PXD028307

PXD028307 is an original dataset announced via ProteomeXchange.

Title	Characterization of CD44s glycoproteoforms in bladder tumours and bladder cancer cell culture models
Description	Bladder cancer (BC) is a major health concern retaining high mortality rates when diagnosed at advanced stages. In this context, the clinical management of BC requires the introduction of new biomarkers and molecular targets capable to elicit precision medicine therapeutical approaches. A promising candidate is cluster of differentiation 44 (CD44), a multifunctional and heavily glycosylated transmembrane protein, involved in cell-cell and cell-matrix adhesion, and a transducer of several oncogenic signalling cascades. CD44 has been widely explored as a marker of BC aggressiveness and cancer stem cells (CSC), but this is a highly heterogenic protein and the lack of molecular tools for precise molecular characterization has led to conflicting results, delaying clinical application. CD44 molecular variability results from the number of proteoforms arising from alternative splicing. The human CD44 gene consists of 17 exons, and while the exons 1-5 are constitutively expressed, exons 6-14 are subjected to alternative splicing, generating a myriad of different variants whose functional implications are yet to be fully understood. Furthermore, this number of proteoforms is greatly amplified by O-GalNAc glycosylation, which is predicted to mostly occur in the protein variable regions. This microheterogeneity and its relevance for BC can only be addressed by obtaining a comprehensive characterization at the protein level. Herein, we devised a strategy, combining transcriptomics, glycomics and mass spectrometry based proteomics data, to interrogate CD44 proteoform expression in a series of BC cell culture models showing different aggressiveness (5637 and T24) and a sample pool from formalin fixed paraffin embedded (FFPE) tumours. Glycoengeneered T24 cells expressing the Tn antigen (T24 C1GALT1 knockout (KO)) were also analysed.
HostingRepository	PRIDE
AnnounceDate	2022-05-19
AnnouncementXML	Submission_2022-05-19_08:16:01.130.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	André Silva
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	O-glycosylated residue
Instrument	Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-09 08:20:50	ID requested
⏵ 1	2022-05-19 08:16:02	announced

Gaiteiro C, Soares J, Relvas-Santos M, Peixoto A, Ferreira D, Paulo P, Brand, ã, o A, Fernandes E, Azevedo R, Palmeira C, Freitas R, Miranda A, Os, ó, rio H, Prieto J, Lima L, Silva AMN, Santos LL, Ferreira JA, Glycoproteogenomics characterizes the CD44 splicing code associated with bladder cancer invasion. Theranostics, 12(7):3150-3177(2022) [pubmed]

submitter keyword: Bladder Cancer, CD44, alternative splicing, glycosylation, glycoproteogenomics

José Alexandre Ferreira
contact affiliation	Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal
contact email	jose.a.ferreira@ipoporto.min-saude.pt
lab head
André Silva
contact affiliation	REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Portugal
contact email	andre.silva@fc.up.pt
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/2022/05/PXD028307

PRIDE project URI

• PRIDE
  1. PXD028307
     1. Label: PRIDE project
     2. Name: Characterization of CD44s glycoproteoforms in bladder tumours and bladder cancer cell culture models