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The oncolytic adenovirus Delta-24-RGD in combination with ONC201 displays a potent antitumor effect in pediatric high-grade glioma models [RNA-seqI]

GSE243223 Homo sapiens (human) RNA-seq (gene expression) 52 samples Submitted 2024/05/09 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 52 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
Homo sapiens (human)
Samples
52 samples: 16 conditions, mostly in triplicateGroups 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
The oncolytic adenovirus Delta-24-RGD in combination with ONC201 induces a potent antitumor response in pediatric high-grade and diffuse midline glioma modelsNeuro-oncology · 2024
Summary (written by the submitters)
Background: Pediatric high-grade gliomas (pHGGs), including diffuse midline gliomas (DMGs) are aggressive pediatric tumors harboring one of the poorest prognoses. Previous preclinical and clinical studies have demonstrated that oncolytic adenovirus Delta-24-RGD and the imipridone ONC201 are two promising therapies for these type of tumors as single agents.
Read the full summary ↓
However, the combination of both agents has not been previously evaluated. Methods: Potential negative effects of ONC201 on the production of functional viruses were assessed by immunoblotting and replication assays. Antitumor effect was evaluated in a panel of human and murine pHGG and DMG cell lines. RNAseq, mTORC1 pathway analysis, Seahorse Stress Test, mitochondrial DNA content, and pH2A.X immunofluorescence were used to perform mechanistical studies. Models of both diseases were used to assess the efficacy of the combination in vivo. Tumor immune microenvironment was evaluated using flow cytometry. Results: ONC201 cotreatment with Delta-24-RGD did not affect the virus replication capability in human and murine pHGG and DMG models in vitro. Cytotoxicity analysis showed that cotreatment was either synergistic or additive. Mechanistically, combination treatment produces an increase of nuclear DNA damage and maintains the metabolic perturbation and mitochondrial damage caused by each agent alone. Delta-24-RGD/ONC201 cotreatment extends the overall survival of mice implanted with human and murine pHGG and DMG cells, independently of H3 mutational status. Finally, combination treatment in murine DMG models revealed a proinflammatory phenotype reshaping of the tumor microenvironment. Conclusions: Delta-24-RGD/ONC201 combination improves the efficacy of each agent alone in vitro and in vivo models, maintaining transcriptional and phenotypical changes, producing exacerbated nuclear DNA damage, and leading to an augmented antitumor immune response.
Published in
The oncolytic adenovirus Delta-24-RGD in combination with ONC201 induces a potent antitumor response in pediatric high-grade and diffuse midline glioma models
de la Nava D, Ausejo-Mauleon I, Laspidea V et al. · Neuro-oncology 2024 · PMID 38554031 · doi:10.1093/neuonc/noae066
This dataset
Open GSE243223 in finder → Find more human 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 GSE243223_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 PRJNA1017427 and SRA study SRP460562. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38554031) ↗
Study design
16 conditions, mostly in triplicate
TP54_C ×4 TP54_D24RGD ×4 TP54_ONC201 ×4 TP54_D24RGDONC201 ×4 CHLA03_C ×3 CHLA03_D24RGD ×3 CHLA03_ONC201 ×3 CHLA03_D24RGDONC201 ×3 +8 more

Supports a between-group comparison across 52 samples.

How we read this: 16 replicated groups read from 52 sample titles; they account for 52 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

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

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