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Brandt L, Angelino P, Martinez R, Cristinelli S, Ciuffi A. Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro through Cell Activation Dynamics. Cells 2023; 12:2689. [PMID: 38067117 PMCID: PMC10706042 DOI: 10.3390/cells12232689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.
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Affiliation(s)
- Ludivine Brandt
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Paolo Angelino
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
- Translational Data Science (TDS)-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland; (L.B.)
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2
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Kulkarni S, Endsley JJ, Lai Z, Bradley T, Sharan R. Single-Cell Transcriptomics of Mtb/HIV Co-Infection. Cells 2023; 12:2295. [PMID: 37759517 PMCID: PMC10529032 DOI: 10.3390/cells12182295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection continues to pose a significant healthcare burden. HIV co-infection during TB predisposes the host to the reactivation of latent TB infection (LTBI), worsening disease conditions and mortality. There is a lack of biomarkers of LTBI reactivation and/or immune-related transcriptional signatures to distinguish active TB from LTBI and predict TB reactivation upon HIV co-infection. Characterizing individual cells using next-generation sequencing-based technologies has facilitated novel biological discoveries about infectious diseases, including TB and HIV pathogenesis. Compared to the more conventional sequencing techniques that provide a bulk assessment, single-cell RNA sequencing (scRNA-seq) can reveal complex and new cell types and identify more high-resolution cellular heterogeneity. This review will summarize the progress made in defining the immune atlas of TB and HIV infections using scRNA-seq, including host-pathogen interactions, heterogeneity in HIV pathogenesis, and the animal models employed to model disease. This review will also address the tools needed to bridge the gap between disease outcomes in single infection vs. co-infection. Finally, it will elaborate on the translational benefits of single-cell sequencing in TB/HIV diagnosis in humans.
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Affiliation(s)
- Smita Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Janice J. Endsley
- Departments of Microbiology & Immunology and Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, The University of Texas Health San Antonio, San Antonio, TX 78229, USA;
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA;
- Departments of Pediatrics and Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO 66160, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO 64108, USA
| | - Riti Sharan
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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3
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Rindler AE, Kuster H, Neumann K, Leemann C, Braun DL, Metzner KJ, Günthard HF. A Novel High Throughput, Parallel Infection Assay for Determining the Replication Capacities of 346 Primary HIV-1 Isolates of the Zurich Primary HIV-1 Infection Study in Primary Cells. Viruses 2021; 13:404. [PMID: 33806576 PMCID: PMC8000554 DOI: 10.3390/v13030404] [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: 02/03/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 replication capacity is an important characteristic to understand the replication competence of single variants or virus populations. It can further aid in the understanding of HIV-1 pathogenicity, disease progression, and drug resistance mutations. To effectively study RC, many assays have been established. However, there is still demand for a high throughput replication capacity assay using primary cells which is robust and reproducible. In this study, we established such an assay and validated it using 346 primary HIV-1 isolates from patients enrolled in the Zurich Primary HIV Infection study (ZPHI) and two control viruses, HIV-1 JR-CSFWT and HIV-1 JR-CSFK65R_M184V. Replication capacity was determined by measuring the viral growth on PBMCs over 10 days by longitudinally transferring cell culture supernatant to TZM-bl reporter cells. By utilizing the TZM-bl luciferase reporter assay, we determined replication capacity by measuring viral infectivity. The simplicity of the experimental setup allowed for all 346 primary HIV-1 isolates to be replicated at one time. Although the infectious input dose for each virus was normalized, a broad range of replication capacity values over 4 logs was observed. The approach was confirmed by two repeated experiments and we demonstrated that the reproducibility of the replication capacity values is statistically comparable between the two separate experiments. In summary, these results endorse our high throughput replication capacity assay as reproducible and robust and can be utilized for large scale HIV-1 replication capacity experiments in primary cells.
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Affiliation(s)
- Audrey E. Rindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
- Life Sciences Graduate School, University of Zürich, 8057 Zürich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Dominique L. Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, 8091 Zürich, Switzerland; (A.E.R.); (H.K.); (K.N.); (C.L.); (D.L.B.)
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland
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4
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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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5
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Single-cell analysis identifies cellular markers of the HIV permissive cell. PLoS Pathog 2017; 13:e1006678. [PMID: 29073251 PMCID: PMC5658171 DOI: 10.1371/journal.ppat.1006678] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
Cellular permissiveness to HIV infection is highly heterogeneous across individuals. Heterogeneity is also found across CD4+ T cells from the same individual, where only a fraction of cells gets infected. To explore the basis of permissiveness, we performed single-cell RNA-seq analysis of non-infected CD4+ T cells from high and low permissive individuals. Transcriptional heterogeneity translated in a continuum of cell states, driven by T-cell receptor-mediated cell activation and was strongly linked to permissiveness. Proteins expressed at the cell surface and displaying the highest correlation with T cell activation were tested as biomarkers of cellular permissiveness to HIV. FACS sorting using antibodies against several biomarkers of permissiveness led to an increase of HIV cellular infection rates. Top candidate biomarkers included CD25, a canonical activation marker. The combination of CD25 high expression with other candidate biomarkers led to the identification of CD298, CD63 and CD317 as the best biomarkers for permissiveness. CD25highCD298highCD63highCD317high cell population showed an enrichment of HIV-infection of up to 28 fold as compared to the unsorted cell population. The purified hyper-permissive cell subpopulation was characterized by a downregulation of interferon-induced genes and several known restriction factors. Single-cell RNA-seq analysis coupled with functional characterization of cell biomarkers provides signatures of the "HIV-permissive cell".
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6
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RNA editing by ADAR1 regulates innate and antiviral immune functions in primary macrophages. Sci Rep 2017; 7:13339. [PMID: 29042669 PMCID: PMC5645456 DOI: 10.1038/s41598-017-13580-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
ADAR1-dependent A-to-I editing has recently been recognized as a key process for marking dsRNA as self, therefore, preventing innate immune activation and affecting the development and resolution of immune-mediated diseases and infections. Here, we have determined the role of ADAR1 as a regulator of innate immune activation and modifier of viral susceptibility in primary myeloid and lymphoid cells. We show that ADAR1 knockdown significantly enhanced interferon, cytokine and chemokine production in primary macrophages that function as antiviral paracrine factors, rendering them resistant to HIV-1 infection. ADAR1 knockdown induced deregulation of the RLRs-MAVS signaling pathway, by increasing MDA5, RIG-I, IRF7 and phospho-STAT1 expression, an effect that was partially rescued by pharmacological blockade of the pathway. In summary, our results demonstrate a role of ADAR1 in regulating innate immune function in primary macrophages, suggesting that macrophages may play an essential role in disease associated to ADAR1 dysfunction. We also show that viral inhibition is exclusively dependent on innate immune activation consequence of ADAR1 knockdown, pointing towards ADAR1 as a potential target to boost antiviral immune response.
