Introduction Development of resistance to tamoxifen is an important clinical issue in the treatment of breast cancer. parallel sequencing to analyze a well-established tamoxifen-resistant cell line model (TAMR) consisting of 4 resistant and one parental cell line. Another tamoxifen-resistant cell line model system (LCC1/LCC2) was used to validate the DNA methylation and gene expression results. Results Significant differences were observed in global gene expression and DNA methylation profiles between the parental tamoxifen-sensitive cell line and the 4 tamoxifen-resistant TAMR sublines. The 4 TAMR cell lines exhibited higher methylation levels as well as an inverse relationship between gene expression and DNA Araloside VII methylation in the promoter regions. A Araloside VII panel of genes including and exhibited lower gene expression in resistant vs. parental cells and concurrent increased promoter Sp7 CGI methylation in resistant vs. parental cell lines. A major part of the methylation gene expression and pathway alterations observed in the TAMR model were also present in the LCC1/LCC2 cell line model. More importantly high expression of and alterations of other and gene family members as well as RB-related pocket protein genes in TAMR highlighted stem cell-associated pathways as being central in the resistant cells Araloside VII and imply that cancer-initiating cells/cancer stem-like cells may be involved in tamoxifen resistance in this model. Conclusion Our data highlight the likelihood that resistant cells emerge from cancer-initiating cells/cancer stem-like cells and imply that these cells may gain further advantage in growth via epigenetic mechanisms. Illuminating the expression and DNA methylation features of putative cancer-initiating cells/cancer stem cells may suggest novel strategies to overcome tamoxifen resistance. Introduction Around 80% of breast cancer patients present with primary breast tumors that are estrogen receptor (ER) alpha-positive suggesting that this tumor is dependent on estrogen for growth [1 2 Accordingly most of these patients are offered endocrine therapy which currently consists of the anti-estrogen tamoxifen or aromatase inhibitors. These drugs can be used successfully both in the adjuvant and advanced disease settings. Tamoxifen belongs to the selective ER modulator class of drugs that act both as antagonists and as agonists in an ER-dependent and tissue-dependent manner . For example in breast cancer tissue tamoxifen acts as a competitive estrogen antagonist by competing with estrogen for binding to ER thereby inhibiting the growth of estrogen-dependent breast cancer cells . However about one-third of primary ER-positive breast tumors do not benefit from adjuvant tamoxifen treatment resulting in disease recurrence . In metastatic disease disease progression eventually occurs in most patients receiving tamoxifen treatment. Acquired endocrine resistance is suggested to develop as a result of a complex set of molecular changes including specific gene expression alterations and/or modifications and loss of ER . These changes have been observed in models of tamoxifen resistance and in ER-positive breast cancer patients with recurrent disease following endocrine treatment . As it is currently not possible to predict sensitivity/resistance to endocrine treatment in ER-positive breast cancer patients new tests to identify endocrine-resistant ER-positive breast cancer are being developed using different molecular markers . Several distinct molecular mechanisms may lead to tamoxifen resistance and within individual tumors different cancer cells may use different mechanisms complicating the evaluation of tamoxifen resistance mechanism(s) when examining whole tumor samples. These obstacles Araloside VII have led to studies of isogenic tamoxifen-resistant breast cancer cell line model systems that may have some advantages in pinpointing individual resistance mechanisms. The estrogen-responsive and tamoxifen-sensitive human breast cancer cell line MCF-7 [9 10 and its derived tamoxifen-resistant sub-lines MCF-7/TAMR-1 MCF-7/TAMR-4 MCF-7/TAMR-7 and MCF-7/TAMR-8 [11 12 constitute a well-established.