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Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [snRNA-seq]

GSE298139 Homo sapiens (human) Single-nucleus RNA-seq 16 samples Submitted 2026/07/08 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 16 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Homo sapiens (human)
Samples
16 samples: 16 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Molecular changes during AT/RT progression associated with epithelial-mesenchymal transition and extracellular matrix changesActa neuropathologica · 2026
Summary (written by the submitters)
Atypical teratoid/rhabdoid tumors (AT/RT) are the most common malignant brain tumors during infancy and associated with a dismal prognosis. 50% of the patients suffer from progressions or recurrences, but the underlying mechanisms remain largely unknown. To identify mechanisms of progression and recurrence, we performed single-nucleus RNA sequencing of eight primary-recurrence pairs.
Read the full summary ↓
Tumor cells and cells of the tumor microenvironment (TME) were analysed separately. Therapy-resistant tumor cells were identified through the comparison of global gene expression profiles between primary and recurrent tumor cell populations using CIBERSORT. Histology, in vitro experiments, bulk RNA sequencing, and survival analyses were performed to validate our findings. Paired primary and recurrent AT/RT tumor samples showed significant differences in their gene expression profiles. The TME of AT/RT recurrences was characterized by enrichment of CD1A+ CD207+ dendritic cells (DCs), which were per se associated with inferior survival in relapsed patients. Differentially expressed genes of AT/RT-MYC primary tumor cells that potentially persist after therapy, were involved in the organization of the extracellular matrix (ECM), developmental processes, and diverse immune signalling pathways. In addition, recurrences demonstrated a significantly higher proportion of cells undergoing partial epithelial-mesenchymal transition (pEMT) compared to primary tumors, a feature that we confirmed following treating AT/RT-MYC tumor cells in vitro. Finally, patients with primary tumors strongly expressing respective genes displayed a significantly worse survival. We identified pEMT, ECM remodeling, and enrichment of CD1A+ CD207+ DCs as potential mechanisms of therapy resistance in AT/RT which could be employed to improve therapy in the future.
Published in
Molecular changes during AT/RT progression associated with epithelial-mesenchymal transition and extracellular matrix changes
Altendorf L, Althammer A, Roy R et al. · Acta neuropathologica 2026 · PMID 42384079 · doi:10.1007/s00401-026-03050-1
This dataset
Open GSE298139 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 GSE298139_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 PRJNA1268413 and SRA study SRP588121. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42384079) ↗
Study design
16 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 16 sample titles: 16 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
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