PXD041733

PXD041733 is an original dataset announced via ProteomeXchange.

Title	Proteomic Analysis of the Urothelial Cancer Landscape
Description	Urothelial cancer is a challenging disease with a wide tumor-biological spec-trum. Most molecular classification attempts are transcriptome-based and re-late only indirectly to the therapeutically relevant protein level. We improve preanalytical preparation of clinical samples for proteome analyses and char-acterize a comprehensive cohort of 434 samples with 242 tumors and 192 paired normal mucosae. We evaluate sample-wise tumor specificity and rank biomarkers by target relevance. We identify five tumor clusters that add prog-nostic information independent from histopathological groups. In silico drug prediction suggests efficacy of several compounds hitherto not in clinical use. Both, in silico as well as in vitro data, indicate predictive value of the proteo-mic clusters for these drugs. Comparative validation on external transcriptom-ic data confirms prognostic relevance and contextualizes proteomic and tran-scriptomic classifications. A real-world diagnostic approach based on im-munohistochemistry further validates our proteomic data but underlines the necessity of omics scale molecular analyses for personalized oncology.
HostingRepository	PRIDE
AnnounceDate	2024-06-16
AnnouncementXML	Submission_2024-06-15_23:16:35.322.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hannah Voß
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-22 08:33:09	ID requested
⏵ 1	2024-06-15 23:16:36	announced

Dressler FF, Diedrichs F, Sabtan D, Hinrichs S, Krisp C, Gemoll T, Hennig M, Mackedanz P, Schlotfeldt M, Vo, ß H, Offermann A, Kirfel J, Roesch MC, Struck JP, Kramer MW, Merseburger AS, Gratzke C, Schoeb DS, Miernik A, Schl, ü, ter H, Wetterauer U, Zubarev R, Perner S, Wolf P, V, é, gv, á, ri Á, Proteomic analysis of the urothelial cancer landscape. Nat Commun, 15(1):4513(2024) [pubmed]

10.1038/s41467-024-48096-5;

submitter keyword: Proteome Analysis,Urothelial Cancer, Multi-Cernter Study, Personalized Oncology, Data integration

Franz F. Dressler
contact affiliation	Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
contact email	franz-friedrich.dressler@charite.de
lab head
Hannah Voß
contact affiliation	University Medical Center Hamburg Eppendorf, Institute of Clinical Chemistry and Laboratory Medicine, Group of Mass Spectrometric Proteomics
contact email	ha.voss@uke.de
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/2024/06/PXD041733

PRIDE project URI

• PRIDE
  1. PXD041733
     1. Label: PRIDE project
     2. Name: Proteomic Analysis of the Urothelial Cancer Landscape