FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer
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ABSTRACT:
PROVIDER: PRJNA512997 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8393430.fastq.gz | Fastqsanger.gz | |||
| SRR8393440.fastq.gz | Fastqsanger.gz | |||
| SRR8393431.fastq.gz | Fastqsanger.gz | |||
| SRR8393441.fastq.gz | Fastqsanger.gz | |||
| SRR8393432.fastq.gz | Fastqsanger.gz |
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Project description:Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Here, we have demonstrated that FOXA1 overexpression in estrogen receptor-positive breast cancer cells drives genome-wide enhancer reprogramming to activate pro-metastatic transcriptional programs. Specifically, FOXA1 overexpression generated more gained chromatin binding regions than the lost regions with decreased FOXA1 binding. Furthermore, FOXA1 overexpression led to establishment of more gained enhancers marked with increased H3K27ac and/or H3K4me1 than the lost enhancers with decreased signals of these two histone marks. In addition, these altered enhancers were highly coordinated with FOXA1-chromatin binding (cistrome) and the alteration of transcriptome due to FOXA1 overexpression, suggesting the direct engagement of high FOXA1 in enhancer reprogramming. The coordination between FOXA1 cistrome, enhancer reprogramming, and transcriptome also exists in the tamoxifen-resistant MCF7 cell model with endogenous FOXA1 gene amplification. Overall, our study supports the notion that FOXA1 overexpression promotes enhancer reprogramming in ER-positive breast cancer to activate gene expression associated with endocrine resistance and metastasis.
2019-12-18 | GSE124654 | GEO
Project description:Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Here, we have demonstrated that FOXA1 overexpression in estrogen receptor-positive breast cancer cells drives genome-wide enhancer reprogramming to activate pro-metastatic transcriptional programs. We have identified the hypoxia-inducible transcription factor HIF-2α as the top FOXA1-engaged super-enhancer target induced by FOXA1 overexpression, activating pro-metastatic gene signatures associated with poor breast cancer outcome. Using two different siRNA sequences, we identified 917 and 1,107 genes commonly down- and up-regulated (FDR < 0.05), respectively, upon HIF-2α knockdown in tamoxifen-resistant MCF7L cells. The enriched GO terms of the down-regulated genes were predominantly linked to tumor metastatic traits. GSEA showed that this HIF-2α-dependent gene set was significantly enriched in the transcriptomes of the TCGA ER+ breast tumors expressing high HIF-2α, but not high HIF-1α. We show the selective efficacy of a HIF-2α antagonist (PT2385), currently in clinical trial for renal cell carcinoma, in repressing migration and clonogenicity of endocrine-resistant breast cancer cells expressing high FOXA1. Our study suggests that targeting HIF-2α is a new approach blocking the aberrant transcriptional programs under high FOXA1-induced enhancer reprogramming in treating endocrine-resistant and metastatic breast cancer.
2019-12-18 | GSE124655 | GEO
Project description:FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer [ChIP-seq]
| PRJNA513000 | ENA
Project description:FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer [RNA-seq]
| PRJNA513001 | ENA
Project description:Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Hyperactive FOXA1 signaling due to gene amplification or overexpression has been reported in estrogen receptor-positive (ER+) endocrine-resistant metastatic breast cancer. However, the molecular mechanisms by which FOXA1 up-regulation promotes these processes and the key downstream targets of the FOXA1 oncogenic network remain elusive. Here, we demonstrate that FOXA1 overexpression in ER+ breast cancer cells drives genome-wide enhancer reprogramming to activate prometastatic transcriptional programs. Up-regulated FOXA1 employs superenhancers (SEs) to synchronize transcriptional reprogramming in endocrine-resistant breast cancer cells, reflecting an early embryonic development process. We identify the hypoxia-inducible transcription factor hypoxia-inducible factor-2α (HIF-2α) as the top high FOXA1-induced SE target, mediating the impact of high FOXA1 in activating prometastatic gene sets and pathways associated with poor clinical outcome. Using clinical ER+/HER2- metastatic breast cancer datasets, we show that the aberrant FOXA1/HIF-2α transcriptional axis is largely nonconcurrent with the ESR1 mutations, suggesting different mechanisms of endocrine resistance and treatment strategies. We further demonstrate the selective efficacy of an HIF-2α antagonist, currently in clinical trials for advanced kidney cancer and recurrent glioblastoma, in reducing the clonogenicity, migration, and invasion of endocrine-resistant breast cancer cells expressing high FOXA1. Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer.
