GEO series

A β-1,3/1,6-glucan from Durvillaea Antarctica enhances anti-tumor effects of immune checkpoint inhibitor antibodies II

GSE242577 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2024/12/31 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 15 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: 15 samples: 5 × tumor, vehicle, i.v., vs 5 × tumor, anti-PD-1 antibodies, i.v vs 5 × tumor,BG136 + anti-PD-1 antibodies, i.vGroups 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)

Immunotherapy has emerged as a frontline approach in cancer management, aiming to enhance the adaptive immune response against tumors. However, its limited efficacy across a narrow range of tumor types necessitates the exploration of novel strategies that target innate immunity. Therapeutic modulation of pattern recognition receptors (PRRs) and innate immune cells holds promise in tumor eradication.

Read the full summary ↓

β-glucan, a pathogen-associated molecular pattern (PAMP), acts as an immunostimulator, bridging the innate and adaptive immune responses. It exhibits low toxicity and high compatibility with various antitumor strategies. Plenty of clinical trials are ongoing to evaluate β-glucan-based cancer immunotherapy and shows promising clinical benefits across multiple cancer types. A soluble β-1,3/1,6-glucan with high purity from Durvillaea Antarctica (BG136) was reported previously by our group to exhibit pan antitumor effects alone as an immune stimulator. In current study, we proved the antitumor activity of BG136 in combination with anti-PD-1 antibodies in MC38 syngeneic tumor model in vivo. Integrated transcriptomic and metabolomic analyses suggest that BG136 enhances the antitumor immunity of anti-PD-1 antibodies by reprogramming tumor microenvironment to more proinflammatory status. There are more innate and adaptive immune cell infiltration and activation, enhanced lipid metabolism, decreased ascorbate and aldarate metabolism. These findings provide mechanistic insights supporting the potent antitumor efficacy of BG136 in combination with immune checkpoint inhibitor antibodies.

This dataset

Open GSE242577 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 GSE242577_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 PRJNA1013965 and SRA study SRP459138. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 × tumor, vehicle, i.v., vs 5 × tumor, anti-PD-1 antibodies, i.v vs 5 × tumor,BG136 + anti-PD-1 antibodies, i.v

Supports a between-group comparison across 15 samples.

How we read this: 3 replicated groups read from 15 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

GSM7766142 tumor, vehicle, i.v., rep1 tumor, vehicle, i.v.,
GSM7766143 tumor, vehicle, i.v., rep2 tumor, vehicle, i.v.,
GSM7766144 tumor, vehicle, i.v., rep3 tumor, vehicle, i.v.,
GSM7766145 tumor, vehicle, i.v., rep4 tumor, vehicle, i.v.,
GSM7766146 tumor, vehicle, i.v., rep5 tumor, vehicle, i.v.,
GSM7766147 tumor, anti-PD-1 antibodies, i.v. rep1 tumor, anti-PD-1 antibo…
GSM7766148 tumor, anti-PD-1 antibodies, i.v. rep2 tumor, anti-PD-1 antibo…
GSM7766149 tumor, anti-PD-1 antibodies, i.v. rep3 tumor, anti-PD-1 antibo…
GSM7766150 tumor, anti-PD-1 antibodies, i.v. rep4 tumor, anti-PD-1 antibo…
GSM7766151 tumor, anti-PD-1 antibodies, i.v. rep5 tumor, anti-PD-1 antibo…
GSM7766152 tumor,BG136 + anti-PD-1 antibodies, i.v. rep1 tumor,BG136 + anti-PD-1…
GSM7766153 tumor,BG136 + anti-PD-1 antibodies, i.v. rep2 tumor,BG136 + anti-PD-1…
GSM7766154 tumor,BG136 + anti-PD-1 antibodies, i.v. rep3 tumor,BG136 + anti-PD-1…
GSM7766155 tumor,BG136 + anti-PD-1 antibodies, i.v. rep4 tumor,BG136 + anti-PD-1…
GSM7766156 tumor,BG136 + anti-PD-1 antibodies, i.v. rep5 tumor,BG136 + anti-PD-1…

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