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Arman MS, Hasan MZ. A computational exploration of global and temporal dynamics of selection pressure on HIV-1 Vif polymorphism. Virus Res 2024; 341:199323. [PMID: 38237808 PMCID: PMC10831783 DOI: 10.1016/j.virusres.2024.199323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Virion infectivity factor (Vif), an accessory protein of HIV-1 (human immunodeficiency virus type 1), antagonizes host APOBEC3 protein (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3) or A3 via proteasomal degradation, facilitating viral replication. HLA (Human leukocyte antigens) alleles, host restriction factors, and error-prone reverse transcription contribute to the global polymorphic dynamics of HIV, impacting effective vaccine design. Our computational analysis of over 50,000 HIV-1 M vif sequences from the Los Alamos National Laboratory (LANL) database (1998-2021) revealed positive selection pressure on the vif gene (nonsynonymous to synonymous ratio, dn/ds=1.58) and an average entropy score of 0.372 in protein level. Interestingly, over the years (1998-2021), a decreasing trend of dn/ds (1.68 to 1.47) and an increasing trend of entropy (0.309 to 0.399) was observed. The predicted mutational frequency against Vif consensus sequence decreased over time (slope = -0.00024, p < 0.0001). Sequence conservation was observed in Vif functional motifs F1, F2, F3, G, BC box, and CBF β binding region, while variability was observed mainly in N- and C- terminal and Zinc finger region, which were dominantly under immune pressure by host HLA-I-restricted CD8+ T cell. Computational analysis of ∆∆Gstability through protein stability prediction tools suggested that missense mutation may affect Vif stability, especially in the Vif-A3 binding interface. Notably, mutations R17K and Y44F in F1 and G box were predicted to destabilize the Vif-A3 binding interface by altering bond formations with adjacent amino acids. Therefore, our analysis demonstrates Vif adaptation with host physiology by maintaining sequence conservation, especially in A3 interacting functional motifs, highlighting important therapeutic candidate regions of Vif against HIV-1 infections.
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Affiliation(s)
- Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md Zafrul Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
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2
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Cochrane CR, Angelovich TA, Byrnes SJ, Waring E, Guanizo AC, Trollope GS, Zhou J, Vue J, Senior L, Wanicek E, Eddine JJ, Gartner MJ, Jenkins TA, Gorry PR, Brew BJ, Lewin SR, Estes JD, Roche M, Churchill MJ. Intact HIV Proviruses Persist in the Brain Despite Viral Suppression with ART. Ann Neurol 2022; 92:532-544. [PMID: 35867351 PMCID: PMC9489665 DOI: 10.1002/ana.26456] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Human immunodeficiency virus (HIV) persistence in blood and tissue reservoirs, including the brain, is a major barrier to HIV cure and possible cause of comorbid disease. However, the size and replication competent nature of the central nervous system (CNS) reservoir is unclear. Here, we used the intact proviral DNA assay (IPDA) to provide the first quantitative assessment of the intact and defective HIV reservoir in the brain of people with HIV (PWH). METHODS Total, intact, and defective HIV proviruses were measured in autopsy frontal lobe tissue from viremic (n = 18) or virologically suppressed (n = 12) PWH. Total or intact/defective proviruses were measured by detection of HIV pol or the IPDA, respectively, through use of droplet digital polymerase chain reaction (ddPCR). HIV-seronegative individuals were included as controls (n = 6). RESULTS Total HIV DNA was present at similar levels in brain tissues from untreated viremic and antiretroviral (ART)-suppressed individuals (median = 22.3 vs 26.2 HIV pol copies/106 cells), reflecting a stable CNS reservoir of HIV that persists despite therapy. Furthermore, 8 of 10 viremic and 6 of 9 virally suppressed PWH also harbored intact proviruses in the CNS (4.63 vs 12.7 intact copies/106 cells). Viral reservoirs in CNS and matched lymphoid tissue were similar in the composition of intact and/or defective proviruses, albeit at lower levels in the brain. Importantly, CNS resident CD68+ myeloid cells in virally suppressed individuals harbored HIV DNA, directly showing the presence of a CNS resident HIV reservoir. INTERPRETATION Our results demonstrate the first evidence for an intact, potentially replication competent HIV reservoir in the CNS of virally suppressed PWH. ANN NEUROL 2022;92:532-544.
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Affiliation(s)
- Catherine R. Cochrane
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of MedicineThe Royal Melbourne Hospital, The University of MelbourneMelbourneVICAustralia
| | - Thomas A. Angelovich
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Life SciencesBurnet InstituteMelbourneVICAustralia,Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Sarah J. Byrnes
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Emily Waring
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of MedicineThe Royal Melbourne Hospital, The University of MelbourneMelbourneVICAustralia
| | - Aleks C. Guanizo
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Gemma S. Trollope
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of MedicineThe Royal Melbourne Hospital, The University of MelbourneMelbourneVICAustralia
| | - Jingling Zhou
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Judith Vue
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Lachlan Senior
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Emma Wanicek
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Janna Jamal Eddine
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Matthew J. Gartner
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Trisha A. Jenkins
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia
| | - Paul R. Gorry
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of Infectious DiseasesAlfred Hospital and Monash UniversityMelbourneVICAustralia,Department of Microbiology and ImmunologyThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Bruce J. Brew
- Peter Duncan Neurosciences Unit, Departments of Neurology and Immunology St Vincent's HospitalSydney, University of New South Wales and University of Notre DameSydneyNew South WalesAustralia
| | - Sharon R. Lewin
- Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia,Department of Infectious DiseasesAlfred Hospital and Monash UniversityMelbourneVICAustralia,Victorian Infectious Diseases ServiceRoyal Melbourne Hospital at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon National Primate Research CentreOregon Health & Science UniversityPortlandORUSA
| | - Michael Roche
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Department of Infectious DiseasesThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
| | - Melissa J. Churchill
- Emerging Infections Program, School of Health and Biomedical SciencesRMIT UniversityMelbourneVICAustralia,Life SciencesBurnet InstituteMelbourneVICAustralia,Departments of Microbiology and MedicineMonash UniversityMelbourneVICAustralia
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3
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Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021; 13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
Abstract
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic.
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Affiliation(s)
| | - Dominique Fournelle
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jana Schockaert
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | | | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Fatima Mostefai
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - Frederic Saab
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | | | - Martin A Smith
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Sofie Pattijn
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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4
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Ikeda T, Yue Y, Shimizu R, Nasser H. Potential Utilization of APOBEC3-Mediated Mutagenesis for an HIV-1 Functional Cure. Front Microbiol 2021; 12:686357. [PMID: 34211449 PMCID: PMC8239295 DOI: 10.3389/fmicb.2021.686357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The introduction of combination antiretroviral therapy (cART) has managed to control the replication of human immunodeficiency virus type 1 (HIV-1) in infected patients. However, a complete HIV-1 cure, including a functional cure for or eradication of HIV-1, has yet to be achieved because of the persistence of latent HIV-1 reservoirs in adherent patients. The primary source of these viral reservoirs is integrated proviral DNA in CD4+ T cells and other non-T cells. Although a small fraction of this proviral DNA is replication-competent and contributes to viral rebound after the cessation of cART, >90% of latent viral reservoirs are replication-defective and some contain high rates of G-to-A mutations in proviral DNA. At least in part, these high rates of G-to-A mutations arise from the APOBEC3 (A3) family proteins of cytosine deaminases. A general model has shown that the HIV-1 virus infectivity factor (Vif) degrades A3 family proteins by proteasome-mediated pathways and inactivates their antiviral activities. However, Vif does not fully counteract the HIV-1 restriction activity of A3 family proteins in vivo, as indicated by observations of A3-mediated G-to-A hypermutation in the proviral DNA of HIV-1-infected patients. The frequency of A3-mediated hypermutation potentially contributes to slower HIV-1/AIDS disease progression and virus evolution including the emergence of cytotoxic T lymphocyte escape mutants. Therefore, combined with other strategies, the manipulation of A3-mediated mutagenesis may contribute to an HIV-1 functional cure aimed at cART-free remission. In this mini-review, we discuss the possibility of an HIV-1 functional cure arising from manipulation of A3 mutagenic activity.
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Affiliation(s)
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Yuan Yue
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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5
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Gaba A, Flath B, Chelico L. Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses. Viruses 2021; 13:1084. [PMID: 34200141 PMCID: PMC8228377 DOI: 10.3390/v13061084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The transmission of viruses from animal hosts into humans have led to the emergence of several diseases. Usually these cross-species transmissions are blocked by host restriction factors, which are proteins that can block virus replication at a specific step. In the natural virus host, the restriction factor activity is usually suppressed by a viral antagonist protein, but this is not the case for restriction factors from an unnatural host. However, due to ongoing viral evolution, sometimes the viral antagonist can evolve to suppress restriction factors in a new host, enabling cross-species transmission. Here we examine the classical case of this paradigm by reviewing research on APOBEC3 restriction factors and how they can suppress human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). APOBEC3 enzymes are single-stranded DNA cytidine deaminases that can induce mutagenesis of proviral DNA by catalyzing the conversion of cytidine to promutagenic uridine on single-stranded viral (-)DNA if they escape the HIV/SIV antagonist protein, Vif. APOBEC3 degradation is induced by Vif through the proteasome pathway. SIV has been transmitted between Old World Monkeys and to hominids. Here we examine the adaptations that enabled such events and the ongoing impact of the APOBEC3-Vif interface on HIV in humans.
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Affiliation(s)
- Amit Gaba
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
| | - Ben Flath
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
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6
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Human TRIM5α: Autophagy Connects Cell-Intrinsic HIV-1 Restriction and Innate Immune Sensor Functioning. Viruses 2021; 13:v13020320. [PMID: 33669846 PMCID: PMC7923229 DOI: 10.3390/v13020320] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) persists as a global health concern, with an incidence rate of approximately 2 million, and estimated global prevalence of over 35 million. Combination antiretroviral treatment is highly effective, but HIV-1 patients that have been treated still suffer from chronic inflammation and residual viral replication. It is therefore paramount to identify therapeutically efficacious strategies to eradicate viral reservoirs and ultimately develop a cure for HIV-1. It has been long accepted that the restriction factor tripartite motif protein 5 isoform alpha (TRIM5α) restricts HIV-1 infection in a species-specific manner, with rhesus macaque TRIM5α strongly restricting HIV-1, and human TRIM5α having a minimal restriction capacity. However, several recent studies underscore human TRIM5α as a cell-dependent HIV-1 restriction factor. Here, we present an overview of the latest research on human TRIM5α and propose a novel conceptualization of TRIM5α as a restriction factor with a varied portfolio of antiviral functions, including mediating HIV-1 degradation through autophagy- and proteasome-mediated mechanisms, and acting as a viral sensor and effector of antiviral signaling. We have also expanded on the protective antiviral roles of autophagy and outline the therapeutic potential of autophagy modulation to intervene in chronic HIV-1 infection.
