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Delviks-Frankenberry KA, Ojha CR, Hermann KJ, Hu WS, Torbett BE, Pathak VK. Potent dual block to HIV-1 infection using lentiviral vectors expressing fusion inhibitor peptide mC46- and Vif-resistant APOBEC3G. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:794-809. [PMID: 37662965 PMCID: PMC10470399 DOI: 10.1016/j.omtn.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023]
Abstract
Gene therapy strategies that effectively inhibit HIV-1 replication are needed to reduce the requirement for lifelong antiviral therapy and potentially achieve a functional cure. We previously designed self-activating lentiviral vectors that efficiently delivered and expressed a Vif-resistant mutant of APOBEC3G (A3G-D128K) to T cells, which potently inhibited HIV-1 replication and spread with no detectable virus. Here, we developed vectors that express A3G-D128K, membrane-associated fusion inhibitor peptide mC46, and O6-methylguanine-DNA-methyltransferase (MGMT) selectable marker for in vivo selection of transduced CD34+ hematopoietic stem and progenitor cells. MGMT-selected T cell lines MT4, CEM, and PM1 expressing A3G-D128K (with or without mC46) potently inhibited NL4-3 infection up to 45 days post infection with no detectable viral replication. Expression of mC46 was sufficient to block infection >80% in a single-cycle assay. Importantly, expression of mC46 provided a selective advantage to the A3G-D128K-modified T cells in the presence of replication competent virus. This combinational approach to first block HIV-1 entry with mC46, and then block any breakthrough infection with A3G-D128K, could provide an effective gene therapy treatment and a potential functional cure for HIV-1 infection.
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Affiliation(s)
- Krista A. Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chet R. Ojha
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Kip J. Hermann
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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Koma T, Doi N, Takemoto M, Watanabe K, Yamamoto H, Nakashima S, Adachi A, Nomaguchi M. The Expression Level of HIV-1 Vif Is Optimized by Nucleotide Changes in the Genomic SA1D2prox Region during the Viral Adaptation Process. Viruses 2021; 13:2079. [PMID: 34696508 PMCID: PMC8537775 DOI: 10.3390/v13102079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
HIV-1 Vif plays an essential role in viral replication by antagonizing anti-viral cellular restriction factors, a family of APOBEC3 proteins. We have previously shown that naturally-occurring single-nucleotide mutations in the SA1D2prox region, which surrounds the splicing acceptor 1 and splicing donor 2 sites of the HIV-1 genome, dramatically alter the Vif expression level, resulting in variants with low or excessive Vif expression. In this study, we investigated how these HIV-1 variants with poor replication ability adapt and evolve under the pressure of APOBEC3 proteins. Adapted clones obtained through adaptation experiments exhibited an altered replication ability and Vif expression level compared to each parental clone. While various mutations were present throughout the viral genome, all replication-competent adapted clones with altered Vif expression levels were found to bear them within SA1D2prox, without exception. Indeed, the mutations identified within SA1D2prox were responsible for changes in the Vif expression levels and altered the splicing pattern. Moreover, for samples collected from HIV-1-infected patients, we showed that the nucleotide sequences of SA1D2prox can be chronologically changed and concomitantly affect the Vif expression levels. Taken together, these results demonstrated the importance of the SA1D2prox nucleotide sequence for modulating the Vif expression level during HIV-1 replication and adaptation.
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Affiliation(s)
- Takaaki Koma
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
| | - Naoya Doi
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
| | - Mai Takemoto
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Kyosuke Watanabe
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Hideki Yamamoto
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Satoshi Nakashima
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
- Faculty of Medicine, Tokushima University, Tokushima 770-8503, Japan
| | - Akio Adachi
- Department of Microbiology, Kansai Medical University, Osaka 573-1010, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8503, Japan; (T.K.); (N.D.); (M.T.); (K.W.); (H.Y.); (S.N.)
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Tamalet C, Devaux C, Dubourg G, Colson P. Resistance to human immunodeficiency virus infection: a rare but neglected state. Ann N Y Acad Sci 2020; 1485:22-42. [PMID: 33009659 DOI: 10.1111/nyas.14452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV-infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV-free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV-1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.
