of primers that could detect varied and specific methylation profiling in genomic DNA isolated from four different cell lines. Five permutations of nine arbitrary primers were determined for the following experiments based on the above test. We then examined the methylation profiling alterations of CpG islands in 31 breast cancer tissue samples relative to their adjacent non-neoplastic tissues with modified MSRF that replaced silver staining with denatured high-performance liquid chromatography for size fraction. We found that two pairs of primers could reveal specific alterations of CpG methylation in the examined tissues, and 83.9% (26/31) of breast cancer tissues exhibited specific CpG island methylation profiling relative to their adjacent non-neoplastic tissues. Size fraction analysis revealed that hypermethylation of CpG islands was responsible for the aberrant methylation profiling in breast cancer tissues. Our work not only established a relative high-throughput, genome-wide and economic method to detect methylation alterations of CpG island profiling, but also revealed that hypermethylation of CpG islands was more prevalent than hypomethylation across the entire genome in our examined cancer tissues. The methylation profiling alterations revealed by two primer pairs used in the present study might be a novel marker for breast cancer.