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7
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Nemeth J, Vongrad V, Metzner KJ, Strouvelle VP, Weber R, Pedrioli P, Aebersold R, Günthard HF, Collins BC. In Vivo and in Vitro Proteome Analysis of Human Immunodeficiency Virus (HIV)-1-infected, Human CD4 + T Cells. Mol Cell Proteomics 2017; 16:S108-S123. [PMID: 28223351 DOI: 10.1074/mcp.m116.065235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/03/2017] [Indexed: 01/06/2023] Open
Abstract
Host-directed therapies against HIV-1 are thought to be critical for long term containment of the HIV-1 pandemic but remain elusive. Because HIV-1 infects and manipulates important effectors of both the innate and adaptive immune system, identifying modulations of the host cell systems in humans during HIV-1 infection may be crucial for the development of immune based therapies. Here, we quantified the changes of the proteome in human CD4+ T cells upon HIV-1 infection, both in vitro and in vivo A SWATH-MS approach was used to measure the proteome of human primary CD4+ T cells infected with HIV-1 in vitro as well as CD4+ T cells from HIV-1-infected patients with paired samples on and off antiretroviral treatment. In the in vitro experiment, the proteome of CD4+ T cells was quantified over a time course following HIV-1 infection. 1,725 host cell proteins and 4 HIV-1 proteins were quantified, with 145 proteins changing significantly during the time course. Changes in the proteome peaked 24 h after infection, concomitantly with significant HIV-1 protein production. In the in vivo branch of the study, CD4+ T cells from viremic patients and those with no detectable viral load after treatment were sorted, and the proteomes were quantified. We consistently detected 895 proteins, 172 of which were considered to be significantly different between the viremic patients and patients undergoing successful treatment. The proteome of the in vitro-infected CD4+ T cells was modulated on multiple functional levels, including TLR-4 signaling and the type 1 interferon signaling pathway. Perturbations in the type 1 interferon signaling pathway were recapitulated in CD4+ T cells from patients. The study shows that proteome maps generated by SWATH-MS indicate a range of functionally significant changes in the proteome of HIV-infected human CD4+ T cells. Exploring these perturbations in more detail may help identify new targets for immune based interventions.
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Affiliation(s)
- Johannes Nemeth
- From the ‡Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091.,§Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093
| | - Valentina Vongrad
- From the ‡Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091.,‖Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Karin J Metzner
- From the ‡Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091.,‖Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Victoria P Strouvelle
- From the ‡Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091.,‖Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Rainer Weber
- From the ‡Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091
| | - Patrick Pedrioli
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093.,**Faculty of Science, University of Zurich, Zurich 8057; and
| | - Huldrych F Günthard
- From the ‡Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich 8091; .,‖Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Ben C Collins
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093;
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8
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Rausell A, Muñoz M, Martinez R, Roger T, Telenti A, Ciuffi A. Innate immune defects in HIV permissive cell lines. Retrovirology 2016; 13:43. [PMID: 27350062 PMCID: PMC4924258 DOI: 10.1186/s12977-016-0275-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/14/2016] [Indexed: 11/29/2022] Open
Abstract
Background Primary CD4+ T cells and cell lines differ in their permissiveness to HIV infection. Impaired innate immunity may contribute to this different phenotype. Findings We used transcriptome profiling of 1503 innate immunity genes in primary CD4+ T cells and permissive cell lines. Two clusters of differentially expressed genes were identified: a set of 249 genes that were highly expressed in primary cells and minimally expressed in cell lines and a set of 110 genes with the opposite pattern. Specific to HIV, HEK293T, Jurkat, SupT1 and CEM cell lines displayed unique patterns of downregulation of genes involved in viral sensing and restriction. Activation of primary CD4+ T cells resulted in reversal of the pattern of expression of those sets of innate immunity genes. Functional analysis of prototypical innate immunity pathways of permissive cell lines confirmed impaired responses identified in transcriptome analyses. Conclusion Integrity of innate immunity genes and pathways needs to be considered in designing gain/loss functional genomic screens of viral infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0275-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Rausell
- Clinical Bioinformatics lab, Imagine Institute, Paris Descartes University - Sorbonne Paris Cité, 75015, Paris, France.
| | - Miguel Muñoz
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Thierry Roger
- Infectious Diseases Service, Department of Medicine, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Amalio Telenti
- Genetic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
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9
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Krapp C, Hotter D, Gawanbacht A, McLaren PJ, Kluge SF, Stürzel CM, Mack K, Reith E, Engelhart S, Ciuffi A, Hornung V, Sauter D, Telenti A, Kirchhoff F. Guanylate Binding Protein (GBP) 5 Is an Interferon-Inducible Inhibitor of HIV-1 Infectivity. Cell Host Microbe 2016; 19:504-14. [PMID: 26996307 DOI: 10.1016/j.chom.2016.02.019] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/02/2016] [Accepted: 02/26/2016] [Indexed: 12/26/2022]
Abstract
Guanylate binding proteins (GBPs) are an interferon (IFN)-inducible subfamily of guanosine triphosphatases (GTPases) with well-established activity against intracellular bacteria and parasites. Here we show that GBP5 potently restricts HIV-1 and other retroviruses. GBP5 is expressed in the primary target cells of HIV-1, where it impairs viral infectivity by interfering with the processing and virion incorporation of the viral envelope glycoprotein (Env). GBP5 levels in macrophages determine and inversely correlate with infectious HIV-1 yield over several orders of magnitude, which may explain the high donor variability in macrophage susceptibility to HIV. Antiviral activity requires Golgi localization of GBP5, but not its GTPase activity. Start codon mutations in the accessory vpu gene from macrophage-tropic HIV-1 strains conferred partial resistance to GBP5 inhibition by increasing Env expression. Our results identify GBP5 as an antiviral effector of the IFN response and may explain the increased frequency of defective vpu genes in primary HIV-1 strains.
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Affiliation(s)
- Christian Krapp
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Ali Gawanbacht
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Paul J McLaren
- National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3P6, Canada
| | - Silvia F Kluge
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Katharina Mack
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elisabeth Reith
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Susanne Engelhart
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital Center, University of Lausanne, 1015 Switzerland
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Amalio Telenti
- J. Craig Venter Institute, Capricorn Ln, La Jolla, CA 92037, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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10
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Leng J, Ho HP, Buzon MJ, Pereyra F, Walker BD, Yu XG, Chang EJ, Lichterfeld M. A cell-intrinsic inhibitor of HIV-1 reverse transcription in CD4(+) T cells from elite controllers. Cell Host Microbe 2015; 15:717-728. [PMID: 24922574 DOI: 10.1016/j.chom.2014.05.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/30/2014] [Accepted: 04/23/2014] [Indexed: 01/22/2023]
Abstract
HIV-1 reverse transcription represents the predominant target for pharmacological inhibition of viral replication, but cell-intrinsic mechanisms that can block HIV-1 reverse transcription in a clinically significant way are poorly defined. We find that effective HIV-1 reverse transcription depends on the phosphorylation of viral reverse transcriptase by host cyclin-dependent kinase (CDK) 2 at a highly conserved Threonine residue. CDK2-dependent phosphorylation increased the efficacy and stability of viral reverse transcriptase and enhanced viral fitness. Interestingly, p21, a cell-intrinsic CDK inhibitor that is upregulated in CD4(+) T cells from "elite controllers," potently inhibited CDK2-dependent phosphorylation of HIV-1 reverse transcriptase and significantly reduced the efficacy of viral reverse transcription. These data suggest that p21 can indirectly block HIV-1 reverse transcription by inhibiting host cofactors supporting HIV-1 replication and identify sites of viral vulnerability that are effectively targeted in persons with natural control of HIV-1 replication.
