PXD055002

PXD055002 is an original dataset announced via ProteomeXchange.

Title	Development of a proteomic workflow for the identification of heparan sulfate proteoglycan-binding substrates of ADAM17 - Evaluation of heparin effects on sample preparation PreOmics
Description	Ectodomain shedding, which is the proteolytic release of transmembrane proteins from the cell surface, is crucial for cell-to-cell communication and other biological processes. The metalloproteinase ADAM17 mediates ectodomain shedding of over 50 transmembrane proteins ranging from cytokines and growth factors, such as TNF and EGFR ligands, to signaling receptors and adhesion molecules. Yet, the ADAM17 sheddome is only partly defined and biological functions of the protease have not been fully characterized. Some ADAM17 substrates (e.g. HB-EGF) are known to bind to heparan sulfate proteoglycans (HSPG), and we hypothesised that such substrates would be under-represented in traditional secretome analyses, due to their binding to cell surface or pericellular HSPGs. Thus, to identify novel HSPG-binding ADAM17 substrates, we developed a proteomic workflow that involves addition of heparin to solubilize HSPG-binding proteins from the cell layer, thereby allowing their mass spectrometry detection by heparin-secretome (HEP-SEC) analysis. Applying this methodology to murine embryonic fibroblasts stimulated with an ADAM17 activator enabled us to identify 46 transmembrane proteins that were shed in response to ADAM17 activation. This included known HSPG-binding ADAM17 substrates (i.e. HB-EGF, CX3CL1) and 17 novel HSPG-binding putative ADAM17 substrates. Two of these, MHC-I and IL1RL1, were validated as ADAM17 substrates by immunoblotting.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_00:34:32.066.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matteo Calligaris
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-19 07:07:14	ID requested
⏵ 1	2025-05-07 00:34:32	announced

10.1002/pmic.202400076;

Calligaris M, Span, ò DP, Puccio MC, M, ü, ller SA, Bonelli S, Lo Pinto M, Zito G, Blobel CP, Lichtenthaler SF, Troeberg L, Scilabra SD, Development of a Proteomic Workflow for the Identification of Heparan Sulphate Proteoglycan-Binding Substrates of ADAM17. Proteomics, 24(23-24):e202400076(2024) [pubmed]

submitter keyword: sheddome,ADAM17, ectodomain shedding, heparin, disintegrin metalloproteinases, secretome

Simone Dario Scilabra
contact affiliation	Proteomics group, Ri.MED Foundation, Palermo, Italy
contact email	sdscilabra@fondazionerimed.com
lab head
Matteo Calligaris
contact affiliation	Università di Udine
contact email	matteo.calligaris@uniud.it
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/PXD055002

PRIDE project URI

• PRIDE
  1. PXD055002
     1. Label: PRIDE project
     2. Name: Development of a proteomic workflow for the identification of heparan sulfate proteoglycan-binding substrates of ADAM17 - Evaluation of heparin effects on sample preparation PreOmics