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7
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Granadillo Rodríguez M, Flath B, Chelico L. The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead. Open Biol 2020; 10:200188. [PMID: 33292100 PMCID: PMC7776566 DOI: 10.1098/rsob.200188] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse 'off-target' cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the APOBEC 'off-target' activity are overexpression in a non-normal cell type, nuclear localization and replication stress. The resulting uracil-induced mutations contribute to genomic variation, which may result in neutral, beneficial or harmful consequences for the cancer. This review summarizes the functional and biochemical basis of the APOBEC3 enzyme activity and highlights their relationship with the most well-studied cancers in this particular context such as breast, lung, bladder, and human papillomavirus-associated cancers. We focus on APOBEC3A, APOBEC3B and APOBEC3H haplotype I because they are the leading candidates as sources of somatic mutations in these and other cancers. Also, we discuss the prognostic value of the APOBEC3 expression in drug resistance and response to therapies.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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8
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Hopfensperger K, Richard J, Stürzel CM, Bibollet-Ruche F, Apps R, Leoz M, Plantier JC, Hahn BH, Finzi A, Kirchhoff F, Sauter D. Convergent Evolution of HLA-C Downmodulation in HIV-1 and HIV-2. mBio 2020; 11:e00782-20. [PMID: 32665270 PMCID: PMC7360927 DOI: 10.1128/mbio.00782-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
HLA-C-mediated antigen presentation induces the killing of human immunodeficiency virus (HIV)-infected CD4+ T cells by cytotoxic T lymphocytes (CTLs). To evade killing, many HIV-1 group M strains decrease HLA-C surface levels using their accessory protein Vpu. However, some HIV-1 group M isolates lack this activity, possibly to prevent the activation of natural killer (NK) cells. Analyzing diverse primate lentiviruses, we found that Vpu-mediated HLA-C downregulation is not limited to pandemic group M but is also found in HIV-1 groups O and P as well as several simian immunodeficiency viruses (SIVs). We show that Vpu targets HLA-C primarily at the protein level, independently of its ability to suppress NF-κB-driven gene expression, and that in some viral lineages, HLA-C downregulation may come at the cost of efficient counteraction of the restriction factor tetherin. Remarkably, HIV-2, which does not carry a vpu gene, uses its accessory protein Vif to decrease HLA-C surface expression. This Vif activity requires intact binding sites for the Cullin5/Elongin ubiquitin ligase complex but is separable from its ability to counteract APOBEC3G. Similar to HIV-1 Vpu, the degree of HIV-2 Vif-mediated HLA-C downregulation varies considerably among different virus isolates. In agreement with opposing selection pressures in vivo, we show that the reduction of HLA-C surface levels by HIV-2 Vif is accompanied by increased NK cell-mediated killing. In summary, our results highlight the complex role of HLA-C in lentiviral infections and demonstrate that HIV-1 and HIV-2 have evolved at least two independent mechanisms to decrease HLA-C levels on infected cells.IMPORTANCE Genome-wide association studies suggest that HLA-C expression is a major determinant of viral load set points and CD4+ T cell counts in HIV-infected individuals. On the one hand, efficient HLA-C expression enables the killing of infected cells by cytotoxic T lymphocytes (CTLs). On the other hand, HLA-C sends inhibitory signals to natural killer (NK) cells and enhances the infectivity of newly produced HIV particles. HIV-1 group M viruses modulate HLA-C expression using the accessory protein Vpu, possibly to balance CTL- and NK cell-mediated immune responses. Here, we show that the second human immunodeficiency virus, HIV-2, can use its accessory protein Vif to evade HLA-C-mediated restriction. Furthermore, our mutational analyses provide insights into the underlying molecular mechanisms. In summary, our results reveal how the two human AIDS viruses modulate HLA-C, a key component of the antiviral immune response.
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Affiliation(s)
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, Maryland, USA
| | - Marie Leoz
- Normandie Université, UNIROUEN, UNICAEN, GRAM 2.0, Rouen, France
| | - Jean-Christophe Plantier
- Normandie Université, UNIROUEN, UNICAEN, GRAM 2.0, Rouen University Hospital, Department of Virology, Laboratory Associated with the National Reference Center on HIV, Rouen, France
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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9
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Antar AA, Jenike KM, Jang S, Rigau DN, Reeves DB, Hoh R, Krone MR, Keruly JC, Moore RD, Schiffer JT, Nonyane BA, Hecht FM, Deeks SG, Siliciano JD, Ho YC, Siliciano RF. Longitudinal study reveals HIV-1-infected CD4+ T cell dynamics during long-term antiretroviral therapy. J Clin Invest 2020; 130:3543-3559. [PMID: 32191639 PMCID: PMC7324206 DOI: 10.1172/jci135953] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Proliferation of CD4+ T cells harboring HIV-1 proviruses is a major contributor to viral persistence in people on antiretroviral therapy (ART). To determine whether differential rates of clonal proliferation or HIV-1-specific cytotoxic T lymphocyte (CTL) pressure shape the provirus landscape, we performed an intact proviral DNA assay (IPDA) and obtained 661 near-full-length provirus sequences from 8 individuals with suppressed viral loads on ART at time points 7 years apart. We observed slow decay of intact proviruses but no changes in the proportions of various types of defective proviruses. The proportion of intact proviruses in expanded clones was similar to that of defective proviruses in clones. Intact proviruses observed in clones did not have more escaped CTL epitopes than intact proviruses observed as singlets. Concordantly, total proviruses at later time points or observed in clones were not enriched in escaped or unrecognized epitopes. Three individuals with natural control of HIV-1 infection (controllers) on ART, included because controllers have strong HIV-1-specific CTL responses, had a smaller proportion of intact proviruses but a distribution of defective provirus types and escaped or unrecognized epitopes similar to that of the other individuals. This work suggests that CTL selection does not significantly check clonal proliferation of infected cells or greatly alter the provirus landscape in people on ART.
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Affiliation(s)
- Annukka A.R. Antar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katharine M. Jenike
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sunyoung Jang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Danielle N. Rigau
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Melissa R. Krone
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Jeanne C. Keruly
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Bareng A.S. Nonyane
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Howard Hughes Medical Institute, Baltimore, Maryland, USA
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10
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Amorim CF, Novais FO, Nguyen BT, Misic AM, Carvalho LP, Carvalho EM, Beiting DP, Scott P. Variable gene expression and parasite load predict treatment outcome in cutaneous leishmaniasis. Sci Transl Med 2019; 11:eaax4204. [PMID: 31748229 PMCID: PMC7068779 DOI: 10.1126/scitranslmed.aax4204] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
Abstract
Patients infected with Leishmania braziliensis develop chronic lesions that often fail to respond to treatment with antiparasite drugs. To determine whether genes whose expression is highly variable in lesions between patients might influence disease outcome, we obtained biopsies of lesions from patients before treatment with pentavalent antimony and performed transcriptomic profiling on these clinical samples. We identified genes that were highly variably expressed between patients, and the variable expression of these genes correlated with treatment outcome. Among the most variable genes in all the patients were components of the cytolytic pathway, and the expression of these genes correlated with parasite load in the skin. We demonstrated that treatment failure was linked to the cytolytic pathway activated during infection. Using a host-pathogen marker profile of as few as three genes, we showed that eventual treatment outcome could be predicted before the start of treatment in two separate cohorts of patients with cutaneous leishmaniasis (n = 21 and n = 25). These findings raise the possibility of point-of-care diagnostic screening to identify patients at high risk of treatment failure and provide a rationale for a precision medicine approach to drug selection in cutaneous leishmaniasis. This work more broadly demonstrates the value of identifying genes of high variability in other diseases to better understand and predict diverse clinical outcomes.
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Affiliation(s)
- Camila Farias Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Fernanda O Novais
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Ba T Nguyen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Ana M Misic
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA
| | - Lucas P Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia 40110-060, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, 40296-710, Brazil
| | - Edgar M Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia 40110-060, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, 40296-710, Brazil
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA.
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, PA 19104-4539, USA.
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11
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Interplay between Intrinsic and Innate Immunity during HIV Infection. Cells 2019; 8:cells8080922. [PMID: 31426525 PMCID: PMC6721663 DOI: 10.3390/cells8080922] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Restriction factors are antiviral components of intrinsic immunity which constitute a first line of defense by blocking different steps of the human immunodeficiency virus (HIV) replication cycle. In immune cells, HIV infection is also sensed by several pattern recognition receptors (PRRs), leading to type I interferon (IFN-I) and inflammatory cytokines production that upregulate antiviral interferon-stimulated genes (ISGs). Several studies suggest a link between these two types of immunity. Indeed, restriction factors, that are generally interferon-inducible, are able to modulate immune responses. This review highlights recent knowledge of the interplay between restriction factors and immunity inducing antiviral defenses. Counteraction of this intrinsic and innate immunity by HIV viral proteins will also be discussed.
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12
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Schönfeld M, Knackmuss U, Chandorkar P, Hörtnagl P, Hope TJ, Moris A, Bellmann-Weiler R, Lass-Flörl C, Posch W, Wilflingseder D. Co- but not Sequential Infection of DCs Boosts Their HIV-Specific CTL-Stimulatory Capacity. Front Immunol 2019; 10:1123. [PMID: 31178863 PMCID: PMC6542955 DOI: 10.3389/fimmu.2019.01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 05/02/2019] [Indexed: 11/27/2022] Open
Abstract
Pathogenic bacteria and their microbial products activate dendritic cells (DCs) at mucosal surfaces during sexually transmitted infections (STIs) and therefore might also differently shape DC functions during co-infection with HIV-1. We recently illustrated that complement (C) coating of HIV-1 (HIV-C), as primarily found during the acute phase of infection before appearance of HIV-specific antibodies, by-passed SAMHD1-mediated restriction in DCs and therefore mediated an increased DC activation and antiviral capacity. To determine whether the superior antiviral effects of HIV-C-exposed DCs also apply during STIs, we developed a co-infection model in which DCs were infected with Chlamydia spp. simultaneously (HIV-C/Chlam-DCs or HIV/Chlam-DCs) or a sequential infection model, where DCs were exposed to Chlamydia for 3 or 24 h (Chlam-DCs) followed by HIV-1 infection. Co-infection of DCs with HIV-1 and Chlamydia significantly boosted the CTL-stimulatory capacity compared to HIV-1-loaded iDCs and this boost was independent on the opsonization pattern. This effect was lost in the sequential infection model, when opsonized HIV-1 was added delayed to Chlamydia-loaded DCs. The reduction in the CTL-stimulatory capacity of Chlam-DCs was not due to lower HIV-1 binding or infection compared to iDCs or HIV-C/Chlam-DCs, but due to altered fusion and internalization mechanisms within DCs. The CTL-stimulatory capacity of HIV-C in Chlam-DCs correlated with significantly reduced viral fusion compared to iDCs and HIV-C/Chlam-DCs and illustrated considerably increased numbers of HIV-C-containing vacuoles than iDCs. The data indicate that Chlamydia co-infection of DCs mediates a transient boost of their HIV-specific CTL-stimulatory and antiviral capacity, while in the sequential infection model this is reversed and associated with hazard to the host.
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Affiliation(s)
- Manuela Schönfeld
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ulla Knackmuss
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Parul Chandorkar
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Paul Hörtnagl
- Central Institute for Blood Transfusion and Immunological Department, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas John Hope
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Arnaud Moris
- Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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13
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Role of co-expressed APOBEC3F and APOBEC3G in inducing HIV-1 drug resistance. Heliyon 2019; 5:e01498. [PMID: 31025011 PMCID: PMC6475876 DOI: 10.1016/j.heliyon.2019.e01498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023] Open
Abstract
The APOBEC3 enzymes can induce mutagenesis of HIV-1 proviral DNA through the deamination of cytosine. HIV-1 overcomes this restriction through the viral protein Vif that induces APOBEC3 proteasomal degradation. Within this dynamic host-pathogen relationship, the APOBEC3 enzymes have been found to be beneficial, neutral, or detrimental to HIV-1 biology. Here, we assessed the ability of co-expressed APOBEC3F and APOBEC3G to induce HIV-1 resistance to antiviral drugs. We found that co-expression of APOBEC3F and APOBEC3G enabled partial resistance of APOBEC3F to Vif-mediated degradation with a corresponding increase in APOBEC3F-induced deaminations in the presence of Vif, in addition to APOBEC3G-induced deaminations. We recovered HIV-1 drug resistant variants resulting from APOBEC3-induced mutagenesis, but these variants were less able to replicate than drug resistant viruses derived from RT-induced mutations alone. The data support a model in which APOBEC3 enzymes cooperate to restrict HIV-1, promoting viral inactivation over evolution to drug resistance.
