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The efficacy of LCMV-based cancer vaccines is unleashed by intratumoral injections of polyI:C (II)

GSE256478 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/04/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × Vehicle (PBS) flank left control treated tumor vs 4 × C) flank right treated tumor vs 4 × BO-112 flank right treated tumor vs 3 × C) flank left treated tumorGroups 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
Efficacy of LCMV-based cancer immunotherapies is unleashed by intratumoral injections of polyI:CJournal for immunotherapy of cancer · 2024
Summary (written by the submitters)
Background Lymphocytic choriomeningitis virus (LCMV) belongs to the Arenavirus family known for inducing strong cytotoxic T-cell responses in both mice and humans. LCMV has been engineered for the development of anti-tumor vaccines, currently undergoing evaluation in phase I/II clinical trials. Initial findings have demonstrated safety and an exceptional ability to induce and expand tumor-specific T lymphocytes.
Read the full summary ↓
Combination strategies to maximize the anti-tumor effectiveness of LCMV-based vaccines are required. Methods We assessed the anti-tumor therapeutic effects of intratumoral administration of polyinosinic:polycytidylic acid (poly(I:C)) and systemic vaccination using an LCMV-vector expressing non-oncogenic versions of the E6 and E7 antigens of human papillomavirus 16 (artLCMV-E7E6) in a bilateral model engrafting TC-1/A9 cells. This cell line, derived from the parental TC-1, exhibits low MHC class I expression and is highly immune-resistant. The mechanisms underlying the combination's efficacy were investigated through bulk RNAseq, flow cytometry analyses of the tumor microenvironment, selective depletions using antibodies and clodronate liposomes, Batf3 deficient mice, and in vivo bioluminescence experiments. Finally, we assessed the anti-tumor effectiveness of the combining of LCMV-E6E7 with BO-112, a GMP-grade poly(I:C) formulated in polyethyleneimine, currently under evaluation in clinical trials. Results Intratumoral injection of poly(I:C) enhanced the anti-tumor efficacy of artLCMV-E7E6 in both injected and non-injected tumor lesions. The combined treatment resulted in a significant delay in tumor growth and often complete eradication of several tumor lesions, leading to significantly improved survival compared to monotherapies. While intratumoral administration of poly(I:C) did not impact LCMV vector biodistribution or transgene expression, it significantly modified leukocyte infiltrates within the tumor microenvironment and amplified systemic efficacy through proinflammatory cytokines/chemokines such as CCL3, CCL5, CXCL10, TNF, IFNα, and IL12p70. Upregulation of MHC on tumor cells and a reconfiguration of the gene expression programs related to tumor vasculature, leukocyte migration, and the activation profile of tumor-infiltrating CD8+ T lymphocytes were observed. Indeed, the anti-tumor effect relied on the functions of CD8+ T lymphocytes and macrophages. The synergistic efficacy of the combination was further confirmed when BO-112 was included. Conclusion Intratumoral injection of poly(I:C) sensitizes MHClow tumors to the anti-tumor effects of artLCMV-E7E6, resulting in a potent therapeutic synergy
Published in
Efficacy of LCMV-based cancer immunotherapies is unleashed by intratumoral injections of polyI:C
Gomar C, Di Trani CA, Bella A et al. · Journal for immunotherapy of cancer 2024 · PMID 38631714 · doi:10.1136/jitc-2023-008287
This dataset
Open GSE256478 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 GSE256478_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 PRJNA1079764 and SRA study SRP491401. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38631714) ↗
Study design
4 × Vehicle (PBS) flank left control treated tumor vs 4 × C) flank right treated tumor vs 4 × BO-112 flank right treated tumor vs 3 × C) flank left treated tumor

Supports a between-group comparison across 15 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 15 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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