Our findings have several important implications for the understanding of breast cancer. First, we have definitively identified distinct epigenomic subtypes of breast cancer and documented the existence of a global CIMP in breast cancer. Aberrant hypermethylation of genes has been described in breast cancer previously (26
), and the methylation state of specific genes has been linked to outcome (52
). However, the existence of a global B-CIMP has remained elusive before our study.
Our global approach robustly identified the B-CIMP as a characteristic of a subset of hormone-positive tumors. The ER has a profound effect on transcriptional activation and repression of many genes, and it may be that these changes contribute to patterning the epigenome. However, from our data, it does not appear that ER/PR positivity alone dictates B-CIMP status because our analysis above repeatedly identified a subset of hormone-positive tumors that were not positive for CIMP. Perhaps, other genetic or epigenetic events are important in dictating epigenomic fate in these tumors. Also, there may exist other epigenomic subgroups of breast cancer within the major methylome subclasses that we describe here. Additional studies will be required to address this possibility.
In our study, B-CIMP+
tumors demonstrated a lower propensity for metastasis and a better clinical outcome than B-CIMP−
tumors. The association of better clinical outcome with CIMP+
tumors could be seen across multiple malignancies (breast, colon, and glioma) (2
). In these tumors, it may be that the epigenomic defects causing the CIMP initially helped promote neoplastic transformation but inactivate genes that facilitate tumor aggressiveness in later stages of cancer progression. It is important to note, however, that the association of methylation at CIMP genes with good clinical outcome is not universally applicable to methylation at all genes. Methylation of specific candidate genes or groups of genes has been associated with poorer prognosis, and these genes may have an effect on tumor aggressiveness independent of the CIMP (27
). Genes such as these, including CDKN2A, PTPRD
, and BRCA1
, were not included among the B-CIMP loci.
The genomic basis of prognostic transcriptional signatures is unclear. Our data demonstrate that aberrations in the DNA methylome explain many of the mRNA expression differences that underlie these signatures. The tight association of these changes with a genome-wide concerted hypermethylation phenotype and their enrichment for PcG targets argues against the inactivation of these genes as being sporadic events. Rather, the B-CIMP phenotype is consistent with a global, systematic derangement in epigenetic regulation. The methylome profiles we have derived and the associated CIMP repression signature provide a previously unknown mechanistic link between breast cancers with differing metastatic behavior and transcriptional signatures that predict metastatic relapse. However, although we show that methylation-associated gene silencing underlies many metastasis-associated gene expression changes, genetic changes are undoubtedly important as well. Indeed, mutations of a number of genes such as BRCA1, PTEN
, and ERBB2
have been shown to be associated with an increased risk of metastasis (5
). The relationship between these mutations and the B-CIMP phenotype remains to be elucidated, and it is likely that both genetic and epigenetic alterations contribute to the metastatic phenotype. BRCA1 has recently been shown to up-regulate DNMT1, which may help explain the association between BRCA1 mutation, basal-type tumors, and the lack of methylation we have observed in our study among HR−
breast cancers (60
). Future studies will be required to define any potential causal relationship between mutations and derangements in the epigenomic landscape.
Our data show a large-scale consensus between CIMP genes from different human cancers. The CIMP in these different malignancies target many of the same genes, which are PcG targets. We speculate that these similarities reflect common mechanistic foundations. Despite their similarities, differences do exist between the PcG targets that comprise the B-, C-, and G-CIMP, which may reflect a degree of tissue or organ specificity.
In summary, these data provide an epigenomic framework for understanding the transcriptomic signatures present in breast cancers with differing metastatic behaviors. Our findings may enable the development of new molecular diagnostics that more accurately reflect the epigenomic underpinnings of breast cancer prognosis. These diagnostics may help further refine our ability to implement personalized medicine for breast cancer patients.