PXD039469 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteomic profiling of advanced melanoma to predict therapeutic response to anti-PD-1 therapy |
Description | Despite high clinical need, hardly any biomarker can accurately predict if patients with metastatic melanoma will respond to anti-PD-1 therapy. In this multicenter study we applied depletion and enrichment methods prior to different proteomic techniques to analyze the discovery cohort (n=56) and discovered several significantly regulated proteins as well as commonly enriched processes such as neutrophil degranulation, cell-substrate adhesion, and extracellular matrix organization. We then analyzed two independent serum cohorts (n=96; n=17) confirming significant differences between R and NR. In addition, literature-based validation revealed 30 markers overlapping with previously published signatures, and survival analysis revealed that overexpression of 17 markers correlated with lower overall survival in melanoma patients. Primary melanoma tumor cells from NR also exhibit a distinctive immunophenotype characterized by CD29, CD49e, CD91, CD105, CD151, CD157, CD248 and CD280, and the TME could represent a potential target for therapy. Ultimately, this led to a potential marker signature with 8 key markers identified in at least two independent serum cohorts: CFHR3, CRP, LRG1, LYVE1, MMRN1, S100A8, SAA2, and TIMP1. |
HostingRepository | PRIDE |
AnnounceDate | 2023-08-18 |
AnnouncementXML | Submission_2023-08-18_06:28:17.639.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | ChristopherGerner |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-01-16 08:06:01 | ID requested | |
⏵ 1 | 2023-08-18 06:28:18 | announced | |
2 | 2024-10-22 06:00:40 | announced | 2024-10-22: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Serum depletion, proteomics, SWATH/DIA mass spectrometry, Glycoproteomics, timsTOF,Predictive biomarker, Immunotherapy |
Contact List
ChristopherGerner |
contact affiliation | University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry |
contact email | christopher.gerner@univie.ac.at |
lab head | |
ChristopherGerner |
contact affiliation | University of Vienna |
contact email | christopher.gerner@univie.ac.at |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039469
- Label: PRIDE project
- Name: Proteomic profiling of advanced melanoma to predict therapeutic response to anti-PD-1 therapy