GEO series

Adenoviral Vectored Neoantigen Vaccine Augments Hyperexpanded CD8+ T Cell Control of Tumor Challenge in Mice

GSE264579 Mus musculus (mouse) Single-cell RNA-seq 32 samples Submitted 2025/02/14 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 32 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: 32 samples: 32 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: Adenoviral-vectored neoantigen vaccine augments hyperexpanded CD8(+) T cell control of tumor challenge in miceJournal for immunotherapy of cancer · 2024

Summary (written by the submitters)

Neoantigens are promising immunogens for cancer vaccines and are traditionally delivered as adjuvanted peptide vaccines. Our goal was to understand how an adenoviral vectored neoantigen vaccine would induce tumor immunity compared to a peptide neoantigen vaccine. We generated adenovirus serotype 26 (Ad26) vaccines encoding MC38-specific neoantigens and compared them to an adjuvanted peptide MC38 neoantigen vaccine.

Read the full summary ↓

The single-shot Ad26 vaccines induced greater neoantigen specific IFN- CD8+ T cell immune responses than the two-shot adjuvanted peptide vaccine in mice, and Ad26.VP22.7Epi also provided superior protective efficacy compared to the peptide vaccine following tumor challenge. Ad26.VP22.7Epi induced a robust immunodominant CD8+ T cell response against the Adpgk neoantigen, while the peptide vaccine induced lower responses against both Adpgk and Reps1 neoantigens. Tumor infiltrating lymphocytes (TILs) from both vaccine groups were analyzed using scRNA-seq and TCR-seq. Vaccinated mice showed increased CD8+ T cell infiltration, with the peptide vaccine inducing more infiltrating CD8+ T cells than the Ad26.VP22.7Epi vaccine. However, Ad26.VP22.7Epi induced CD8+ T cells showed more upregulation of T cell maturation, activation, and Th1 pathways compared to peptide vaccine induced CD8+ T cells, suggesting improved functional T cell quality. TCR-seq of these TILs also demonstrated that Ad26.VP22.7Epi generated larger T cell hyperexpanded clones compared to the peptide vaccine. These results suggest that the Ad26.VP22.7Epi vaccine led to improved tumor control compared with the peptide vaccine due to increased T cell hyperexpansion and functional activation. Our data suggest that future cancer vaccine development strategies should focus on inducing functional hyperexpanded CD8+ T cell responses and not only maximizing tumor infiltrating CD8+ T cell numbers.

Published in

Adenoviral-vectored neoantigen vaccine augments hyperexpanded CD8(+) T cell control of tumor challenge in mice

Dagotto G, Colarusso A, Patio RC et al. · Journal for immunotherapy of cancer 2024 · PMID 39694702 · doi:10.1136/jitc-2024-009644

This dataset

Open GSE264579 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 GSE264579_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 PRJNA1103182 and SRA study SRP503359. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39694702) ↗

Study design

32 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 32 sample titles: 32 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

GSM8223007 G1M1 Gene Expression
GSM8223008 G1M1 V(D)J Sequencing
GSM8223009 G1M10 Gene Expression
GSM8223010 G1M10 V(D)J Sequencing
GSM8223011 G1M11 Gene Expression
GSM8223012 G1M11 V(D)J Sequencing
GSM8223013 G1M3 Gene Expression
GSM8223014 G1M3 V(D)J Sequencing
GSM8223015 G1M6 Gene Expression
GSM8223016 G1M6 V(D)J Sequencing
GSM8223017 G2M11 Gene Expression
GSM8223018 G2M11 V(D)J Sequencing
GSM8223019 G2M13 Gene Expression
GSM8223020 G2M13 V(D)J Sequencing
GSM8223021 G2M14 Gene Expression
GSM8223022 G2M14 V(D)J Sequencing
GSM8223023 G2M4 Gene Expression
GSM8223024 G2M4 V(D)J Sequencing
GSM8223025 G2M8 Gene Expression
GSM8223026 G2M8 V(D)J Sequencing
GSM8223027 G3M1 Gene Expression
GSM8223028 G3M1 V(D)J Sequencing
GSM8223029 G3M11 Gene Expression
GSM8223030 G3M11 V(D)J Sequencing
GSM8223031 G3M13 Gene Expression
GSM8223032 G3M13 V(D)J Sequencing
GSM8223033 G3M14 Gene Expression
GSM8223034 G3M14 V(D)J Sequencing
GSM8223035 G3M4 Gene Expression
GSM8223036 G3M4 V(D)J Sequencing
GSM8223037 G3M5 Gene Expression
GSM8223038 G3M5 V(D)J Sequencing

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