PXD044107

PXD044107 is an original dataset announced via ProteomeXchange.

Title	Comparative quantitative proteomic analysis of melanoma subtypes, nevus-associated melanoma, and corresponding nevi
Description	A substantial part of cutaneous malignant melanomas develops from benign nevi. However, the precise molecular events driving the transformation from benign to malignant melanoma are not well understood. We used laser microdissection and mass spectrometry to analyze the proteomes of melanoma subtypes, including superficial spreading melanomas (SSM, n=17), nodular melanomas (NM, n=17), and acral melanomas (AM, n=15). Furthermore, we compared the proteomes of nevi cells and melanoma cells within the same specimens (nevus-associated melanoma (NAM, n=14)). In total, we quantified 7,935 proteins. Despite the genomic and clinical differences of the melanoma subtypes, our analysis revealed relatively similar proteomes, except for the upregulation of proteins involved in immune activation in NM vs AM. Examining NAM versus nevi, we found 1,725 differentially expressed proteins. Among these proteins were 140 that overlapped with cancer hallmarks, tumor suppressors, and regulators of metabolism and cell cycle. Pathway analysis indicated aberrant activation of the RAS/MAPK and PI3K-AKT-mTOR pathways, as well as the Hippo-YAP pathway. Using a classifier, we identified six proteins capable of distinguishing melanoma from nevi samples. Our study represents the first comprehensive comparative analysis of the proteome in melanoma subtypes and associated nevi, offering new insights into the biological behavior of these distinct entities.
HostingRepository	PRIDE
AnnounceDate	2024-01-29
AnnouncementXML	Submission_2024-01-28_16:28:05.134.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julie Breinholt Kjær Sølberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-26 08:12:25	ID requested
⏵ 1	2024-01-28 16:28:05	announced

Naimy S, S, ø, lberg JBK, Kuczek DE, L, ø, vendorf MB, Bzorek M, Litman T, Mund A, Rahbek Gjerdrum LM, Clark RA, Mann M, Dyring-Andersen B, Comparative Quantitative Proteomic Analysis of Melanoma Subtypes, Nevus-Associated Melanoma, and Corresponding Nevi. J Invest Dermatol, ():(2024) [pubmed]

10.1016/j.jid.2023.12.011;

submitter keyword: Human, nevus-associated melanoma, proteomics, microdissection, skin cancer, skin, melanoma subtypes, FFPE, nevi, malignant melanoma

Beatrice Dyring-Andersen
contact affiliation	Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark Leo Foundation Skin Immunology Research Center, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
contact email	beatrice.dyring-andersen@regionh.dk
lab head
Julie Breinholt Kjær Sølberg
contact affiliation	Department of allergy and skin, Gentofte Hospital, Gentofte
contact email	julie.soelberg@regionh.dk
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/2024/01/PXD044107

PRIDE project URI

• PRIDE
  1. PXD044107
     1. Label: PRIDE project
     2. Name: Comparative quantitative proteomic analysis of melanoma subtypes, nevus-associated melanoma, and corresponding nevi