GEO series

Induced loss of TREX1 in host cells inflames the tumor micromilieu and invigorates CTL-mediated cancer control

GSE268792 Mus musculus (mouse) RNA-seq (gene expression) 2 samples Submitted 2025/05/04 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 2 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: 2 samples
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: Systemic Inactivation of TREX1 Induces Selective Inflammation of the Tumor Microenvironment and Invigorated T-cell-Mediated Tumor ControlCancer research · 2025

Summary (written by the submitters)

Activation of local innate immunity in tumor tissue, aiming at induction of adaptive responses, is a major concept in cancer immunotherapy. The cGAS/STING pathway triggers type I IFN and pro-inflammatory cytokine responses upon detection of cytosolic DNA and can robustly enhance anti-tumor immunity. The DNase 3’ repair exonuclease 1 (TREX1) is a central component of cellular DNA disposal preventing accumulation of endogenous DNA in the cytosol, activation of cGAS and cell-intrinsic innate immune responses.

Read the full summary ↓

While constitutive TREX1-deficiency causes severe mendelian autoimmunity, temporary pharmacological inhibition of the enzyme may represent an efficient means to activate anti-tumor immunity. Induced inactivation of the Trex1 gene in mice (TREX1 iKO) resulted in improved immune control of established syngeneic tumors that was type I IFN- and CD8+ T cell-dependent. This was associated with a dramatic increase of immune cell infiltration of tumor tissue while other (non-tumor) tissues were not or marginally affected. TREX1 iKO triggered an inflammatory switch of intra-tumoral monocyte, macrophage and dendritic cell populations, associated with enhanced antigen presentation capacity. Invigoration of CD8 T cell responses was reflected in robust increase in cells differentiating along the exhaustion trajectory but expressing significant signatures of effector function. Combination of TREX1 iKO with immune checkpoint inhibition synergistically promoted tumor control. In addition to improved anti-tumor immunity upon loss of TREX1 in host cells, we also show that cancer cell-specific TREX1 deficiency synergizes with irradiation and checkpoint inhibition to enable tumor rejection and formation of long-term memory. We conclude that pharmacological TREX1 inhibition is a promising therapeutic approach to boost anti-tumor immunity.

Published in

Systemic Inactivation of TREX1 Induces Selective Inflammation of the Tumor Microenvironment and Invigorated T-cell-Mediated Tumor Control

Marinkovic E, Chen M, Schubert N et al. · Cancer research 2025 · PMID 40354626 · doi:10.1158/0008-5472.CAN-24-2262

This dataset

Open GSE268792 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 GSE268792_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 PRJNA1118762 and SRA study SRP511083. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40354626) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

Datasets on a similar topic

GSE290383 Induced loss of TREX1 in host cells inflames the tumor micromilieu and invigorates CTL-mediated cancer control 12 samples shares trex1, ctl-mediated, micromilieu, invigorates, inflames, induced, control, loss
GSE207859 Transcriptome changes in multiple tissues of Trex1 knockout mouse after SN-011 administration 24 samples shares trex1
GSE226594 The effect of the STING antagonist on the gene expression changes in the kidney of Trex1 -/- mice 9 samples shares trex1
GSE143826 Transcriptome changes in BMDM cells of Trex1 knockout mouse before and after STING antagonists treatments 8 samples shares trex1
GSE322841 GPR30-mediated NETs degradation via Trex1 in heart failure of aged female mice 6 samples shares trex1
GSE271340 Single-cell sequencing of CD45-positive and CD45 negative cells from the lungs of WT, Trex1 KO, Trex1;Ifngr1 DKO, and cGas-KI/+;Vav-icre mice 4 samples shares trex1
GSE11698 Microarray of Trex1 WT and Trex1 KO hearts on RAG2KO background 6 samples shares trex1
GSE275905 Targeted release of a bispecific fusion protein SIRPα/Siglec-10 by oncolytic adenovirus reinvigorates tumor associated macrophages to improve therapeutic outcomes in solid tumors 11 samples shares invigorates

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