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Flt3L -expanded conventional type I dendritic cells formed in the tumor prime “stem-like” T cells in the draining lymph nodes to evoke enhanced responses to immunotherapy [1]

GSE291668 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/10/02 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 10 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
10 samples: 5 × 24JK Tumors (Day16) vs 5 × 24JK-FLT3L Tumors (Day16)Groups 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
Flt3L-mediated tumor cDC1 expansion enhances immunotherapy by priming stem-like CD8(+) T cells in lymph nodesNature immunology · 2026
Summary (written by the submitters)
Immune checkpoint blockade (ICB) evokes anti-tumor immunity through the reinvigoration of tumor-specific T cell responses but it is only effective in a subset of patients. T cell differentiation status is a critical determinant of response, with less differentiated cells demonstrating an enhanced capacity to proliferate following ICB.
Read the full summary ↓
Given recent data indicating that conventional type 1 dendritic cells (cDC1) maintain precursor exhausted (TPEX) cells, we hypothesized that expansion of cDC1s could enhance responses to ICB. Treatment of mice with Flt3L simultaneously expanded cDC1s and CD62L+SLAMF6+CD8+ T cells in both tumors and draining lymph nodes. The formation of these CD62L+SLAMF6+ CD8+ T cells is dependent on the transcription factor Myb, CCR7+ XCR1+DCs and lymph node egress. Hence, we demonstrate that the lymph node is a critical site for the effect of Flt3L on T cell differentiation state. We hypothesized that the promotion of this phenotype would enable more effective responses to ICB. Indeed, the combination of Flt3L and anti-CTLA4 led to significantly enhanced therapeutic responses and was associated with the emergence of a unique CD8+ T cell subset characterized by the expression of IL-21R.
Published in
Flt3L-mediated tumor cDC1 expansion enhances immunotherapy by priming stem-like CD8(+) T cells in lymph nodes
Lai J, Chan CW, Armitage JD et al. · Nature immunology 2026 · PMID 41667622 · doi:10.1038/s41590-026-02419-4
This dataset
Open GSE291668 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 GSE291668_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 PRJNA1234612 and SRA study SRP569722. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41667622) ↗
Study design
5 × 24JK Tumors (Day16) vs 5 × 24JK-FLT3L Tumors (Day16)

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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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