⮝ Full datasets listing
PXD078649
PXD078649 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Identification and Characterization of Adrenergic and Mesenchymal Cancer Cell States in Neuroblastoma Using Spatial-Omics |
| Description | 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. 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. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-08-20 |
| AnnouncementXML | Submission_2026-08-20_07:14:28.011.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Zuofei Yuan |
| SpeciesList | scientific name: human; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | instrument model |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-05-20 23:40:58 | ID requested | |
| ⏵ 1 | 2026-08-20 07:14:28 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Neuroblastoma, intratumoral heterogeneity, immunotherapy, single-cell biology, DatasetType:Proteomics |
Contact List
| Anthony A High | |
|---|---|
| contact affiliation | St. Jude Children's Research Hospital |
| contact email | anthony.high@stjude.org |
| lab head | |
| Zuofei Yuan | |
| contact affiliation | St. Jude Children's Research Hospital |
| contact email | zuo-fei.yuan@stjude.org |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive-ftp.ucsd.edu/v13/MSV000101912/ |
