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NRF2 Activation in Cancer Cells Suppresses Immune Infiltration into Tumor Microenvironment

GSE299332 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2025/08/20 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 7 conditions, mostly with about 4 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
NRF2 activation in cancer cells suppresses immune infiltration into the tumor microenvironmentiScience · 2025
Summary (written by the submitters)
Clinical observations have revealed that NRF2 hyperactivation in cancer cells is often associated with immune suppression in the tumor microenvironment. However, it remains unclear whether NRF2 hyperactivation directly reduces immune cell infiltration into tumors. To address this question, we established a syngeneic mouse model using transplantation of 3LL lung cancer-derived cells with either NRF2 hyperactivation via Keap1 gene deletion or concomitant Keap1-Nrf2 gene deletion.
Read the full summary ↓
A series of flowcytometry, histological analysis, and comprehensive gene expression profiling demonstrated that immune cell infiltration was significantly reduced in KEAP1-deleted tumors, with marked decrease in CD45-positive cells, particularly myeloid and monocytic populations. In contrast, concomitant deletion of NRF2 restored immune cell infiltration in the KEAP1-deleted tumors. These findings provide convincing lines of evidence that NRF2 activation in cancer cells suppresses immune cell infiltration into tumors. Our study sheds light on the mechanistic basis by which NRF2 activation contributes to cancer malignancy.
Published in
NRF2 activation in cancer cells suppresses immune infiltration into the tumor microenvironment
Wen H, Suzuki T, Zhang A et al. · iScience 2025 · PMID 41035689 · doi:10.1016/j.isci.2025.113519
This dataset
Open GSE299332 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 GSE299332_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 PRJNA1273922 and SRA study SRP591256. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41035689) ↗
Study design
7 conditions, mostly with about 4 replicates each
3LL_cell_WT ×4 3LL_cell_K0 ×4 3LL_cell_K0N0 ×4 3LL_tumor_WT_A ×4 3LL_tumor_K0_A ×4 3LL_tumor_K0_B ×4 3LL_tumor_K0N0_B ×4

Supports a between-group comparison across 28 samples.

How we read this: 7 replicated groups read from 28 sample titles; they account for 28 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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