PXD060290

PXD060290 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic characterization of muscle invasive bladder cancer
Description	To explore potential chemoresistance mechanisms and identify therapeutic opportunities in muscle invasive bladder cancer (MIBC), we conducted comprehensive proteogenomic characterization of 46 pre- and 14 post-treatment MIBC tumors incorporating genomics, transcriptomics, proteomics, and phosphoproteomics. Multi-omics clustering not only recapitulated established molecular subtypes, but also revealed subtypes associated with chemotherapy sensitivity. Protein isoform level analysis identified protein abundance of a short isoform of ATAD1 and RAF family proteins as biomarkers of chemosensitivity. Integration of proteomic and phosphoproteomic data revealed Wnt signaling via GSK3B-S9 phosphorylation and the JAK/STAT pathway as potential targets to overcome chemoresistance. Correlations between PD-L1 and TROP-2/NECTIN-4 indicate an additive benefit of combination therapy targeting these proteins. Overall, this study serves as a valuable resource for researchers and clinicians aiming to better understand and treat chemoresistant MIBC.
HostingRepository	PRIDE
AnnounceDate	2025-09-22
AnnouncementXML	Submission_2025-09-21_22:49:31.602.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Holt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-28 12:08:23	ID requested
⏵ 1	2025-09-21 22:49:32	announced

Holt MV, Dou Y, Young MN, Saltzman AB, Anurag M, Lei JT, Jain A, Leng M, Kim BJ, Dobrolecki LE, Faucher SF, Savage S, Wang C, Shi Z, Villanueva H, Kremers K, Drinnon KD, Castro PD, Ittmann MM, Khatani MM, Kim SH, Ellis MJ, Zhang B, Malovannaya A, Lerner SP, Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer. Cell Rep Med, 6(8):102255(2025) [pubmed]

10.1016/j.xcrm.2025.102255;

submitter keyword: TMT, Cancer,Bladder Cancer

Matthew Holt
contact affiliation	Baylor College of Medicine
contact email	mvholt@bcm.edu
lab head
Matthew Holt
contact affiliation	BCM
contact email	mvholt@bcm.edu
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/2025/09/PXD060290

PRIDE project URI

• PRIDE
  1. PXD060290
     1. Label: PRIDE project
     2. Name: Proteogenomic characterization of muscle invasive bladder cancer