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In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation (TAD18)

GSE273610 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/03/10 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 14 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
14 samples: 6 conditions, mostly in duplicateGroups 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
In vivo armed macrophages curb liver metastasis through tumor-reactive T-cell rejuvenationNature communications · 2025
Summary (written by the submitters)
Despite recent progress in cancer treatment, liver metastases persist as an unmet clinical need. This is partly attributable to the immunosuppressive microenvironment of liver metastases, which inhibits immune activation. To unleash anti-tumoral immune responses against liver metastases, we armed liver and tumor-associated macrophages to coordinately express tumor antigens (TAs), IFNα and IL-12.
Read the full summary ↓
The combination of TAs with both cytokines yielded the most potent therapeutic response, resulting in the eradication of established liver metastases in several mouse models of the disease. Mechanistically, armed macrophages expanded tumor reactive CD8+ T cells, which in the presence of IFNα and IL-12 acquired features of progenitor exhausted T cells and killed cancer cells independently of CD4+ T cell help. IFNα and IL-12 produced within the liver tissue by armed macrophages rewired cell interactions within the tumor microenvironment and reprogrammed antigen presenting cells to further support T cell effector functions. Tumor reactive T cell rejuvenation and strong therapeutic activity were observed in distinct liver metastasis mouse models of colorectal cancer and melanoma, expressing either surrogate tumor antigens, naturally occurring private neoantigens or tumor-associated antigens. Altogether, our findings support the translational potential of in vivo armed liver macrophages expressing TA and immune-activating cytokines to expand and rejuvenate tumor reactive T cells for the treatment of liver metastases.
Published in
In vivo armed macrophages curb liver metastasis through tumor-reactive T-cell rejuvenation
Notaro M, Borghetti M, Bresesti C et al. · Nature communications 2025 · PMID 40216735 · doi:10.1038/s41467-025-58369-2
This dataset
Open GSE273610 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 GSE273610_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 PRJNA1142496 and SRA study SRP523551. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40216735) ↗
Study design
6 conditions, mostly in duplicate
Liver, liOVA_IL12, ×2 Tumor, liOVA_IL12, ×2 Liver, liOVA_IFNa, ×2 Tumor, liOVA_IFNa, ×2 Liver, liOVA_IL12_INFa, ×2 Tumor, liOVA_IL12_INFa, ×2 Liver, liOVA ×1 Tumor, liOVA ×1

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 14 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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