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Affiliation(s)
- Jin Leng
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Hsin-Pin Ho
- Department of Chemistry, York College and the Graduate Center, City University of New York, New York, NY, USA
| | - Maria J Buzon
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Florencia Pereyra
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Emmanuel J Chang
- Department of Chemistry, York College and the Graduate Center, City University of New York, New York, NY, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
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11
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Simple mathematical models do not accurately predict early SIV dynamics. Viruses 2015; 7:1189-217. [PMID: 25781919 PMCID: PMC4379566 DOI: 10.3390/v7031189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 02/07/2023] Open
Abstract
Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results suggest that, in order to appropriately model early HIV/SIV dynamics, additional factors must be considered in the model development. These may include variability in monkey susceptibility to infection, within-host competition between different viruses for target cells at the initial site of virus replication in the mucosa, innate immune response, and possibly the inclusion of several different tissue compartments. The sobering news is that while an increase in model complexity is needed to explain the available experimental data, testing and rejection of more complex models may require more quantitative data than is currently available.
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Ruiz A, Pauls E, Badia R, Riveira-Muñoz E, Clotet B, Ballana E, Esté JA. Characterization of the influence of mediator complex in HIV-1 transcription. J Biol Chem 2014; 289:27665-76. [PMID: 25100719 DOI: 10.1074/jbc.m114.570341] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
HIV-1 exploits multiple host proteins during infection. siRNA-based screenings have identified new proteins implicated in different pathways of the viral cycle that participate in a broad range of cellular functions. The human Mediator complex (MED) is composed of 28 elements and represents a fundamental component of the transcription machinery, interacting with the RNA polymerase II enzyme and regulating its ability to express genes. Here, we provide an evaluation of the MED activity on HIV replication. Knockdown of 9 out of 28 human MED proteins significantly impaired viral replication without affecting cell viability, including MED6, MED7, MED11, MED14, MED21, MED26, MED27, MED28, and MED30. Impairment of viral replication by MED subunits was at a post-integration step. Inhibition of early HIV transcripts was observed by siRNA-mediated knockdown of MED6, MED7, MED11, MED14, and MED28, specifically affecting the transcription of the nascent viral mRNA transactivation-responsive element. In addition, MED14 and MED30 were shown to have special relevance during the formation of unspliced viral transcripts (p < 0.0005). Knockdown of the selected MED factors compromised HIV transcription induced by Tat, with the strongest inhibitory effect shown by siMED6 and siMED14 cells. Co-immunoprecipitation experiments suggested physical interaction between MED14 and HIV-1 Tat protein. A better understanding of the mechanisms and factors controlling HIV-1 transcription is key to addressing the development of new strategies required to inhibit HIV replication or reactivate HIV-1 from the latent reservoirs.
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Affiliation(s)
- Alba Ruiz
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eduardo Pauls
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Roger Badia
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eva Riveira-Muñoz
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Bonaventura Clotet
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Ester Ballana
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - José A Esté
- From the AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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13
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Riveira-Muñoz E, Ruiz A, Pauls E, Permanyer M, Badia R, Mothe B, Crespo M, Clotet B, Brander C, Ballana E, Esté JA. Increased expression of SAMHD1 in a subset of HIV-1 elite controllers. J Antimicrob Chemother 2014; 69:3057-60. [PMID: 25063780 DOI: 10.1093/jac/dku276] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES SAMHD1 and the CDKN1A (p21) cyclin-dependent kinase inhibitor have been postulated to mediate HIV-1 restriction in CD4+ cells. We have shown that p21 affects HIV replication through its effect on SAMHD1. Thus, we aimed at evaluating the expression of SAMHD1 and p21 in different HIV+ phenotypic groups. PATIENTS AND METHODS We evaluated SAMHD1 and CDKN1A mRNA expression in CD4+ T cells from HIV+ individuals including elite controllers (n = 12), individuals who control HIV without the need for antiretroviral treatment, viraemic progressors (n = 10) and HIV-1 seronegative healthy donors (n = 14). Immunological variables were measured by flow cytometry. RESULTS We show that a subset of HIV+ elite controllers with lower T cell proliferation levels (Ki67+ cells) expressed higher SAMHD1 compared with healthy donors or viraemic progressors. Conversely, there was no difference in p21 expression before or after T cell activation with a bispecific CD3/CD8 antibody. CONCLUSIONS Our results suggest that SAMHD1 may play a role in controlling virus replication in HIV+ individuals and slow the rate of disease progression.
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Affiliation(s)
- Eva Riveira-Muñoz
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Alba Ruiz
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eduardo Pauls
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Marc Permanyer
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Roger Badia
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Beatriz Mothe
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Manel Crespo
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Bonaventura Clotet
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Christian Brander
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ester Ballana
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - José A Esté
- AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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Pollicita M, Surdo M, Di Santo F, Cortese MF, Fabeni L, Fedele V, Malet I, Marcelin AG, Calvez V, Ceccherini-Silberstein F, Perno CF, Svicher V. Comparative replication capacity of raltegravir-resistant strains and antiviral activity of the new-generation integrase inhibitor dolutegravir in human primary macrophages and lymphocytes. J Antimicrob Chemother 2014; 69:2412-9. [DOI: 10.1093/jac/dku144] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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15
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Herrera-Carrillo E, Paxton WA, Berkhout B. The search for a T cell line for testing novel antiviral strategies against HIV-1 isolates of diverse receptor tropism and subtype origin. J Virol Methods 2014; 203:88-96. [PMID: 24698763 DOI: 10.1016/j.jviromet.2014.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/18/2014] [Accepted: 03/21/2014] [Indexed: 11/16/2022]
Abstract
The world-wide HIV epidemic is characterized by increasing genetic diversity with multiple viral subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs). Antiretroviral drug design and basic virology studies have largely focused on HIV-1 subtype B. There have been few direct comparisons by subtype, perhaps due to the lack of uniform and standardized culture systems for the in vitro propagation of diverse HIV-1 subtypes. Although peripheral blood mononuclear cells (PBMCs) are major targets and reservoirs of HIV, PBMCs culturing is relatively difficult and not always reproducible. In addition, long-term experiments cannot be performed because PBMCs are short-lived cells. We faced these problems during the in vitro testing of an experimental RNA interference (RNAi) based gene therapy. Therefore, many T cell lines that support HIV-1 infection were tested and compared for replication of HIV-1 isolates, including viruses that use different receptors and diverse subtypes. The PM1 T cell line was comparable to PBMCs for culturing of any of the HIV-1 strains and subtypes. The advantage of PM1 cells in long-term cultures for testing the safety and efficacy of an RNAi-based gene therapy was demonstrated. PM1 may thus provide a valuable research tool for studying new anti-HIV therapies.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - William A Paxton
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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16
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Susceptibility to CD8 T-cell-mediated killing influences the reservoir of latently HIV-1-infected CD4 T cells. J Acquir Immune Defic Syndr 2014; 65:1-9. [PMID: 23846565 DOI: 10.1097/qai.0b013e3182a1bc81] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND HIV-1 establishes a lifelong infection in the human body, but host factors that influence viral persistence remain poorly understood. Cell-intrinsic characteristics of CD4 T cells, the main target cells for HIV-1, may affect the composition of the latent viral reservoir by altering the susceptibility to CD8 T-cell-mediated killing. RESULTS We observed that susceptibilities of CD4 T cells to CD8 T-cell-mediated killing, as determined in direct ex vivo assays, were significantly higher in persons with natural control of HIV-1 (elite controllers) than in individuals effectively treated with antiretroviral therapy. These differences were most pronounced in naive and in terminally differentiated CD4 T cells and corresponded to a reduced viral reservoir size in elite controllers. Interestingly, the highest susceptibility to CD8 T-cell-mediated killing and lowest reservoirs of cell-associated HIV-1 DNA was consistently observed in elite controllers expressing the protective HLA class I allele B57. CONCLUSIONS These data suggest that the functional responsiveness of host CD4 T cells to cytotoxic effects of HIV-1-specific CD8 T cells can contribute to shaping the structure and composition of the latently infected CD4 T-cell pool.
