PXD012263

PXD012263 is an original dataset announced via ProteomeXchange.

Title	Functional proteomic atlas of HIV-infection in primary human CD4+ T cells
Description	Viruses manipulate host cells to enhance their replication, and the identification of host factors targeted by viruses has led to key insights in both viral pathogenesis and cellular physiology. We previously described global changes in cellular protein levels during human immunodeficiency virus (HIV) infection using transformed CEM-T4 T cells as a model. In this study, we develop an HIV reporter virus displaying a streptavidin-binding affinity tag at the surface of infected cells, allowing facile one-step selection with streptavidin-conjugated magnetic beads. We use this system to obtain pure populations of HIV-infected primary human CD4+ T cells for detailed proteomic analysis, including quantitation of >9,000 proteins across 4 different donors, and temporal profiling during T cell activation. Remarkably, amongst 650 cellular proteins significantly perturbed during HIV infection of primary T cells (q<0.05), almost 50% are regulated directly or indirectly by the viral accessory proteins Vpr, Vif, Nef and Vpu. The remainder have not been previously characterised, but include novel Vif-dependent targets FMR1 and DPH7, and 192 targets not identified and/or regulated in T cell lines, such as AIRD5A and PTPN22. We therefore provide a high-coverage functional proteomic atlas of HIV infection, and a mechanistic account of HIV-dependent changes in its natural target cell.
HostingRepository	PRIDE
AnnounceDate	2019-03-08
AnnouncementXML	Submission_2019-05-27_01:16:54.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD012263
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	James Williamson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Acetylhypusine; TMT6plex; Oxidation; MappingA; Carbamidomethyl
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-08 00:28:51	ID requested
1	2019-03-08 01:37:57	announced
⏵ 2	2019-05-27 01:16:56	announced	Updated publication reference for PubMed record(s): 30857592.

Naamati A, Williamson JC, Greenwood EJ, Marelli S, Lehner PJ, Matheson NJ, Functional proteomic atlas of HIV infection in primary human CD4+ T cells. Elife, 8():(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Proteomics, HIV, Primary T-Cells

Nicholas J Matheson
contact affiliation	Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
contact email	njm25@cam.ac.uk
lab head
James Williamson
contact affiliation	University of Cambridge
contact email	jcw76@cam.ac.uk
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/2019/03/PXD012263

PRIDE project URI

• PRIDE
  1. PXD012263
     1. Label: PRIDE project
     2. Name: Functional proteomic atlas of HIV-infection in primary human CD4+ T cells