PXD023684

PXD023684 is an original dataset announced via ProteomeXchange.

Title	Allotype-specific glycosylation and cellular localization of HLA class I proteins
Description	Presentation of self- and foreign peptide antigens by human leukocyte antigen (HLA) complexes at the cell surface is a key process in our immune response. The alpha-chain, the part of the HLA class I complex that contains the peptide binding groove, is one of the most polymorphic proteins in the human proteome. All HLA class I alpha-chains carry a conserved N-glycosylation site, but little is known about its nature and function. Here, we report an in-depth characterization of the N-glycosylation features in HLA class I molecules. In three cell lines we observe that different HLA-A alpha-chains carry similar glycosylation, distinctly different from the HLA-B, HLA-C and HLA-F alpha-chains. HLA-B alpha-chains carry mostly mature glycans, HLA-C and HLA-F alpha-chains carry predominantly high-mannose, whereas HLA-A molecules display the broadest variety of glycan characteristics. We hypothesized that these glycosylation features are directly linked to the cellular localization of the HLA complexes. Analyzing HLA class I complexes from plasma and inner membrane enriched fractions revealed confirmed that most HLA-B complexes can be found in the plasma membrane, most HLA-C and HLA-F molecules reside in the ER and Golgi membrane and HLA-A molecules are more equally distributed over all these cellular compartments. As peptide-binding and specificity is cellular compartment dependent, we corroborate from our data that standard measurements of HLA peptide-antigens from whole cell extracts likely do not exclusively capture the antigen repertoires presented at the cell surface, but also those still within the cell. Our data indicate that standard protein quantification of HLA alpha-chains does not correlate with cell surface expression levels, while analysis of glycopeptides provides allotype and compartment specific quantification.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_00:29:56.369.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Max Hoek
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue; glycosylated residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-19 22:30:37	ID requested
⏵ 1	2022-02-17 00:29:57	announced

Hoek M, Demmers LC, Wu W, Heck AJR, Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins. J Proteome Res, 20(9):4518-4528(2021) [pubmed]

submitter keyword: HLA, MHC, glycoproteomics

Albert J.R. Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
contact email	A.J.R.Heck@uu.nl
lab head
Max Hoek
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
contact email	m.hoek@uu.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023684
     1. Label: PRIDE project
     2. Name: Allotype-specific glycosylation and cellular localization of HLA class I proteins