PXD027006

PXD027006 is an original dataset announced via ProteomeXchange.

Title	Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV‐2 S1 Spike Glycoprotein
Description	Cytotoxic T-lymphocytes are critical determinants of SARS-CoV-2 infection severity and long-term immunity. A hallmark of COVID-19 is its highly variable severity and breadth of immune responses between individuals. To address the underlying mechanisms behind this phenomenon we analyzed the proteolytic processing of S1 spike glycoprotein by 10 common allotypes of ER aminopeptidase 1 (ERAP1), an intracellular enzyme that generates antigenic peptides. We utilized a systematic proteomic approach that allows the concurrent analysis of hundreds of trimming reactions. While all ERAP1 allotypes produced optimal ligands for HLA molecules, including known SARS-CoV-2 epitopes, they presented major differences in peptide sequences produced, suggesting allotype-dependent sequence biases. Allotype 10, previously suggested to be enzymatically deficient, was rather found to be functionally distinct from other allotypes. Our findings suggest that common ERAP1 allotypes can be a major source of heterogeneity in antigen processing and through this mechanism contribute to variable immune responses to COVID-19.
HostingRepository	PRIDE
AnnounceDate	2021-11-25
AnnouncementXML	Submission_2021-11-25_08:08:43.480.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martina Samiotaki
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-30 05:12:37	ID requested
⏵ 1	2021-11-25 08:08:43	announced

Dataset with its publication pending

ProteomeXchange project tag: Covid-19

submitter keyword: ERAP1, peptidomics, Allotypic variation, SARS-CoV‐2 S1 Spike Glycoprotein

Efstratios Stratikos
contact affiliation	Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15784, Athens, Greece
contact email	estratikos@chem.uoa.gr
lab head
Martina Samiotaki
contact affiliation	Protein Analysis Laboratory B.S.R.C. "Alexander Fleming", Alexander Fleming Street 34 16672, Vari, Greece
contact email	samiotaki@fleming.gr
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/2021/11/PXD027006

PRIDE project URI

• PRIDE
  1. PXD027006
     1. Label: PRIDE project
     2. Name: Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV‐2 S1 Spike Glycoprotein