PXD018151

PXD018151 is an original dataset announced via ProteomeXchange.

Title	Deciphering and predicting CD4+ T cell immunodominance of Influenza virus hemagglutinin
Description	The importance of CD4+ T helper (Th) cells is well appreciated in view of their essential role in the elicitation of antibody and cytotoxic T cell responses. However, the mechanisms that determine the selection of immunodominant epitopes within complex protein antigens remain elusive. Here, we used ex vivo stimulation of memory T cells and screening of naïve and memory T cell libraries, combined with T cell cloning and TCR sequencing, to dissect the human naïve and memory CD4+ T cell repertoire against the influenza pandemic H1 hemagglutinin (H1-HA). We found that naïve CD4+ T cells have a broad repertoire, being able to recognize naturally processed as well as cryptic peptides spanning the whole H1-HA sequence. In contrast, memory Th cells were primarily directed against just a few immunodominant peptides that were readily detected by mass spectrometry-based MHC-II peptidomics and predicted by structural accessibility analysis. Collectively, these findings reveal the presence of a broad repertoire of naïve T cells specific for cryptic H1-HA peptides, and demonstrate that antigen processing represents a major constraint determining immunodominance.
HostingRepository	PRIDE
AnnounceDate	2024-02-07
AnnouncementXML	Submission_2024-02-07_03:31:29.965.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Antonino Cassotta
SpeciesList	scientific name: Influenza A virus (A/California/07-00002/2009(H1N1)); NCBI TaxID: 2060328; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-23 06:31:47	ID requested
1	2020-06-28 23:15:09	announced
⏵ 2	2024-02-07 03:31:30	announced	2024-02-07: Updated project metadata.

10.1084/jem.20200206;

Cassotta A, Paparoditis P, Geiger R, Mettu RR, Landry SJ, Donati A, Benevento M, Foglierini M, Lewis DJM, Lanzavecchia A, Sallusto F, Deciphering and predicting CD4+ T cell immunodominance of influenza virus hemagglutinin. J Exp Med, 217(10):(2020) [pubmed]

submitter keyword: peptidomics, Influenza, MHC-II, moDC, EBV-B, antigen presentation,human, hemagglutinin

Federica Sallusto
contact affiliation	Institute for Research in Biomedicine Università della Svizzera italiana (USI), Faculty of Biomedical Sciences Via Vincenzo Vela 6 6500 Bellinzona, Switzerland
contact email	federica.sallusto@irb.usi.ch
lab head
Antonino Cassotta
contact affiliation	Institute for Research in Biomedicine, Università della Svizzera italiana
contact email	antonino.cassotta@irb.usi.ch
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/2020/06/PXD018151

PRIDE project URI

• PRIDE
  1. PXD018151
     1. Label: PRIDE project
     2. Name: Deciphering and predicting CD4+ T cell immunodominance of Influenza virus hemagglutinin