PXD042231

PXD042231 is an original dataset announced via ProteomeXchange.

Title	The HLA-II immunopeptidome of SARS-CoV-2
Description	Weingarten-Gabbay S, Chen D, Sarkizova S, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. 2023. Targeted synthetic vaccines have the potential to transform our response to viral outbreaks; yet the design of these vaccines requires a comprehensive knowledge of viral immunogens, including T-cell epitopes. Having previously mapped the SARS-CoV-2 HLA-I landscape, here we report viral peptides that are naturally processed and loaded onto HLA-II complexes in infected cells. We identified over 500 unique viral peptides from canonical proteins, as well as overlapping internal open reading frames (ORFs), revealing, for the first time, the contribution of internal ORFs to the HLA-II peptide repertoire. Most HLA-II peptides co-localized with the known CD4+ T cell epitopes in COVID-19 patients, including a finding that two reported immunodominant regions in the SARS-CoV-2 membrane protein were formed at the level of HLA-II presentation. We observed that the HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for the majority of the HLA-II peptidome and non-structural and non-canonical proteins accounting for the majority of the HLA-I peptidome. These findings suggest that the future vaccines should incorporate multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize their effectiveness.
HostingRepository	MassIVE
AnnounceDate	2024-01-11
AnnouncementXML	Submission_2024-01-11_09:22:03.833.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karl Clauser
SpeciesList	scientific name: SARS-CoV-2; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	unknown modification; unknown modification; unknown modification
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-15 06:02:25	ID requested
⏵ 1	2024-01-11 09:22:04	announced

no publication

submitter keyword: immunopeptidome, SARS-CoV-2

Steven A. Carr
contact affiliation	Broad Institute of MIT and Harvard
contact email	scarr@broadinstitute.org
lab head
Karl Clauser
contact affiliation	Broad Institute of MIT and Harvard
contact email	clauser@broadinstitute.org
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000091943/