Chromatin profile-based identification of a novel ER-positive breast cancer subgroup with reduced ER-responsive element accessibility

Abstract

Background Oestrogen receptor (ER) signalling-dependent cancer cell growth is one of the major features of ER-positive breast cancer (BC). Inhibition of ER function is a standard and effective treatment for ER-positive tumours; however, ~20% of patients with ER-positive BC experience early or late recurrence. In this study, we examined intertumour heterogeneity from an epigenetic perspective based on the hypothesis that the intrinsic difference in epigenetic states around ER signalling pathway underlies endocrine therapy resistance. Methods We performed transposase-accessible chromatin sequencing (ATAC-seq) analysis of 42 BC samples, including 35 ER-positive(+) human epidermal growth factor receptor 2 (HER2)-negative(−) and 7 triple-negative tumours. We also reanalysed ATAC-seq data of 45 ER + /HER2 − tumours in the Cancer Genome Atlas (TCGA) BC cohort to validate our observations. Results We conducted a comprehensive analysis of cis-regulatory elements (CREs) using ATAC-seq, identifying three subgroups based on chromatin accessibility profiles. We identified a subgroup of ER-positive BCs with a distinctive chromatin accessibility pattern including reduced accessibility to ER-responsive elements (EREs). The same subgroup was also observed in TCGA BC cohort. Despite the reduced accessibility to EREs, the expression of ER and potential ER target genes were not decreased in these tumours. Conclusion Our findings highlight the existence of a subset of ER-positive BCs with unchanged ER expression but reduced EREs accessibility that cannot be distinguished by conventional immunostaining for ER. Future studies should determine whether these tumours are associated with resistance to endocrine therapy.

Identification of lineage-specific epigenetic regulators FOXA1 and GRHL2 through chromatin accessibility profiling in breast cancer cell lines

“…1a ). A large proportion of these CREs were located in distal regions, including distal intergenic and intronic regions, whereas promoter elements constituted only 21.7% of the total CREs, consistent with previous findings [ 6 , 7 ].

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“…Subsequently, we performed peak calling analysis using MACS2. To generate a counts matrix, we employed a method established previously [ 6 , 7 ] ( Supplementary Methods ). ChIPseeker was used for peak annotation [ 40 ].…”

“…However, previous studies have highlighted heterogeneity extending beyond gene expression across breast tumors [ 5 , 6 ]. For example, we previously showed that a subset of estrogen receptor-positive (ER+) breast cancers displays reduced accessibility to ER-responsive elements, potentially leading to poor outcomes [ 7 ]. These findings underscore the critical need to identify epigenetic states for a more comprehensive understanding of breast cancer heterogeneity.…”

Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

“…A higher infiltration of T and B cells was observed in cluster CA-C and higher proportions of endothelial cells and fibroblasts were observed in cluster CA-B (Figure 6B). These predictions are consistent with the infiltration level estimations reported in the original publication, although no differences in macrophages infiltration was observed between the ER+/HER2-subgroups in our case (64).…”

“…These predictions are consistent with the infiltration level estimations reported in the original publication, although no differences in macrophages infiltration was observed between the ER+/HER2-subgroups in our case (Kumegawa et al 2023).…”