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Geretz A, Ehrenberg PK, Clifford RJ, Laliberté A, Prelli Bozzo C, Eiser D, Kundu G, Yum LK, Apps R, Creegan M, Gunady M, Shangguan S, Sanders-Buell E, Sacdalan C, Phanuphak N, Tovanabutra S, Russell RM, Bibollet-Ruche F, Robb ML, Michael NL, Ake JA, Vasan S, Hsu DC, Hahn BH, Kirchhoff F, Thomas R. Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo. Sci Transl Med 2023; 15:eadg0873. [PMID: 37531416 DOI: 10.1126/scitranslmed.adg0873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene PTMA, which encodes prothymosin α. This association was genome-wide significant (Padjusted < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
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Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Daina Eiser
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauren K Yum
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Mohamed Gunady
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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