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14
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Borzooee F, Joris KD, Grant MD, Larijani M. APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome. Front Immunol 2019; 9:3032. [PMID: 30687306 PMCID: PMC6338068 DOI: 10.3389/fimmu.2018.03032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022] Open
Abstract
APOBEC3G (A3G) is a host enzyme that mutates the genomes of retroviruses like HIV. Since A3G is expressed pre-infection, it has classically been considered an agent of innate immunity. We and others previously showed that the impact of A3G-induced mutations on the HIV genome extends to adaptive immunity also, by generating cytotoxic T cell (CTL) escape mutations. Accordingly, HIV genomic sequences encoding CTL epitopes often contain A3G-mutable “hotspot” sequence motifs, presumably to channel A3G action toward CTL escape. Here, we studied the depths and consequences of this apparent viral genome co-evolution with A3G. We identified all potential CTL epitopes in Gag, Pol, Env, and Nef restricted to several HLA class I alleles. We simulated A3G-induced mutations within CTL epitope-encoding sequences, and flanking regions. From the immune recognition perspective, we analyzed how A3G-driven mutations are predicted to impact CTL-epitope generation through modulating proteasomal processing and HLA class I binding. We found that A3G mutations were most often predicted to result in diminishing/abolishing HLA-binding affinity of peptide epitopes. From the viral genome evolution perspective, we evaluated enrichment of A3G hotspots at sequences encoding CTL epitopes and included control sequences in which the HIV genome was randomly shuffled. We found that sequences encoding immunogenic epitopes exhibited a selective enrichment of A3G hotspots, which were strongly biased to translate to non-synonymous amino acid substitutions. When superimposed on the known mutational gradient across the entire length of the HIV genome, we observed a gradient of A3G hotspot enrichment, and an HLA-specific pattern of the potential of A3G hotspots to lead to CTL escape mutations. These data illuminate the depths and extent of the co-evolution of the viral genome to subvert the host mutator A3G.
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Affiliation(s)
- Faezeh Borzooee
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Krista D Joris
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Michael D Grant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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15
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Colomer-Lluch M, Ruiz A, Moris A, Prado JG. Restriction Factors: From Intrinsic Viral Restriction to Shaping Cellular Immunity Against HIV-1. Front Immunol 2018; 9:2876. [PMID: 30574147 PMCID: PMC6291751 DOI: 10.3389/fimmu.2018.02876] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/22/2018] [Indexed: 01/20/2023] Open
Abstract
Antiviral restriction factors are host cellular proteins that constitute a first line of defense blocking viral replication and propagation. In addition to interfering at critical steps of the viral replication cycle, some restriction factors also act as innate sensors triggering innate responses against infections. Accumulating evidence suggests an additional role for restriction factors in promoting antiviral cellular immunity to combat viruses. Here, we review the recent progress in our understanding on how restriction factors, particularly APOBEC3G, SAMHD1, Tetherin, and TRIM5α have the cell-autonomous potential to induce cellular resistance against HIV-1 while promoting antiviral innate and adaptive immune responses. Also, we provide an overview of how these restriction factors may connect with protein degradation pathways to modulate anti-HIV-1 cellular immune responses, and we summarize the potential of restriction factors-based therapeutics. This review brings a global perspective on the influence of restrictions factors in intrinsic, innate, and also adaptive antiviral immunity opening up novel research avenues for therapeutic strategies in the fields of drug discovery, gene therapy, and vaccines to control viral infections.
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Affiliation(s)
- Marta Colomer-Lluch
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Alba Ruiz
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Arnaud Moris
- Sorbonne Université, INSERM U1135, CNRS ERL 8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute, Universitat Autonoma de Barcelona, Badalona, Spain
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16
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Budczies J, Seidel A, Christopoulos P, Endris V, Kloor M, Győrffy B, Seliger B, Schirmacher P, Stenzinger A, Denkert C. Integrated analysis of the immunological and genetic status in and across cancer types: impact of mutational signatures beyond tumor mutational burden. Oncoimmunology 2018; 7:e1526613. [PMID: 30524909 DOI: 10.1080/2162402x.2018.1526613] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/25/2022] Open
Abstract
Harnessing the immune system by checkpoint blockade has greatly expanded the therapeutic options for advanced cancer. Since the efficacy of immunotherapies is influenced by the molecular make-up of the tumor and its crosstalk with the immune system, comprehensive analysis of genetic and immunologic tumor characteristics is essential to gain insight into mechanisms of therapy response and resistance. We investigated the association of immune cell contexture and tumor genetics including tumor mutational burden (TMB), copy number alteration (CNA) load, mutant allele heterogeneity (MATH) and specific mutational signatures (MutSigs) using TCGA data of 5722 tumor samples from 21 cancer types. Among all genetic variables, MutSigs associated with DNA repair deficiency and AID/APOBEC gene activity showed the strongest positive correlations with immune parameters. For smoking-related and UV-light-exposure associated MutSigs a few positive correlations were identified, while MutSig 1 (clock-like process) correlated non-significantly or negatively with the major immune parameters in most cancer types. High TMB was associated with high immune cell infiltrates in some but not all cancer types, in contrast, high CNA load and high MATH were mostly associated with low immune cell infiltrates. While a bi- or multimodal distribution of TMB was observed in colorectal, stomach and endometrial cancer where its levels were associated with POLE/POLD1 mutations and MSI status, TMB was unimodal distributed in the most other cancer types including NSCLC and melanoma. In summary, this study uncovered specific genetic-immunology associations in major cancer types and suggests that mutational signatures should be further investigated as interesting candidates for response prediction beyond TMB.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Charité University Hospital, Berlin, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Berlin and Heidelberg partner sites, Germany
| | - Anja Seidel
- Institute of Pathology, Charité University Hospital, Berlin, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Kloor
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, Heidelberg, Germany
| | - Balázs Győrffy
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary.,MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Barbara Seliger
- Institute of Medical Immunology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Berlin and Heidelberg partner sites, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Berlin and Heidelberg partner sites, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité University Hospital, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin and Heidelberg partner sites, Germany
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17
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Pang W, Song JH, Lu Y, Zhang XL, Zheng HY, Jiang J, Zheng YT. Host Restriction Factors APOBEC3G/3F and Other Interferon-Related Gene Expressions Affect Early HIV-1 Infection in Northern Pig-Tailed Macaque ( Macaca leonina). Front Immunol 2018; 9:1965. [PMID: 30210504 PMCID: PMC6120991 DOI: 10.3389/fimmu.2018.01965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/09/2018] [Indexed: 01/07/2023] Open
Abstract
The northern pig-tailed macaques (NPMs) lack TRIM5α, an antiviral restriction factor, and instead have TRIM5-CypA. In our previous study, we demonstrated that HIV-1NL4-3 successfully infected NPMs and formed a long-term viral reservoir in vivo. However, the HIV-1-infected NPMs showed relatively high viremia in the first 6 weeks of infection, which declined thereafter suggesting that HIV-1 NL4-3 infection in these animals was only partly permissive. To optimize HIV-1 infection in NPMs therefore, we generated HIV-1NL4-R3A and stHIV-1sv, and infected NPMs with these viruses. HIV-1NL4-R3A and stHIV-1sv can replicate persistently in NPMs during 41 weeks of acute infection stage. Compared to the HIV-1NL4-R3A, stHIV-1sv showed a notably higher level of replication, and the NPMs infected with the latter induced a more robust neutralizing antibody but a weaker cellular immune response. In addition, IFN-I signaling was significantly up-regulated with the viral replication, and was higher in the stHIV-1sv infected macaques. Consequently, the sequences of pro-viral env showed fewer G-A hyper-mutations in stHIV-1sv, suggesting that vif gene of SIV could antagonize the antiviral effects of APOBEC3 proteins in NPMs. Taken together, NPMs infected with HIV-1NL4-R3A and stHIV-1sv show distinct virological and immunological features. Furthermore, interferon-related gene expression might play a role in controlling primary HIV-1NL4-R3A and stHIV-1sv replication in NPMs. This result suggests NPM is a potential HIV/AIDS animal model.
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Affiliation(s)
- Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jia-Hao Song
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Institute of Health Sciences, Anhui University, Hefei, China
| | - Ying Lu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiao-Liang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jin Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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18
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Borzooee F, Asgharpour M, Quinlan E, Grant MD, Larijani M. Viral subversion of APOBEC3s: Lessons for anti-tumor immunity and tumor immunotherapy. Int Rev Immunol 2018; 37:151-164. [PMID: 29211501 DOI: 10.1080/08830185.2017.1403596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
APOBEC3s (A3) are endogenous DNA-editing enzymes that are expressed in immune cells including T lymphocytes. A3s target and mutate the genomes of retroviruses that infect immune tissues such as the human immunodeficiency virus (HIV). Therefore, A3s were classically defined as host anti-viral innate immune factors. In contrast, we and others showed that A3s can also benefit the virus by mediating escape from adaptive immune recognition and drugs. Crucially, whether A3-mediated mutations help or hinder HIV, is not up to chance. Rather, the virus has evolved multiple mechanisms to actively and maximally subvert A3 activity. More recently, extensive A3 mutational footprints in tumor genomes have been observed in many different cancers. This suggests a role for A3s in cancer initiation and progression. On the other hand, multiple anti-tumor activities of A3s have also come to light, including impact on immune checkpoint molecules and possible generation of tumor neo-antigens. Here, we review the studies that reshaped the view of A3s from anti-viral innate immune agents to host factors exploited by HIV to escape from immune recognition. Viruses and tumors share many attributes, including rapid evolution and adeptness at exploiting mutations. Given this parallel, we then discuss the pro- and anti-tumor roles of A3s, and suggest that lessons learned from studying A3s in the context of anti-viral immunity can be applied to tumor immunotherapy.
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Affiliation(s)
- Faezeh Borzooee
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mahdi Asgharpour
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Emma Quinlan
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Michael D Grant
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mani Larijani
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
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19
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Covino DA, Gauzzi MC, Fantuzzi L. Understanding the regulation of APOBEC3 expression: Current evidence and much to learn. J Leukoc Biol 2017; 103:433-444. [DOI: 10.1002/jlb.2mr0717-310r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/28/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
| | | | - Laura Fantuzzi
- National Center for Global Health; Istituto Superiore di Sanità; Rome Italy
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20
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Abstract
PURPOSE OF REVIEW HIV-1 infection is of global importance, and still incurs substantial morbidity and mortality. Although major pharmacologic advances over the past two decades have resulted in remarkable HIV-1 control, a cure is still forthcoming. One approach to a cure is to exploit natural mechanisms by which the host restricts HIV-1. Herein, we review past and recent discoveries of HIV-1 restriction factors, a diverse set of host proteins that limit HIV-1 replication at multiple levels, including entry, reverse transcription, integration, translation of viral proteins, and packaging and release of virions. RECENT FINDINGS Recent studies of intracellular HIV-1 restriction have offered unique molecular insights into HIV-1 replication and biology. Studies have revealed insights of how restriction factors drive HIV-1 evolution. Although HIV-1 restriction factors only partially control the virus, their importance is underscored by their effect on HIV-1 evolution and adaptation. The list of host restriction factors that control HIV-1 infection is likely to expand with future discoveries. A deeper understanding of the molecular mechanisms of regulation by these factors will uncover new targets for therapeutic control of HIV-1 infection.
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Affiliation(s)
- Mary Soliman
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Geetha Srikrishna
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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21
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Sumner RP, Thorne LG, Fink DL, Khan H, Milne RS, Towers GJ. Are Evolution and the Intracellular Innate Immune System Key Determinants in HIV Transmission? Front Immunol 2017; 8:1246. [PMID: 29056936 PMCID: PMC5635324 DOI: 10.3389/fimmu.2017.01246] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/19/2017] [Indexed: 01/05/2023] Open
Abstract
HIV-1 is the single most important sexually transmitted disease in humans from a global health perspective. Among human lentiviruses, HIV-1 M group has uniquely achieved pandemic levels of human-to-human transmission. The requirement to transmit between hosts likely provides the strongest selective forces on a virus, as without transmission, there can be no new infections within a host population. Our perspective is that evolution of all of the virus-host interactions, which are inherited and perpetuated from host-to-host, must be consistent with transmission. For example, CXCR4 use, which often evolves late in infection, does not favor transmission and is therefore lost when a virus transmits to a new host. Thus, transmission inevitably influences all aspects of virus biology, including interactions with the innate immune system, and dictates the biological niche in which the virus exists in the host. A viable viral niche typically does not select features that disfavor transmission. The innate immune response represents a significant selective pressure during the transmission process. In fact, all viruses must antagonize and/or evade the mechanisms of the host innate and adaptive immune systems that they encounter. We believe that viewing host-virus interactions from a transmission perspective helps us understand the mechanistic details of antiviral immunity and viral escape. This is particularly true for the innate immune system, which typically acts from the very earliest stages of the host-virus interaction, and must be bypassed to achieve successful infection. With this in mind, here we review the innate sensing of HIV, the consequent downstream signaling cascades and the viral restriction that results. The centrality of these mechanisms to host defense is illustrated by the array of countermeasures that HIV deploys to escape them, despite the coding constraint of a 10 kb genome. We consider evasion strategies in detail, in particular the role of the HIV capsid and the viral accessory proteins highlighting important unanswered questions and discussing future perspectives.
