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Mitochondrial respiration is necessary for CD8 T cell proliferation and cell fate

GSE296763 Mus musculus (mouse) RNA-seq (gene expression) 99 samples Submitted 2025/06/20 Platform GPL19057Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 99 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
99 samples: 22 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
Mitochondrial respiration is necessary for CD8(+) T cell proliferation and cell fateNature immunology · 2025
Summary (written by the submitters)
CD8 T cell proliferation and memory formation are linked to changes in metabolism, which has important implications for improving CD8 T cell fitness in therapies against chronic infections and cancer. The mitochondrial electron transport chain (ETC) is essential for antigen-specific CD8 T cell proliferation. Mitochondrial ETC function is linked to the generation of ATP, production of metabolites to sustain proliferation, and signaling molecules including reactive oxygen species (ROS), which determine T cell function and fate.
Read the full summary ↓
However, it is not fully understood which mitochondrial ETC functions are necessary for CD8 T cell proliferation in vivo. Here we report that impairing mitochondrial complex III function, which diminishes respiration, proton pumping linked to ATP production, and superoxide production, decreases CD8 T cell proliferation and memory formation. CD8 T cells lacking functional mitochondrial complex III also exhibit an exhausted-like phenotype following acute stimulation. The expression of Ciona intestinalis alternative oxidase (AOX), which accepts electrons from coenzyme Q, thus compensating for the loss of mitochondrial complex III function without generating ROS or proton pumping, restores respiration, proliferation and largely prevents the exhausted phenotype in vitro and in vivo. However, AOX did not sustain memory CD8 T cells, suggesting mitochondrial complex III ROS is necessary for optimal memory formation. These findings demonstrate that the primary function of the mitochondrial ETC in CD8 T cells is enabling respiration to sustain proliferation and memory formation as well as to prevent an exhausted phenotype.
Published in
Mitochondrial respiration is necessary for CD8(+) T cell proliferation and cell fate
Steinert EM, Furtado Bruza B, Danchine VD et al. · Nature immunology 2025 · PMID 40670617 · doi:10.1038/s41590-025-02202-x
This dataset
Open GSE296763 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 GSE296763_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 PRJNA1261015 and SRA study SRP584302. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40670617) ↗
Study design
22 conditions, mostly with about 5 replicates each
In_Vitro_Activation_WT_Naïve ×6 Direct_Infection_WT_Activated ×5 Direct_Infection_WT_Naïve ×5 Direct_Infection_KO_Activated ×5 Direct_Infection_KO_Naïve ×5 Adoptive_Transfer_WT_Activated ×5 Adoptive_Transfer_WT+AOX_Activated ×5 Adoptive_Transfer_WT_Naïve ×5 +14 more

Supports a between-group comparison across 99 samples.

How we read this: 22 replicated groups read from 99 sample titles; they account for 99 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

+ 59 more — browse all 99 samples with per-sample file links →

Datasets on a similar topic

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