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The T-cell niche tunes immune function through modulation of the cytoskeleton and TCR-antigen forces

GSE335537 Mus musculus (mouse) RNA-seq (gene expression) 9 samples Submitted 2026/06/20 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 9 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
9 samples: 3 × T Cell unconditioned media treated vs 3 × T Cell adipocyte conditioned media treated vs 3 × T Cell stromal conditioned media treatedGroups 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.
Summary (written by the submitters)
Obesity has become a major public health crisis given its rampant growth and association with an increased risk for cancer. Cancer patients who present with obesity tend to have increased tumor burden and decreased T-cell function, yet it remains unclear how obesity compromises T-cell mediated immunity. To address this, we modeled the adipose niche using the secretome of cultured adipocytes and assessed the impact of these factors on T-cell function.
Read the full summary ↓
We found that these secretomes altered antigen-specific T-cell receptor triggering and activation. RNA-sequencing analysis identified changes in cytoskeletal regulation and actin polymerization in T-cells exposed to the adipocyte secretome. Molecular force measurements were consistent and showed that T-cells exposed to the adipocyte niche display dampened force transmission to the TCR-antigen complex. Conversely, exposure to the control stromal cell secretome lead to enhanced TCR forces. These results were then validated in diet-induced obese mice and human donor T-cells. Importantly, secretome-mediated TCR force modulation mirrored the changes in T-cell functional responses in human T-cells using the FDA-approved immunotherapy, blinatumomab. Thus, the adipocyte niche contributes to T-cell dysfunction through cytoskeletal modulation and reduces TCR triggering by dampening TCR forces consistent with the mechanosensor model of T-cell activation.
This dataset
Open GSE335537 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 GSE335537_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 PRJNA1478840 and SRA study SRP709891. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × T Cell unconditioned media treated vs 3 × T Cell adipocyte conditioned media treated vs 3 × T Cell stromal conditioned media treated

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.