PXD021177

PXD021177 is an original dataset announced via ProteomeXchange.

Title	Characterization of the HLA class I Ligandome from Extracellular vesicles
Description	Extracellular vesicles have shown promise in the field of anti-tumor vaccines. EVs are antigen-presenting entities capable of eliciting potent T-cell responses and have therefore being explored as cell-free based peptide vaccine vectors. However, whether the EV ligandome sufficiently resembles the cell ligandome as to preserve antigenicity and immunogenicity of the ligands is still a crucial aspect to be addressed. In particular, when aiming to use EVs as cell-free vaccine vectors. To understand whether HLA-I complexes homing to EVs display the same ligand sequence features and characteristics than those homing to the cell surface, we used a highly sensitive MS-based immunopeptidomics approach to generate a comprehensive side-by-side analysis of the EV and whole-cell (WC) ligandomes. In this work we identified thousands of ligands derived from both EVs and WCs, which allowed a deep characterization of important ligand properties such as the occurrence of PTMs in both ligandomes. Our results indicate that EVs are as good as cells when it comes to antigen presentation, since the sequence properties of the antigens were conserved in EVs and WCs ligandomes. Interestingly, EVs were enriched in HLA-B ligands and cysteinylated peptides, which can ultimately affect the antigenicity and immunogenicity of the ligands and should be taken into consideration when developing cell-free EV-based peptide vaccination approaches.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:51:37.634.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julia Bauzá Martinez
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; cysteinylation (disulfide with free L-cysteine); phosphorylated residue; monohydroxylated residue; deamidated L-asparagine
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-27 23:17:48	ID requested
1	2021-07-05 01:53:11	announced
⏵ 2	2023-11-14 08:51:38	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP)

submitter keyword: EV vaccines, extracellular vesicles, immunopeptidomics,Ligandome, HLA-I

Wei Wu
contact affiliation	1 Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands 2 Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	W.Wu1@uu.nl
lab head
Julia Bauzá Martinez
contact affiliation	Utrecht University
contact email	j.bauzamartinez@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021177
     1. Label: PRIDE project
     2. Name: Characterization of the HLA class I Ligandome from Extracellular vesicles