GEO series

CD4 T cell therapy counteracts inflammaging and senescence by preserving gut barrier integrity

GSE266095 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/08/04 Platform GPL23479

At a glance

RNA-seq (gene expression) · mouse · 11 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: 11 samples: 5 × Colon, KO+adoptive transfer, sample vs 3 × Colon, control, sample vs 3 × Colon, KO, sampleGroups 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: CD4 T cell therapy counteracts inflammaging and senescence by preserving gut barrier integrityScience immunology · 2025

Summary (written by the submitters)

Healthy aging relies on a symbiotic host–microbiota relationship. The age-associated decline of the immune system can pose a threat in this delicate equilibrium. In this work, we investigated how the functional deterioration of T cells can impact host–microbiota symbiosis and gut barrier integrity and the implications of this deterioration for inflammaging, senescence, and health decline.

Read the full summary ↓

Using the Tfamfl/flCd4Cre mouse model, we found that T cell failure compromised gut immunity leading to a decrease in T follicular and regulatory T (Treg) cells and an accumulation of highly proinflammatory and cytotoxic T cells. These alterations were associated with intestinal barrier disruption and gut dysbiosis. Microbiota depletion or adoptive transfer of total CD4 T cells or a Treg cell–enriched pool prevented gut barrier dysfunction and mitigated premature inflammaging and senescence, ultimately enhancing healthspan in this mouse model. Thus, a competent CD4 T cell compartment is critical to ensure healthier aging by promoting host–microbiota mutualism and gut barrier integrity.

Published in

CD4 T cell therapy counteracts inflammaging and senescence by preserving gut barrier integrity

Gómez de Las Heras MM, Carrasco E, Pérez-Manrique M et al. · Science immunology 2025 · PMID 40749035 · doi:10.1126/sciimmunol.adv0985

This dataset

Open GSE266095 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 GSE266095_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 PRJNA1105872 and SRA study SRP504580. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40749035) ↗

Study design

5 × Colon, KO+adoptive transfer, sample vs 3 × Colon, control, sample vs 3 × Colon, KO, sample

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 11 sample titles; they account for 11 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

GSM8240535 Colon, KO+adoptive transfer, sample 1 Colon, KO+adoptive tran…
GSM8240536 Colon, KO+adoptive transfer, sample 2 Colon, KO+adoptive tran…
GSM8240537 Colon, KO+adoptive transfer, sample 3 Colon, KO+adoptive tran…
GSM8240538 Colon, KO+adoptive transfer, sample 4 Colon, KO+adoptive tran…
GSM8240539 Colon, KO+adoptive transfer, sample 6 Colon, KO+adoptive tran…
GSM8240540 Colon, control, sample 1 Colon, control, sample
GSM8240541 Colon, control, sample 2 Colon, control, sample
GSM8240542 Colon, control, sample 3 Colon, control, sample
GSM8240543 Colon, KO, sample 1 Colon, KO, sample
GSM8240544 Colon, KO, sample 3 Colon, KO, sample
GSM8240545 Colon, KO, sample 4 Colon, KO, sample

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