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Affiliation(s)
- Rebecca P. Sumner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Lucy G. Thorne
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Doug L. Fink
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Hataf Khan
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Richard S. Milne
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Greg J. Towers
- Division of Infection and Immunity, University College London, London, United Kingdom
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22
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Grant M, Larijani M. Evasion of adaptive immunity by HIV through the action of host APOBEC3G/F enzymes. AIDS Res Ther 2017; 14:44. [PMID: 28893290 PMCID: PMC5594601 DOI: 10.1186/s12981-017-0173-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/11/2017] [Indexed: 01/11/2023] Open
Abstract
APOBEC3G (A3G) and APOBEC3F (A3F) are DNA-mutating enzymes expressed in T cells, dendritic cells and macrophages. A3G/F have been considered innate immune host factors, based on reports that they lethally mutate the HIV genome in vitro. In vivo, A3G/F effectiveness is limited by viral proteins, entrapment in inactive complexes and filtration of mutations during viral life cycle. We hypothesized that the impact of sub-lethal A3G/F action could extend beyond the realm of innate immunity confined to the cytoplasm of infected cells. We measured recognition of wild type and A3G/F-mutated epitopes by cytotoxic T lymphocytes (CTL) from HIV-infected individuals and found that A3G/F-induced mutations overwhelmingly diminished CTL recognition of HIV peptides, in a human histocompatibility-linked leukocyte antigen (HLA)-dependent manner. Furthermore, we found corresponding enrichment of A3G/F-favored motifs in CTL epitope-encoding sequences within the HIV genome. These findings illustrate that A3G/F‐mediated mutations mediate immune evasion by HIV in vivo. Therefore, we suggest that vaccine strategies target T cell or antibody epitopes that are not poised for mutation into escape variants by A3G/F action.
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Silver ZA, Watkins DI. The role of MHC class I gene products in SIV infection of macaques. Immunogenetics 2017; 69:511-519. [PMID: 28695289 PMCID: PMC5537376 DOI: 10.1007/s00251-017-0997-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 04/30/2017] [Indexed: 01/27/2023]
Abstract
Human immunodeficiency virus (HIV) remains among the most significant public health threats worldwide. Despite three decades of research following the discovery of HIV, a preventive vaccine remains elusive. The study of HIV elite controllers has been crucial to elaborate the genetic and immunologic determinants that underlie control of HIV replication. Coordinated studies of elite control in humans have, however, been limited by variability among infecting viral strains, host genotype, and the uncertainty of the timing and route of infection. In this review, we discuss the role of nonhuman primate (NHP) models for the elucidation of the immunologic correlates that underlie control of AIDS virus replication. We discuss the importance of major histocompatibility complex class I (MHC-I) alleles in activating CD8+ T-cell populations that promote control of both HIV and simian immunodeficiency virus (SIV) replication. Provocatively, we make the argument that T-cell subsets recognizing the HIV/SIV viral infectivity factor (Vif) protein may be crucial for control of viral replication. We hope that this review demonstrates how an in-depth understanding of the MHC-I gene products associated with elite control of HIV/SIV, and the epitopes that they present, can provide researchers with a glimpse into the protective immune responses that underlie AIDS nonprogression.
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Affiliation(s)
- Zachary A Silver
- Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL, USA. .,Department of Pathology, University of Miami Miller School of Medicine, Miami, FL, USA.
| | - David I Watkins
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL, USA
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24
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Iizuka T, Wakae K, Nakamura M, Kitamura K, Ono M, Fujiwara H, Muramatsu M. APOBEC3G is increasingly expressed on the human uterine cervical intraepithelial neoplasia along with disease progression. Am J Reprod Immunol 2017; 78. [PMID: 28590025 DOI: 10.1111/aji.12703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/14/2017] [Indexed: 12/15/2022] Open
Abstract
PROBLEM APOBEC3G (A3G) is a cytidine deaminase that exhibits antiviral activity by introducing C-to-T hypermutation in viral DNA. We recently observed the distinct presence of C-to-T hypermutation of human papillomavirus DNA in uterine cervical intraepithelial neoplasia (CIN), suggesting the possible involvement of A3G in the mutation-inducing process. Consequently, we investigated the association of A3G expression with CIN progression in this study. METHOD OF STUDY Patients who had undergone cervical conization due to CIN1 (n=11), CIN2 (n=9), CIN3 (n=12), and micro-invasive squamous cell carcinoma (n=2) were included. The expression profiles of A3G and p16 proteins in cervical lesions and A3G-positive immune cells around the lesions were examined by immunohistochemistry. RESULTS Immunoreactive A3G protein was detected in the CIN and squamous cell carcinoma lesions. Its expression intensity and positive areas were increased and spread in accordance with the progression of CIN, respectively. The co-expression of p16 was observed on the A3G-positive atypical cells. The numbers of A3G-positive immune cells in CIN3 lesions were significantly higher than those of CIN1-2 lesions. CONCLUSION These findings indicate that A3G is associated with CIN, suggesting its important roles in human papillomavirus-induced pathophysiological processes such as CIN progression and viral elimination.
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Affiliation(s)
- Takashi Iizuka
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan.,Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Kousho Wakae
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Mitsuhiro Nakamura
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Koichi Kitamura
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Masanori Ono
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Hiroshi Fujiwara
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Masamichi Muramatsu
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
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25
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Cardinaud S, Urrutia A, Rouers A, Coulon PG, Kervevan J, Richetta C, Bet A, Maze EA, Larsen M, Iglesias MC, Appay V, Graff-Dubois S, Moris A. Triggering of TLR-3, -4, NOD2, and DC-SIGN reduces viral replication and increases T-cell activation capacity of HIV-infected human dendritic cells. Eur J Immunol 2017; 47:818-829. [PMID: 28266028 DOI: 10.1002/eji.201646603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/02/2017] [Accepted: 02/27/2017] [Indexed: 11/06/2022]
Abstract
A variety of signals influence the capacity of dendritic cells (DCs) to mount potent antiviral cytotoxic T-cell (CTL) responses. In particular, innate immune sensing by pathogen recognition receptors, such as TLR and C-type lectines, influences DC biology and affects their susceptibility to HIV infection. Yet, whether the combined effects of PPRs triggering and HIV infection influence HIV-specific (HS) CTL responses remain enigmatic. Here, we dissect the impact of innate immune sensing by pathogen recognition receptors on DC maturation, HIV infection, and on the quality of HS CTL activation. Remarkably, ligand-driven triggering of TLR-3, -4, NOD2, and DC-SIGN, despite reducing viral replication, markedly increased the capacity of infected DCs to stimulate HS CTLs. This was exemplified by the diversity and the quantity of cytokines produced by HS CTLs primed by these DCs. Infecting DCs with viruses harboring members of the APOBEC family of antiviral factors enhanced the antigen-presenting skills of infected DCs. Our results highlight the tight interplay between innate and adaptive immunity and may help develop innovative immunotherapies against viral infections.
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Affiliation(s)
- Sylvain Cardinaud
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
- INSERM, U955, IMRB Equipe-16, Vaccine Research Institute-VRI, Creteil, France
| | - Alejandra Urrutia
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Angeline Rouers
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Pierre-Grégoire Coulon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Jérome Kervevan
- INSERM, U955, IMRB Equipe-16, Vaccine Research Institute-VRI, Creteil, France
| | - Clémence Richetta
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Anne Bet
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Emmanuel A Maze
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Martin Larsen
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Maria-Candela Iglesias
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Victor Appay
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Stéphanie Graff-Dubois
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
| | - Arnaud Moris
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections - CIMI-Paris, Paris, France
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26
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Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang SH, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho YC. Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape. Cell Host Microbe 2017; 21:494-506.e4. [PMID: 28407485 DOI: 10.1016/j.chom.2017.03.008] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/07/2017] [Accepted: 03/16/2017] [Indexed: 12/31/2022]
Abstract
Despite antiretroviral therapy, HIV-1 persists in memory CD4+ T cells, creating a barrier to cure. The majority of HIV-1 proviruses are defective and considered clinically irrelevant. Using cells from HIV-1-infected individuals and reconstructed patient-derived defective proviruses, we show that defective proviruses can be transcribed into RNAs that are spliced and translated. Proviruses with defective major splice donors (MSDs) can activate novel splice sites to produce HIV-1 transcripts, and cells with these proviruses can be recognized by HIV-1-specific cytotoxic T lymphocytes (CTLs). Further, cells with proviruses containing lethal mutations upstream of CTL epitopes can also be recognized by CTLs, potentially through aberrant translation. Thus, CTLs may change the landscape of HIV-1 proviruses by preferentially targeting cells with specific types of defective proviruses. Additionally, the expression of defective proviruses will need to be considered in the measurement of HIV-1 latency reversal.
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Affiliation(s)
- Ross A Pollack
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - R Brad Jones
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Mihaela Pertea
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Katherine M Bruner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa R Martin
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Allison S Thomas
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Adam A Capoferri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Szu-Han Huang
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Sara Karandish
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Haiping Hao
- Deep Sequencing & Microarray Core, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Patrick C Yong
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Colin Kovacs
- Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Maple Leaf Medical Clinic, Toronto, ON M5G 1K2, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, ON M5G 1K2, Canada
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Ya-Chi Ho
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Jimenez-Moyano E, Ruiz A, Kløverpris HN, Rodriguez-Plata MT, Peña R, Blondeau C, Selwood DL, Izquierdo-Useros N, Moris A, Clotet B, Goulder P, Towers GJ, Prado JG. Nonhuman TRIM5 Variants Enhance Recognition of HIV-1-Infected Cells by CD8+ T Cells. J Virol 2016; 90:8552-62. [PMID: 27440884 PMCID: PMC5021395 DOI: 10.1128/jvi.00819-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Tripartite motif-containing protein 5 (TRIM5) restricts human immunodeficiency virus type 1 (HIV-1) in a species-specific manner by uncoating viral particles while activating early innate responses. Although the contribution of TRIM5 proteins to cellular immunity has not yet been studied, their interactions with the incoming viral capsid and the cellular proteasome led us to hypothesize a role for them. Here, we investigate whether the expression of two nonhuman TRIM5 orthologs, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), both of which are potent restrictors of HIV-1, could enhance immune recognition of infected cells by CD8(+) T cells. We illustrate how TRIM5 restriction improves CD8(+) T-cell-mediated HIV-1 inhibition. Moreover, when TRIM5 activity was blocked by the nonimmunosuppressive analog of cyclosporine (CsA), sarcosine-3(4-methylbenzoate)-CsA (SmBz-CsA), we found a significant reduction in CD107a/MIP-1β expression in HIV-1-specific CD8(+) T cells. This finding underscores the direct link between TRIM5 restriction and activation of CD8(+) T-cell responses. Interestingly, cells expressing RhT5 induced stronger CD8(+) T-cell responses through the specific recognition of the HIV-1 capsid by the immune system. The underlying mechanism of this process may involve TRIM5-specific capsid recruitment to cellular proteasomes and increase peptide availability for loading and presentation of HLA class I antigens. In summary, we identified a novel function for nonhuman TRIM5 variants in cellular immunity. We hypothesize that TRIM5 can couple innate viral sensing and CD8(+) T-cell activation to increase species barriers against retrovirus infection. IMPORTANCE New therapeutics to tackle HIV-1 infection should aim to combine rapid innate viral sensing and cellular immune recognition. Such strategies could prevent seeding of the viral reservoir and the immune damage that occurs during acute infection. The nonhuman TRIM5 variants, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), are attractive candidates owing to their potency in sensing HIV-1 and blocking its activity. Here, we show that expression of RhT5 and TCyp in HIV-1-infected cells improves CD8(+) T-cell-mediated inhibition through the direct activation of HIV-1-specific CD8(+) T-cell responses. We found that the potency in CD8(+) activation was stronger for RhT5 variants and capsid-specific CD8(+) T cells in a mechanism that relies on TRIM5-dependent particle recruitment to cellular proteasomes. This novel mechanism couples innate viral sensing with cellular immunity in a single protein and could be exploited to develop innovative therapeutics for control of HIV-1 infection.
