Genome-wide DNA methylation assessment of ‘BRCA1-like’ early-onset breast cancer: Data from the Australian Breast Cancer Family Registry

Highlights

• Some young women have widespread blood derived DNA methylation at the BRCA1 promoter

• These women also have reduced blood derived DNA methylation at TWIST2 and CTBP1

• Corresponding tumour DNA from these women have elevated methylation at BRCA1

• These tumours also have other DMR when compared to other breast cancer molecular subtypes.

Abstract

Breast cancers arising in women carrying a germline mutation in BRCA1 are typically high-grade, early-onset and have distinct morphological features (BRCA1-like). However, the majority of early-onset breast cancers of this morphological type are not associated with germline BRCA1 mutations or constitutional BRCA1 promoter methylation. We aimed to assess DNA methylation across the genome for associations with the “BRCA1-like” morphology. Genome-wide methylation in blood-derived DNA was measured using the Infinium HumanMethylation450K BeadChip assay for women under the age of 40 years participating in the Australian Breast Cancer Family Study (ABCFS) diagnosed with: i) BRCA1-like breast cancer (n = 30); and ii) breast cancer without BRCA1-like morphological features (non BRCA1-like; n = 30), and age-matched unaffected women (controls; n = 30). Corresponding tumour-derived DNA from 43 of the affected women was also assessed. Methylation of blood-derived DNA was found to be elevated across 17 consecutive marks in the BRCA1 promoter region and decreased at several other genomic regions (including TWIST2 and CTBP1) for 7 women (23%) diagnosed with BRCA1-like breast cancer compared with women in the other groups. Corresponding tumour-derived DNA available from 5 of these 7 women had elevated methylation within the BRCA1 and SPHK2 promoter region and decreased methylation within the ADAP1, IGF2BP3 and SPATA13 promoter region when compared with the other breast tumours. These methylation marks could be biomarkers of risk for BRCA1-like breast cancer, and could be responsible in part for their distinctive morphological features and biology. As such, they may assist with prevention and targeted therapies for this cancer subtype.

Introduction

Breast cancers arising in women who carry a germline mutation in BRCA1 are often high grade and early-onset, with poor prognosis and limited treatment options (Anders et al., 2010). These breast cancers also have distinct morphological features that include a high mitotic index, high nuclear grade, little or no tubule formation, pushing margins, necrosis, lymphocytic infiltrate and trabecular, circumscribed and syncytial growth patterns (Armes et al., 1998b; Eisinger et al., 1996; Johannsson et al., 1997; Lakhani et al., 1998). Breast cancers with a large number of these features are commonly referred to as “BRCA1-like”, irrespective of their germline BRCA1 mutation status.

Approximately 25% of all women diagnosed with BRCA1-like breast cancer before the age of 40 years carry an identifiable BRCA1 germline mutation, suggesting the majority are due to other mechanisms that result in the same histological pattern (Southey et al., 2011). We previously detected blood-derived DNA methylation at the BRCA1 promoter region in approximately 30% of young women diagnosed with BRCA1-like breast cancers (who were not known to carry a BRCA1 germline mutation). These methylation marks were associated with a 3.5-fold (95% CI, 1.4–10.5) increased risk of early-onset breast cancer (Wong et al., 2011). A similar association was reported by Iwamoto et al. (2011) in the Japanese population (OR 1.73 95% CI, 1.01–2.96) although the association was not specific to any age group or histological type (Iwamoto et al., 2011). BRCA1 promoter methylation has been well-described in tumour-derived DNA from BRCA1-like breast cancers, including the tumours from women with elevated blood-derived DNA methylation at this region (Dobrovic and Simpfendorfer, 1997; Snell et al., 2008; Wong et al., 2011).

Until recently, research in this area has been limited by low-resolution molecular techniques with the capacity to measure only a single or a small number of methylation marks. It was, therefore, not known if the BRCA1 promoter methylation observed in these BRCA1-like breast cancers (both in blood and tumour-derived DNA) was specific to the BRCA1 promoter, part of an extended methylation signature, or even a genome-wide phenomenon. Here, we hypothesize that aberrant DNA methylation marks, not restricted to the BRCA1 promoter region, are associated with the BRCA1-like breast cancers.

To test this, we measured genome-wide methylation in blood-derived and tumour-derived DNA samples from women with early-onset breast cancer (selected by tumour morphology), and age-matched unaffected women (controls) from the ABCFS using the Illumina HM450K Beadchip assay.