GEO series

Immune checkpoint blockade augments lymphodepleting chemotherapy-induced antitumor immunity by expanding effector CD8+ T cell clones in preclinical models of cancer

GSE307388 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/06/10 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 12 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.

Summary (written by the submitters)

Cancer treatment using immune checkpoint blockade (ICB) with anti-programmed cell death protein (PD)-1 and anti-cytotoxic T lymphocyte associated protein (CTLA)-4 has been successful. However, primary and acquired resistance limits clinical benefit. To improve the effectiveness of ICB therapies, strategies that reorchestrate anti-tumor immunity through mechanism-based drug combinations are being actively explored.

Read the full summary ↓

The alkylating chemotherapeutic agent, cyclophosphamide (CTX), has direct tumoricidal and immunomodulatory properties, including the induction of homeostatic proliferation of T cells. Since ICB suppresses inhibitory signals in T cells, we hypothesized that ICB could augment CTX-induced homeostatic proliferation of antigen-specific T cells, thereby resetting the T cell receptor (TCR) repertoire in favor of tumor-specific T cells. Here, we show that a single dose of CTX one day prior to starting aPD-1+aCTLA-4 is sufficient to delay tumor progression in established melanoma and prolong survival in tumor-bearing mice in preclinical models. These effects extended to other lymphodepleting treatments, such as Gemcitabine and radiation therapy. The anti-tumor immune response was mainly driven by the clonal expansion of activated/effector CD8+ tumor infiltrating lymphocytes. Furthermore, combined CTX and aPD-1+aCTLA-4 treatment demonstrated efficacy across additional preclinical tumor models, including colorectal cancer and triple negative breast cancer. Overall, our findings highlight that the combination of CTX and aPD-1+aCTLA-4 represents a clinically relevant approach in the treatment of ICB-refractory tumors.

This dataset

Open GSE307388 in finder → Find more mouse 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 GSE307388_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 PRJNA1320634 and SRA study SRP617769. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

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

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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

GSM9223198 PBS IgG GEX
GSM9223199 PBS combo GEX
GSM9223200 CTX IgG GEX
GSM9223201 CTX combo GEX
GSM9223202 PBS IgG ADT
GSM9223203 PBS combo ADT
GSM9223204 CTX IgG ADT
GSM9223205 CTX combo ADT
GSM9223206 PBS IgG VDJ
GSM9223207 PBS combo VDJ
GSM9223208 CTX IgG VDJ
GSM9223209 CTX combo VDJ

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