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Affiliation(s)
| | - Alba Ruiz
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Henrik N Kløverpris
- KwaZulu-Natal Research Institute for TB and HIV, University of KwaZulu-Natal, Durban, South Africa
| | | | - Ruth Peña
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Caroline Blondeau
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - David L Selwood
- The Wolfson Institute for Biomedical Research, University College London, United Kingdom
| | | | - Arnaud Moris
- Sorbonne Universités, UPMC University Paris 6, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections-Paris, Paris, France
| | - Bonaventura Clotet
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Julia G Prado
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
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28
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Desimmie BA, Burdick RC, Izumi T, Doi H, Shao W, Alvord WG, Sato K, Koyanagi Y, Jones S, Wilson E, Hill S, Maldarelli F, Hu WS, Pathak VK. APOBEC3 proteins can copackage and comutate HIV-1 genomes. Nucleic Acids Res 2016; 44:7848-65. [PMID: 27439715 PMCID: PMC5027510 DOI: 10.1093/nar/gkw653] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/31/2023] Open
Abstract
Although APOBEC3 cytidine deaminases A3G, A3F, A3D and A3H are packaged into virions and inhibit viral replication by inducing G-to-A hypermutation, it is not known whether they are copackaged and whether they can act additively or synergistically to inhibit HIV-1 replication. Here, we showed that APOBEC3 proteins can be copackaged by visualization of fluorescently-tagged APOBEC3 proteins using single-virion fluorescence microscopy. We further determined that viruses produced in the presence of A3G + A3F and A3G + A3H, exhibited extensive comutation of viral cDNA, as determined by the frequency of G-to-A mutations in the proviral genomes in the contexts of A3G (GG-to-AG) and A3D, A3F or A3H (GA-to-AA) edited sites. The copackaging of A3G + A3F and A3G + A3H resulted in an additive increase and a modest synergistic increase (1.8-fold) in the frequency of GA-to-AA mutations, respectively. We also identified distinct editing site trinucleotide sequence contexts for each APOBEC3 protein and used them to show that hypermutation of proviral DNAs from seven patients was induced by A3G, A3F (or A3H), A3D and A3G + A3F (or A3H). These results indicate that APOBEC3 proteins can be copackaged and can comutate the same genomes, and can cooperate to inhibit HIV replication.
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Affiliation(s)
- Belete A Desimmie
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ryan C Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hibiki Doi
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei Shao
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Gregory Alvord
- Statistical Consulting, Data Management Services, Inc., Frederick, MD 21702, USA
| | - Kei Sato
- Institute of Virus Research, Kyoto University, Kyoto, 606-8057, Japan CREST, Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Yoshio Koyanagi
- Institute of Virus Research, Kyoto University, Kyoto, 606-8057, Japan
| | - Sara Jones
- Leidos Biomedical Research, Inc., Bethesda, MD 20892, USA
| | - Eleanor Wilson
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shawn Hill
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Frank Maldarelli
- Clinical Retrovirology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer. BMC Genomics 2016; 17:643. [PMID: 27527602 PMCID: PMC4986275 DOI: 10.1186/s12864-016-3001-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/08/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ovarian cancer is a highly complex heterogeneous malignancy in respect of tumor anatomy, tumor microenvironment including pro-/antitumor immunity and inflammation; still, it is generally treated as single disease. Thus, further approaches to investigate novel aspects of ovarian cancer pathogenesis aiming to provide a personalized strategy to clinical decision making are of high priority. Herein we assessed the contribution of the AID/APOBEC family and their associated genes given the remarkable ability of AID and APOBECs to edit DNA/RNA, and as such, providing tools for genetic and epigenetic alterations potentially leading to reprogramming of tumor cells, stroma and immune cells. RESULTS We structured the study by three consecutive analytical modules, which include the multigene-based expression profiling in a cohort of patients with primary serous ovarian cancer using a self-created AID/APOBEC-associated gene signature, building up of multivariable survival models with high predictive accuracy and nomination of top-ranked candidate/target genes according to their prognostic impact, and systems biology-based reconstruction of the AID/APOBEC-driven disease-relevant mechanisms using transcriptomics data from ovarian cancer samples. We demonstrated that inclusion of the AID/APOBEC signature-based variables significantly improves the clinicopathological variables-based survival prognostication allowing significant patient stratification. Furthermore, several of the profiling-derived variables such as ID3, PTPRC/CD45, AID, APOBEC3G, and ID2 exceed the prognostic impact of some clinicopathological variables. We next extended the signature-/modeling-based knowledge by extracting top genes co-regulated with target molecules in ovarian cancer tissues and dissected potential networks/pathways/regulators contributing to pathomechanisms. We thereby revealed that the AID/APOBEC-related network in ovarian cancer is particularly associated with remodeling/fibrotic pathways, altered immune response, and autoimmune disorders with inflammatory background. CONCLUSIONS The herein study is, to our knowledge, the first one linking expression of entire AID/APOBECs and interacting genes with clinical outcome with respect to survival of cancer patients. Overall, data propose a novel AID/APOBEC-derived survival model for patient risk assessment and reconstitute mapping to molecular pathways. The established study algorithm can be applied further for any biologically relevant signature and any type of diseased tissue.
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30
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Maelfait J, Bridgeman A, Benlahrech A, Cursi C, Rehwinkel J. Restriction by SAMHD1 Limits cGAS/STING-Dependent Innate and Adaptive Immune Responses to HIV-1. Cell Rep 2016; 16:1492-1501. [PMID: 27477283 PMCID: PMC4978700 DOI: 10.1016/j.celrep.2016.07.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/20/2016] [Accepted: 07/01/2016] [Indexed: 01/08/2023] Open
Abstract
SAMHD1 is a restriction factor for HIV-1 infection. SAMHD1 mutations cause the autoinflammatory Aicardi-Goutières syndrome that is characterized by chronic type I interferon (IFN) secretion. We show that the spontaneous IFN response in SAMHD1-deficient cells and mice requires the cGAS/STING cytosolic DNA-sensing pathway. We provide genetic evidence that cell-autonomous control of lentivirus infection in myeloid cells by SAMHD1 limits virus-induced production of IFNs and the induction of co-stimulatory markers. This program of myeloid cell activation required reverse transcription, cGAS and STING, and signaling through the IFN receptor. Furthermore, SAMHD1 reduced the induction of virus-specific cytotoxic T cells in vivo. Therefore, virus restriction by SAMHD1 limits the magnitude of IFN and T cell responses. This demonstrates a competition between cell-autonomous virus control and subsequent innate and adaptive immune responses, a concept with important implications for the treatment of infection. Spontaneous IFN production in SAMHD1-deficient cells requires cGAS and STING During HIV-1 infection, SAMHD1 limits activation of myeloid cells cGAS and STING detect HIV-1 infection in SAMHD1-deficient cells and induce IFN SAMHD1 prevents virus-specific CD8 T cell responses in vivo
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Affiliation(s)
- Jonathan Maelfait
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adel Benlahrech
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chiara Cursi
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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Coulon PG, Richetta C, Rouers A, Blanchet FP, Urrutia A, Guerbois M, Piguet V, Theodorou I, Bet A, Schwartz O, Tangy F, Graff-Dubois S, Cardinaud S, Moris A. HIV-Infected Dendritic Cells Present Endogenous MHC Class II-Restricted Antigens to HIV-Specific CD4+ T Cells. THE JOURNAL OF IMMUNOLOGY 2016; 197:517-32. [PMID: 27288536 DOI: 10.4049/jimmunol.1600286] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
Abstract
It is widely assumed that CD4(+) T cells recognize antigenic peptides (epitopes) derived solely from incoming, exogenous, viral particles or proteins. However, alternative sources of MHC class II (MHC-II)-restricted Ags have been described, in particular epitopes derived from newly synthesized proteins (so-called endogenous). In this study, we show that HIV-infected dendritic cells (DC) present MHC-II-restricted endogenous viral Ags to HIV-specific (HS) CD4(+) T cells. This endogenous pathway functions independently of the exogenous route for HIV Ag presentation and offers a distinct possibility for the immune system to activate HS CD4(+) T cells. We examined the implication of autophagy, which plays a crucial role in endogenous viral Ag presentation and thymic selection of CD4(+) T cells, in HIV endogenous presentation. We show that infected DC do not use autophagy to process MHC-II-restricted HIV Ags. This is unlikely to correspond to a viral escape from autophagic degradation, as infecting DC with Nef- or Env-deficient HIV strains did not impact HS T cell activation. However, we demonstrate that, in DC, specific targeting of HIV Ags to autophagosomes using a microtubule-associated protein L chain 3 (LC3) fusion protein effectively enhances and broadens HS CD4(+) T cell responses, thus favoring an endogenous MHC-II-restricted presentation. In summary, in DC, multiple endogenous presentation pathways lead to the activation of HS CD4(+) T cell responses. These findings will help in designing novel strategies to activate HS CD4(+) T cells that are required for CTL activation/maintenance and B cell maturation.
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Affiliation(s)
- Pierre-Grégoire Coulon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | - Clémence Richetta
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | - Angéline Rouers
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | - Fabien P Blanchet
- CNRS, FRE3689, Université de Montpellier, Centre d'Études d'Agents Pathogènes et Biotechnologies pour la Santé, 34293 Montpellier, France
| | - Alejandra Urrutia
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | - Mathilde Guerbois
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75724 Paris, France
| | - Vincent Piguet
- Department of Dermatology and Wound Healing, Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Ioannis Theodorou
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France; Département d'Immunologie, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, 75013 Paris, France; and
| | - Anne Bet
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | | | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75724 Paris, France
| | - Stéphanie Graff-Dubois
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | - Sylvain Cardinaud
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France
| | - Arnaud Moris
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre d'Immunologie et des Maladies Infectieuses, U1135, CNRS 8255, F-75013 Paris, France; Département d'Immunologie, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, 75013 Paris, France; and
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32
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Knisbacher BA, Gerber D, Levanon EY. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet 2016; 32:16-28. [PMID: 26608778 DOI: 10.1016/j.tig.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel.
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33
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Stavrou S, Ross SR. APOBEC3 Proteins in Viral Immunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:4565-70. [PMID: 26546688 PMCID: PMC4638160 DOI: 10.4049/jimmunol.1501504] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Apolipoprotein B editing complex 3 family members are cytidine deaminases that play important roles in intrinsic responses to infection by retroviruses and have been implicated in the control of other viruses, such as parvoviruses, herpesviruses, papillomaviruses, hepatitis B virus, and retrotransposons. Although their direct effect on modification of viral DNA has been clearly demonstrated, whether they play additional roles in innate and adaptive immunity to viruses is less clear. We review the data regarding the various steps in the innate and adaptive immune response to virus infection in which apolipoprotein B editing complex 3 proteins have been implicated.
