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Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical models

GSE310501 Mus musculus (mouse) RNA-seq (gene expression) 31 samples Submitted 2025/11/25 Platform GPL34328
At a glance

RNA-seq (gene expression) · mouse · 31 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
31 samples: 6 conditions, mostly with about 5 replicates eachGroups 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
Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical modelsScientific reports · 2026
Summary (written by the submitters)
Mesothelioma is a cancer derived from mesothelial cells, most commonly arising from the pleura or the peritoneum. Immune checkpoint therapy (ICT) has shown survival benefit for pleural mesothelioma, but little is known about the response in peritoneal mesothelioma. Most preclinical mesothelioma models involve subcutaneous cancer cell implantation, which lacks the relevant tumour microenvironment of peritoneal mesothelioma and does not resemble the clinical presentation.
Read the full summary ↓
We therefore set out to explore the influence of location on the mesothelioma tumour microenvironment, comparing pleural, peritoneal, and subcutaneous models using identical cell line-derived syngeneic mesotheliomas. We found that the peritoneal location conferred an anti-inflammatory tumour microenvironment, characterised by low IFN, TNFα, and STAT signalling activity, low immune cell infiltration and a gene signature associated with non-response to ICT. ICT was effective in subcutaneous models, but the same cell line-derived tumours were irresponsive when inoculated intraperitoneally. Together, these findings show that peritoneal location is associated with an immune suppressive tumour microenvironment.
Published in
Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical models
Orozco Morales ML, Lansley SM, Chin WL et al. · Scientific reports 2026 · PMID 41735480 · doi:10.1038/s41598-026-41431-4
This dataset
Open GSE310501 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 GSE310501_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 PRJNA1364153 and SRA study SRP644663. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41735480) ↗
Study design
6 conditions, mostly with about 5 replicates each
RNA extracted from AB1-mCherry pleural whole … ×6 RNA extracted from AB1-mCherry subcutaneous w… ×5 RNA extracted from AB1-mCherry peritoneal who… ×5 RNA extracted from AB1-mCherry sorted cells f… ×5 RNA extracted from AB1-mCherry sorted cells f… ×5 RNA extracted from AB1-mCherry sorted cells f… ×5

Supports a between-group comparison across 31 samples.

How we read this: 6 replicated groups read from 31 sample titles; they account for 31 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
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