GEO series

Tumor-derived miR-9-5p-loaded EVs regulate cholesterol homeostasis to promote breast cancer liver metastasis in mice.

GSE222708 Mus musculus (mouse) RNA-seq (gene expression) 27 samples Submitted 2024/08/31 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 27 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: Mus musculus (mouse)
Samples: 27 samples: 9 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.
Paper: Tumor-derived miR-9-5p-loaded EVs regulate cholesterol homeostasis to promote breast cancer liver metastasis in miceNature communications · 2024

Summary (written by the submitters)

Cancer cells secrete extracellular vesicles (EV) encapsulating bioactive cargoes to facilitate inter-organ communication in vivo and are emerging as critical mediators of tumor progression and metastasis, a condition which is often accompanied by a dysregulated cholesterol metabolism. Whether EVs are involved in the control of cholesterol homeostasis during tumor metastasis is still undefined and warrant further investigation.

Read the full summary ↓

Here, we find that breast cancer-derived exosomal miR-9-5p induces the expression of HMGCR and CH25H, two enzymes involved in cholesterol synthesis and the conversion of 25-hydroxycholesterol from cholesterol by targeting INSIG1, INSIG2 and ATF3 genes in the liver. Notably, in vivo miR-9-5p antagomir treatment and genetic CH25H ablation prevents tumor metastasis in a mouse model of breast cancer. Thus, our findings reveal the regulatory mechanism of tumor-derived miR-9-5p in liver metastasis by linking oxysterol metabolism and Kupffer cell polarization, shedding light on future applications for cancer diagnosis and treatment.

Published in

Tumor-derived miR-9-5p-loaded EVs regulate cholesterol homeostasis to promote breast cancer liver metastasis in mice

Li MX, Hu S, Lei HH et al. · Nature communications 2024 · PMID 39627188 · doi:10.1038/s41467-024-54706-z

This dataset

Open GSE222708 in finder → Find more mouse RNA-seq datasets →

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 GSE222708_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 PRJNA923237 and SRA study SRP416980. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39627188) ↗

Study design

9 conditions, mostly in triplicate

Liver PBS ×3 Liver MCF-10A EV ×3 Liver MDA-MB-231EV ×3 RAW264.7 vehicle ×3 RAW264.7 25-HC ×3 Liver tumor free ×3 Liver tumor bearing ×3 Liver 231/Rab27A KD ×3 +1 more

Supports a case/control comparison: 6 samples read as cases, 3 as controls.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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

GSM6927905 Liver PBS_1 Liver PBS
GSM6927906 Liver PBS_2 Liver PBS
GSM6927907 Liver PBS_3 Liver PBS
GSM6927908 Liver MCF-10A EV_1 Liver MCF-10A EV
GSM6927909 Liver MCF-10A EV_2 Liver MCF-10A EV
GSM6927910 Liver MCF-10A EV_3 Liver MCF-10A EV
GSM6927911 Liver MDA-MB-231EV_1 Liver MDA-MB-231EV
GSM6927912 Liver MDA-MB-231EV_2 Liver MDA-MB-231EV
GSM6927913 Liver MDA-MB-231EV_3 Liver MDA-MB-231EV
GSM6927914 RAW264.7 vehicle_1 RAW264.7 vehicle
GSM6927915 RAW264.7 vehicle_2 RAW264.7 vehicle
GSM6927916 RAW264.7 vehicle_3 RAW264.7 vehicle
GSM6927917 RAW264.7 25-HC_1 RAW264.7 25-HC
GSM6927918 RAW264.7 25-HC_2 RAW264.7 25-HC
GSM6927919 RAW264.7 25-HC_3 RAW264.7 25-HC
GSM6929221 Liver tumor free_1 Liver tumor free
GSM6929222 Liver tumor free_2 Liver tumor free
GSM6929223 Liver tumor free_3 Liver tumor free
GSM6929224 Liver tumor bearing_1 Liver tumor bearing
GSM6929225 Liver tumor bearing_2 Liver tumor bearing
GSM6929226 Liver tumor bearing_3 Liver tumor bearing
GSM6929227 Liver 231/Rab27A KD_1 Liver 231/Rab27A KD
GSM6929228 Liver 231/Rab27A KD_2 Liver 231/Rab27A KD
GSM6929229 Liver 231/Rab27A KD_3 Liver 231/Rab27A KD
GSM6929230 Liver 231/miR-9 KO_1 Liver 231/miR-9 KO
GSM6929231 Liver 231/miR-9 KO_2 Liver 231/miR-9 KO
GSM6929232 Liver 231/miR-9 KO_3 Liver 231/miR-9 KO

Datasets on a similar topic

GSE222707 Cancer-cell-secreted miR-9-5p regulates cholesterol homeostasis to promote tumor metastasis [TF TB Rab27AKD miR-9KO] 12 samples shares cholesterol, homeostasis, metastasis, regulate, promote
GSE272476 Neutrophils exposed to a cholesterol metabolite secrete extracellular vesicles that promote epithelial-mesenchymal transition and stemness in breast cancer cells [RNA-seq] 30 samples shares cholesterol, promote, breast
GSE54371 Secretory Antibodies in Breast Milk Promote Long-Term Intestinal Homeostasis by Regulating the Gut Microbiota and Host Gene Expression. 16 samples shares homeostasis, promote, breast
GSE318897 L-DOPA treatment promotes sustained neurovascular and synaptic homeostasis in the diabetic retina 53 samples shares homeostasis, promote
GSE310017 Disease-associated mutations on the STAT5B SH2 domain regulate cholesterol and lipid metabolism in liver [RNA-Seq liver] 37 samples shares cholesterol, regulate
GSE240578 MAD2-dependent insulin receptor endocytosis regulates metabolic homeostasis 20 samples shares homeostasis, regulate
GSE334363 PDE5a Inhibition Restricts Cancer Metastasis by Disrupting NPC1-Mediated Cholesterol Trafficking Through a Non-canonical cGMP-Dependent Pathway 18 samples shares cholesterol, metastasis
GSE276731 Fibroblast growth factor receptor signaling modulates cholesterol storage in a SOAT1-dependent manner to promote mammary tumor cell invasion 18 samples shares cholesterol, promote

Search all mouse 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.