Functional proteomic atlas of HIV infection in primary human CD4+ T cells

Elife. 2019 Mar 12:8:e41431. doi: 10.7554/eLife.41431.

Abstract

Viruses manipulate host cells to enhance their replication, and the identification of cellular factors targeted by viruses has led to key insights into both viral pathogenesis and cell biology. In this study, we develop an HIV reporter virus (HIV-AFMACS) 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, and quantitate approximately 9000 proteins across multiple donors on a dynamic background of T cell activation. Amongst 650 HIV-dependent changes (q < 0.05), we describe novel Vif-dependent targets FMR1 and DPH7, and 192 proteins not identified and/or regulated in T cell lines, such as ARID5A and PTPN22. We therefore provide a high-coverage functional proteomic atlas of HIV infection, and a mechanistic account of host factors subverted by the virus in its natural target cell.

Keywords: HIV; human; immunology; infectious disease; inflammation; magnetic cell selection; microbiology; primary human CD4+ T cell; proteomics; virus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CD4-Positive T-Lymphocytes / cytology*
  • CD4-Positive T-Lymphocytes / virology*
  • Cell Separation
  • Cluster Analysis
  • DNA-Binding Proteins / chemistry
  • Fragile X Mental Retardation Protein / chemistry
  • Gene Expression Regulation*
  • Green Fluorescent Proteins / chemistry
  • HIV Infections / metabolism*
  • HIV-1 / physiology
  • Humans
  • Hydrogen-Ion Concentration
  • Lentivirus
  • Lymphocyte Activation
  • Magnetics
  • Methyltransferases / chemistry
  • Protein Binding
  • Protein Tyrosine Phosphatase, Non-Receptor Type 22 / chemistry
  • Proteome*
  • Proteomics
  • Streptavidin / chemistry
  • Virus Replication
  • vif Gene Products, Human Immunodeficiency Virus / chemistry

Substances

  • ARID5A protein, human
  • DNA-Binding Proteins
  • FMR1 protein, human
  • Proteome
  • vif Gene Products, Human Immunodeficiency Virus
  • vif protein, Human immunodeficiency virus 1
  • Fragile X Mental Retardation Protein
  • Green Fluorescent Proteins
  • Streptavidin
  • DPH7 protein, human
  • Methyltransferases
  • PTPN22 protein, human
  • Protein Tyrosine Phosphatase, Non-Receptor Type 22