PXD005234

PXD005234 is an original dataset announced via ProteomeXchange.

Title	In vivo and in vitro proteome analysis of HIV-1 infected, human CD4+ T cells
Description	Host directed therapies against HIV-1 are thought to be critical for long term containment of the HIV-1 pandemic but remain elusive. Since HIV-1 infects and manipulates important effectors of both the innate and adaptive immune system, identifying modulations of the host cell systems in humans during HIV-1 infection may be crucial for the development of immune based therapies. Here, we quantified the changes of the proteome in human CD4+ T cells upon HIV-1 infection, both in vitro and in vivo. A SWATH-MS approach was used to measure the proteome of human primary CD4+ T cells infected with HIV-1 in vitro as well as CD4+ T cells from HIV-1 infected patients with paired samples on and off antiretroviral treatment. In the in vitro experiment, the proteome of CD4+ T cells was quantified over a time course following HIV-1 infection. 1,725 host cell proteins and 4 HIV-1 proteins were quantified, with 145 proteins changing significantly during the time course. Changes in the proteome peaked 24 hours after infection, concomitantly with significant HIV-1 protein production. In the in vivo branch of the study, CD4+ T cells from viremic patients and those with no detectable viral load after treatment were sorted and the proteomes quantified. We consistently detected 895 proteins, 172 of which were considered to be significantly different between viraemic patients and patients undergoing successful treatment. The proteome of in vitro infected CD4+ T cells was modulated on multiple functional levels, including TLR-4 signalling and the type 1 interferon signalling pathway. Perturbations in the type 1 interferon signalling pathway were recapitulated in CD4+ T cells from patients. The study shows that proteome maps generated by SWATH-MS indicate a range of functionally significant changes in the proteome of HIV infected human CD4+ T cells. Exploring these perturbations in more detail may help identify new targets for immune based interventions.
HostingRepository	PRIDE
AnnounceDate	2017-02-28
AnnouncementXML	Submission_2017-02-28_06:02:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ben Collins
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-10-27 23:58:58	ID requested
⏵ 1	2017-02-28 06:02:07	announced

Nemeth J, Vongrad V, Metzner KJ, Strouvelle VP, Weber R, Pedrioli P, Aebersold R, G, ü, nthard HF, Collins BC, T Cells. Mol Cell Proteomics, 16(4 suppl 1):S108-S123(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: HIV, SWATH, CD4 T cell

Ben Collins
contact affiliation	Department of Biology Institute of Molecular Systems Biology ETH Zurich Switzerland
contact email	collins@imsb.biol.ethz.ch
lab head
Ben Collins
contact affiliation	ETH Zurich
contact email	collins@imsb.biol.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005234
     1. Label: PRIDE project
     2. Name: In vivo and in vitro proteome analysis of HIV-1 infected, human CD4+ T cells