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Affiliation(s)
- Spyridon Stavrou
- Department of Microbiology, Abramson Cancer Center, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6142
| | - Susan R Ross
- Department of Microbiology, Abramson Cancer Center, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6142
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Abstract
UNLABELLED Monocyte-derived dendritic cells (MDDC) stimulate CD8 cytotoxic T lymphocytes (CTL) by presenting endogenous and exogenous viral peptides via major histocompatibility complex class I (MHC-I) molecules. MDDC are poorly susceptible to HIV-1, in part due to the presence of SAMHD1, a cellular enzyme that depletes intracellular deoxynucleoside triphosphates (dNTPs) and degrades viral RNA. Vpx, an HIV-2/SIVsm protein absent from HIV-1, antagonizes SAMHD1 by inducing its degradation. The impact of SAMHD1 on the adaptive cellular immune response remains poorly characterized. Here, we asked whether SAMHD1 modulates MHC-I-restricted HIV-1 antigen presentation. Untreated MDDC or MDDC pretreated with Vpx were exposed to HIV-1, and antigen presentation was examined by monitoring the activation of an HIV-1 Gag-specific CTL clone. SAMHD1 depletion strongly enhanced productive infection of MDDC as well as endogenous HIV-1 antigen presentation. Time-lapse microscopy analysis demonstrated that in the absence of SAMHD1, the CTL rapidly killed infected MDDC. We also report that various transmitted/founder (T/F) HIV-1 strains poorly infected MDDC and, as a consequence, did not stimulate CTL. Vesicular stomatitis virus glycoprotein (VSV-G) pseudotyping of T/F alleviated a block in viral entry and induced antigen presentation only in the absence of SAMHD1. Furthermore, by using another CTL clone that mostly recognizes incoming HIV-1 antigens, we demonstrate that SAMHD1 does not influence exogenous viral antigen presentation. Altogether, our results demonstrate that the antiviral activity of SAMHD1 impacts antigen presentation by DC, highlighting the link that exists between restriction factors and adaptive immune responses. IMPORTANCE Upon viral infection, DC may present antigens derived from incoming viral material in the absence of productive infection of DC or from newly synthesized viral proteins. In the case of HIV, productive infection of DC is blocked at an early postentry step. This is due to the presence of SAMHD1, a cellular enzyme that depletes intracellular levels of dNTPs and inhibits viral reverse transcription. We show that the depletion of SAMHD1 in DCs strongly stimulates the presentation of viral antigens derived from newly produced viral proteins, leading to the activation of HIV-1-specific cytotoxic T lymphocytes (CTL). We further show in real time that the enhanced activation of CTL leads to killing of infected DCs. Our results indicate that the antiviral activity of SAMHD1 not only impacts HIV replication but also impacts antigen presentation by DC. They highlight the link that exists between restriction factors and adaptive immune responses.
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van den Berg LM, Cardinaud S, van der Aar AMG, Sprokholt JK, de Jong MAWP, Zijlstra-Willems EM, Moris A, Geijtenbeek TBH. Langerhans Cell-Dendritic Cell Cross-Talk via Langerin and Hyaluronic Acid Mediates Antigen Transfer and Cross-Presentation of HIV-1. THE JOURNAL OF IMMUNOLOGY 2015; 195:1763-73. [PMID: 26170391 DOI: 10.4049/jimmunol.1402356] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
Human epidermal and mucosal Langerhans cells (LCs) express the C-type lectin receptor langerin that functions as a pattern recognition receptor. LCs are among the first immune cells to interact with HIV-1 during sexual transmission. In this study, we demonstrate that langerin not only functions as a pattern recognition receptor but also as an adhesion receptor mediating clustering between LCs and dendritic cells (DCs). Langerin recognized hyaluronic acid on DCs and removal of these carbohydrate structures partially abrogated LC-DC clustering. Because LCs did not cross-present HIV-1-derived Ags to CD8(+) T cells in a cross-presentation model, we investigated whether LCs were able to transfer Ags to DCs. LC-DC clustering led to maturation of DCs and facilitated Ag transfer of HIV-1 to DCs, which subsequently induced activation of CD8(+) cells. The rapid transfer of Ags to DCs, in contrast to productive infection of LCs, suggests that this might be an important mechanism for induction of anti-HIV-1 CD8(+) T cells. Induction of the enzyme hyaluronidase-2 by DC maturation allowed degradation of hyaluronic acid and abrogated LC-DC interactions. Thus, we have identified an important function of langerin in mediating LC-DC clustering, which allows Ag transfer to induce CTL responses to HIV-1. Furthermore, we showed this interaction is mediated by hyaluronidase-2 upregulation after DC maturation. These data underscore the importance of LCs and DCs in orchestrating adaptive immunity to HIV-1. Novel strategies might be developed to harness this mechanism for vaccination.
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Affiliation(s)
- Linda M van den Berg
- Department of Experimental Immunology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Sylvain Cardinaud
- Center for Immunology and Microbial Infections-Paris, University Pierre and Marie Curie Paris 06, University Sorbonne, F-75013 Paris, France; Center for Immunology and Microbial Infections-Paris, INSERM, U1135, F-75013 Paris, France; Center for Immunology and Microbial Infections-Paris, French National Centre for Scientific Research, ERL 8255, F-75013 Paris, France
| | - Angelic M G van der Aar
- Department of Experimental Immunology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Joris K Sprokholt
- Department of Experimental Immunology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Marein A W P de Jong
- Department of Experimental Immunology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | | | - Arnaud Moris
- Center for Immunology and Microbial Infections-Paris, University Pierre and Marie Curie Paris 06, University Sorbonne, F-75013 Paris, France; Center for Immunology and Microbial Infections-Paris, INSERM, U1135, F-75013 Paris, France; Center for Immunology and Microbial Infections-Paris, French National Centre for Scientific Research, ERL 8255, F-75013 Paris, France; Department of Immunology, AP-HP University Medical Center Paris Area, F-75013 Paris, France
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands;
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36
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Complement-Opsonized HIV-1 Overcomes Restriction in Dendritic Cells. PLoS Pathog 2015; 11:e1005005. [PMID: 26121641 PMCID: PMC4485899 DOI: 10.1371/journal.ppat.1005005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/05/2015] [Indexed: 11/19/2022] Open
Abstract
DCs express intrinsic cellular defense mechanisms to specifically inhibit HIV-1 replication. Thus, DCs are productively infected only at very low levels with HIV-1, and this non-permissiveness of DCs is suggested to go along with viral evasion. We now illustrate that complement-opsonized HIV-1 (HIV-C) efficiently bypasses SAMHD1 restriction and productively infects DCs including BDCA-1 DCs. Efficient DC infection by HIV-C was also observed using single-cycle HIV-C, and correlated with a remarkable elevated SAMHD1 T592 phosphorylation but not SAMHD1 degradation. If SAMHD1 phosphorylation was blocked using a CDK2-inhibitor HIV-C-induced DC infection was also significantly abrogated. Additionally, we found a higher maturation and co-stimulatory potential, aberrant type I interferon expression and signaling as well as a stronger induction of cellular immune responses in HIV-C-treated DCs. Collectively, our data highlight a novel protective mechanism mediated by complement opsonization of HIV to effectively promote DC immune functions, which might be in the future exploited to tackle HIV infection. We here give insight into a substantial novel way of dendritic cell modulation at least during acute HIV-1 infection by triggering integrin receptor signaling. We found that complement-opsonization of the virus is able to relieve SAMHD1 restriction in DCs, thereby initiating strong maturation and co-stimulatory capacity of the cells and stimulating efficient cellular and humoral antiviral immune responses. This newly described way of DC modulation by complement might be exploited to find novel therapeutic targets promoting DC immune functions against HIV.
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37
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Simon V, Bloch N, Landau NR. Intrinsic host restrictions to HIV-1 and mechanisms of viral escape. Nat Immunol 2015; 16:546-53. [PMID: 25988886 PMCID: PMC6908429 DOI: 10.1038/ni.3156] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/24/2015] [Indexed: 02/06/2023]
Abstract
To replicate in their hosts, viruses have to navigate the complexities of the mammalian cell, co-opting mechanisms of cellular physiology while defeating restriction factors that are dedicated to halting their progression. Primate lentiviruses devote a relatively large portion of their coding capacity to counteracting restriction factors by encoding accessory proteins dedicated to neutralizing the antiviral function of these intracellular inhibitors. Research into the roles of the accessory proteins has revealed the existence of previously undetected intrinsic defenses, provided insight into the evolution of primate lentiviruses as they adapt to new species and uncovered new targets for the development of therapeutics. This Review discusses the biology of the restriction factors APOBEC3, SAMHD1 and tetherin and the viral accessory proteins that counteract them.
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Affiliation(s)
- Viviana Simon
- Department of Microbiology, The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicolin Bloch
- Department of Microbiology, NYU School of Medicine, New York, New York, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU School of Medicine, New York, New York, USA
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38
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Armitage AE, Deforche K, Welch JJ, Van Laethem K, Camacho R, Rambaut A, Iversen AKN. Possible footprints of APOBEC3F and/or other APOBEC3 deaminases, but not APOBEC3G, on HIV-1 from patients with acute/early and chronic infections. J Virol 2014; 88:12882-94. [PMID: 25165112 PMCID: PMC4248940 DOI: 10.1128/jvi.01460-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/21/2014] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Members of the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like-3 (APOBEC3) innate cellular cytidine deaminase family, particularly APOBEC3F and APOBEC3G, can cause extensive and lethal G-to-A mutations in HIV-1 plus-strand DNA (termed hypermutation). It is unclear if APOBEC3-induced mutations in vivo are always lethal or can occur at sublethal levels that increase HIV-1 diversification and viral adaptation to the host. The viral accessory protein Vif counteracts APOBEC3 activity by binding to APOBEC3 and promoting proteasome degradation; however, the efficiency of this interaction varies, since a range of hypermutation frequencies are observed in HIV-1 patient DNA. Therefore, we examined "footprints" of APOBEC3G and APOBEC3F activity in longitudinal HIV-1 RNA pol sequences from approximately 3,000 chronically infected patients by determining whether G-to-A mutations occurred in motifs that were favored or disfavored by these deaminases. G-to-A mutations were more frequent in APOBEC3G-disfavored than in APOBEC3G-favored contexts. In contrast, mutations in APOBEC3F-disfavored contexts were relatively rare, whereas mutations in contexts favoring APOBEC3F (and possibly other deaminases) occurred 16% more often than average G-to-A mutations. These results were supported by analyses of >500 HIV-1 env sequences from acute/early infection. IMPORTANCE Collectively, our results suggest that APOBEC3G-induced mutagenesis is lethal to HIV-1, whereas mutagenesis caused by APOBEC3F and/or other deaminases may result in sublethal mutations that might facilitate viral diversification. Therefore, Vif-specific cytotoxic T lymphocyte (CTL) responses and drugs that manipulate the interplay between Vif and APOBEC3 may have beneficial or detrimental clinical effects depending on how they affect the binding of Vif to various members of the APOBEC3 family.