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17
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Abstract
Early studies of HIV infection dynamics suggested that virus-producing HIV-infected cells had an average half-life of approximately 1 day. However, whether this average behavior is reflective of the dynamics of individual infected cells is unclear. Here, we use HIV-enhanced green fluorescent protein (EGFP) constructs and flow cytometry sorting to explore the dynamics of cell infection, viral protein production, and cell death in vitro. By following the numbers of productively infected cells expressing EGFP over time, we show that infected cell death slows down over time. Although infected cell death in vivo could be very different, our results suggest that the constant decay of cell numbers observed in vivo during antiretroviral treatment could reflect a balance of cell death and delayed viral protein production. We observe no correlation between viral protein production and death rate of productively infected cells, showing that viral protein production is not likely to be the sole determinant of the death of HIV-infected cells. Finally, we show that all observed features can be reproduced by a simple model in which infected cells have broad distributions of productive life spans, times to start viral protein production, and viral protein production rates. This broad spectrum of the level and timing of viral protein production provides new insights into the behavior and characteristics of HIV-infected cells.
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18
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Telenti A. Host polymorphism in steps of the HIV-1 lifecycle after entry and other genetic variants influencing HIV-1 pathogenesis. Curr Opin HIV AIDS 2012; 1:232-40. [PMID: 19372815 DOI: 10.1097/01.coh.0000221598.79906.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Dominant host factors modifying the susceptibility to HIV-1 include diversity in the major histocompatibility complex class I, and alleles of chemokine and chemokine receptor genes. Additional host factors, particularly those determining cell permissiveness to viral replication, are expected to play a significant role in HIV-1 pathogenesis. RECENT FINDINGS A growing number of publications (n = 32) propose new variants (n = 27) modifying HIV-1 susceptibility in genes (n = 17) needed for the viral lifecycle, in antiviral innate defense, and in a number of soluble and membrane proteins. SUMMARY Although there are multiple publications describing putative associations of host genetic variants and susceptibility to HIV-1, most reports are yet to be confirmed by subsequent publications, or have led to conflicting data among laboratories.
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Affiliation(s)
- Amalio Telenti
- Institute of Microbiology and University Hospital, University of Lausanne, Lausanne, Switzerland
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19
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Host Genomic Profiling in Human Immunodeficiency Virus Infection. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Bol SM, Moerland PD, Limou S, van Remmerden Y, Coulonges C, van Manen D, Herbeck JT, Fellay J, Sieberer M, Sietzema JG, van 't Slot R, Martinson J, Zagury JF, Schuitemaker H, van 't Wout AB. Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS One 2011; 6:e17190. [PMID: 21364930 PMCID: PMC3045405 DOI: 10.1371/journal.pone.0017190] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/21/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART), macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. METHODOLOGY/PRINCIPAL FINDINGS Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96) or high (n = 96) p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16 × 10(-5)). While the association was not genome-wide significant (p<1 × 10(-7)), we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034). Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84 × 10(-6)). In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048). CONCLUSIONS/SIGNIFICANCE These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo.
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Affiliation(s)
- Sebastiaan M. Bol
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Perry D. Moerland
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center of the University of Amsterdam, The Netherlands
- Netherlands Bioinformatics Center (NBIC), Nijmegen, The Netherlands
| | - Sophie Limou
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Yvonne van Remmerden
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Cédric Coulonges
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Daniëlle van Manen
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jacques Fellay
- Center for Human Genome Variation, Duke University, Durham, North Carolina, United States of America
| | - Margit Sieberer
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Jantine G. Sietzema
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ruben van 't Slot
- Complex Genetics Section, Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeremy Martinson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jean-François Zagury
- Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
- Université Paris 12, INSERM U955, Paris, France
| | - Hanneke Schuitemaker
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van 't Wout
- Landsteiner Laboratory, Sanquin Research, Department of Experimental Immunology, and Center for Infection and Immunity Amsterdam (CINIMA) at the Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Rogers TF, Lim SY, Sundsvold TJ, Chan T, Hsu A, Letvin NL. Variability in a dominant block to SIV early reverse transcription in rhesus monkey cells predicts in vivo viral replication and time to death. Virol J 2010; 7:79. [PMID: 20416115 PMCID: PMC2874537 DOI: 10.1186/1743-422x-7-79] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 04/26/2010] [Indexed: 11/11/2022] Open
Abstract
While it has long been appreciated that there is considerable variability in host containment of HIV/SIV replication, the determinants of that variability are not fully understood. Previous studies demonstrated that the degree of permissivity of a macaque's peripheral blood mononuclear cells (PBMC) for infection with simian immunodeficiency virus (SIV) in vitro predicted that animal's peak plasma virus RNA levels following SIV infection in vivo. The present study was conducted to define the mechanisms underlying the variable intrinsic susceptibility of rhesus monkey PBMC to SIVsmE660 infection. In a cohort of 15 unrelated Indian-origin rhesus monkeys, infectability of PBMC of individual animals with SIVsmE660, as defined by tissue culture infectious dose (TCID50), varied by more than 3 logs and was a stable phenotype over time. Susceptibility of a monkey's PBMC to wild type SIVsmE660 infection correlated with the susceptibility of that monkey's PBMC to infection with VSV-G pseudotyped SIVsm543-GFP. Moreover, the permissivity of an individual monkey's PBMC for infection with this construct correlated with the permissivity of a B-lymphoblastoid cell line (B-LCL) generated from PBMC of the same animal. We found that the degree of intrinsic resistance of monkey B-LCL correlated with the copy number of early reverse transcription (ERT) SIV DNA. The resistance of monkey B-LCL to SIVsmE660 replication could be abrogated by preincubation of cells with the SIV virus-like particles (VLPs) and SIV resistance phenotype could be transferred to a SIV susceptible B-LCL through cell fusion. Finally, we observed a positive correlation between susceptibility of monkey B-LCL to SIV infection with a VSV-G pseudotyped SIV-GFP construct in vitro and both the peak plasma virus RNA levels in vivo and time to death following wild type SIV infection. These findings suggest that a dominant early RT restricting factor that can be saturated by SIV capsid may contribute to the variable resistance to SIV infection in rhesus monkey B-LCL and that this differential intrinsic susceptibility contributes to the clinical outcome of an SIV infection.
