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Metabolic Dependencies in Medulloblastoma Reflect Underlying Cellular Origins

GSE318970 Homo sapiens (human) RNA-seq (gene expression) 33 samples Submitted 2026/08/01 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 33 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)
Topic
MedulloblastomaThis series is part of our curated briefing on it.
Samples
33 samples: 6 conditions, mostly with about 8 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.
Summary (written by the submitters)
Medulloblastoma (MB) is the most common malignant brain tumour of childhood and comprises molecularly and clinically distinct subgroups arising from defined neuronal progenitor populations. Despite extensive genomic characterization, therapeutic strategies have remained largely unchanged for decades, and outcomes for high-risk disease remain poor.
Read the full summary ↓
Here, we identify a conserved and lineage-encoded metabolic dependency that distinguishes MB from other brain tumours. Using genome-wide CRISPR–Cas9 dropout screens across SHH, TP53-mutant SHH, and MYC-amplified Group 3 MB models, we uncover mitochondrial respiration as a core fitness requirement shared across subgroups. Unbiased metabolomic profiling of primary patient tumours reveals that MB occupies a distinct metabolic state characterized by depletion of glycolytic intermediates relative to ependymoma and glioma, independent of subgroup or MYC status. This metabolic configuration mirrors neuronal bioenergetics and reflects suppressed glycolytic capacity rather than oncogene-driven reprogramming. Consistent with this rigidity, MB cells fail to compensate for mitochondrial inhibition by upregulating glycolysis and are exquisitely sensitive to pharmacologic complex I blockade. In orthotopic patient-derived xenograft models, complex I inhibitors including IACS-010759 and metformin significantly extend survival across high-risk MB subgroups. Together, these findings establish oxidative phosphorylation as a lineage-constrained metabolic vulnerability in MB and provide a strong rationale for therapeutic targeting of mitochondrial respiration in this disease.
This dataset
Open GSE318970 in finder → Find more human RNA-seq datasets → Medulloblastoma landscape →
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 GSE318970_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 PRJNA1420898 and SRA study SRP675916. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 8 replicates each
SJMBSHH-13-5634 IACS Treated ×8 SJMBSHH-13-5634 vehicle ×8 SJMBSHH-14-4106 vehicle ×5 2112FH vehicle ×5 SJMBSHH-14-4106 IACS Treated ×4 2112FH IACS Treated ×3

Supports a case/control comparison: 15 samples read as cases, 18 as controls.

How we read this: 6 replicated groups read from 33 sample titles; they account for 33 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
More Medulloblastoma datasets

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