CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells

Ujjwal Rathore, Paige Haas, Vigneshwari Easwar Kumar, Joseph Hiatt, Kelsey M. Haas, Mehdi Bouhaddou, Danielle L. Swaney, Erica Stevenson, Lorena Zuliani-Alvarez, Michael J. McGregor, Autumn Turner-Groth, Charles Ochieng Olwal, Yaw Bediako, Hannes Braberg, Margaret Soucheray, Melanie Ott, Manon Eckhardt, Judd F. Hultquist, Alexander Marson, Robyn M. Kaake*Nevan J. Krogan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

During HIV infection of CD4+ T cells, ubiquitin pathways are essential to viral replication and host innate immune response; however, the role of specific E3 ubiquitin ligases is not well understood. Proteomics analyses identified 116 single-subunit E3 ubiquitin ligases expressed in activated primary human CD4+ T cells. Using a CRISPR-based arrayed spreading infectivity assay, we systematically knocked out 116 E3s from activated primary CD4+ T cells and infected them with NL4-3 GFP reporter HIV-1. We found 10 E3s significantly positively or negatively affected HIV infection in activated primary CD4+ T cells, including UHRF1 (pro-viral) and TRAF2 (anti-viral). Furthermore, deletion of either TRAF2 or UHRF1 in three JLat models of latency spontaneously increased HIV transcription. To verify this effect, we developed a CRISPR-compatible resting primary human CD4+ T cell model of latency. Using this system, we found that deletion of TRAF2 or UHRF1 initiated latency reactivation and increased virus production from primary human resting CD4+ T cells, suggesting these two E3s represent promising targets for future HIV latency reversal strategies.

Original languageEnglish (US)
JournalmBio
Volume15
Issue number4
DOIs
StatePublished - Apr 2024

Keywords

  • CRISPR screen
  • HIV latency
  • human immunodeficiency virus
  • resting primary T cells
  • ubiquitin E3 ligases

ASJC Scopus subject areas

  • Microbiology
  • Virology

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