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Temporal proteomic analysis of total cellular proteome of HIV-1 infected cells

E. Greenwood, N. Matheson, J Williamson eLife 2016

Graphical Abstract - Greenwood, E. et al. Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection,Cell Rep. 2019 Apr 30; 27(5): 1579–1596.e7.

Figure 1. Greenwood, E. et al. Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection,Cell Rep. 2019 Apr 30; 27(5): 1579–1596.e7.

We have a longstanding interest in deciphering how viruses manipulate endogenous cell surface receptors. Starting from the finding that many viruses downregulate MHC-I expression we wanted to develop an approach to provide a systematic unbiased view of the multititude of cellular pathways that viruses manipulate, both at the cell surface and inside the cell. We developed and applied complementary proteomic and genetic approaches to provide a comprehensive understanding of how viruses remodel their host cell environment.


Our initial focus was the plasma membrane, the critical interface for cell communication, and led to the development of ‘plasma membrane profiling’, a systematic, quantitative approach to detect virus-induced changes in the abundance of cell surface proteins. This was applied to latent HCMV infection, a major clinical problem in the immune-compromised and has led to the development of new approaches to prevent latent CMV transmission.

The application of systematic quantitative proteomics changes our understanding of how and why viruses remodel infected cells. Viral genes which hitherto were assigned individual substrates e.g. HIV-Vif degradation of APOBECs, are clearly more complex. Our proteomic approaches revealed novel cellular therapeutic targets.


Exploiting multiplexed proteomic technology, together with our collaborators, we have mapped the cell surface and total protein changes over the time course of CMV, KSHV and HIV infection, providing a unique overview of viral remodelling of the host cell, identifying novel NK- and T-cell ligands, and unrecognised cell-surface viral proteins as therapeutic targets.


Applying this technology to HIV-infected T-cells identified antiviral resistance factors (SERINC3/5) as HIV Nef targets, amino acid transporters as HIV Vpu targets and the intracellular phosphatase PP2A as an unanticipated and evolutionarily conserved target of HIV Vif20. Indeed, regulation of the host phosphoproteome is a key function for Vif and promotes the phosphorylation of >200 cellular proteins.


Our discovery that HIV Vpr targets multiple host proteins and drives systems-level changes in HIV-infected cells changed our view of this viral accessory protein6. These pioneering proteomic approaches provide a systems framework for the study of any virus, enabling in-depth analysis of key aspects of viral life cycles and pathogenesis which were previously unavailable.



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Matheson NJ, Sumner J, Wals K, Rapiteanu R, Weekes MP, Vigan R, Weinelt J, Schindler M, Antrobus R, Costa ASH, Frezza C, Clish CB, Neil SJD, Lehner PJ. Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. Cell, Host and Microbe (2015) 18(4):409-23 PMID: 26439863 doi: 10.1016/j.chom.2015.09.003.


Greenwood EJD, Matheson NJ, Wals K, van den Boomen DJ,  Antrobus R, Williamson JC, Lehner PJ. Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants. eLife (2016);5:e18296 PMID: 27690223 doi: 10.7554/eLife.18296.


Gabaev I,  Williamson JC, Crozier TWM, Schulz TF, Lehner PJ. Quantitative proteomics analysis of lytic KSHV infection in human endothelial cells reveals novel targets of viral immune modulation. Cell Reports 2020 Oct 13;33(2):108249. PMID: 33053346 doi: 10.1016/108249

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