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Hypoxia-Enhanced Podoplanin-Defined Tumour Plasticity Drives CCR7-Mediated Lymphatic Metastasis in Breast Cancer

GSE313218 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2025/12/17 Platform GPL21626

At a glance

Single-cell RNA-seq · mouse · 24 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 24 samples: 6 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.

Summary (written by the submitters)

Background: Lymphatic metastasis is strongly associated with poor prognosis. Although the chemokine receptor CCR7 is a well-established promoter of lymphatic dissemination, its prognostic relevance remains weak. We show that tumour cell plasticity, defined by upregulation of podoplanin (PDPN) and promoted by hypoxia, intersects with CCR7 function in triple-negative breast cancer (TNBC).

Read the full summary ↓

Methods: In vivo and in vitro studies using a CCR7-expressing TNBC mouse model were combined with transcriptomic profiling. Human relevance was assessed using scRNA-seq datasets from cell lines and primary tumours, as well as the METABRIC breast cancer cohorts (n = 1784). Results: A PDPN-defined epithelial–mesenchymal transition (EMT) state—promoted by hypoxia—was required for efficient CCR7-driven lymphatic metastasis and tumour progression. PDPN-expression was linked to elevated tumour cell collagen-expression and suppression of interferon-signalling, features associated with an immune-cold microenvironment. PDPN-expression with effects on interferon and collagen programs were observed across murine and human TNBC/basal-like cell lines. In primary TNBC, PDPN-expression correlated with EMT, collagen, and hypoxia signatures, mirroring murine findings. In METABRIC, high CCR7–PDPN co-expression predicted poor survival in lymph node–positive patients, whereas either marker alone lacked prognostic value. Conclusions: PDPN is a tumour-cell-associated biomarker of plasticity in TNBC, revealing synergy between specific hypoxia-induced EMT-states and CCR7 in promoting lymphatic dissemination and poor prognosis.

This dataset

Open GSE313218 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 GSE313218_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 PRJNA1378922 and SRA study SRP654478. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

X2 batch 1 ×4 X2 batch 2 ×4 CCR7 batch 1 ×4 CCR7 PDPN batch 1 ×4 CCR7 PDPN batch 2 ×4 X2 PDPN ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM9364383 X2 batch 1 replicate 1 X2 batch 1
GSM9364384 X2 batch 1 replicate 2 X2 batch 1
GSM9364385 X2 batch 1 replicate 3 X2 batch 1
GSM9364386 X2 batch 1 replicate 4 X2 batch 1
GSM9364387 X2 batch 2 replicate 1 X2 batch 2
GSM9364388 X2 batch 2 replicate 2 X2 batch 2
GSM9364389 X2 batch 2 replicate 3 X2 batch 2
GSM9364390 X2 batch 2 replicate 4 X2 batch 2
GSM9364391 CCR7 batch 1 replicate 1 CCR7 batch 1
GSM9364392 CCR7 batch 1 replicate 2 CCR7 batch 1
GSM9364393 CCR7 batch 1 replicate 3 CCR7 batch 1
GSM9364394 CCR7 batch 1 replicate 4 CCR7 batch 1
GSM9364395 CCR7 PDPN batch 1 replicate 1 CCR7 PDPN batch 1
GSM9364396 CCR7 PDPN batch 1 replicate 2 CCR7 PDPN batch 1
GSM9364397 CCR7 PDPN batch 1 replicate 3 CCR7 PDPN batch 1
GSM9364398 CCR7 PDPN batch 1 replicate 4 CCR7 PDPN batch 1
GSM9364399 CCR7 PDPN batch 2 replicate 1 CCR7 PDPN batch 2
GSM9364400 CCR7 PDPN batch 2 replicate 2 CCR7 PDPN batch 2
GSM9364401 CCR7 PDPN batch 2 replicate 3 CCR7 PDPN batch 2
GSM9364402 CCR7 PDPN batch 2 replicate 4 CCR7 PDPN batch 2
GSM9364403 X2 PDPN replicate 1 X2 PDPN
GSM9364404 X2 PDPN replicate 2 X2 PDPN
GSM9364405 X2 PDPN replicate 3 X2 PDPN
GSM9364406 X2 PDPN replicate 4 X2 PDPN

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