One key component of the cancer epigenome is an altered DNA methylation pattern by global hypomethylation and promoter localized hypermethylation [1
]. These methylation changes can result in an alteration in structure and function of DNA, such as unwanted activation of repeat elements, abnormal transcriptional regulation of genes involved in cancer initiation and progression, and predisposition to genomic instability through disruption of chromosome replication control [2
Numerous studies have paid attention to the difference of DNA methylation profiles between malignant breast cells and normal control, regardless of their origins [4
]. Molecular subtype taxonomy of breast cancers and breast cancer cell lines is more and more important, and the identified new biomarkers that inflect cell origin might be promising targets for disease treatment [6
]. MCF-7 and MDA-MB-231 are widely used breast cancer cell lines in cancer research [9
]. Both cell lines were established from metastatic cells in pleural effusions collected from two individual ductal invasive breast cancers [9
]. MCF-7 is classified as a luminal (epithelium)-like cell line with relatively low invasive potential, whereas MDA-MB-231 is a mesenchymal-like cell line which is highly invasive [6
]. Comparison of the two cell lines in terms of DNA copy number variation (CNV) and gene expression profiles have been performed [6
]. However, a comprehensive picture of DNA methylation patterns, DNA copy number alterations and gene expression levels genome wide for the two cell lines remains to be established.
A detailed exploration of the role of DNA methylation in tumorigenesis depends on sensitive methods to precisely describe DNA methylation states genome wide. Methylation-specific digital karyotyping (MSDK) is one such powerful method [12
], which combines the use of methylation-sensitive restriction enzyme digestion and sequencing by a SAGE-like method to achieve genome-wide DNA methylation maps [12
]. However, this technique is limited by a relatively low throughput and a high cost of sequencing. Solexa 1G Genome Analyzer is a new generation sequencer which can perform massively parallel signature sequencing. Thus, it has been applied in epigenetic studies to improve currently existing techniques [14
]. In the present study, we establish a method, modified methylation-specific digital karyotyping (MMSDK) on the basis of the combination of original MSDK [12
] and the new sequencing technique using Solexa 1G Genome Analyzer. In the original MSDK method ditags are produced followed by clone sequencing. In MMSDK tags are directly amplified by PCR using a pair of universal primers and subsequently sequenced using a Solexa sequencer. Finally, tags (reads) are mapped back to the human genome. We chose MCF-7 and MDA-MB-231 as representatives for luminal-like and mesenchymal-like subtypes, respectively, and used these cell lines for comparative analysis by MMSDK, array comparative genomic hybridization (aCGH) and gene expression microarray analysis to explore the correlation between DNA methylation, genomic stability and gene expression. We demonstrate that MMSDK is a genome-wide, high-throughput and cost-effective method to analyze DNA methylation in large genomes such as the human and that MMSDK can be used to reveal connections between genomic, epigenetic and transcriptional features.