GEO series

Fusion-positive rhabdomyosarcoma oncofusions share a common interactome

GSE285855 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2026/04/09 Platform GPL30882

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 10 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.
Paper: Fusion-positive rhabdomyosarcoma oncofusions share a common interactomeNature communications · 2026

Summary (written by the submitters)

The sole reoccurring oncogenic mutation in the pediatric cancer of fusion-positive rhabdomyosarcoma is a reciprocal translocation giving rise to a transcriptional oncofusion comprised of the N-terminus of the PAX3 transcription factor encoding DNA-binding domains fused in-frame to the C-terminus of the FOXO1 transcription factor encoding a transactivation domain.

Read the full summary ↓

However, a host of new translocations have been detected in this cancer that are known or predicted to encode a protein comprised of the same PAX3 or its paralog PAX7 N-terminus, but with very different C-terminal fusion partners. How such different oncofusions cause the identical cancer was unknown. Here we show that these oncofusions are functionally interchangeable and engage a common interactome of proteins and activate a core shared transcriptional program. Interestingly, this common interactome contains the C-terminal fusion partners or their paralogs of all tested oncofusions, as well as the C-terminal fusion partner of a novel oncofusion. We thus suggest that oncofusions originate in rhabdomyosarcoma from the same DNA-binding domain fused to proteins within a common interactome, which in turn engages a core set of genes giving rise to this cancer.

Published in

Fusion-positive rhabdomyosarcoma oncofusions share a common interactome

Zimmerman SP, Delaney CD, Lau BK et al. · Nature communications 2026 · PMID 42209514 · doi:10.1038/s41467-026-73749-y

This dataset

Open GSE285855 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE285855_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1206223 and SRA study SRP555231. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42209514) ↗

Samples in this study

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

+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

GSE279336 Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma [CUT&Run] 34 samples shares rhabdomyosarcoma, fusion-positive
GSE279337 Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma 40 samples shares rhabdomyosarcoma, fusion-positive
GSE240308 Longitudinal biopsies of fusion-positive rhabdomyosarcoma orthotopic xenografts 16 samples shares rhabdomyosarcoma, fusion-positive
GSE332748 PAX3::FOXO1-Targeting PROTAC Induces Myogenic Differentiation of Fusion-Positive Rhabdomyosarcoma Cells 6 samples shares rhabdomyosarcoma, fusion-positive
GSE279335 Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma [RNA-Seq] 6 samples shares rhabdomyosarcoma, fusion-positive
GSE319092 Integrated Multi-Omics and Interactome Analysis of CDK8 Inhibition Reveals Erythroid Differentiation Programs and BET Synergy in AML Stem-like Cells 135 samples shares interactome
GSE259305 TurboCas: A method for locus-specific labeling of genomic regions and isolating their associated protein interactome [ChIPseq] 52 samples shares interactome
GSE303151 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma [CUT&RUN] 50 samples shares rhabdomyosarcoma

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