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Affiliation(s)
- Thomas F Rogers
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Bol SM, van Remmerden Y, Sietzema JG, Kootstra NA, Schuitemaker H, van't Wout AB. Donor variation in in vitro HIV-1 susceptibility of monocyte-derived macrophages. Virology 2009; 390:205-11. [PMID: 19535121 DOI: 10.1016/j.virol.2009.05.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 03/15/2009] [Accepted: 05/24/2009] [Indexed: 11/17/2022]
Abstract
Primary human cells from different donors vary in their susceptibility to in vitro infection with HIV-1. In order to perform genetic analysis to identify host factors that affect HIV-1 susceptibility, it is important that a clear phenotype is defined. Here, we report a standardized method to study variation for in vitro HIV-1 infection in monocyte-derived macrophages (MDM) from large numbers of individuals. With this assay, HIV-1 susceptibility of MDM from 489 different donors shows more than 3 log variation and a good correlation with the 32 base pair deletion in the CCR5 co-receptor (ccr5 Delta 32 genotype) of the donors. However, in 7 of 12 donors completely resistant to infection with CCR5-using HIV-1, this was not explained by the ccr5 Delta 32 genotype, showing evidence that other host factors are likely to influence HIV-1 replication in MDM. Infections with VSV-G pseudotyped HIV-1 indeed confirmed the existence of post-entry level restrictions in MDM.
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Affiliation(s)
- Sebastiaan M Bol
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center of The University of Amsterdam, Amsterdam, The Netherlands
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Chable-Bessia C, Meziane O, Latreille D, Triboulet R, Zamborlini A, Wagschal A, Jacquet JM, Reynes J, Levy Y, Saib A, Bennasser Y, Benkirane M. Suppression of HIV-1 replication by microRNA effectors. Retrovirology 2009; 6:26. [PMID: 19272132 PMCID: PMC2657893 DOI: 10.1186/1742-4690-6-26] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 03/09/2009] [Indexed: 12/31/2022] Open
Abstract
The rate of HIV-1 gene expression is a key step that determines the kinetics of virus spread and AIDS progression. Viral entry and gene expression were described to be the key determinants for cell permissiveness to HIV. Recent reports highlighted the involvement of miRNA in regulating HIV-1 replication post-transcriptionally. In this study we explored the role of cellular factors required for miRNA-mediated mRNA translational inhibition in regulating HIV-1 gene expression. Here we show that HIV-1 mRNAs associate and co-localize with components of the RNA Induced Silencing Complex (RISC), and we characterize some of the proteins required for miRNA-mediated silencing (miRNA effectors). RCK/p54, GW182, LSm-1 and XRN1 negatively regulate HIV-1 gene expression by preventing viral mRNA association with polysomes. Interestingly, knockdown of RCK/p54 or DGCR8 resulted in virus reactivation in PBMCs isolated from HIV infected patients treated with suppressive HAART.
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Affiliation(s)
- Christine Chable-Bessia
- Institut de Génétique Humaine CNRS UPR1142, Laboratoire de Virologie Moléculaire, Montpellier, France.
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Speelmon EC, Livingston-Rosanoff D, Desbien AL, Lee J, Wick WD, Hladik F, McElrath MJ. Impaired viral entry cannot explain reduced CD4+ T cell susceptibility to HIV type 1 in certain highly exposed individuals. AIDS Res Hum Retroviruses 2008; 24:1415-27. [PMID: 19000021 DOI: 10.1089/aid.2007.0256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rare individuals report repeated unprotected HIV-1 sexual exposures, yet remain seronegative for years. We investigated the possibility that reduced in vitro CD4(+) T cell susceptibility to HIV-1 infection protects such highly exposed seronegative (ES) individuals. Susceptibility to three R5-tropic HIV-1 isolates, regardless of inoculating dose, was remarkably similar between 81 ES and 33 low-risk controls. In 94% (99/105) of donors, we observed a 1.36 log-unit range in HIV-1(JR-CSF) production, with similar results for HIV-1(1192). The median frequency of intracellular Gag(+) T cells after single-round infection was similar in ES (5.2%) and controls (7.2%), p = 0.456. However, in repeated testing, CD4(+) T cells from two controls (6.1%) and four ES (4.9%) exhibited a 10- to 2500-fold reduction in HIV-1 production and required 5- to 12-fold greater HIV-1(1192) and HIV-1(JR-CSF) inocula to establish infection (TCID(50)). Reduced viral entry cannot explain the low producer phenotype; no differences in CCR5 receptor density or beta-chemokine production were observed. In conclusion, we have identified a remarkably narrow range of HIV-1 susceptibility in seronegative donors regardless of risk activity, which can be applied as a benchmark to assess vaccine-induced antiviral effector activities. However, CD4(+) T cells from a subset of individuals demonstrated reduced HIV-1 susceptibility unexplained by impaired entry, lending support to the possibility that cellular restriction of HIV-1 may account for continued seronegativity in some of those having repeated sexual exposure. Identifying the host-virus interactions responsible for diminished in vitro susceptibility may contribute to the development of novel therapeutic strategies.
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Affiliation(s)
- Emily C. Speelmon
- Medical Scientist Training Program, University of Washington, Seattle, Washington 98105
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98105
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Devon Livingston-Rosanoff
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Anthony L. Desbien
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Jean Lee
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - W. David Wick
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Florian Hladik
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98105
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington 98105
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26
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Anzinger JJ, Olinger GG, Spear GT. Donor variability in HIV binding to peripheral blood mononuclear cells. Virol J 2008; 5:95. [PMID: 18706090 PMCID: PMC2538508 DOI: 10.1186/1743-422x-5-95] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 08/15/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV infection of cells varies greatly between individuals, with multiple steps in the replication cycle potentially contributing to the variability. Although entry and post-entry variability of HIV infection levels in cells has been demonstrated, variability in HIV binding has not been examined. In this study, we examined variability of HIV binding to peripheral blood mononuclear cells (PBMC) from different donors. RESULTS HIV binding to PBMC varied up to 3.9-fold between individuals and was independent of CD4. Replication of HIV in donor PBMC required CD4 and paralleled virus binding trends of donor PBMC. To assess the stability of virus binding phenotypes over time, HIV was bound to donors with low- and high-binding phenotypes. The binding phenotypes were maintained when tested weekly over a 4-week period for 3 of 4 donors, while one high-binding donor decreased to lower binding on the 4th week. The low- and high-binding phenotypes were also preserved across different HIV strains. Experiments performed to determine if there was an association between HIV binding levels and specific cell subset levels within PBMC showed no correlation, suggesting that HIV binds to multiple cell subsets. CONCLUSION These results show that differences exist in HIV binding to donor PBMC. Our data also show that HIV binding to donor PBMC is CD4-independent and can change over time, suggesting that virus binding variability is due to differences in the expression of changeable cell-surface host factors. Taken together, this study highlights the impact of cell-surface factors in HIV binding to, and infection of, PBMC which likely represents an important step in HIV infection in vivo.
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Affiliation(s)
- Joshua J Anzinger
- Section of Experimental Atherosclerosis, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, Building 10, Room 5N111, Bethesda, Maryland 20892, USA.
