Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Abstract

Background: Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

Results: To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells.

Discussion: Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway.

Conclusions: Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.

Keywords: Breast cancer subtypes; Chromatin states; Epigenetics; Histone modifications.

Fig. 1

Cells and histone modifications collected in LONESTAR project. a Summary of cell lines and histone marks. b Thirteen chromatin states were defined using 5 key histone modifications, the left panel describes the chromatin state annotations and color scheme, the central panel describes the emission coefficients in ChromHMM model, the right panel describes the relative enrichment of coverage in whole genome and in different genomic regions. c Integrated view of whole genome chromatin state landscapes in breast cancer cells and corresponding individual histone modification profiles in MCF7 cells for a region on chromosome 19

Fig. 2

Chromatin states signatures for breast cancer subtypes. a Genome wide subtype specific patterns revealed by chromatin state clustering (chromatin state color scheme same as Fig. 1b). The Heatmap represents the top 1000 highly variable genomic regions clustered according to average linkage distance metric. b Pie chart of major chromatin states categories in subtype specific patterns across all cell lines. c Genebody H3K36me3 occupancy heatmap for genes associated with active transcription states. d Promoter H3K27me3 occupancy heatmap for genes associated with repressive states

Fig. 3

TNBC specific signatures: AFAP-AS1 transcription. a Screen shot of TNBC specific chromatin states and H3K4me3 signals on AFAP1-AS1 promoter and genebody. TNBC specific AFAP1-AS1 expression measured by (b) RNA-seq and (c) q-PCR. Depletion of AFAP1-AS1 in MB231 (d) and HCC1937 cells (e) inhibits cell proliferation (f, g), and colony formation (h, i) respectively