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Cryoablation of primary breast cancer tumors induces a systemic abscopal effect altering TIME (Tumor-Immune Micro-Environment) in distant tumors.

GSE282249 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2024/11/19 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 60 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
60 samples: 15 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.
Paper
Cryoablation of primary breast cancer tumors induces a systemic abscopal effect altering TIME (Tumor Immune Microenvironment) in distant tumorsFrontiers in immunology · 2024
Summary (written by the submitters)
Despite recent advances, triple-negative breast cancer (TNBC) patients remain at high risk for recurrence and metastasis, which creates the need for innovative therapeutic approaches to improve patient outcomes. Cryoablation is a promising, less invasive alternative to surgical resection, capable of inducing tumor necrosis via freeze/thaw cycles.
Read the full summary ↓
Necrotic cell death results in increased inflammatory signals and release of preserved tumor antigens, which have the potential to boost the local and systemic anti-tumor immune response. Thus, compared to surgery, cryoablation enhances the activation of T cells leading to an improved abscopal effect, defined as the occurrence of a systemic response after local treatment. We previously showed with a bilateral-tumor mouse model of TNBC that cryoablation of the primary tumor leads to increased infiltration of distant tumors by tumor infiltrating lymphocytes (TILs) and decreased rates of recurrence and metastasis. However, the early drivers of the cryoablation-generated abscopal effect are still unknown and knowledge of the mechanism could provide insight into improving the anti-tumor immune response through pharmacologic immune modulation in addition to cryoablation. Here we show that cryoablation of mouse mammary carcinomas results in smaller distant tumors that harbor increased frequencies of anti-tumor cells [such as natural killer (NK) cells], accompanied by a systemic increase in the frequency of migratory conventional type 1 dendritic cells (cDC1; CD103+ XCR1+), compared to resection. The changes in cell frequencies are mirrored by the immune gene signature of the distant tumors, with cryoablation inducing genes involved with NK cell activation and leukocyte-mediated toxicity, including IL11ra1 and Pfr1. These results better define the early mechanisms through which cryoablation improves tumor elimination, which is mediated by enhanced frequencies of anti-tumoral cells such as NK and cDC1s at the distant tumor and in the spleen of mice treated with cryoablation, respectively.
Published in
Cryoablation of primary breast cancer tumors induces a systemic abscopal effect altering TIME (Tumor Immune Microenvironment) in distant tumors
Sardela de Miranda F, Martinez-Marin D, Babcock RL et al. · Frontiers in immunology 2024 · PMID 39703517 · doi:10.3389/fimmu.2024.1498942
This dataset
Open GSE282249 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 GSE282249_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 PRJNA1187640 and SRA study SRP546021. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39703517) ↗
Study design
15 conditions, mostly with about 4 replicates each
Mouse 6, abscopal tumor from cryoablation, ×4 Mouse 1, abscopal tumor from resection, ×4 Mouse 1, resected tumor, ×4 Mouse 2, abscopal tumor from resection, ×4 Mouse 2, resected tumor, ×4 Mouse 7, abscopal tumor from cryoablation, ×4 Mouse 8, abscopal tumor from cryoablation, ×4 Mouse 3, abscopal tumor from resection, ×4 +7 more

Supports a between-group comparison across 60 samples.

How we read this: 15 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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