GEO series

The Tumor-Sentinel Lymph Node Immune Migratome Reveals a Key Role for Migratory CCR7+ Dendritic Cells in Response to Immunoradiotherapy [CITE-seq]

GSE276434 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2025/06/07 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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: The tumor-sentinel lymph node immuno-migratome reveals CCR7⁺ dendritic cells drive response to sequenced immunoradiotherapyNature communications · 2025

Summary (written by the submitters)

Surgical ablation or radiation of tumor-draining lymph nodes can eliminate the primary tumor response to immunotherapy, indicating that local tumor response to immunotherapy is mediated by tumor-draining lymph nodes. Here, we show that immunoradiotherapy efficacy is dependent on immune cell migration from tumor to sentinel lymph nodes.

Read the full summary ↓

Using a tamoxifen-inducible reporter paired with CITE-sequencing in a murine model of oral cancer, we characterized tumor immune cellular migration through lymphatic channels to sentinel lymph nodes at single-cell resolution. Within a structured approach of sequential immunomodulatory radiotherapy and checkpoint inhibition, we demonstrate that lymphatic-sparing, tumor-directed radiotherapy followed by PD-1 inhibition achieves complete and durable tumor responses. Mechanistically, this treatment approach enhances activated, migratory CCR7+ dendritic cell surveillance across the tumor-sentinel lymph node axis, revealing a shift from their canonical role in promoting tolerance to driving antitumor immunity. Overall, this work supports rationally sequencing immune-sensitizing, lymphatic-preserving, tumor-directed radiotherapy followed by immune checkpoint inhibition to optimize the tumor response. By characterizing the tumor-sentinel lymph node immunomigratome that drives durable antitumor response, we reveal a therapeutic opportunity to enhance the response to immunotherapy by optimizing activated dendritic cell migration to tumor-draining sentinel nodes.

Published in

The tumor-sentinel lymph node immuno-migratome reveals CCR7⁺ dendritic cells drive response to sequenced immunoradiotherapy

Saddawi-Konefka R, Msari RA, Tang S et al. · Nature communications 2025 · PMID 40675962 · doi:10.1038/s41467-025-61780-4

This dataset

Open GSE276434 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 GSE276434_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1157367 and SRA study SRP530604. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40675962) ↗

Study design

16 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 4 samples read as cases, 4 as controls.

How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. 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

GSM8498483 tumor, ctrl, rep1, GEX
GSM8498484 tumor, ctrl, rep2, GEX
GSM8498485 tumor, irt, rep1, GEX
GSM8498486 tumor, irt, rep2, GEX
GSM8498487 sln, ctrl, rep1, GEX
GSM8498488 sln, ctrl, rep2, GEX
GSM8498489 sln, irt, rep1, GEX
GSM8498490 sln, irt, rep4, GEX
GSM8498491 tumor, ctrl, rep1, CSP
GSM8498492 tumor, ctrl, rep2, CSP
GSM8498493 tumor, irt, rep1, CSP
GSM8498494 tumor, irt, rep2, CSP
GSM8498495 sln, ctrl, rep1, CSP
GSM8498496 sln, ctrl, rep2, CSP
GSM8498497 sln, irt, rep1, CSP
GSM8498498 sln, irt, rep4, CSP

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