PXD028874

PXD028874 is an original dataset announced via ProteomeXchange.

Title	The HLA ligandome comprises a limited repertoire of O-GlcNAcylated antigens preferentially associated with HLA-B07:02
Description	Mass-spectrometry based immunopeptidomics has provided unprecedented insights into antigen presentation, not only charting an enormous ligandome of self-antigens, but also cancer neo-antigens and peptide antigens harbouring post-translational modifications. Here we concentrate on the latter, focusing on the small subset of HLA Class I peptides (less than 1%) that has been observed to be post-translationally modified (PTM) by a O-linked N-acetylglucosamine (GlcNAc). Just like neo-antigens these modified antigens may have specific immunomodulatory functions. Here we compiled from literature, and a new dataset originating from JY B cell lymphoblastoid line cells, a concise albeit comprehensive list of O-GlcNAcylated HLA class I peptides. The cumulative list of O-GlcNAcylated HLA peptides originates from diverse datasets, entailing normal and cancer cell lines as well as tissue samples. Interestingly, the overlap in detected O-GlcNAcylated HLA peptides as well as their source proteins is strikingly high. From the compiled list we extract that O-GlcNAcylated HLA Class I peptides are preferentially presented by the HLA-B07:02 allele. This allele accommodates a Proline anchoring site at position 2, and a binding groove that can accommodate the recently proposed consensus sequence for O-GlcNAcylation, P(V/A/T/S)g(S/T). Most of the O-GlcNAcylated HLA peptides originate from nuclear proteins, notably transcription factors. The conclusions drawn from the compiled list, may assist to predict novel O-GlcNAcylated HLA antigens, which will likely be presented best by patients harbouring HLA-B7:02, or related, alleles that uses Proline as anchoring residue.
HostingRepository	PRIDE
AnnounceDate	2021-12-03
AnnouncementXML	Submission_2021-12-03_08:30:41.659.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alvaro Sanchez Bernabeu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	O-glycosylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-30 03:35:56	ID requested
⏵ 1	2021-12-03 08:30:42	announced

Dataset with its publication pending

submitter keyword: HLA class I, MHC, O-GlcNAcylation, immunopeptidomics, HLA-B07

Albert JR Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Utrecht Institute for Pharmaceutical Sciences (UIPS)
contact email	A.J.R.Heck@uu.nl
lab head
Alvaro Sanchez Bernabeu
contact affiliation	Utrecht University
contact email	a.sanchezbernabeu@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028874
     1. Label: PRIDE project
     2. Name: The HLA ligandome comprises a limited repertoire of O-GlcNAcylated antigens preferentially associated with HLA-B07:02