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Affiliation(s)
- Catherine Tamalet
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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Inhibition of Vif-Mediated Degradation of APOBEC3G through Competitive Binding of Core-Binding Factor Beta. J Virol 2020; 94:JVI.01708-19. [PMID: 31941780 DOI: 10.1128/jvi.01708-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/27/2019] [Indexed: 12/31/2022] Open
Abstract
Vif counteracts the host restriction factor APOBEC3G (A3G) and other APOBEC3s by preventing the incorporation of A3G into progeny virions. We previously identified Vif mutants with a dominant-negative (D/N) phenotype that interfered with the function of wild-type Vif, inhibited the degradation of A3G, and reduced the infectivity of viral particles by increased packaging of A3G. However, the mechanism of interference remained unclear, in particular since all D/N Vif mutants were unable to bind Cul5 and some mutants additionally failed to bind A3G, ruling out competitive binding to A3G or the E3 ubiquitin ligase complex as the sole mechanism. The goal of the current study was to revisit the mechanism of D/N interference by Vif mutants and analyze the possible involvement of core binding factor beta (CBFβ) in this process. We found a clear correlation of D/N properties of Vif mutants with their ability to engage CBFβ. Only mutants that retained the ability to bind CBFβ exhibited the D/N phenotype. Competition studies revealed that D/N Vif mutants directly interfered with the association of CBFβ and wild-type Vif. Furthermore, overexpression of CBFβ counteracted the interference of D/N Vif mutants with A3G degradation by wild-type Vif. Finally, overexpression of Runx1 mimicked the effect of D/N Vif mutants and inhibited the degradation of A3G by wild-type Vif. Taken together, we identified CBFβ as the key player involved in D/N interference by Vif.IMPORTANCE Of all the accessory proteins encoded by HIV-1 and other primate lentiviruses, Vif has arguably the strongest potential as a target for antiviral therapy. This conclusion is based on the observation that replication of HIV-1 in vivo is critically dependent on Vif. Thus, inhibiting the function of Vif via small-molecule inhibitors or other approaches has significant therapeutic potential. We previously identified dominant-negative (D/N) Vif variants whose expression interferes with the function of virus-encoded wild-type Vif. We now show that D/N interference involves competitive binding of D/N Vif variants to the transcriptional cofactor core binding factor beta (CBFβ), which is expressed in cells in limiting quantities. Overexpression of CBFβ neutralized the D/N phenotype of Vif. In contrast, overexpression of Runx1, a cellular binding partner of CBFβ, phenocopied the D/N Vif phenotype by sequestering endogenous CBFβ. Thus, our results provide proof of principle that D/N Vif variants could have therapeutic potential.
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Delviks-Frankenberry KA, Ackerman D, Timberlake ND, Hamscher M, Nikolaitchik OA, Hu WS, Torbett BE, Pathak VK. Development of Lentiviral Vectors for HIV-1 Gene Therapy with Vif-Resistant APOBEC3G. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:1023-1038. [PMID: 31778955 PMCID: PMC6889484 DOI: 10.1016/j.omtn.2019.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/29/2022]
Abstract
Strategies to control HIV-1 replication without antiviral therapy are needed to achieve a functional cure. To exploit the innate antiviral function of restriction factor cytidine deaminase APOBEC3G (A3G), we developed self-activating lentiviral vectors that efficiently deliver HIV-1 Vif-resistant mutant A3G-D128K to target cells. To circumvent APOBEC3 expression in virus-producing cells, which diminishes virus infectivity, a vector containing two overlapping fragments of A3G-D128K was designed that maintained the gene in an inactive form in the virus-producer cells. However, during transduction of target cells, retroviral recombination between the direct repeats reconstituted an active A3G-D128K in 89%-98% of transduced cells. Lentiviral vectors that expressed A3G-D128K transduced CD34+ hematopoietic stem and progenitor cells with a high efficiency (>30%). A3G-D128K expression in T cell lines CEM, CEMSS, and PM1 potently inhibited spreading infection of several HIV-1 subtypes by C-to-U deamination leading to lethal G-to-A hypermutation and inhibition of reverse transcription. SIVmac239 and HIV-2 were not inhibited, since their Vifs degraded A3G-D128K. A3G-D128K expression in CEM cells potently suppressed HIV-1 replication for >3.5 months without detectable resistant virus, suggesting a high genetic barrier for the emergence of A3G-D128K resistance. Because of this, A3G-D128K expression in HIV-1 target cells is a potential anti-HIV gene therapy approach that could be combined with other therapies for the treatment and functional cure of HIV-1 infection.
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Affiliation(s)
- Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Daniel Ackerman
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Maria Hamscher
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Olga A Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
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Vpr and Its Cellular Interaction Partners: R We There Yet? Cells 2019; 8:cells8111310. [PMID: 31652959 PMCID: PMC6912716 DOI: 10.3390/cells8111310] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Vpr is a lentiviral accessory protein that is expressed late during the infection cycle and is packaged in significant quantities into virus particles through a specific interaction with the P6 domain of the viral Gag precursor. Characterization of the physiologically relevant function(s) of Vpr has been hampered by the fact that in many cell lines, deletion of Vpr does not significantly affect viral fitness. However, Vpr is critical for virus replication in primary macrophages and for viral pathogenesis in vivo. It is generally accepted that Vpr does not have a specific enzymatic activity but functions as a molecular adapter to modulate viral or cellular processes for the benefit of the virus. Indeed, many Vpr interacting factors have been described by now, and the goal of this review is to summarize our current knowledge of cellular proteins targeted by Vpr.
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