A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV

Elife. 2018 Dec 6:7:e39823. doi: 10.7554/eLife.39823.

Abstract

Interferon (IFN) inhibits HIV replication by inducing antiviral effectors. To comprehensively identify IFN-induced HIV restriction factors, we assembled a CRISPR sgRNA library of Interferon Stimulated Genes (ISGs) into a modified lentiviral vector that allows for packaging of sgRNA-encoding genomes in trans into budding HIV-1 particles. We observed that knockout of Zinc Antiviral Protein (ZAP) improved the performance of the screen due to ZAP-mediated inhibition of the vector. A small panel of IFN-induced HIV restriction factors, including MxB, IFITM1, Tetherin/BST2 and TRIM5alpha together explain the inhibitory effects of IFN on the CXCR4-tropic HIV-1 strain, HIV-1LAI, in THP-1 cells. A second screen with a CCR5-tropic primary strain, HIV-1Q23.BG505, described an overlapping, but non-identical, panel of restriction factors. Further, this screen also identifies HIV dependency factors. The ability of IFN-induced restriction factors to inhibit HIV strains to replicate in human cells suggests that these human restriction factors are incompletely antagonized.

Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Keywords: CRISPR; HIV; infectious disease; interferon-stimulated genes; microbiology; restriction factor; screen; virus; virus replication.

Publication types

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

MeSH terms

  • Antigens, CD / genetics
  • Antigens, CD / immunology
  • Antigens, Differentiation / genetics
  • Antigens, Differentiation / immunology
  • Antiviral Restriction Factors
  • CRISPR-Cas Systems
  • Carrier Proteins / genetics
  • Carrier Proteins / immunology
  • Cell Line, Tumor
  • Epithelial Cells / drug effects
  • Epithelial Cells / immunology*
  • Epithelial Cells / virology
  • GPI-Linked Proteins / genetics
  • GPI-Linked Proteins / immunology
  • Gene Editing / methods*
  • Gene Expression Regulation
  • Genetic Vectors / chemistry
  • Genetic Vectors / immunology
  • HEK293 Cells
  • HIV-1 / drug effects
  • HIV-1 / genetics*
  • HIV-1 / growth & development
  • HIV-1 / immunology
  • Host-Pathogen Interactions*
  • Humans
  • Interferon-alpha / pharmacology
  • Lentivirus / genetics
  • Lentivirus / metabolism
  • Myxovirus Resistance Proteins / genetics
  • Myxovirus Resistance Proteins / immunology
  • Nuclear Proteins / deficiency
  • Nuclear Proteins / genetics*
  • Nuclear Proteins / immunology
  • Phosphotransferases (Alcohol Group Acceptor) / deficiency
  • Phosphotransferases (Alcohol Group Acceptor) / genetics*
  • Phosphotransferases (Alcohol Group Acceptor) / immunology
  • RNA-Binding Proteins
  • Receptors, CCR5 / genetics
  • Receptors, CCR5 / immunology
  • Receptors, CXCR4 / genetics
  • Receptors, CXCR4 / immunology
  • Repressor Proteins
  • Signal Transduction
  • THP-1 Cells
  • Tripartite Motif Proteins
  • Ubiquitin-Protein Ligases
  • Viral Tropism / genetics
  • Virus Assembly / drug effects
  • Virus Replication / drug effects

Substances

  • Antigens, CD
  • Antigens, Differentiation
  • Antiviral Restriction Factors
  • BST2 protein, human
  • CCR5 protein, human
  • CXCR4 protein, human
  • Carrier Proteins
  • GPI-Linked Proteins
  • Interferon-alpha
  • MX2 protein, human
  • Myxovirus Resistance Proteins
  • Nuclear Proteins
  • RNA-Binding Proteins
  • Receptors, CCR5
  • Receptors, CXCR4
  • Repressor Proteins
  • Tripartite Motif Proteins
  • YLPM1 protein, human
  • leu-13 antigen
  • TRIM5 protein, human
  • Ubiquitin-Protein Ligases
  • Phosphotransferases (Alcohol Group Acceptor)