FOXA1 represses the molecular phenotype of basal breast cancer cells

Abstract

Breast cancer is a heterogeneous disease comprised of multiple subtypes. Luminal subtype tumors confer a more favorable patient prognosis, which is in part, attributed to estrogen receptor-α (ER) positivity and anti-hormone responsiveness. Expression of the forkhead box transcription factor, FOXA1, similarly correlates with the luminal subtype and patient survival, but is also present in a subset of ER-negative tumors. FOXA1 is also consistently expressed in luminal breast cancer cell lines even in the absence of ER. In contrast, breast cancer cell lines representing the basal subtype do not express FOXA1. To delineate an ER-independent role for FOXA1 in maintaining the luminal phenotype, and hence a more favorable prognosis, we performed cDNA microarray analyses on FOXA1-positive, ER-positive (MCF7, T47D) or FOXA1-positive, ER-negative (MDA-MB-453, SKBR3) luminal cell lines in the presence or absence of transient FOXA1 silencing. This resulted in three FOXA1 transcriptomes: (1) a luminal-signature (consistent across cell lines), (2) an ER-positive signature (restricted to MCF7 and T47D) and (3) an ER-negative signature (restricted to MDA-MB-453 and SKBR3). Gene Set Enrichment Analyses (GSEA) revealed FOXA1 silencing causes a partial transcriptome shift from luminal to basal gene expression signatures. FOXA1 binds to a subset of both luminal and basal genes within luminal breast cancer cells, and loss of FOXA1 increases enhancer RNA (eRNA) transcription for a representative basal gene (CD58). These data suggest FOXA1 directly represses basal signature genes. Functionally, FOXA1 silencing increases migration and invasion of luminal cancer cells, both characteristics of basal subtype cells. We conclude FOXA1 controls plasticity between basal and luminal breast cancer cells, not only by inducing luminal genes, but also by repressing the basal phenotype, and thus aggressiveness. Although it has been proposed that FOXA1-targeting agents may be useful for treating luminal tumors, these data suggest that this approach may promote transitions toward more aggressive cancers.

GABA(A) Receptor Pi (GABRP) Stimulates Basal-like Breast Cancer Cell Migration through Activation of Extracellular-regulated Kinase 1/2 (ERK1/2)

“…5C). Although we and others have observed subtype plasticity in breast cancer cell lines following alterations in subtype-specifying genes (29,36), the decrease in the basal-like cytokeratins with GABRP knockdown was not accompanied with an up-regulation of KRT19, a luminal-specific cytokeratin (Fig. 5, B and C).…”

“…Migration-Migration assays were performed as described (29). Briefly, 50,000 viable cells, as determined by trypan blue exclusion, were seeded into the top of uncoated 24-well transwell inserts (Corning) in either serum-free RPMI media (HCC70) or RPMI media containing 1% FBS (HCC1187).…”

“…Quantitative Real-time PCR-RNA processing, DNase I treatment and reverse transcription was performed as described (29). Applied Biosystems TaqMan Gene Expression Assays included: GAPDH, Hs99999905_m1; GABRP, Hs00959454_m1; KRT5, Hs00361185_m1; KRT6B, Hs00745492_s1; KRT14, Hs00559328_m1; KRT17, Hs00356958_m1; KRT19, Hs00761767_ s1.…”

Forkhead box a2 (FOXA2) is essential for uterine function and fertility

“…Both FOXA1 and FOXA2 are pioneer transcription factors with essential roles in the development of and estrogen signaling in the liver (43). In breast cancer cells, FOXA factors and ESR1 are frequently bound to adjacent cis-regulatory elements in the genome, and recruitment of ESR1 to those binding sites is dependent on FOXA factors (42,44). Of note, the majority of uterine gland-specific genes (Cxcl15, Prss29, Spink3, Ttr, and Wfdc3) studied here are bound by FOXA2 in ChIP sequencing (ChIP-seq) analyses of GD 3.5 mouse uteri (18).…”

Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data

“…As expected, we identified the estrogen receptor (ESR1), which is the most relevant marker for breast cancer subtyping in histochemistry, as one of the top features. The other top features are FOXA1, which has been identified as a tumor suppressor [19] and MLPH, which is not known to be associated with breast cancer, but has an experimentally verified interaction to RAB27A, which was shown to promote proliferation in human glioma cells [20]. Furthermore, we identified FOXC1 as a top feature, which is of the same family of transcription factors as FOXA1 and which was shown to play a role in NF-κB signaling in basal breast cancer cells [21].…”