GEO series

RNA-seq analysis of MDA-MB-231 and MDA-MB-453 cells treated with abemaciclib and/or fulvestrant

GSE336730 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/06/29 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: 8 conditions, mostly in triplicateGroups 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.

Summary (written by the submitters)

The retinoblastoma protein (Rb) is a tumour suppressor best known for repressing E2F transcription factors and halting cell cycle progression. In hormone receptor-positive (HR+) breast cancer, CDK4/6 inhibitors activate Rb by preventing its phosphorylation, forming a key component of current endocrine therapy regimens. How pharmacologically activated Rb remodels chromatin and influences transcription beyond cell cycle arrest remains poorly understood.

Read the full summary ↓

Here we show that CDK4/6 inhibition induces redistribution of hypo-phosphorylated Rb to promoters and enhancers. While Rb predictably binds to cell cycle gene promoters to repress transcription, at other sites it unexpectedly promotes expression of oestrogen-responsive genes by integrating into oestrogen receptor (ER)-rich transcriptional hubs. CDK4/6 inhibition enhances ER target gene expression in breast cancer cells, patient-derived xenografts, and clinical HR+ breast cancer samples in an Rb-dependent manner. This reprogramming is mediated in part by KDM5A, whose interaction with Rb contributes to gene regulation at these loci. Critically, components of this Rb-driven ER transcriptional program are pro-proliferative. In endocrine-sensitive tumours, this can be neutralised with anti-oestrogen therapy, explaining therapeutic synergy. In endocrine-resistant settings such as ESR1-mutant breast cancer, the program persists, limiting therapeutic efficacy. These findings reframe Rb as a dual-function transcriptional regulator that, while enforcing cell cycle arrest, can also activate programs that counteract its tumour suppressor function.

This dataset

Open GSE336730 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 GSE336730_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 PRJNA1482501 and SRA study SRP712923. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in triplicate

M231 DMSO RNAseq ×3 M231 abemaciclib RNAseq ×3 M231 Fulvestrant RNAseq ×3 M231 abemaciclib and fulvestrant combination … ×3 M453 DMSO RNAseq ×3 M453 abemaciclib RNAseq ×3 M453 Fulvestrant RNAseq ×3 M453 abemaciclib and fulvestrant combination … ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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

GSM9841444 M231 DMSO RNAseq replicate 1 M231 DMSO RNAseq
GSM9841445 M231 DMSO RNAseq replicate 2 M231 DMSO RNAseq
GSM9841446 M231 DMSO RNAseq replicate 3 M231 DMSO RNAseq
GSM9841447 M231 abemaciclib RNAseq replicate 1 M231 abemaciclib RNAseq
GSM9841448 M231 abemaciclib RNAseq replicate 2 M231 abemaciclib RNAseq
GSM9841449 M231 abemaciclib RNAseq replicate 3 M231 abemaciclib RNAseq
GSM9841450 M231 Fulvestrant RNAseq replicate 1 M231 Fulvestrant RNAseq
GSM9841451 M231 Fulvestrant RNAseq replicate 2 M231 Fulvestrant RNAseq
GSM9841452 M231 Fulvestrant RNAseq replicate 3 M231 Fulvestrant RNAseq
GSM9841453 M231 abemaciclib and fulvestrant combination RNAseq replicate 1 M231 abemaciclib and fu…
GSM9841454 M231 abemaciclib and fulvestrant combination RNAseq replicate 2 M231 abemaciclib and fu…
GSM9841455 M231 abemaciclib and fulvestrant combination RNAseq replicate 3 M231 abemaciclib and fu…
GSM9841456 M453 DMSO RNAseq replicate 1 M453 DMSO RNAseq
GSM9841457 M453 DMSO RNAseq replicate 2 M453 DMSO RNAseq
GSM9841458 M453 DMSO RNAseq replicate 3 M453 DMSO RNAseq
GSM9841459 M453 abemaciclib RNAseq replicate 1 M453 abemaciclib RNAseq
GSM9841460 M453 abemaciclib RNAseq replicate 2 M453 abemaciclib RNAseq
GSM9841461 M453 abemaciclib RNAseq replicate 3 M453 abemaciclib RNAseq
GSM9841462 M453 Fulvestrant RNAseq replicate 1 M453 Fulvestrant RNAseq
GSM9841463 M453 Fulvestrant RNAseq replicate 2 M453 Fulvestrant RNAseq
GSM9841464 M453 Fulvestrant RNAseq replicate 3 M453 Fulvestrant RNAseq
GSM9841465 M453 abemaciclib and fulvestrant combination RNAseq replicate 1 M453 abemaciclib and fu…
GSM9841466 M453 abemaciclib and fulvestrant combination RNAseq replicate 2 M453 abemaciclib and fu…
GSM9841467 M453 abemaciclib and fulvestrant combination RNAseq replicate 3 M453 abemaciclib and fu…

More Breast cancer datasets

GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing
GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
GSE336729 RNA-seq analysis of CAMA-1 cells treated with abemaciclib and/or fulvestrant 12 samples shares abemaciclib, fulvestrant, rna-seq, treated
GSE316771 RNA-seq analysis of MDA-MB-231 triple-negative breast cancer cells treated with CIr2 for 24 h 6 samples shares mda-mb-231, rna-seq, treated
GSE185760 RNA-Seq of MDA-MB-231 human triple-negative breast cancer cells treated with a copper chelator 9 samples shares mda-mb-231, rna-seq, treated

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.