PXD063253 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | The GF-NEO Discovery Platform: A Systems-Level Approach to Analyzing and Validating Fusion Neoantigens in Pediatric Cancer |
| Description | Gene fusions (GFs) are critical events in pediatric oncology, often serving as oncogenic drivers. However, fusion proteins and their derived neoantigens (GF-NEOs) remain underexplored for targeted immunotherapy. We developed ProteoFusioNEO, a computational tool for in silico translation of transcriptomic data, analyzing 5,190 pediatric cancer patients and 935 cell lines, yielding 382 and 446 fusion proteins. We highlight that GFs generate multiple translational outcomes with 97% being in-frame in patients. Fusion junctions exhibit the sequence motif [KQE][DG] which partly reflects the nature of exon–exon junctions albeit with additional hydrophilicity. Moreover, GF-NEOs abundance may be shaped by the motif, offering insights into fusion protein biology. Finally, a multipronged validation strategy using in vitro and in vivo systems confirms the GF-NEOs presentation through mass spectrometry-based proteomics and immunopeptidomics. Multiple GF-NEOs encoded by two versions of the ETV6-RUNX1 fusion were validated, paving the way for targeted immunotherapy development. |
| HostingRepository | PRIDE |
| AnnounceDate | 2025-11-26 |
| AnnouncementXML | Submission_2025-11-26_14:39:54.850.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD063253 |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Christopher Savoie |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue |
| Instrument | Orbitrap Eclipse |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-04-23 16:52:54 | ID requested | |
| ⏵ 1 | 2025-11-26 14:39:55 | announced | |
Publication List
Keyword List
Contact List
| Isabelle Sirois |
|---|
| contact affiliation | Sainte-Justine Hospital Research Center (CRCHUSJ) |
| contact email | isabelle.sirois.hsj@ssss.gouv.qc.ca |
| lab head | |
| Christopher Savoie |
|---|
| contact affiliation | Centre de recherche du CHU Sainte-Justine (CRCHUSJ) |
| contact email | christopher.savoie.hsj@ssss.gouv.qc.ca |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD063253
- Label: PRIDE project
- Name: The GF-NEO Discovery Platform: A Systems-Level Approach to Analyzing and Validating Fusion Neoantigens in Pediatric Cancer
