GEO series

Identification and Characterization of Adrenergic and Mesenchymal Cancer Cell States in Neuroblastoma Using Spatial-Omics

GSE331531 Homo sapiens (human) Other 7 samples Submitted 2026/08/20 Platform GPL33762

At a glance

human · 7 samples

Organism: Homo sapiens (human)
Topic: NeuroblastomaThis series is part of our curated briefing on it.
Samples: 7 samples: 7 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage and cell lines derived from neuroblastoma patients have features of either adrenergic neurons (ADRN) or mesenchymal cells (MES). However, identification of MES neuroblastoma cells in patient tumors has been challenging and controversial. This may be due to inter- or intra-patient tumor heterogeneity or discrepancies between the established neuroblastoma cell lines and patient tumors.

Read the full summary ↓

To characterize the intra- and inter-patient cellular heterogeneity, we analyzed 54 neuroblastoma tumors, spanning a broad range of clinical, genetic, and histologic features. We combined single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, spatial transcriptomics, and spatial proteomics. We discovered that the tumor cells are in distinct cellular neighborhoods from the non-malignant immune and stromal cells, but we could not identify MES neuroblastoma cells using the established gene expression signatures developed from cell lines. However, using ADRN/MES gene expression signatures developed from early passage orthotopic patient-derived xenografts, we were able to identify MES neuroblastoma tumor cells. We validated our results using RNA-seq, RNA in situ hybridization, immunostaining, chromatin profiling, spatial transcriptomics, functional studies in organoids, and electron microscopy. MES neuroblastoma tumor cells were more likely to be found in high-risk, MYCN amplified post-treatment samples. Taken together, our results demonstrate that MES neuroblastoma tumor cells are present in patient tumors and may correlate with response to therapy and outcome.

This dataset

Open GSE331531 in finder → Find more human datasets → Neuroblastoma landscape →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE331531_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1468545. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 7 sample titles: 7 distinct titles with little repetition. 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

GSM9749285 SJNBL012407_X1_output-XETG00580__0046445__MAST-97__20251009__161536
GSM9749287 SJNBL033705_D1_output-XETG00580__0046443__MAST-925-PATIENT__20251009_161536
GSM9749288 SJNBL033705_X1_output-XETG00580__0046443__Region_2__20251009__161536
GSM9982048 SJST34567_46414
GSM9982049 SJST36813_46354
GSM9982050 SJST36909_46426
GSM9982051 SJNBL031239_46178

More Neuroblastoma datasets

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GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples same disease briefing · shares neuroblastoma
GSE12494 SNP data from Neuroblastoma samples 262 samples same disease briefing · shares neuroblastoma
GSE16476 Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma 88 samples same disease briefing · shares neuroblastoma
GSE130612 Multi-omics analysis of neuroblastoma cells reveals a diversity of malignant transformations 64 samples same disease briefing · shares neuroblastoma
GSE153823 Effect of ASCL1 phosphorylation status on chromatin binding and target regulation in neuroblastoma 52 samples same disease briefing · shares neuroblastoma
GSE112914 Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression 44 samples same disease briefing · shares neuroblastoma

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