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Prelli Bozzo C, Laliberté A, De Luna A, Pastorio C, Regensburger K, Krebs S, Graf A, Blum H, Volcic M, Sparrer KMJ, Kirchhoff F. Replication competent HIV-guided CRISPR screen identifies antiviral factors including targets of the accessory protein Nef. Nat Commun 2024; 15:3813. [PMID: 38714682 PMCID: PMC11076291 DOI: 10.1038/s41467-024-48228-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/24/2024] [Indexed: 05/10/2024] Open
Abstract
Innate antiviral factors are essential for effective defense against viral pathogens. However, the identity of major restriction mechanisms remains elusive. Current approaches to discover antiviral factors usually focus on the initial steps of viral replication and are limited to a single round of infection. Here, we engineered libraries of >1500 replication-competent HIV-1 constructs each expressing a single gRNAs to target >500 cellular genes for virus-driven discovery of antiviral factors. Passaging in CD4+ T cells robustly enriched HIV-1 encoding sgRNAs against GRN, CIITA, EHMT2, CEACAM3, CC2D1B and RHOA by >50-fold. Using an HIV-1 library lacking the accessory nef gene, we identified IFI16 as a Nef target. Functional analyses in cell lines and primary CD4+ T cells support that the HIV-driven CRISPR screen identified restriction factors targeting virus entry, transcription, release and infectivity. Our HIV-guided CRISPR technique enables sensitive discovery of physiologically relevant cellular defense factors throughout the entire viral replication cycle.
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Affiliation(s)
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Aurora De Luna
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Chiara Pastorio
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Kerstin Regensburger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center, LMU Munich, 81377, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis Gene Center, LMU Munich, 81377, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis Gene Center, LMU Munich, 81377, Munich, Germany
| | - Meta Volcic
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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2
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Jadhav S, Nema V. Association of Viral and Host Genetic Architecture with the Status of Neurocognitive Disorder in HIV-Infected Individuals. AIDS Res Hum Retroviruses 2023; 39:688-698. [PMID: 37335040 DOI: 10.1089/aid.2022.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
The polymorphisms in host genes such as CCR5, CCR2, stromal derived factor (SDF), and MBL (mannose-binding lectin) as well as the viral nef gene have been shown to influence human immunodeficiency virus (HIV) infection, followed by the development of HIV-associated neurocognitive disorder (HAND). In this preliminary study with a limited number of samples, we have tried to associate the genetic polymorphism from the host and viral genetic factors with the neurocognitive status along with immuno-virological parameters. The total RNA was isolated from 10 unlinked plasma samples containing 5 samples from each group with and without HAND based on the International HIV Dementia Scale (IHDS) score <9.5 and >9.5, respectively. The CCR5, CCR2, SDF, MBL, and HIV nef genes were amplified and digested with restriction enzymes, except for the nef gene amplicon. Restrictions fragment length polymorphism (RFLP) was used to determine whether allelic variations were present in the digested host gene products, while sequencing was done for HIV nef amplicons without digestion. CCR5 delta 32 heterozygous variants were present in two samples from the HAND group. Three samples with HAND showed SDF-1 3' heterozygous allelic variant, while the MBL-2 gene presented with a homozygous mutant allele (D/D) in codon 52, heterozygous mutant allele (A/B) in codon 54, and codon 57 (A/C) for all samples except IHDS-2 irrespective of dementia status. Furthermore, amino acid alignment of Nef sequences confirmed the heterogeneity, while prediction of the human leukocyte antigen binding epitopes further explored its effect on functional motifs with variable binding efficiency such as epitopes GAFDLSFFL (aa 83) and LTFGWCFKL (aa 138) binding with HLA molecules at 60% and 80%, respectively. Thus, host genetics evidently influence predisposition to HIV infection and HAND. The genetic variability in the nef gene from both groups resulted in altering the functionality of specific domains and showing its impact on the progression of the disease, which needs to be explored.
