GEO DataSets

(Submitter supplied) To assess the global effects of HOXC11 in endocrine resistant breast cancer cells we performed RNA-seq on LY2 cells which were transfected with either siRNA targeting HOXC11 (siHOXC11) or a scrambled negative control siRNA (scrHOXC11) in the presence of 4-OH-tamoxifen (10-8M). Knockdown was verified by Taq-man qRT-PCR prior to library preparation. RNA (10µg) was extracted using an Oligotex mRNA kit (Qiagen) as per manufacturer’s instructions (n=4). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

8 Samples

Download data: XLSX

(Submitter supplied) The androgen receptor (AR) has emerged as a candidate target for the treatment of breast cancer. In this study, we sought to characterize the functional consequences of AR knockdown using a siRNA-mediated approach in a tamoxifen-resistant (TamR) derivative of MCF7 breast cancer cell line.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

6 Samples

Download data: CEL

(Submitter supplied) Acquired resistance to aromatase inhibitor (AI) therapy is a major clinical problem in the treatment of breast cancer. The detailed mechanisms of how tumour cells develop this resistance remain unclear. Here estrogen receptor ChIPseq analysis identifies adaptations of the ER in response to prolonged letrozole treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL10999 GPL11154

8 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) To elucidate the molecular mechanisms of tamoxifen resistance in breast cancer, we performed gene array analysis and identified 366 genes with altered expression in four unique tamoxifen resistant (TamR) cell lines vs the parental tamoxifen sensitive MCF7/S0.5 cell line. Most of these genes were funcationally linked to cell proliferation, death and control gene expression, and include FYN, PRKCA, ITPR1, DPYD, DACH1, LYN, GBP1 and PRLR. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

18 Samples

Download data: CEL

(Submitter supplied) Anti-estrogens and aromatase inhibitors are important drugs in the treatment of estrogen-dependent breast cancer. In order to investigate the effects of these drugs on gene expression in breast cancer cells, we treated estrogen receptor-positive MCF-7 cells, stably transfected with the aromatase gene (known as MCF-7aro cells), with testosterone, 17β-estradiol, two aromatase inhibitors (letrozole and anastrozole), and an anti-estrogen (tamoxifen). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1873

Platform:

GPL96

18 Samples

Download data: CEL, EXP

Analysis of estrogen receptor positive, aromatase transfected MCF-7 cells after treatment with an antiestrogen (AE) or an aromatase inhibitor (AI). AEs and AIs are used to treat estrogen-dependent breast cancer. Cells also treated with androgen which is converted to estrogen by aromatase.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 6 agent, 4 other sets

Platform:

GPL96

Series:

GSE2225

18 Samples

Download data: CEL, EXP

(Submitter supplied) The aim of this study is to identify the differentially expressed genes in upon Akt3 over-expression after estrogen and tamoxifen treatment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

7 Samples

Download data: TXT

(Submitter supplied) Postmenopausal breast cancer patients benefit from aromatase inhibitors (AIs) that reduce the levels of estrogens critical for the growth of estrogen receptor (ER)-positive tumors. Unfortunately, many tumors are resistant to AI, and we are only beginning to understand the complex mechanisms underlying treatment resistance. Here we set out to determine whether epigenetic changes could contribute to therapy resistance. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL5082

2 Samples

Download data: BAR, CEL

(Submitter supplied) We performed RNA-sequencing on 7 tamoxifen-resistant (MCF-7 Tam1, T-47D Tam1, T-47D Tam2, ZR-75-1 Tam1, ZR-75-1 Tam2, BT474 Tam1 and BT-474 Tam2) and their isogenic parental (MCF-7, T-47D, ZR-75-1 and BT-474) breast cancer cell lines. The tamoxifen-resistant cell lines were generated from the parentel cell lines by continuous administration of 1 µM 4-OH-tamoxifen for eight to twelve months. RNA- sequencing was performed to determine the changes in the expression of genes in the resistant clones as well as pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL11154

11 Samples

Download data: TXT

(Submitter supplied) Approximately 30% of women diagnosed with ERα breast cancer relapse with metastatic disease following adjuvant treatment with endocrine therapies. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain (TAD) undergoes epigenetic reprogramming in cells that develop resistance to aromatase inhibitors (AI), leading to keratin 80 (KRT80) upregulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TSV

