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Pertussis toxin-induced lymphocytosis enhances anti-tumor immune environments and improves the anti-PD1 treatment response in a squamous cell carcinoma model.

GSE311831 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/08/05 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
Pertussis toxin-induced lymphocytosis shifts the tumor microenvironment toward immune activation via CXCL9 signalingCancer immunology, immunotherapy : CII · 2026
Summary (written by the submitters)
Elevation of the neutrophil-to-lymphocyte ratio (NLR) in cancer patients predicts a worse prognosis, and NLR is a good discriminator in response to anti-tumor immune checkpoint inhibitors. However, the therapeutic potential of NLR normalization to enhance the efficacy of anti-tumor immunotherapy has not been investigated. In this study, we chose pertussis toxin (PTX) as an agent to induce lymphocytosis and lower NLR.
Read the full summary ↓
PTX decreased NLR in squamous cell carcinoma (SCC)-tumor-bearing mice and shifted the tumors from low to high immune scores. PTX-induced elevation of CXCL9 led to lymphocytosis and increased immune cell infiltration in tumor tissues. The combination treatment with PTX and anti-PD1 antibody significantly suppressed in vivo SCC tumor growth, compared to anti-PD1 treatment alone. The combination treatment induced a larger proportion of T cells in the tumor microenvironment, and these findings were associated with an increase in terminally differentiated CD8 T cells and their augmented Ki-67 expression. In addition, tumor-specific IFN-γ production was augmented in animals treated with anti-PD1 antibody and combination treatments, but not with PTX alone. In summary, PTX can induce high lymphocyte infiltration into tumor tissue, leading to the NLR normalization and a favorable immune environment for immune checkpoint inhibitors.
Published in
Pertussis toxin-induced lymphocytosis shifts the tumor microenvironment toward immune activation via CXCL9 signaling
Cho JK, Lee K, Shin DY et al. · Cancer immunology, immunotherapy : CII 2026 · PMID 42209867 · doi:10.1007/s00262-026-04436-6
This dataset
Open GSE311831 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 GSE311831_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 PRJNA1370977 and SRA study SRP649775. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42209867) ↗
Study design
8 conditions, mostly in triplicate
G1 - Tumor single cell, M# ×3 G1 - Lymph node, M# ×3 G2 - Tumor single cell, P toxin-induced, M# ×3 G2 - Lymph node, P toxin-induced, M# ×3 G5 - Tumor single cell, M# ×3 G5 - Lymph node, M# ×3 G6 - Tumor single cell, P toxin-induced, M# ×3 G6 - Lymph node, P toxin-induced, M# ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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
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