Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.

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State: Public
Version: Final published version
License: Not specified
Serval ID
serval:BIB_97FD3CF01470
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection.
Journal
Scientific reports
Author(s)
Golumbeanu M., Desfarges S., Hernandez C., Quadroni M., Rato S., Mohammadi P., Telenti A., Beerenwinkel N., Ciuffi A.
ISSN
2045-2322 (Electronic)
ISSN-L
2045-2322
Publication state
Published
Issued date
18/01/2019
Peer-reviewed
Oui
Volume
9
Number
1
Pages
213
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
Throughout the HIV-1 replication cycle, complex host-pathogen interactions take place in the infected cell, leading to the production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while counteracting intracellular defense mechanisms. We investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptomic, proteomic, and phosphoproteomic expression changes in infected and uninfected SupT1 CD4+ T cells at five time points of the viral replication process. By means of a Gaussian mixed-effects model implemented in the new R/Bioconductor package TMixClust, we clustered host genes based on their temporal expression patterns. We identified a proteo-transcriptomic gene expression signature of 388 host genes specific for HIV-1 replication. Comprehensive functional analyses of these genes confirmed the previously described roles of some of the genes and revealed novel key virus-host interactions affecting multiple molecular processes within the host cell, including signal transduction, metabolism, cell cycle, and immune system. The results of our analysis are accessible through a freely available, dedicated and user-friendly R/Shiny application, called PEACHi2.0. This resource constitutes a catalogue of dynamic host responses to HIV-1 infection that provides a basis for a more comprehensive understanding of virus-host interactions.
Keywords
CD4-Positive T-Lymphocytes/metabolism, Gene Expression Profiling/methods, HIV Infections/genetics, HIV Infections/virology, HIV-1/genetics, HIV-1/metabolism, HIV-1/pathogenicity, Host-Pathogen Interactions/genetics, Humans, Proteome/genetics, Proteomics/methods, Signal Transduction, Transcriptome/genetics, Virus Latency/genetics, Virus Replication/genetics
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2019 13:44
Last modification date
21/11/2022 8:25
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