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Al-Jabri AA, Lambkin R, Oxford JS. Lack of Evidence for Complete Resistance of Peripheral Blood Mononuclear Cells to HIV-1 and HIV-2 Infection. Viral Immunol 2008; 21:83-90. [DOI: 10.1089/vim.2007.0092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ali A. Al-Jabri
- SQU, Microbiology and Immunology, Muscat, Oman, University of London, London, U.K
| | - Robert Lambkin
- Medical Microbiology and Retroscreen Virology, University of London, London, U.K
| | - John S. Oxford
- Medical Microbiology and Retroscreen Virology, University of London, London, U.K
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Loeuillet C, Deutsch S, Ciuffi A, Robyr D, Taffé P, Muñoz M, Beckmann JS, Antonarakis SE, Telenti A. In vitro whole-genome analysis identifies a susceptibility locus for HIV-1. PLoS Biol 2008; 6:e32. [PMID: 18288889 PMCID: PMC2245987 DOI: 10.1371/journal.pbio.0060032] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 01/03/2008] [Indexed: 12/13/2022] Open
Abstract
Advances in large-scale analysis of human genomic variability provide unprecedented opportunities to study the genetic basis of susceptibility to infectious agents. We report here the use of an in vitro system for the identification of a locus on HSA8q24.3 associated with cellular susceptibility to HIV-1. This locus was mapped through quantitative linkage analysis using cell lines from multigeneration families, validated in vitro, and followed up by two independent association studies in HIV-positive individuals. Single nucleotide polymorphism rs2572886, which is associated with cellular susceptibility to HIV-1 in lymphoblastoid B cells and in primary T cells, was also associated with accelerated disease progression in one of two cohorts of HIV-1-infected patients. Biological analysis suggests a role of the rs2572886 region in the regulation of the LY6 family of glycosyl-phosphatidyl-inositol (GPI)-anchored proteins. Genetic analysis of in vitro cellular phenotypes provides an attractive approach for the discovery of susceptibility loci to infectious agents.
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Affiliation(s)
- Corinne Loeuillet
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Samuel Deutsch
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | | | - Miguel Muñoz
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jacques S Beckmann
- Department of Medical Genetics, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospital of Geneva, Geneva, Switzerland
| | - Amalio Telenti
- Institute of Microbiology, University Hospital, University of Lausanne, Lausanne, Switzerland
- Swiss HIV Cohort Study, Lausanne, Switzerland
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WFDC1/ps20 is a novel innate immunomodulatory signature protein of human immunodeficiency virus (HIV)-permissive CD4+ CD45RO+ memory T cells that promotes infection by upregulating CD54 integrin expression and is elevated in HIV type 1 infection. J Virol 2007; 82:471-86. [PMID: 17942534 DOI: 10.1128/jvi.00939-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Understanding why human immunodeficiency virus (HIV) preferentially infects some CD4(+) CD45RO(+) memory T cells has implications for antiviral immunity and pathogenesis. We report that differential expression of a novel secreted factor, ps20, previously implicated in tissue remodeling, may underlie why some CD4 T cells are preferentially targeted. We show that (i) there is a significant positive correlation between endogenous ps20 mRNA in diverse CD4 T-cell populations and in vitro infection, (ii) a ps20(+) permissive cell can be made less permissive by antibody blockade- or small-interference RNA-mediated knockdown of endogenous ps20, and (iii) conversely, a ps20(low) cell can be more permissive by adding ps20 exogenously or engineering stable ps20 expression by retroviral transduction. ps20 expression is normally detectable in CD4 T cells after in vitro activation and interleukin-2 expansion, and such oligoclonal populations comprise ps20(positive) and ps20(low/negative) isogenic clones at an early differentiation stage (CD45RO(+)/CD25(+)/CD28(+)/CD57(-)). This pattern is altered in chronic HIV infection, where ex vivo CD4(+) CD45RO(+) T cells express elevated ps20. ps20 promoted HIV entry via fusion and augmented CD54 integrin expression; both of these effects were reversed by anti-ps20 antibody. We therefore propose ps20 to be a novel signature of HIV-permissive CD4 T cells that promotes infection in an autocrine and paracrine manner and that HIV has coopted a fundamental role of ps20 in promoting cell adhesion for its benefit. Disrupting the ps20 pathway may therefore provide a novel anti-HIV strategy.
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30
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Lama J, Planelles V. Host factors influencing susceptibility to HIV infection and AIDS progression. Retrovirology 2007; 4:52. [PMID: 17651505 PMCID: PMC1978541 DOI: 10.1186/1742-4690-4-52] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 07/25/2007] [Indexed: 12/21/2022] Open
Abstract
Transmission of HIV first results in an acute infection, followed by an apparently asymptomatic period that averages ten years. In the absence of antiretroviral treatment, most patients progress into a generalized immune dysfunction that culminates in death. The length of the asymptomatic period varies, and in rare cases infected individuals never progress to AIDS. Other individuals whose behavioral traits put them at high-risk of HIV transmission, surprisingly appear resistant and never succumb to infection. These unique cases highlight the fact that susceptibility to HIV infection and progression to disease are complex traits modulated by environmental and genetic factors. Recent evidence has indicated that natural variations in host genes can influence the outcome of HIV infection and its transmission. In this review we summarize the available literature on the roles of cellular factors and their genetic variation in modulating HIV infection and disease progression.
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Affiliation(s)
- Juan Lama
- La Jolla Institute for Molecular Medicine, 4570 Executive Drive, Suite 100, San Diego, California 92121, USA
- RetroVirox, Inc. 4570 Executive Drive, Suite 100, San Diego, California 92121, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East #2100 – Room 2520, Salt Lake City, Utah 84112, USA
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31
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Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Goldstein DB. A whole-genome association study of major determinants for host control of HIV-1. Science 2007; 317:944-7. [PMID: 17641165 PMCID: PMC1991296 DOI: 10.1126/science.1143767] [Citation(s) in RCA: 971] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding why some people establish and maintain effective control of HIV-1 and others do not is a priority in the effort to develop new treatments for HIV/AIDS. Using a whole-genome association strategy, we identified polymorphisms that explain nearly 15% of the variation among individuals in viral load during the asymptomatic set-point period of infection. One of these is found within an endogenous retroviral element and is associated with major histocompatibility allele human leukocyte antigen (HLA)-B*5701, whereas a second is located near the HLA-C gene. An additional analysis of the time to HIV disease progression implicated two genes, one of which encodes an RNA polymerase I subunit. These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents.
