PXD043984-1

PXD043984 is an original dataset announced via ProteomeXchange.

Title	Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling
Description	The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observe that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of HIV-infected individuals, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that are targets for vaccination strategies and might reveal the existence of viral microproteins or pseudogenes.
HostingRepository	PRIDE
AnnounceDate	2025-01-15
AnnouncementXML	Submission_2025-01-15_05:09:23.939.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Annika Nelde
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-21 06:00:07	ID requested
⏵ 1	2025-01-15 05:09:24	announced

Dataset with its publication pending

submitter keyword: HIV-1, ribosome profiling, immunopeptidome

Juliane Walz
contact affiliation	Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
contact email	juliane.walz@med.uni-tuebingen.de
lab head
Annika Nelde
contact affiliation	Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
contact email	annika.nelde@uni-tuebingen.de
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/2025/01/PXD043984

PRIDE project URI

• PRIDE
  1. PXD043984
     1. Label: PRIDE project
     2. Name: Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling