GEO series

AMBRA1 as a novel positive regulator of the SHH pathway in medulloblastoma [scRNA-seq]

GSE288463 Homo sapiens (human) Single-cell RNA-seq 2 samples Submitted 2026/03/09 Platform GPL34281

At a glance

Single-cell RNA-seq · human · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: MedulloblastomaThis series is part of our curated briefing on it.
Samples: 2 samples
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)

AMBRA1 (Autophagy and Beclin 1 Regulator 1) is a versatile scaffold protein involved in disparate processes including autophagy, cell cycle regulation, and tumorigenesis. While AMBRA1 is primarily recognized as a tumor suppressor, its dual function as a tumor promoter has garnered increasing attention. However, the role of AMBRA1 remains largely unexplored in many malignancies, particularly in brain tumors.

Read the full summary ↓

Leveraging multiomic analysis of the largest human medulloblastoma (MB) cohort, we identify significantly elevated AMBRA1 protein levels in the Sonic Hedgehog subgroup (MBSHH) compared to other MB variants. Notably, AMBRA1 protein abundance, independent of its mRNA expression, correlates with poor prognosis, positioning AMBRA1 as a biomarker for MBSHH. Mechanistically, AMBRA1 enhances SHH signaling by stabilizing GLI1, the pathway's final effector, by inhibiting the βTrCP-mediated degradation of GLI1. Additionally, AMBRA1 protein stability is modulated by the REN E3 ubiquitin ligase, a tumor suppressor gene and antagonist of the SHH pathway. Genetic inhibition of AMBRA1 significantly blocks MBSHH growth in murine and patient-derived pre-clinical models, highlighting its therapeutic potential. Moreover, combining AMBRA1 knock-down with FDA-approved SHH inhibitors amplifies tumor suppression. These findings uncover the AMBRA1/βTrCP/REN axis as a key regulatory mechanism in SHH signaling, providing actionable insights into targeted therapies for MBSHH.

This dataset

Open GSE288463 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 GSE288463_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1217811 and SRA study SRP560877. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

More Medulloblastoma datasets

GSE288462 AMBRA1 as a novel positive regulator of the SHH pathway in medulloblastoma [RNA-Seq] 8 samples same disease briefing · shares ambra1, shh, medulloblastoma, regulator, positive
GSE253557 Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq] 39 samples same disease briefing · shares medulloblastoma, scrna-seq
GSE263652 Human cerebellar organoids to study medulloblastoma pathogenesis and treatment. [scRNA-Seq] 17 samples same disease briefing · shares medulloblastoma, scrna-seq
GSE131347 PELP1 regulate medulloblastoma progression via NF-κB pathway 4 samples same disease briefing · shares medulloblastoma
GSE294901 Measles oncolytic virus as an immunotherapy for recurrent/refractory pediatric medulloblastoma and atypical teratoid rhabdoid tumor: results from PNOC005 84 samples same disease briefing · shares medulloblastoma
GSE269909 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq] 50 samples same disease briefing · shares medulloblastoma
GSE323995 CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [RNA-Seq 3] 48 samples same disease briefing · shares medulloblastoma
GSE318970 Metabolic Dependencies in Medulloblastoma Reflect Underlying Cellular Origins 33 samples same disease briefing · shares medulloblastoma

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.