Proteomic profiling of HIV-infected T-cells by SWATH mass spectrometry

Jason DeBoer; Melinda S Wojtkiewicz; Nicole Haverland; Yan Li; Emma Harwood; Emily Leshen; Joseph W George; Pawel Ciborowski; Michael Belshan

doi:10.1016/j.virol.2018.01.025

Proteomic profiling of HIV-infected T-cells by SWATH mass spectrometry

Virology. 2018 Mar:516:246-257. doi: 10.1016/j.virol.2018.01.025.

Authors

Jason DeBoer¹, Melinda S Wojtkiewicz², Nicole Haverland², Yan Li¹, Emma Harwood², Emily Leshen¹, Joseph W George¹, Pawel Ciborowski³, Michael Belshan⁴

Affiliations

¹ Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA.
² Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
³ Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA.
⁴ Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; The Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA. Electronic address: michaelbelshan@creighton.edu.

Abstract

Viral pathogenesis results from changes in host cells due to virus usurpation of the host cell and the innate cellular responses to thwart infection. We measured global changes in protein expression and localization in HIV-1 infected T-cells using subcellular fractionation and the Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) proteomic platform. Eight biological replicates were performed in two independent experimental series. In silico merging of both experiments identified 287 proteins with altered expression (p < .05) between control and infected cells- 172 in the cytoplasm, 84 in the membrane, and 31 in nuclei. 170 of the proteins are components of the NIH HIV interaction database. Multiple Reaction Monitoring and traditional immunoblotting validated the altered expression of several factors during infection. Numerous factors were found to affect HIV infection in gain- and loss-of-expression infection assays, including the intermediate filament vimentin which was found to be required for efficient infection.

Keywords: HIV-1; Host response to infection; Proteomics; SWATH-MS; Vimentin.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

HIV Infections / genetics
HIV Infections / metabolism*
HIV Infections / virology
HIV-1 / physiology*
Humans
Proteins / chemistry*
Proteins / genetics
Proteins / metabolism
Proteomics
T-Lymphocytes / chemistry*
T-Lymphocytes / metabolism
T-Lymphocytes / virology
Tandem Mass Spectrometry

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding