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Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases

GSE263625 Mus musculus (mouse) Single-cell RNA-seq 19 samples Submitted 2025/02/06 Platform GPL17021Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 19 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
19 samples: 4 × CMG vs 4 × TMG vs 4 × TA-MACGroups 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
Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastasesCancer cell · 2025
Summary (written by the submitters)
Melanoma is one of the solid tumor types with the highest risk of brain metastasis. However, the biology of melanoma brain metastasis and the contribution of the brain immune microenvironment to the responses to therapies remain insufficiently characterized. By using preclinical models and single-cell transcriptomics, we identify microglia, as critical regulators of melanoma biology in the brain.
Read the full summary ↓
We show that activation of the Rela/NF-kB pathway in microglia promotes melanoma brain metastasis and that targeting this pathway elicits microglia reprogramming towards a pro-inflammatory phenotype that enhances anti-tumor immunity and reduces brain metastatic burden. Additionally, canonical and pro-inflammatory microglial markers in melanoma brain metastasis correlate with better responses to immune checkpoint inhibitors in patients and we show that Rela/NF-kB targeting improves responses to these therapies in the brain. Thus, we propose targeting Rela/NF-kB in activated microglia as a strategy to promote anti-tumor immunity and to improve the response to immune checkpoint inhibitors in melanoma brain metastasis.
Published in
Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases
Rodriguez-Baena FJ, Marquez-Galera A, Ballesteros-Martinez P et al. · Cancer cell 2025 · PMID 39919736 · doi:10.1016/j.ccell.2025.01.008
This dataset
Open GSE263625 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 GSE263625_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1098587 and SRA study SRP500694. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39919736) ↗
Study design
4 × CMG vs 4 × TMG vs 4 × TA-MAC

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 19 sample titles; they account for 12 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
Datasets on a similar topic

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