GEO series

Reciprocal regulation of extracellular matrix proteins by EWS-FLI1 and AP-1 in Ewing sarcoma cells

GSE263503 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/09/30 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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)
Samples: 12 samples: 3 × EW8 vs 3 × EW8_doxy vs 3 × TC71 vs 3 × TC71_doxyGroups 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: EWS-FLI1 and Activator Protein-1 (AP-1) Reciprocally Regulate Extracellular-Matrix Proteins in Ewing sarcoma CellsInternational journal of molecular sciences · 2024

Summary (written by the submitters)

Ribonucleotide reductase (RNR) is the rate limiting enzyme in the synthesis of deoxyribonucleotides and the target of multiple chemotherapy drugs, including gemcitabine and hydroxyurea. In previous work, we identified that inhibition of RNR in Ewing sarcoma tumors upregulates the expression levels of multiple members of the activator protein-1 (AP-1) transcription factor family, including c-Jun and c-Fos, and downregulates the expression of c-Myc.

Read the full summary ↓

However, the broader functions and downstream targets of AP-1, which are highly context- and cell-dependent, are unknown in Ewing sarcoma tumors. Consequently, in this work, we used genetically defined models, transcriptome profiling, and gene set enrichment analysis to identify that AP-1 and EWS-FLI1, the driver oncogene in most Ewing sarcoma tumors, reciprocally regulate the expression of multiple extracellular matrix proteins, including fibronectins, integrins, and collagens. AP-1 expression in Ewing sarcoma cells also drives, coincident with these perturbations in gene and protein expression, changes in cell morphology and phenotype. Furthermore, we also identified that the EWS-FLI1 oncoprotein dysregulates the expression of multiple AP-1 proteins, aligning with previous reports demonstrating genetic and physical interactions between EWS-FLI1 and AP-1. Overall, these results provide novel insight into the distinct, EWS-FLI1-dependent features of Ewing sarcoma tumors and identify a novel, reciprocal regulation of extracellular matrix components by EWS-FLI1 and AP-1.

Published in

EWS-FLI1 and Activator Protein-1 (AP-1) Reciprocally Regulate Extracellular-Matrix Proteins in Ewing sarcoma Cells

Croushore EE, Stipp CS, Gordon DJ · International journal of molecular sciences 2024 · PMID 39201282 · doi:10.3390/ijms25168595

This dataset

Open GSE263503 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 GSE263503_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 PRJNA1097654 and SRA study SRP500372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39201282) ↗

Study design

3 × EW8 vs 3 × EW8_doxy vs 3 × TC71 vs 3 × TC71_doxy

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8193706 EW8_1 EW8
GSM8193707 EW8_2 EW8
GSM8193708 EW8_3 EW8
GSM8193709 EW8_doxy_1 EW8_doxy
GSM8193710 EW8_doxy_2 EW8_doxy
GSM8193711 EW8_doxy_3 EW8_doxy
GSM8193712 TC71_1 TC71
GSM8193713 TC71_2 TC71
GSM8193714 TC71_3 TC71
GSM8193715 TC71_doxy_1 TC71_doxy
GSM8193716 TC71_doxy_2 TC71_doxy
GSM8193717 TC71_doxy_3 TC71_doxy

Datasets on a similar topic

GSE272960 EWS-FLI1 Expression in Human Embryonic Mesenchymal Stem Cells Leads to Defective DNA Damage Repair and Ewing Sarcoma 24 samples shares ews-fli1, sarcoma, ewing
GSE265940 Overexpression of extracellular matrix proteins, increased cell death and reduced cell proliferation contribute to the pathophysiology of microphthalmia across in vitro patient-derived models 48 samples shares extracellular, proteins, matrix
GSE249697 Transcriptional changes of the extracellular matrix in chronic thromboembolic pulmonary hypertension governs right ventricle remodeling and recovery 135 samples shares extracellular, matrix
GSE255359 High mechanical conditioning by tumor extracellular matrix stiffness is a predictive biomarker for anti-fibrotic therapy in HER2-negative breast cancer 108 samples shares extracellular, matrix
GSE208732 Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-seq] 102 samples shares extracellular, matrix
GSE249696 Transcriptional changes of the extracellular matrix in chronic thromboembolic pulmonary hypertension governs right ventricle remodeling and recovery [ext395_rnaseq] 95 samples shares extracellular, matrix
GSE289930 Proteogenomic Characterization of Primary Oral Cancer Unveils Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked to Lymph Node Metastasis [RNA-seq] 33 samples shares extracellular, matrix
GSE288678 Combinatorial Extracellular Matrix Tissue Chips for Optimizing Mesenchymal Stromal Cell Microenvironment and Manufacturing 24 samples shares extracellular, matrix

Search all human RNA-seq datasets in GEO →

Share this dataset

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.