(Submitter supplied) Background: Invasive lobular breast carcinoma (ILC) is a histological subtype of breast cancer that is characterized by loss of E-cadherin, and high expression of estrogen receptor alpha (ER). Many patients with ILC are effectively treated with adjuvant aromatase inhibitors (AIs), however, acquired AI resistance remains a significant problem. Methods: To identify underlying mechanisms of acquired antiestrogen resistance in ILC, we developed a total of 6 long-term estrogen-deprived (LTED) variant cell lines of the human ILC cell lines SUM44PE (SUM44; 2 lines) and MDA-MB-134VI (MM134; 4 lines). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

27 Samples

Download data: CSV

(Submitter supplied) We profiled primary breast cancer, nodal and liver metastatic tumours from three patients. At the time of initial diagnosis, all three patients presented with luminal breast cancer with adjacent nodal metastasis. They all received 5 years of enodrine therapy and all subsequently developed liver metastasis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Endocrine therapy is the most important treatment modality of breast cancer patients whose tumors express the estrogen receptor  (ER). The androgen receptor (AR) is also expressed in the vast majority (80-90%) of ER-positive tumors. However, AR-targeting drugs are not used in clinical practice, but have been evaluated in multiple trials and preclinical studies. We performed a genome-wide study to identify genetic context-dependent AR signaling induced by either AR agonist (dihydrotestosterone [DHT]), or AR antagonist (enzalutamide [Enz]), known as pharmacogenomic expression quantitative expression loci (PGx-eQTLs), utilizing a previously well characterized lymphoblastic cell line panel.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

120 Samples

Download data: TXT

(Submitter supplied) Endocrine therapy resistance remains a critical problem in the treatment of estrogen receptor alpha (ERα) breast cancer. Endocrine therapies target ERα via different modes of action. Drug resistance involves drug specific remodeling of the transcriptional and regulatory landscape. Using epigenomics and transcriptomics, we demonstrate that resistance to aromatase inhibitors (AI) induces phenotypical changes through epigenetic activation of cholesterol biosynthesis (CB) and keratin 80. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL11154

10 Samples

Download data: BED, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: WIG

(Submitter supplied) The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. While SRC-1 typically functions to activate gene expression, some evidence has pointed towards a potential role in repression. This study looks into the effects of a stable knockdown of SRC-1 in a tamoxifen resistant cell line, LY2, and the effects of this knock down on the methylation landscape.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: WIG

(Submitter supplied) The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. SRC-1's role in affecting the transcriptome of the breast cancer endocrine resistant setting is uncovered through this RNA-seq analysis of LY2 cells grown with or without the presence of SRC-1

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n=11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21613

16 Samples

Download data: TXT

(Submitter supplied) Background: Unlike estrogen receptor (ER) negative breast cancer, ER-positive breast cancer outcomes are less influenced by lymphocyte content, indicating a need for investigation of checkpoint targets and immune tolerance mechanisms that may be specific to this disease subset. Methods: A supervised analysis of microarray data from the Alliance/ACOSOG Z1031 trial was conducted to identify upregulated genes in Luminal B breast cancers that exhibited persistent tumor proliferation despite aromatase inhibitor therapy (33 cases Ki67 >10%) versus Luminal B breast cancers that were more sensitive (33 cases Ki67 <10%).  Results: This study identified thirty genes (Pearson’s r>0.4 with Ki67 as a continuous variable). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

603 Samples

Download data: TXT

(Submitter supplied) A series of MCF-7 variants were previously developed that are estrogen-dependent for growth (MCF-7:WS8 cells), or resistant to estrogen deprivation/vulnerable to fast (MCF-7:5C) and delayed (MCF-7:2A) E2-inducible apoptosis. To identify miRNAs associated with aromatase inhibitor (AI)-resistance and vulnerability to E2-induced apoptosis, estrogen deprivation-resistant 5C and 2A cells were compared to estrogen-dependent WS8 cells and among each other.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

12 Samples

Download data: CEL