 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 27, 2023 |
| Title |
Cell plasticity in neuroblastoma |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain poorly defined. Our results now document spontaneous plasticity in several neuroblastoma models between noradrenergic and mesenchymal tumor states and show that this plasticity is reversible and relies on epigenetic reprogramming. We demonstrate that an in vivo microenvironment provides a powerful pressure towards a noradrenergic identity for these models. Interestingly, single-cell RNA-seq analyses of 18 tumor biopsies and 15 PDX models revealed that tumor cells systematically exhibit a noradrenergic identity. Yet, our data highlight a population of noradrenergic tumor cells with mesenchymal features, demonstrating that the plasticity described in cellular models between both identities is relevant in neuroblastoma patients. Our work also emphasizes that both external cues of the environment and intrinsic factors influence plasticity and cell identity in neuroblastoma.
|
| |
|
| Overall design |
ChIP-seq data of neuroblastoma cell lines and xenografts (H3K27ac)
|
| Web link |
https://doi.org/10.1101/2021.01.07.425710
|
| |
|
| Contributor(s) |
Thirant C, Janoueix-Lerosey I |
| Citation(s) |
37142597 |
| Submission date |
Jul 22, 2020 |
| Last update date |
Aug 02, 2023 |
| Contact name |
Agathe Peltier |
| Organization name |
Institut Curie
|
| Department |
Centre de recherche
|
| Lab |
U830
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (20)
|
| GSM6429312 |
SK-N-SH CD44neg Input, ChIP-seq |
| GSM6429313 |
SK-N-SHm CD44pos H3K27ac, ChIP-seq |
| GSM6429314 |
SK-N-SHm CD44pos Input, ChIP-seq |
| GSM6429315 |
SK-N-SHm CD44neg H3K27ac, ChIP-seq |
| GSM6429316 |
SK-N-SHm CD44neg Input, ChIP-seq |
| GSM6429321 |
xenograft SH-SY5Y rep1 H3K27ac, ChIP-seq |
| GSM6429322 |
xenograft SH-SY5Y rep1 Input, ChIP-seq |
| GSM6429323 |
xenograft SH-SY5Y rep2 H3K27ac, ChIP-seq |
| GSM6429324 |
xenograft SH-SY5Y rep2 Input, ChIP-seq |
| GSM6429325 |
xenograft SK-N-SH CD44pos rep1 H3K27ac, ChIP-seq |
| GSM6429326 |
xenograft SK-N-SH CD44pos rep1 Input, ChIP-seq |
| GSM6429327 |
xenograft SK-N-SH CD44pos rep2 H3K27ac, ChIP-seq |
| GSM6429328 |
xenograft SK-N-SH CD44pos rep2 Input, ChIP-seq |
| GSM6429329 |
xenograft SK-N-SH CD44neg rep1 H3K27ac, ChIP-seq |
| GSM6429330 |
xenograft SK-N-SH CD44neg rep1 Input, ChIP-seq |
| GSM6429331 |
xenograft SK-N-SH CD44neg rep2 H3K27ac, ChIP-seq |
| GSM6429332 |
xenograft SK-N-SH CD44neg rep2 Input, ChIP-seq |
|
| Relations |
| BioProject |
PRJNA647862 |
| SRA |
SRP273102 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE154907_RAW.tar |
1.8 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...