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The Alb-R26Met liver cancer mouse model recapitulates molecular features and heterogeneity of hepatocellular carcinoma patients

GSE271709 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/02/07 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 12 × advanced liver tumour AlbR26Met vs 6 × mutant liver healty AlbR26MetGroups 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
Tracing specificity of immune landscape remodeling associated with distinct anticancer treatmentsiScience · 2025
Summary (written by the submitters)
We have generated an inside-out genetic mouse model of liver cancer, the Alb-R26Met mice, in which slightly increased levels of the wild-type form of the MET Receptor Tyrosine Kinase (RTK) occurs specifically in the liver following the deletion of a stop cassette by the Cre recombinase. This genetic combination is obtained by crossing the R26stopMet with Alb-Cre mice.
Read the full summary ↓
The Alb-R26Met mice spontaneously develop liver tumours and model the whole tumorigenic program. These tumours correspond to HCC patients belonging to the proliferative-progenitor subset. Importantly, the Alb-R26Met model recapitulates several features of HCC patients, including the molecular heterogeneity, the temporal heterogeneity of tumour onset, and the resistance to RTK inhibitors used in the clinic for HCC treatment. This unique genetic setting offered us the possibility to compare the transcriptomic profile of Alb-R26Met non-tumoral livers with Alb-R26Met advanced liver tumours. Outcomes offer an overall vision of how gene expression switches during a tumorigenic process modelled by the Alb-R26Met mice. Importantly, as tumorigenesis in the Alb-R26Met genetic setting occurs in an immune-competent context, outcomes offers as well the possibility to explore the profound changes in the immune microenvironment in the liver tumours, by performing deconvolution of RNAseq data.
Published in
Tracing specificity of immune landscape remodeling associated with distinct anticancer treatments
Cannet F, Sequera C, Veloso PM et al. · iScience 2025 · PMID 40124507 · doi:10.1016/j.isci.2025.112071
This dataset
Open GSE271709 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 GSE271709_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 PRJNA1132968 and SRA study SRP518522. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40124507) ↗
Study design
12 × advanced liver tumour AlbR26Met vs 6 × mutant liver healty AlbR26Met

Supports a between-group comparison across 18 samples.

How we read this: 2 replicated groups read from 18 sample titles; they account for 18 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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