GEO series

Impact of Sirt2 deficiency on downstream TCR signaling in mouse melanoma tumor-infiltrating T lymphocytes

GSE265880 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/10/15 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 4 × CD4_TILs_Sirt2KO vs 4 × CD4_TILs_WildType vs 4 × CD8_TILs_Sirt2KO vs 4 × CD8_TILs_WildTypeGroups 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: SIRT2-mediated deacetylation of LCK governs the magnitude of T cell receptor signalingNature immunology · 2026

Summary (written by the submitters)

The T-cell receptor (TCR) signaling pathway is a highly regulated system designed to prevent autoimmunity while ensuring effective immune responses. This regulation is typically mediated through phosphorylation, dephosphorylation, and ubiquitination. Sirt2, is a cytoplasmic NAD+-dependent histone deacetylase with anti-aging and antioxidant properties.

Read the full summary ↓

Here we reveal acetylation modulated by Sirt2 as a previously unrecognized process controlling TCR signaling. In our study, we found that the loss of Sirt2 in T cells leads to enhanced TCR signaling following T cell activation. Furthermore, we demonstrated that inhibiting Sirt2 in both murine and human tumor-infiltrating lymphocytes restores TCR responsiveness and enhances their anti-tumor activity. This suggests Sirt2 targeting as a potential therapeutic approach for reactivating exhausted T cells within the tumor microenvironment.

Published in

SIRT2-mediated deacetylation of LCK governs the magnitude of T cell receptor signaling

Hamaidi I, Cheng P, Jun SY et al. · Nature immunology 2026 · PMID 41611868 · doi:10.1038/s41590-025-02377-3

This dataset

Open GSE265880 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 GSE265880_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 PRJNA1104612 and SRA study SRP504017. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41611868) ↗

Study design

4 × CD4_TILs_Sirt2KO vs 4 × CD4_TILs_WildType vs 4 × CD8_TILs_Sirt2KO vs 4 × CD8_TILs_WildType

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM8230783 CD4_TILs_Sirt2KO1 CD4_TILs_Sirt2KO
GSM8230784 CD4_TILs_Sirt2KO2 CD4_TILs_Sirt2KO
GSM8230785 CD4_TILs_Sirt2KO3 CD4_TILs_Sirt2KO
GSM8230786 CD4_TILs_Sirt2KO4 CD4_TILs_Sirt2KO
GSM8230787 CD4_TILs_WildType1 CD4_TILs_WildType
GSM8230788 CD4_TILs_WildType2 CD4_TILs_WildType
GSM8230789 CD4_TILs_WildType3 CD4_TILs_WildType
GSM8230790 CD4_TILs_WildType4 CD4_TILs_WildType
GSM8230791 CD8_TILs_Sirt2KO1 CD8_TILs_Sirt2KO
GSM8230792 CD8_TILs_Sirt2KO2 CD8_TILs_Sirt2KO
GSM8230793 CD8_TILs_Sirt2KO3 CD8_TILs_Sirt2KO
GSM8230794 CD8_TILs_Sirt2KO4 CD8_TILs_Sirt2KO
GSM8230795 CD8_TILs_WildType1 CD8_TILs_WildType
GSM8230796 CD8_TILs_WildType2 CD8_TILs_WildType
GSM8230797 CD8_TILs_WildType3 CD8_TILs_WildType
GSM8230798 CD8_TILs_WildType4 CD8_TILs_WildType

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