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Affiliation(s)
- Jacques Fellay
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Kevin V. Shianna
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Dongliang Ge
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Sara Colombo
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases, University Hospital, 8091 Zürich, Switzerland
| | - Mike Weale
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Kunlin Zhang
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
| | - Curtis Gumbs
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico, San Raffaele Hospital, 20127 Milan, Italy
| | - Andrea Cossarizza
- Department of Biomedical Sciences, Section of General Pathology, University of Modena and Reggio Emilia, School of Medicine, 41100 Modena, Italy
| | - Alessandro Cozzi-Lepri
- Department of Primary Care and Population Sciences, Royal Free and University College Medical School, University College London, London NW3 2PF, UK
| | - Andrea De Luca
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Philippa Easterbrook
- Academic Department of HIV and Genitourinary Medicine, Kings College London, at Guy's, King's, and St. Thomas' Hospitals, London SE5 9RJ, UK
| | - Patrick Francioli
- Service of Infectious Diseases, Department of Medicine and Service of Hospital Preventive Medicine, University Hospital Center, 1011 Lausanne, Switzerland
| | - Simon Mallal
- Centre for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital; and Murdoch University, Perth, WA 6000, Australia
| | - Javier Martinez-Picado
- irsiCaixa Foundation and Hospital Germans Trias i Pujol, 08916 Badalona, Spain; and Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - José M. Miro
- Hospital Clinic–Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, 08036 Barcelona, Spain
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Jason P. Smith
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
| | - Josiane Wyniger
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
| | - Patrick Descombes
- Genomics Platform, National Centre of Competence in Research “Frontiers in Genetics,” University of Geneva, 1211 Geneva, Switzerland
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Norman L. Letvin
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew J. McMichael
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Amalio Telenti
- Institute of Microbiology, University Hospital Center; and University of Lausanne, 1011 Lausanne, Switzerland
- To whom correspondence should be addressed. E-mail: (A.T.); (D.B.G.)
| | - David B. Goldstein
- Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
- To whom correspondence should be addressed. E-mail: (A.T.); (D.B.G.)
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32
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Mok HP, Javed S, Lever A. Stable gene expression occurs from a minority of integrated HIV-1-based vectors: transcriptional silencing is present in the majority. Gene Ther 2007; 14:741-51. [PMID: 17330088 DOI: 10.1038/sj.gt.3302923] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human immunodeficiency virus (HIV)-based vectors are being increasingly used in vitro for gene transfer and in vivo for gene therapy. The proportion of integrated retroviral vectors that are silenced or remain transcriptionally active, and the stability of gene expression in the latter remains poorly explored. To study this, T cells were infected with an HIV-1-based vector construct containing a long terminal repeat-driven reporter gene. Only a small percentage of detectable integrated vector expressed gene product. In clones derived from cells with transcriptionally active vector, gene expression was remarkably stable with more than 80% continuing to express for greater than 18 months. Failure to continue expressing the vector was associated with epigenetic changes. Our data suggest that there are two forms of vector silencing: one occurring immediately after integration affecting the majority of the vectors, and one occurring in the much longer term affecting a small minority of vectors which had previously established expression.
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Affiliation(s)
- H P Mok
- Department of Medicine, University of Cambridge, Level 5, Addenbrooke's Hospital, Cambridge, UK
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33
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Adojaan M, Mölder T, Männik A, Kivisild T, Villems R, Krispin T, Ustav M. High prevalence of the CCR5Delta32 HIV-resistance mutation among Estonian HIV type 1-infected individuals. AIDS Res Hum Retroviruses 2007; 23:193-7. [PMID: 17331026 DOI: 10.1089/aid.2006.0113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this survey was to investigate human immunodeficiency virus type 1 (HIV-1) coreceptor, chemokine receptor 5 (CCR5), polymorphism among Estonian HIV-1-infected individuals. Homozygous CCR5Delta32 genotypes have been associated with resistance to HIV-1 infection; however, inconsistent evidence exists as to whether a single copy of a mutant allele among heterozygotes confers protection from HIV-1 infection. In an Estonian population the frequency of the CCR5Delta32 allele has been found to be among the greatest observed to date. Ironically, Estonia is concomitantly characterized by a very high HIV-1 prevalence. We compared the allele frequencies in a healthy control population to the HIV-positive group. The frequency of heterozygous individuals did not differ significantly between the HIV-positive group and the control population. Allele frequencies were analyzed among different risk groups as well as groups with different HIV genetic backgrounds. We did not find a difference between CCR5Delta32 allele frequencies among intravenous drug users (IDUs) and sexually infected persons. Likewise, the distribution of CCR5Delta32 allele frequencies among patients infected with different subtypes did not differ while data from "pure" subtypes A, B, and CRF06_cpx were pooled and evaluated against unique recombinant forms.
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Affiliation(s)
- Maarja Adojaan
- FIT Biotech Oyj Plc Eesti Filiaal, Institute of Molecular and Cell Biology, University of Tartu, Nooruse 9, Tartu 50411, Estonia
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Sáez-Cirión A, Versmisse P, Truong LX, Chakrabarti LA, Carpentier W, Barré-Sinoussi F, Scott-Algara D, Pancino G. Persistent resistance to HIV-1 infection in CD4 T cells from exposed uninfected Vietnamese individuals is mediated by entry and post-entry blocks. Retrovirology 2006; 3:81. [PMID: 17092330 PMCID: PMC1636660 DOI: 10.1186/1742-4690-3-81] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 11/08/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We have previously reported that CD4 T cells from some exposed uninfected (EU) Vietnamese intravenous drug users are relatively resistant to HIV infection in vitro. Here, we further characterized the restriction of viral replication in CD4 T cells from five EUs and assessed its persistence in serial samples. RESULTS CD4 T cells and/or PBMC sampled during a period of between 2 and 6 years were challenged with replication-competent HIV-1 and other retroviral particles pseudotyped with envelope proteins of various tropisms. CCR5 expression and function in resistant CD4 T cells was evaluated. The step at which HIV-1 replication is restricted was investigated by real-time PCR quantification of HIV-1 reverse transcripts. We identified three patterns of durable HIV-1 restriction in EU CD4 T cells. CD4 T cells from four of the five EU subjects were resistant to HIV-1 R5 infection. In two cases this resistance was associated with low CCR5 surface expression, which was itself associated with heterozygous CCR5 mutations. In the other two cases, CD4 T cells were resistant to HIV-1 R5 infection despite normal CCR5 expression and signaling function, and normal beta-chemokine secretion upon CD4 T cell activation. Instead, restriction appeared to be due to enhanced CD4 T cell sensitivity to beta-chemokines in these two subjects. In the fifth EU subject the restriction involved post-entry steps of viral replication and affected not only HIV-1 but also other lentiviruses. The restriction was not overcome by a high viral inoculum, suggesting that it was not mediated by a saturable inhibitory factor. CONCLUSION Various constitutive mechanisms of CD4 T cell resistance to HIV-1 infection, affecting entry or post-entry steps of viral replication, are associated with resistance to HIV-1 in subjects who remain uninfected despite long-term high-risk behavior.
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Affiliation(s)
- Asier Sáez-Cirión
- Unité de Régulation des Infections Rétrovirales, Institut Pasteur, Paris, France
| | - Pierre Versmisse
- Unité de Régulation des Infections Rétrovirales, Institut Pasteur, Paris, France
| | - Lien X Truong
- Retrovirology and Viral Hepatitis Laboratory, Institut Pasteur, Ho Chi Minh City, Vietnam
| | - Lisa A Chakrabarti
- Laboratoire de Pathogénie Virale Moléculaire, Institut Pasteur, Paris, France
- Unité d'Immunogénétique Cellulaire, Institut Pasteur, Paris, France
| | - Wassila Carpentier
- Laboratoire d'Immunologie Cellulaire, UR INSERM 543, Faculté de Médecine Pitié-Salpétrière, Paris, France
| | | | - Daniel Scott-Algara
- Unité de Régulation des Infections Rétrovirales, Institut Pasteur, Paris, France
| | - Gianfranco Pancino
- Unité de Régulation des Infections Rétrovirales, Institut Pasteur, Paris, France
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35
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Abstract
Genomics is now a core element in the effort to develop a vaccine against HIV-1. Thanks to unprecedented progress in high-throughput genotyping and sequencing, in knowledge about genetic variation in humans, and in evolutionary genomics, it is finally possible to systematically search the genome for common genetic variants that influence the human response to HIV-1. The identification of such variants would help to determine which aspects of the response to the virus are the most promising targets for intervention. However, a key obstacle to progress remains the scarcity of appropriate human cohorts available for genomic research.
