Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells

Ujjwal Rathore; Eli Dugan; Hunter Thornton; Vigneshwari Easwar Kumar; Rama Dajani; Ryan C Burdick; Janet M Young; Zachary Steinhart; Reanna Lao; Krista A Delviks-Frankenberry; Wooyoung Choi; William S Henriques; Ignacia Echeverria; Emma Dann; Ishaan Dureja; Nandini Pathak; Maya M Arce; Justin McKetney; Jennifer M Umhoefer; Simrun Parulekar; Ralf Schmidt; Benjamin J Polacco; Jason Neidleman; Mauricio Montano; Vinh Q Nguyen; Andrej Sali; Jay A Levy; Jeannette L Tenthorey; Yifan Cheng; Nadia R Roan; Danielle L Swaney; Robyn M Kaake; Stacie E Dodgson; Joseph Hiatt; Vinay K Pathak; Harmit S Malik; Nevan J Krogan; Alexander Marson

doi:10.1016/j.cell.2026.03.046

Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells

Cell. 2026 Jun 11;189(12):3651-3668.e31. doi: 10.1016/j.cell.2026.03.046. Epub 2026 Apr 20.

Authors

Ujjwal Rathore¹, Eli Dugan², Hunter Thornton³, Vigneshwari Easwar Kumar³, Rama Dajani³, Ryan C Burdick⁴, Janet M Young⁵, Zachary Steinhart⁶, Reanna Lao⁷, Krista A Delviks-Frankenberry⁴, Wooyoung Choi⁸, William S Henriques⁹, Ignacia Echeverria¹⁰, Emma Dann¹¹, Ishaan Dureja³, Nandini Pathak³, Maya M Arce⁶, Justin McKetney⁷, Jennifer M Umhoefer³, Simrun Parulekar³, Ralf Schmidt¹², Benjamin J Polacco⁷, Jason Neidleman³, Mauricio Montano³, Vinh Q Nguyen¹³, Andrej Sali¹⁰, Jay A Levy¹⁴, Jeannette L Tenthorey¹⁵, Yifan Cheng¹⁶, Nadia R Roan¹⁷, Danielle L Swaney¹⁸, Robyn M Kaake¹⁸, Stacie E Dodgson³, Joseph Hiatt⁶, Vinay K Pathak⁴, Harmit S Malik¹⁹, Nevan J Krogan¹⁸, Alexander Marson²⁰

Affiliations

¹ Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA. Electronic address: ujjwal.rathore@gladstone.ucsf.edu.
² Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
³ Gladstone Institutes, San Francisco, CA, USA.
⁴ Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
⁵ Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.
⁶ Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
⁷ Gladstone Institutes, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
⁸ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
⁹ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
¹⁰ Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
¹¹ Gladstone Institutes, San Francisco, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA.
¹² Gladstone Institutes, San Francisco, CA, USA; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
¹³ Gladstone Institutes, San Francisco, CA, USA; Department of Surgery, University of California, San Francisco, San Francisco, CA, USA.
¹⁴ Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
¹⁵ Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
¹⁶ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
¹⁷ Gladstone Institutes, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
¹⁸ Gladstone Institutes, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
¹⁹ Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA.
²⁰ Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. Electronic address: alexander.marson@ucsf.edu.

Abstract

Host factors that promote or restrict human immunodeficiency virus (HIV) infection in human CD4+ T cells have not been comprehensively identified. We employed orthogonal genome-wide CRISPR activation (CRISPRa) and CRISPR knockout screens in primary CD4+ T cells to discover pro- and anti-HIV host factors systematically. Secondary pooled screens and individual perturbations validated high-confidence hits and revealed diverse mechanisms of action. CRISPRa uncovered multiple potent antiviral factors, including PI16, PPID, SHISA3, and ITM2A. PI16 interacts with host factors involved in HIV fusion and inhibits viral entry, whereas PPID (Cyp40), a paralog of the proviral cyclophilin CypA, binds capsid and reduces nuclear import of the HIV core. Structural modeling, evolutionary analyses, and targeted mutagenesis revealed domains and residues required for PPID-mediated HIV restriction, including non-human primate ortholog substitutions that enhance antiviral activity. Together, these data define the functional HIV-host interaction landscape in primary human T cells and uncover new mechanisms modulating infection.

Keywords: CRISPR; HIV-1; HIV-host interactions; human T cells; immunology; pooled screens; virology.

MeSH terms

CD4-Positive T-Lymphocytes* / immunology
CD4-Positive T-Lymphocytes* / metabolism
CD4-Positive T-Lymphocytes* / virology
HIV Infections* / immunology
HIV Infections* / virology
HIV-1* / physiology
Host-Pathogen Interactions
Humans

Abstract

MeSH terms

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