PXD035206

PXD035206 is an original dataset announced via ProteomeXchange.

Title	Proteogenomics linked to histopathology identifies subtypes and progression biomarkers in malignant melanoma
Description	In this study, proteogenomic analysis coupled with clinical histopathology revealed proteomic subtypes and identified candidate markers, which uncovered tumor biology related to patient survival. A total of 12,695 proteins and 45,356 phosphosites were quantified. This newly generated proteomic data was integrated with a previously published transcriptomic dataset from matched tumor specimens (Cirenajwis et al., 2015). Using consensus clustering, we could identify five melanoma subtypes, which were classified into extracellular, extracellular-immune, mitochondrial, mitochondrial-immune, and extracellular-mitochondrial categories according to/based on the annotations of their highly expressed proteins. The proteomic subtypes displayed differences in phenotype switching, immune surveillance, the levels of known melanoma markers, and were associated with survival. In addition, clinical parameters such as the expression of mutated BRAF V600E protein and the composition of the surrounding tumor microenvironment were found to be good independent indicators of prognosis. Lastly, validation of survival-related proteins in an independent cohort identified five candidate markers for predicting disease progression and patient survival (ADAM10, SCAI, CTNND1, CDK4, FGA). In conclusion, this study provides insights into the complex biology of melanoma while emphasizing/highlighting the importance of the tumor microenvironment. It also offers opportunities to find/indentify novel drug target candidates.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_11:37:29.271.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD035206
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Magdalena Kuras
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-09 09:19:08	ID requested
⏵ 1	2025-05-06 11:37:30	announced

10.6019/PXD035206;

10.3390/cancers17050832;

Kuras M, Betancourt LH, Hong R, Szadai L, Rodriguez J, Horvatovich P, Pla I, Eriksson J, Szeitz B, Deszcz B, Welinder C, Sugihara Y, Ekedahl H, Baldetorp B, Ingvar C, Lundgren L, Lindberg H, Oskolas H, Horvath Z, Rezeli M, Gil J, Appelqvist R, Kem, é, ny LV, Malm J, Sanchez A, Szasz AM, Paw, ł, owski K, Wieslander E, Feny, ö D, Nemeth IB, Marko-Varga G, ve Metastatic Malignant Melanoma. Cancers (Basel), 17(5):(2025) [pubmed]

ProteomeXchange project tag: CPTAC Consortium

submitter keyword: cancer, proteomics, mass spectrometry, melanoma,proteogenomics, metastasis

György Marko-Varga
contact affiliation	8Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, Lund, Sweden
contact email	gyorgy.marko-varga@bme.lth.se
lab head
Magdalena Kuras
contact affiliation	Lund University
contact email	magdalena.kuras@med.lu.se
dataset submitter

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://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD035206

PRIDE project URI

• PRIDE
  1. PXD035206
     1. Label: PRIDE project
     2. Name: Proteogenomics linked to histopathology identifies subtypes and progression biomarkers in malignant melanoma