Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1

Abstract

Breast cancer is a heterogeneous disease and several distinct subtypes exist based on differential gene expression patterns. Molecular apocrine tumours were recently identified as an additional subgroup, characterised as oestrogen receptor negative and androgen receptor positive (ER- AR+), but with an expression profile resembling ER+ luminal breast cancer. One possible explanation for the apparent incongruity is that ER gene expression programmes could be recapitulated by AR. Using a cell line model of ER- AR+ molecular apocrine tumours (termed MDA-MB-453 cells), we map global AR binding events and find a binding profile that is similar to ER binding in breast cancer cells. We find that AR binding is a near-perfect subset of FoxA1 binding regions, a level of concordance never previously seen with a nuclear receptor. AR functionality is dependent on FoxA1, since silencing of FoxA1 inhibits AR binding, expression of the majority of the molecular apocrine gene signature and growth cell growth. These findings show that AR binds and regulates ER cis-regulatory elements in molecular apocrine tumours, resulting in a transcriptional programme reminiscent of ER-mediated transcription in luminal breast cancers.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1

Molecular apocrine breast cancer cells are dependent on AR for growth and transcription. (A) Western blot for AR and ER in MCF-7 breast cancer cells, MDA-MB-453 molecular apocrine breast cancer cells and LNCaP prostate cancer cells. (B) MDA-MB-453 cells were transfected with siControl or siAR. Western blot showing AR silencing. Following AR silencing, MDA-MB-453 colony formation was assessed in a soft agar assay. An example image is shown in (C) and quantification of number and size of colonies from three replicates is shown in (D). *Denotes P-value <0.05. (E) MTT growth assay with MDA-MB-453 cells treated with 1 μM bicalutamide or ethanol control, average of three independent replicates, * denotes P-value <001. (F) AR ChIP of MDA-MB-453 cells after 4 h treatment with vehicle, R1881, bicalutamide or R1881 plus bicalutamide followed by real-time PCR. (G) Transcript levels of a number of genes expressed in luminal tumours were assessed in cells transfected with siControl or two different siRNA to AR, average of three individual replicates.

Figure 2

AR binding in molecular apocrine breast cancer is more similar to ER binding in the breast than AR binding in the prostate. (A) AR binding was mapped in asynchronous MDA-MB-453 breast cancer cells and asynchronous LNCaP prostate cancer cells, and ER binding mapped in asynchronous MCF-7 breast cancer cells. (B) Heatmap showing AR and ER binding signal intensity for overlapping regions in a window of ±5 kb. The heatmap represents binding events ranked from strongest to weakest AR binding in MDA-MB-453 cells, and the adjacent columns represent signal from the corresponding ChIP-sequencing experiment in the MCF7 and LNCaP cells. (C) Example of binding events which are unique or shared by AR in MDA-MB-453 cells. (D) Motifs enriched in AR binding events in MDA-MB-453 cells. (E) A comparison of differentially enriched motifs between the different categories of binding events: Common represents regions bound by AR in MDA-MB-453 and LNCaP cells and by ER in MCF-7 cells; AR/ER is regions shared by AR in MDA-MB-453 and ER in MCF-7 cells; AR/AR represents regions shared by AR in MDA-MB-453 and LNCaP cells; AR unique represents the AR binding sites unique to MDA-MB-453 cells only. (F) Enrichment for AR and Forkhead motif in the centre of the AR MDA-MB-453 binding events.

Figure 3

Almost all AR binding events occur at FoxA1 binding regions. (A) FoxA1 binding was determined by ChIP-seq in MDA-MB-453 breast cancer cells and overlap with AR is shown. (B) The proportion of overlapping AR/FoxA1 binding events is more similar than either the ER/FoxA1 overlap in MCF7 or FoxA1/FoxA1 across the three cell lines. Table shows FoxA1 binding overlap between cell lines in pale orange. FoxA1 and nuclear receptor overlap within the same cell line is in dark orange, that is, AR/FoxA1 MDA-MB-453, AR/FoxA1 LNCaP or ER/FoxA1 MCF7. (C) Example of a genomic region showing AR and FoxA1 binding in MDA-MB-453 cells. (D) Unsupervised clustering GSC Heatmap showing z scores for the comparisons between each ChIP-seq experiment. (E) Re-ChIP showing co-occupancy of AR and FoxA1 on the chromatin in a ligand-dependent manner.

Figure 4

FoxA1 is required for AR binding and transcription of target genes. (A) Western blot showing silencing of FoxA1 in MDA-MB-453 cells. (B) MDA-MB-453 cells were transfected with siControl or siFoxA1. AR ChIP was performed followed by real-time PCR of AR binding regions. (C) MDA-MB-453 cells were transfected with siControl or siFoxA1, total chromatin fraction was collected and western blotted. Total chromatin-associated AR is decreased when FoxA1 is silenced. (D) Microarray analysis of gene expression changes following transfection of siControl or siFoxA1. Only genes with an FDR <0.01 were considered which resulted in 730 FoxA1-dependent genes. (E) The 730 FoxA1-dependent genes were analysed for enriched biological pathways. (F) Soft agar assay following transfection of MDA-MB-453 cells with siControl or siFoxA1. (G) Heatmap showing log2 fold change in gene expression of the 100 gene molecular apocrine signature induced by two different siRNAs targeted to FoxA1. Black box indicates the presence of AR and FoxA1 binding event ±10 kb from TSS of the gene.