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Estrogen Intracellular Retention is Augmented by GRAM Domain Containing Protein ASTER-B in Breast Cancer Cells

GSE267914 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/04/09 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Breast cancerThis series is part of our curated briefing on it.
Samples
24 samples: 12 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Intracellular Retention of Estradiol Is Mediated by GRAM Domain-Containing Protein ASTER-B in Breast Cancer CellsMolecular cancer research : MCR · 2025
Summary (written by the submitters)
Estrogen is the primary mitogen for ER+ BC cells, but how the hormone is retained intracellularly is poorly understood. We found that the ER+ BC cell line MCF-7 retains a substantial amount of hormone even upon removal of the hormone from the culture medium. The effect of acute E2 treatment followed by washout on gene regulation was determined by RNA-seq over an E2 treatment timecourse.
Read the full summary ↓
In agreement with intracellular hormone levels, gene exprssion was also sustained over hours after removal of the hormone. We next identified that ASTER-B, a cholesterol-binding protein, was mislocalized into the nucleus of MCF-7 cells, and was associated with retained E2. By knocking down GRAMD1B (ASTER-B), both E2 retention and its associated gene regulatory programs (ER binding and gene expression) were significantly abrogated. Taken together, this shows E2 retention is required for sustained E2 induction, and that ASTER-B supports accumulation and retention of intracellular E2.
Published in
Intracellular Retention of Estradiol Is Mediated by GRAM Domain-Containing Protein ASTER-B in Breast Cancer Cells
Kim HB, Kraus WL · Molecular cancer research : MCR 2025 · PMID 39804053 · doi:10.1158/1541-7786.MCR-24-0533
This dataset
Open GSE267914 in finder → Find more human RNA-seq datasets → Breast cancer landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE267914_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1113630 and SRA study SRP508821. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39804053) ↗
Study design
12 conditions, mostly in duplicate
DMSO, vehicle control - induction ×2 100nM E2 induction, 40m ×2 100nM E2 induction, 1h ×2 100nM E2 induction, 2h ×2 100nM E2 induction, 3h ×2 100nM E2 induction, 6h replciate ×2 DMSO, vehicle control - washout ×2 100nM E2 washout, 40m + 0m ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
More Breast cancer datasets

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