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Affiliation(s)
- Andrew E Armitage
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Koen Deforche
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Kristel Van Laethem
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - Ricardo Camacho
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Andrew Rambaut
- Institute of Evolutionary Biology. University of Edinburgh, Edinburgh, United Kingdom
| | - Astrid K N Iversen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
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39
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Sato K, Takeuchi JS, Misawa N, Izumi T, Kobayashi T, Kimura Y, Iwami S, Takaori-Kondo A, Hu WS, Aihara K, Ito M, An DS, Pathak VK, Koyanagi Y. APOBEC3D and APOBEC3F potently promote HIV-1 diversification and evolution in humanized mouse model. PLoS Pathog 2014; 10:e1004453. [PMID: 25330146 PMCID: PMC4199767 DOI: 10.1371/journal.ppat.1004453] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/05/2014] [Indexed: 12/02/2022] Open
Abstract
Several APOBEC3 proteins, particularly APOBEC3D, APOBEC3F, and APOBEC3G, induce G-to-A hypermutations in HIV-1 genome, and abrogate viral replication in experimental systems, but their relative contributions to controlling viral replication and viral genetic variation in vivo have not been elucidated. On the other hand, an HIV-1-encoded protein, Vif, can degrade these APOBEC3 proteins via a ubiquitin/proteasome pathway. Although APOBEC3 proteins have been widely considered as potent restriction factors against HIV-1, it remains unclear which endogenous APOBEC3 protein(s) affect HIV-1 propagation in vivo. Here we use a humanized mouse model and HIV-1 with mutations in Vif motifs that are responsible for specific APOBEC3 interactions, DRMR/AAAA (4A) or YRHHY/AAAAA (5A), and demonstrate that endogenous APOBEC3D/F and APOBEC3G exert strong anti-HIV-1 activity in vivo. We also show that the growth kinetics of 4A HIV-1 negatively correlated with the expression level of APOBEC3F. Moreover, single genome sequencing analyses of viral RNA in plasma of infected mice reveal that 4A HIV-1 is specifically and significantly diversified. Furthermore, a mutated virus that is capable of using both CCR5 and CXCR4 as entry coreceptor is specifically detected in 4A HIV-1-infected mice. Taken together, our results demonstrate that APOBEC3D/F and APOBEC3G fundamentally work as restriction factors against HIV-1 in vivo, but at the same time, that APOBEC3D and APOBEC3F are capable of promoting viral diversification and evolution in vivo. Mutation can produce three outcomes in viruses: detrimental, neutral, or beneficial. The first one leads to abrogation of virus replication because of error catastrophe, while the last one lets the virus escape from anti-viral immune system or adapt to the host. Human APOBEC3D, APOBEC3F, and APOBEC3G are cellular cytidine deaminases which cause G-to-A mutations in HIV-1 genome. Here we use a humanized mouse model and demonstrate that endogenous APOBEC3F and APOBEC3G induce G-to-A hypermutation in viral genomes and exert strong anti-HIV-1 activity in vivo. We also reveal that endogenous APOBEC3D and/or APOBEC3F induce viral diversification, which can lead to the emergence of a mutated virus that converts its coreceptor usage. Our results suggest that APOBEC3D and APOBEC3F are capable of promoting viral diversification and functional evolution in vivo.
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Affiliation(s)
- Kei Sato
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Kyoto, Japan
- * E-mail:
| | - Junko S. Takeuchi
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Kyoto, Japan
| | - Naoko Misawa
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Kyoto, Japan
| | - Taisuke Izumi
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Tomoko Kobayashi
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Kyoto, Japan
| | - Yuichi Kimura
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Kyoto, Japan
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Kazuyuki Aihara
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Graduate School of Information Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Mamoru Ito
- Central Institute for Experimental Animals, Kawasaki, Kanagawa, Japan
| | - Dong Sung An
- Division of Hematology and Oncology, University of California, Los Angeles, Los Angeles, California, United States of America
- School of Nursing, University of California, Los Angeles, Los Angeles, California, United States of America
- AIDS Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Yoshio Koyanagi
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Kyoto, Japan
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40
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Moris A, Murray S, Cardinaud S. AID and APOBECs span the gap between innate and adaptive immunity. Front Microbiol 2014; 5:534. [PMID: 25352838 PMCID: PMC4195361 DOI: 10.3389/fmicb.2014.00534] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/24/2014] [Indexed: 12/17/2022] Open
Abstract
The activation-induced deaminase (AID)/APOBEC cytidine deaminases participate in a diversity of biological processes from the regulation of protein expression to embryonic development and host defenses. In its classical role, AID mutates germline-encoded sequences of B cell receptors, a key aspect of adaptive immunity, and APOBEC1, mutates apoprotein B pre-mRNA, yielding two isoforms important for cellular function and plasma lipid metabolism. Investigations over the last ten years have uncovered a role of the APOBEC superfamily in intrinsic immunity against viruses and innate immunity against viral infection by deamination and mutation of viral genomes. Further, discovery in the area of human immunodeficiency virus (HIV) infection revealed that the HIV viral infectivity factor protein interacts with APOBEC3G, targeting it for proteosomal degradation, overriding its antiviral function. More recently, our and others' work have uncovered that the AID and APOBEC cytidine deaminase family members have an even more direct link between activity against viral infection and induction and shaping of adaptive immunity than previously thought, including that of antigen processing for cytotoxic T lymphocyte activity and natural killer cell activation. Newly ascribed functions of these cytodine deaminases will be discussed, including their newly identified roles in adaptive immunity, epigenetic regulation, and cell differentiation. Herein this review we discuss AID and APOBEC cytodine deaminases as a link between innate and adaptive immunity uncovered by recent studies.
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Affiliation(s)
- Arnaud Moris
- Center for Immunology and Microbial Infections, Faculty of Medicine, Université Paris-Sorbonne UPMC Univ Paris 06, Paris, France ; Center for Immunology and Microbial Infections, Institut National de la Santé et de la Recherche Médicale U1135, Paris, France ; Center for Immunology and Microbial Infections, Centre National de la Recherche Scientifique ERL 8255, Paris, France ; Department of Immunology, Hôpital Pitié-Salpêtière Paris, France
| | - Shannon Murray
- Center for Immunology and Microbial Infections, Faculty of Medicine, Université Paris-Sorbonne UPMC Univ Paris 06, Paris, France ; Center for Immunology and Microbial Infections, Institut National de la Santé et de la Recherche Médicale U1135, Paris, France ; Center for Immunology and Microbial Infections, Centre National de la Recherche Scientifique ERL 8255, Paris, France
| | - Sylvain Cardinaud
- Center for Immunology and Microbial Infections, Faculty of Medicine, Université Paris-Sorbonne UPMC Univ Paris 06, Paris, France ; Center for Immunology and Microbial Infections, Institut National de la Santé et de la Recherche Médicale U1135, Paris, France ; Center for Immunology and Microbial Infections, Centre National de la Recherche Scientifique ERL 8255, Paris, France
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41
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Feng Y, Baig TT, Love RP, Chelico L. Suppression of APOBEC3-mediated restriction of HIV-1 by Vif. Front Microbiol 2014; 5:450. [PMID: 25206352 PMCID: PMC4144255 DOI: 10.3389/fmicb.2014.00450] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/06/2014] [Indexed: 12/21/2022] Open
Abstract
The APOBEC3 restriction factors are a family of deoxycytidine deaminases that are able to suppress replication of viruses with a single-stranded DNA intermediate by inducing mutagenesis and functional inactivation of the virus. Of the seven human APOBEC3 enzymes, only APOBEC3-D, -F, -G, and -H appear relevant to restriction of HIV-1 in CD4+ T cells and will be the focus of this review. The restriction of HIV-1 occurs most potently in the absence of HIV-1 Vif that induces polyubiquitination and degradation of APOBEC3 enzymes through the proteasome pathway. To restrict HIV-1, APOBEC3 enzymes must be encapsidated into budding virions. Upon infection of the target cell during reverse transcription of the HIV-1 RNA into (-)DNA, APOBEC3 enzymes deaminate cytosines to form uracils in single-stranded (-)DNA regions. Upon replication of the (-)DNA to (+)DNA, the HIV-1 reverse transcriptase incorporates adenines opposite to the uracils thereby inducing C/G to T/A mutations that can functionally inactivate HIV-1. APOBEC3G is the most studied APOBEC3 enzyme and it is known that Vif attempts to thwart APOBEC3 function not only by inducing its proteasomal degradation but also by several degradation-independent mechanisms, such as inhibiting APOBEC3G virion encapsidation, mRNA translation, and for those APOBEC3G molecules that still become virion encapsidated, Vif can inhibit APOBEC3G mutagenic activity. Although most Vif variants can induce efficient degradation of APOBEC3-D, -F, and -G, there appears to be differential sensitivity to Vif-mediated degradation for APOBEC3H. This review examines APOBEC3-mediated HIV restriction mechanisms, how Vif acts as a substrate receptor for a Cullin5 ubiquitin ligase complex to induce degradation of APOBEC3s, and the determinants and functional consequences of the APOBEC3 and Vif interaction from a biological and biochemical perspective.
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Affiliation(s)
- Yuqing Feng
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
| | - Tayyba T Baig
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan Saskatoon, SK, Canada
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Stonos N, Wootton SK, Karrow N. Immunogenetics of small ruminant lentiviral infections. Viruses 2014; 6:3311-33. [PMID: 25153344 PMCID: PMC4147697 DOI: 10.3390/v6083311] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/11/2022] Open
Abstract
The small ruminant lentiviruses (SRLV) include the caprine arthritis encephalitis virus (CAEV) and the Maedi-Visna virus (MVV). Both of these viruses limit production and can be a major source of economic loss to producers. Little is known about how the immune system recognizes and responds to SRLVs, but due to similarities with the human immunodeficiency virus (HIV), HIV research can shed light on the possible immune mechanisms that control or lead to disease progression. This review will focus on the host immune response to HIV-1 and SRLV, and will discuss the possibility of breeding for enhanced SRLV disease resistance.
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Affiliation(s)
- Nancy Stonos
- Centre for the Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Sarah K Wootton
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Niel Karrow
- Centre for the Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Kim EY, Lorenzo-Redondo R, Little SJ, Chung YS, Phalora PK, Maljkovic Berry I, Archer J, Penugonda S, Fischer W, Richman DD, Bhattacharya T, Malim MH, Wolinsky SM. Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection. PLoS Pathog 2014; 10:e1004281. [PMID: 25080100 PMCID: PMC4117599 DOI: 10.1371/journal.ppat.1004281] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/13/2014] [Indexed: 11/18/2022] Open
Abstract
Human APOBEC3 proteins are cytidine deaminases that contribute broadly to innate immunity through the control of exogenous retrovirus replication and endogenous retroelement retrotransposition. As an intrinsic antiretroviral defense mechanism, APOBEC3 proteins induce extensive guanosine-to-adenosine (G-to-A) mutagenesis and inhibit synthesis of nascent human immunodeficiency virus-type 1 (HIV-1) cDNA. Human APOBEC3 proteins have additionally been proposed to induce infrequent, potentially non-lethal G-to-A mutations that make subtle contributions to sequence diversification of the viral genome and adaptation though acquisition of beneficial mutations. Using single-cycle HIV-1 infections in culture and highly parallel DNA sequencing, we defined trinucleotide contexts of the edited sites for APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H. We then compared these APOBEC3 editing contexts with the patterns of G-to-A mutations in HIV-1 DNA in cells obtained sequentially from ten patients with primary HIV-1 infection. Viral substitutions were highest in the preferred trinucleotide contexts of the edited sites for the APOBEC3 deaminases. Consistent with the effects of immune selection, amino acid changes accumulated at the APOBEC3 editing contexts located within human leukocyte antigen (HLA)-appropriate epitopes that are known or predicted to enable peptide binding. Thus, APOBEC3 activity may induce mutations that influence the genetic diversity and adaptation of the HIV-1 population in natural infection.
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Affiliation(s)
- Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Susan J. Little
- Division of Infectious Diseases, University of California San Diego, San Diego, California, United States of America
| | - Yoon-Seok Chung
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Prabhjeet K. Phalora
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, United Kingdom
| | - Irina Maljkovic Berry
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - John Archer
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Will Fischer
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Douglas D. Richman
- Division of Infectious Diseases, University of California San Diego, San Diego, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Tanmoy Bhattacharya
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Michael H. Malim
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, United Kingdom
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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Nowarski R, Prabhu P, Kenig E, Smith Y, Britan-Rosich E, Kotler M. APOBEC3G inhibits HIV-1 RNA elongation by inactivating the viral trans-activation response element. J Mol Biol 2014; 426:2840-53. [PMID: 24859335 DOI: 10.1016/j.jmb.2014.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Deamination of cytidine residues in viral DNA is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 (HIV-1) replication. dC-to-dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here, we demonstrate that A3G provides an additional layer of defense against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. These results identify A3G as an efficient mutator and that deamination of (-)SSDNA results in an early block of HIV-1 transcription.
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Affiliation(s)
- Roni Nowarski
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Ponnandy Prabhu
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Edan Kenig
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Elena Britan-Rosich
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Moshe Kotler
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel.