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Affiliation(s)
- Amalio Telenti
- Institute of Microbiology, University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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36
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Agarwal S, Nikolai B, Yamaguchi T, Lech P, Somia NV. Construction and use of retroviral vectors encoding the toxic gene barnase. Mol Ther 2006; 14:555-63. [PMID: 16814610 DOI: 10.1016/j.ymthe.2006.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 02/28/2006] [Accepted: 03/20/2006] [Indexed: 01/23/2023] Open
Abstract
Suicide genes for negative selection of cells have been powerful tools in somatic cell genetic studies and in gene therapy. Here we report on the construction, characterization, and utilization of retroviral vectors encoding barnase, a ribonuclease from Bacillus amyloliquefaciens, expression of which results in apoptosis of transduced mammalian cells. High-titer viral vector production was enabled by expression of an inhibitor of barnase (barstar) in transfected cells generating murine leukemia virus (MLV)- and HIV-1-based vectors. To identify cellular genes required for infection we used barnase-encoding vectors in a genetic screen to isolate mutant mammalian cells that are resistant to infection by MLV and HIV-1. We describe one such mutant clone that is inhibited in the infection process after reverse transcription. These results suggest that barnase-encoding vectors should be useful for negative selection strategies examining retroviral infection from entry to integration. Furthermore these vectors could have utility in approaches for gene therapy that require specific cell ablation.
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Affiliation(s)
- Sumit Agarwal
- Department of Genetics, Cell Biology, and Development, Institute of Human Genetics, University of Minnesota, 420 Delaware Street SE, MMC 206, Minneapolis, MN 55455, USA
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Bleiber G, May M, Martinez R, Meylan P, Ott J, Beckmann JS, Telenti A. Use of a combined ex vivo/in vivo population approach for screening of human genes involved in the human immunodeficiency virus type 1 life cycle for variants influencing disease progression. J Virol 2005; 79:12674-80. [PMID: 16188970 PMCID: PMC1235818 DOI: 10.1128/jvi.79.20.12674-12680.2005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Humans differ substantially with respect to susceptibility to human immunodeficiency virus type 1 (HIV-1). We evaluated variants of nine host genes participating in the viral life cycle for their role in modulating HIV-1 infection. Alleles were assessed ex vivo for their impact on viral replication in purified CD4 T cells from healthy blood donors (n = 128). Thereafter, candidate alleles were assessed in vivo in a cohort of HIV-1-infected individuals (n = 851) not receiving potent antiretroviral therapy. As a benchmark test, we tested 12 previously reported host genetic variants influencing HIV-1 infection as well as single nucleotide polymorphisms in the nine candidate genes. This led to the proposition of three alleles of PML, TSG101, and PPIA as potentially associated with differences in progression of HIV-1 disease. In a model considering the combined effects of new and previously reported gene variants, we estimated that their effect might be responsible for lengthening or shortening by up to 2.8 years the period from 500 CD4 T cells/mul to <200 CD4 T cells/mul.
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38
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Karlsson I, Grivel JC, Chen SS, Karlsson A, Albert J, Fenyö EM, Margolis LB. Differential pathogenesis of primary CCR5-using human immunodeficiency virus type 1 isolates in ex vivo human lymphoid tissue. J Virol 2005; 79:11151-60. [PMID: 16103166 PMCID: PMC1193585 DOI: 10.1128/jvi.79.17.11151-11160.2005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the course of human immunodeficiency virus (HIV) disease, CCR5-utilizing HIV type 1 (HIV-1) variants (R5), which typically transmit infection and dominate its early stages, persist in approximately half of the infected individuals (nonswitch virus patients), while in the other half (switch virus patients), viruses using CXCR4 (X4 or R5X4) emerge, leading to rapid disease progression. Here, we used a system of ex vivo tonsillar tissue to compare the pathogeneses of sequential primary R5 HIV-1 isolates from patients in these two categories. The absolute replicative capacities of HIV-1 isolates seemed to be controlled by tissue factors. In contrast, the replication level hierarchy among sequential isolates and the levels of CCR5(+) CD4(+) T-cell depletion caused by the R5 isolates seemed to be controlled by viral factors. R5 viruses isolated from nonswitch virus patients depleted more target cells than R5 viruses isolated from switch virus patients. The high depletion of CCR5(+) cells by HIV-1 isolates from nonswitch virus patients may explain the steady decline of CD4(+) T cells in patients with continuous dominance of R5 HIV-1. The level of R5 pathogenicity, as measured in ex vivo lymphoid tissue, may have a predictive value reflecting whether, in an infected individual, X4 HIV-1 will eventually dominate.
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Affiliation(s)
- Ingrid Karlsson
- Unit of Virology, Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Sweden.
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Rose KM, Marin M, Kozak SL, Kabat D. Regulated production and anti-HIV type 1 activities of cytidine deaminases APOBEC3B, 3F, and 3G. AIDS Res Hum Retroviruses 2005; 21:611-9. [PMID: 16060832 DOI: 10.1089/aid.2005.21.611] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
APOBEC3G and 3F (A3G and A3F) cytidine deaminases incorporate into retroviral cores where they lethally hypermutate nascent DNA reverse transcripts. As substantiated here, the viral infectivity factor (Vif) encoded by human immunodeficiency virus type-1 (HIV-1) binds A3G and A3F and induces their degradation, thereby precluding their incorporation into viral progeny. Previous evidence suggested that A3G is expressed in H9 and other nonpermissive cells that contain this antiviral defense but not in several permissive cells, and that overexpression of A3G or A3F makes permissive cells nonpermissive. Using a broader panel of cell lines, we confirmed a correlation between A3G and cellular abilities to inactivate HIV-1(Deltavif). However, there was a quantitative discrepancy because several cells with weak antiviral activities had similar amounts of wild-type A3G mRNA and protein compared to H9 cells. Antiviral activity of H9 cells was also attenuated in some conditions. These quantitative discrepancies could not be explained by the presence of A3F or other A3G paralogs in some of the cell lines. Thus, A3A, A3B, and A3C had weak but significant anti-HIV-1 activities and did not dominantly interfere with A3G or A3F antiviral functions. Control of A3G synthesis by the protein kinase C/mitogen-activated protein kinase kinase/extracellular signal-regulated kinase pathway was also similar in permissive and nonpermissive cells. A3G in highly permissive cells is degraded by Vif, suggesting that it is not in a sequestered site, and is specifically incorporated in low amounts into HIV-1(Deltavif). Although A3G and/or A3F inactivate HIV-1(Deltavif) and are neutralized by Vif, the antiviral properties of cell lines are also influenced by other cellular and viral factors.
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Affiliation(s)
- Kristine M Rose
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098, USA
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