| S-EPMC6936436 | biostudies-literature
Project description:Phenotypic plasticity has emerged as an important mechanism of therapy resistance in cancers, yet the underlying molecular mechanisms remain unclear. Using an established breast cancer cellular model for endocrine resistance, we show that hormone resistance is associated with enhanced phenotypic plasticity, indicated by a general downregulation of luminal/epithelial differentiation markers and upregulation of basal/mesenchymal invasive markers. Our extensive omics studies, including GRO-seq on enhancer landscapes, demonstrate that the global enhancer gain/loss reprogramming driven by the differential interactions between ER-alpha and other oncogenic transcription factors (TFs), predominantly GATA3 and AP1, profoundly alters breast cancer transcriptional programs. Our functional studies in multiple biological systems support a coordinate role of GATA3 and AP1 in enhancer reprogramming that drives phenotypic plasticity to achieve endocrine resistance or cancer invasive progression. Thus, changes in TF-TF and TF-enhancer interactions can lead to genome-wide enhancer reprogramming, resulting in transcriptional dysregulations that promote plasticity and cancer therapy-resistance progression
2019-05-24 | MSV000083857 | MassIVE
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-12-18 | GSE124656 | GEO
Project description:Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, to date, key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) highly enriched in ER+ endocrine-resistant (EndoR) cells. We identified Secretome14, a CGS subset encoding ER-dependent cancer secretory proteins, strongly predicts poor outcomes of ER+ BC and is elevated in ER+ metastases vs. primary tumors, irrespective to the ESR1 mutations. Parental (P) ER+ BC cells and their endocrine-resistant (EndoR) derivatives, and ER+ BC cells expressing doxycycline (Dox)-inducible ectopic FOXA1 were used in this study. Differential gene expression analysis was performed in EndoR vs. P cells and P cells +Dox vs. -Dox. We found that the FOXA1-CGS was highly enriched in the altered transcriptomes of two ER+ BC cell models (ZR75-1 and T47D) expressing ectopic H-FOXA1. The enriched hallmark gene sets, shared by the H-FOXA1 cell models, include “inflammatory response”, “complement”, and “interferon gamma response” for the H-FOXA1-induced, and “estrogen response early” and “estrogen response late” for the H-FOXA1-repressed genes. These findings point to the common transcriptional profile exhibiting an immune- over estrogen-responsive signature induced by H-FOXA1. In addition, we found that both the tamoxifen-resistant (TamR) and estrogen deprivation-resistant (EDR) derivatives of the 600MPE P cells were enriched for the H-FOXA1-induced CGS and FOXA1/ER-activated Secretome14. Our findings uncover H-FOXA1-induced ER reprogramming driving EndoR and metastasis, possibly via a H-FOXA1/ER-dependent secretome that warrants further studies to clarify its involvement in disease progression of ER+ metastatic BC.
2023-05-21 | GSE175401 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE25314: FoxA1 is a critical determinant of Estrogen Receptor function and endocrine response (part I) GSE25315: FoxA1 is a critical determinant of Estrogen Receptor function and endocrine response (part II) Refer to individual Series
2010-11-17 | E-GEOD-25316 | biostudies-arrayexpress
Project description:Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, to date, key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estrogen receptor-positive (ER+) breast cancer (BC) metastasis in a xenograft mouse model. Mechanistically, H-FOXA1 reprograms ER-chromatin binding to elicit a core gene signature (CGS) and an ER-dependent secretome highly enriched in ER+ endocrine-resistant (EndoR) cells. ER+ BC MCF7-parental (P) cells treated with estrogen deprivation or estrogen, and with doxycycline (Dox)-inducible FOXA1 overexpression were used in this study. We found that a majority of the lost or retained ER binding induced by H-FOXA1 overlapped with the ER binding sites in P cells induced by estrogen vs. tamoxifen treatment. The lost ER binding sites were also significantly enriched for the ER binding under E2 vs. ED, which corresponds to 11% of the total E2-stimulated ER binding, suggesting that H-FOXA1 induces a loss of selective E2-stimulated ER binding sites. In addition, we found that the proportion of H-FOXA1-induced ER-loss regions were significantly enriched for the unique ER binding sites in P vs. tamoxifen-resistant (TamR) cells, yet no enrichment of the ER-gain regions was observed in the unique ER binding in TamR vs. P cells. Our findings uncover H-FOXA1-induced ER reprogramming driving EndoR and metastasis, possibly via a H-FOXA1/ER-dependent secretome that warrants further studies to clarify its involvement in disease progression of ER+ metastatic breast cancer.
2023-05-21 | GSE175418 | GEO