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Monajemi M, Woodworth CF, Zipperlen K, Gallant M, Grant MD, Larijani M. Positioning of APOBEC3G/F mutational hotspots in the human immunodeficiency virus genome favors reduced recognition by CD8+ T cells. PLoS One 2014; 9:e93428. [PMID: 24722422 PMCID: PMC3982959 DOI: 10.1371/journal.pone.0093428] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/05/2014] [Indexed: 11/18/2022] Open
Abstract
Due to constitutive expression in cells targeted by human immunodeficiency virus (HIV), and immediate mode of viral restriction upon HIV entry into the host cell, APOBEC3G (A3G) and APOBEC3F (A3F) have been considered primarily as agents of innate immunity. Recent bioinformatic and mouse model studies hint at the possibility that mutation of the HIV genome by these enzymes may also affect adaptive immunity but whether this occurs in HIV-infected individuals has not been examined. We evaluated whether APOBEC-mediated mutations within common HIV CD8+ T cell epitopes can potentially enhance or diminish activation of HIV-specific CD8+ T cells from infected individuals. We compared ex vivo activation of CD8+ T lymphocytes from HIV-infected individuals by wild type HIV peptide epitopes and synthetic variants bearing simulated A3G/F-induced mutations by measuring interferon-γ (IFN-γ) production. We found that A3G/F-induced mutations consistently diminished HIV-specific CD8+ T cell responses against the common epitopes we tested. If this reflects a significant trend in vivo, then adaptation by HIV to enrich sequences that are favored for mutation by A3G/F (A3G/F hotspots) in portions of its genome that encode immunogenic CD8+ T cell epitopes would favor CTL escape. Indeed, we found the most frequently mutated A3G motif (CCC) is enriched up to 6-fold within viral genomic sequences encoding immunodominant CD8+ T cell epitopes in Gag, Pol and Nef. Within each gene, A3G/F hotspots are more abundant in sequences encoding epitopes that are commonly recognized due to their HLA restriction. Thus, in our system, mutations of the HIV genome, mimicking A3G/F activity, appeared to abrogate or severely reduce CTL recognition. We suggest that the physiological significance of this potential effect in facilitating CTL escape is echoed in the adaptation of the HIV genome to enrich A3G/F hotspots in sequences encoding CTL epitopes that are more immunogenic at the population level.
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Affiliation(s)
- Mahdis Monajemi
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Claire F. Woodworth
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Katrin Zipperlen
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Maureen Gallant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Michael D. Grant
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- * E-mail: (MDG); (ML)
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- * E-mail: (MDG); (ML)
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Maeda K, Almofty SA, Singh SK, Eid MMA, Shimoda M, Ikeda T, Koito A, Pham P, Goodman MF, Sakaguchi N. GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 191:6030-6039. [PMID: 24198285 PMCID: PMC4086635 DOI: 10.4049/jimmunol.1302057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ssDNA-dependent deoxycytidine deaminase apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (A3G) is a potent restrictive factor against HIV-1 virus lacking viral-encoded infectivity factor (Vif) in CD4(+) T cells. A3G antiretroviral activity requires its encapsulation into HIV-1 virions. In this study, we show that germinal center-associated nuclear protein (GANP) is induced in activated CD4(+) T cells and physically interacts with A3G. Overexpression of GANP augments the A3G encapsidation into the virion-like particles and ΔVif HIV-1 virions. GANP is encapsidated in HIV-1 virion and modulates A3G packaging into the cores together with cellular RNAs, including 7SL RNA, and with unspliced HIV-1 genomic RNA. GANP upregulation leads to a significant increase in A3G-catalyzed G→A hypermutation in the viral genome and suppression of HIV-1 infectivity in a single-round viral infection assay. Conversely, GANP knockdown caused a marked increase in HIV-1 infectivity in a multiple-round infection assay. The data suggest that GANP is a cellular factor that facilitates A3G encapsidation into HIV-1 virions to inhibit viral infectivity.
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MESH Headings
- APOBEC-3G Deaminase
- Acetyltransferases/antagonists & inhibitors
- Acetyltransferases/biosynthesis
- Acetyltransferases/chemistry
- Acetyltransferases/genetics
- Acetyltransferases/physiology
- CD4-Positive T-Lymphocytes/immunology
- Cells, Cultured
- Cytidine Deaminase/chemistry
- Cytidine Deaminase/physiology
- Genes, vif
- HIV-1/physiology
- HIV-1/ultrastructure
- Humans
- Intracellular Signaling Peptides and Proteins/antagonists & inhibitors
- Intracellular Signaling Peptides and Proteins/biosynthesis
- Intracellular Signaling Peptides and Proteins/chemistry
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/physiology
- Lymphocyte Activation
- Mutation
- Protein Interaction Mapping
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Small Cytoplasmic/metabolism
- RNA, Small Interfering/pharmacology
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Signal Recognition Particle/metabolism
- Up-Regulation
- Virion/metabolism
- Virion/ultrastructure
- Virulence
- Virus Replication
- vif Gene Products, Human Immunodeficiency Virus/deficiency
- RNA, Small Untranslated
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Affiliation(s)
- Kazuhiko Maeda
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Sarah Ameen Almofty
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Shailendra Kumar Singh
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Mohammed Mansour Abbas Eid
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Terumasa Ikeda
- Department of Retrovirology and Self-Defense, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Atsushi Koito
- Department of Retrovirology and Self-Defense, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Nobuo Sakaguchi
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
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De Pasquale M, Kourteva Y, Allos T, D'Aquila RT. Lower HIV provirus levels are associated with more APOBEC3G protein in blood resting memory CD4+ T lymphocytes of controllers in vivo. PLoS One 2013; 8:e76002. [PMID: 24146808 PMCID: PMC3797809 DOI: 10.1371/journal.pone.0076002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/21/2013] [Indexed: 12/22/2022] Open
Abstract
Immunodeficiency does not progress for prolonged periods in some HLA B57- and/or B27-positive subjects with human immunodeficiency virus type 1 (HIV) infection, even in the absence of antiretroviral therapy (ART). These "controllers" have fewer HIV provirus-containing peripheral blood mononuclear cells than "non-controller" subjects, but lymphocytes that harbor latent proviruses were not specifically examined in studies to date. Provirus levels in resting memory cells that can serve as latent reservoirs of HIV in blood were compared here between controllers and ART-suppressed non-controllers. APOBEC3G (A3G), a cellular factor that blocks provirus formation at multiple steps if not antagonized by HIV virion infectivity factor (Vif), was also studied. HLA-linked HIV control was associated with less provirus and more A3G protein in resting CD4+ T central memory (Tcm) and effector memory (Tem) lymphocytes (provirus: p = 0.01 for Tcm and p = 0.02 for Tem; A3G: p = 0.02 for Tcm and p = 0.02 for Tem). Resting memory T cells with the highest A3G protein levels (>0.5 RLU per unit of actin) had the lowest levels of provirus (<1,000 copies of DNA per million cells) in vivo (p = 0.03, Fisher's exact test). Using two different experimental approaches, Vif-positive viruses with more A3G were found to have decreased virion infectivity ex vivo. These results raise the hypothesis that HIV control is associated with increased cellular A3G that may be packaged into Vif-positive virions to add that mode of inhibition of provirus formation to previously described adaptive immune mechanisms for HIV control.
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Affiliation(s)
- MariaPia De Pasquale
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Yordanka Kourteva
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Tara Allos
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Richard T. D'Aquila
- Division of Infectious Diseases and Northwestern HIV Translational Research Center, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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Misra A, Thippeshappa R, Kimata JT. Macaques as model hosts for studies of HIV-1 infection. Front Microbiol 2013; 4:176. [PMID: 23825473 PMCID: PMC3695370 DOI: 10.3389/fmicb.2013.00176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/11/2013] [Indexed: 12/16/2022] Open
Abstract
Increasing evidence indicates that the host range of primate lentiviruses is in part determined by their ability to counteract innate restriction factors that are effectors of the type 1 interferon (IFN-1) response. For human immunodeficiency virus type 1 (HIV-1), in vitro experiments have shown that its tropism may be narrow and limited to humans and chimpanzees because its replication in other non-human primate species is hindered by factors such as TRIM5α (tripartite motif 5 alpha), APOBEC3G (apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3), and tetherin. Based on these data, it has been hypothesized that primate lentiviruses will infect and replicate in a new species if they are able to counteract and evade suppression by the IFN-1 response. Several studies have tested whether engineering HIV-1 recombinants with minimal amounts of simian immunodeficiency virus sequences would enable replication in CD4+ T cells of non-natural hosts such as Asian macaques and proposed that infection of these macaque species could be used to study transmission and pathogenesis. Indeed, infection of macaques with these viruses revealed that Vif-mediated counteraction of APOBEC3G function is central to cross-species tropism but that other IFN-induced factors may also play important roles in controlling replication. Further studies of these macaque models of infection with HIV-1 derivatives could provide valuable insights into the interaction of lentiviruses and the innate immune response and how lentiviruses adapt and cause disease.
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Affiliation(s)
- Anisha Misra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston, TX, USA
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49
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Vieira VC, Soares MA. The role of cytidine deaminases on innate immune responses against human viral infections. BIOMED RESEARCH INTERNATIONAL 2013; 2013:683095. [PMID: 23865062 PMCID: PMC3707226 DOI: 10.1155/2013/683095] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 05/29/2013] [Accepted: 05/31/2013] [Indexed: 02/06/2023]
Abstract
The APOBEC family of proteins comprises deaminase enzymes that edit DNA and/or RNA sequences. The APOBEC3 subgroup plays an important role on the innate immune system, acting on host defense against exogenous viruses and endogenous retroelements. The role of APOBEC3 proteins in the inhibition of viral infection was firstly described for HIV-1. However, in the past few years many studies have also shown evidence of APOBEC3 action on other viruses associated with human diseases, including HTLV, HCV, HBV, HPV, HSV-1, and EBV. APOBEC3 inhibits these viruses through a series of editing-dependent and independent mechanisms. Many viruses have evolved mechanisms to counteract APOBEC effects, and strategies that enhance APOBEC3 activity constitute a new approach for antiviral drug development. On the other hand, novel evidence that editing by APOBEC3 constitutes a source for viral genetic diversification and evolution has emerged. Furthermore, a possible role in cancer development has been shown for these host enzymes. Therefore, understanding the role of deaminases on the immune response against infectious agents, as well as their role in human disease, has become pivotal. This review summarizes the state-of-the-art knowledge of the impact of APOBEC enzymes on human viruses of distinct families and harboring disparate replication strategies.
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Affiliation(s)
- Valdimara C. Vieira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, No. 37–4 Andar, Bairro de Fátima, 20231-050 Rio de Janeiro, RJ, Brazil
| | - Marcelo A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rua André Cavalcanti, No. 37–4 Andar, Bairro de Fátima, 20231-050 Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, 21949-570 Rio de Janeiro, RJ, Brazil
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50
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Münk C, Jensen BEO, Zielonka J, Häussinger D, Kamp C. Running loose or getting lost: how HIV-1 counters and capitalizes on APOBEC3-induced mutagenesis through its Vif protein. Viruses 2012; 4:3132-61. [PMID: 23202519 PMCID: PMC3509687 DOI: 10.3390/v4113132] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/29/2012] [Accepted: 11/05/2012] [Indexed: 12/24/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) dynamics reflect an intricate balance within the viruses’ host. The virus relies on host replication factors, but must escape or counter its host’s antiviral restriction factors. The interaction between the HIV-1 protein Vif and many cellular restriction factors from the APOBEC3 protein family is a prominent example of this evolutionary arms race. The viral infectivity factor (Vif) protein largely neutralizes APOBEC3 proteins, which can induce in vivo hypermutations in HIV-1 to the extent of lethal mutagenesis, and ensures the production of viable virus particles. HIV-1 also uses the APOBEC3-Vif interaction to modulate its own mutation rate in harsh or variable environments, and it is a model of adaptation in a coevolutionary setting. Both experimental evidence and the substantiation of the underlying dynamics through coevolutionary models are presented as complementary views of a coevolutionary arms race.
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Affiliation(s)
- Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
| | - Björn-Erik O. Jensen
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
| | - Jörg Zielonka
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
- Roche Glycart AG, Schlieren 8952, Switzerland
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.M.); (B.-E.O.J.); (J.Z.); (D.H.)
| | - Christel Kamp
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
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