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Affiliation(s)
- Sushama Jadhav
- Division of Molecular Biology, Indian Council of Medical Research, National AIDS Research Institute, Pune, India
- Symbiosis International University, Pune, India
| | - Vijay Nema
- Division of Molecular Biology, Indian Council of Medical Research, National AIDS Research Institute, Pune, India
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3
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Lamers SL, Fogel GB, Liu ES, Nolan DJ, Rose R, McGrath MS. HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation. Infect Genet Evol 2023; 115:105514. [PMID: 37832752 PMCID: PMC10842591 DOI: 10.1016/j.meegid.2023.105514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND HIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner. METHODS 2253 sequences representing subtypes A1, B, C, and D were aligned and domains with known functional properties were scored based on amino acid physicochemical properties. Following feature generation, we used statistical pruning and evolved neural networks (ENNs) to determine if we could successfully classify subtypes. Next, we used ENNs to identify the top five key Nef physicochemical features applied to specific immunoregulatory domains that differentiated subtypes. A signature pattern analysis was performed to the assess amino acid diversity in sub-domains that differentiated each subtype. RESULTS In validation studies, ENNs successfully differentiated each subtype at A1 (87.2%), subtype B (89.5%), subtype C (91.7%), and subtype D (85.1%). Our feature-based domain scoring, followed by t-tests, and a similar ENN identified subtype-specific domain-associated features. Subtype A1 was associated with alterations in Nef CD4 binding domain; subtype B was associated with alterations with the AP-2 Binding domain; subtype C was associated with alterations in a structural Alpha Helix domain; and, subtype D was associated with alterations in a Beta-Sheet domain. CONCLUSIONS Recent studies have focused on HIV Nef as a driver of immunoregulatory disease in those HIV infected and on ART. Nef acts through a complex mixture of interactions that are directly linked to the key features of the subtype-specific domains we identified with the ENN. The study supports the hypothesis that varied Nef subtypes contribute to subtype-specific disease progression.
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Affiliation(s)
| | | | - Enoch S Liu
- Natural Selection, San Diego, California, USA
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4
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Olabode AS, Mumby MJ, Wild TA, Muñoz-Baena L, Dikeakos JD, Poon AFY. Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses. Mol Biol Evol 2023; 40:msad164. [PMID: 37463439 PMCID: PMC10400143 DOI: 10.1093/molbev/msad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
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Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
| | - Mitchell J Mumby
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Tristan A Wild
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Laura Muñoz-Baena
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
- Department of Microbiology & Immunology, Western University, London, Canada
- Department of Computer Science, Western University, London, Canada
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5
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Ramdas P, Chande A. SERINC5 Mediates a Postintegration Block to HIV-1 Gene Expression in Macrophages. mBio 2023; 14:e0016623. [PMID: 36976020 PMCID: PMC10127607 DOI: 10.1128/mbio.00166-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023] Open
Abstract
HIV-1 antagonizes SERINC5 by redundant mechanisms, primarily through Nef and additionally via envelope glycoprotein. Paradoxically, HIV-1 preserves Nef function to ensure the exclusion of SERINC5 from virion incorporation regardless of the availability of envelope that can confer resistance, suggesting additional roles of the virion-incorporated host factor. Here, we report an unusual mode of SERINC5 action in inhibiting viral gene expression. This inhibition is observed only in the myeloid lineage cells but not in the cells of epithelial or lymphoid origin. We found that SERINC5-bearing viruses induce the expression of RPL35 and DRAP1 in macrophages, and these host proteins intercept HIV-1 Tat from binding to and recruiting a mammalian capping enzyme (MCE1) to the HIV-1 transcriptional complex. As a result, uncapped viral transcripts are synthesized, leading to the inhibition of viral protein synthesis and subsequent progeny virion biogenesis. Cell-type-specific inhibition of HIV-1 gene expression thus exemplifies a novel antiviral function of virion-incorporated SERINC5. IMPORTANCE In addition to Nef, HIV-1 envelope glycoprotein has been shown to modulate SERINC5-mediated inhibition. Counterintuitively, Nef from the same isolates preserves the ability to prevent SERINC5 incorporation into virions, implying additional functions of the host protein. We identify that virion-associated SERINC5 can manifest an antiviral mechanism independent of the envelope glycoprotein to regulate HIV-1 gene expression in macrophages. This mechanism is exhibited by affecting the viral RNA capping and is plausibly adopted by the host to overcome the envelope glycoprotein-mediated resistance to SERINC5 restriction.
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Affiliation(s)
- Pavitra Ramdas
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Ajit Chande
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
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6
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Heinrich F, Thomas CE, Alvarado JJ, Eells R, Thomas A, Doucet M, Whitlatch KN, Aryal M, Lösche M, Smithgall TE. Neutron Reflectometry and Molecular Simulations Demonstrate HIV-1 Nef Homodimer Formation on Model Lipid Bilayers. J Mol Biol 2023; 435:168009. [PMID: 36773691 PMCID: PMC10079580 DOI: 10.1016/j.jmb.2023.168009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
The HIV-1 Nef protein plays a critical role in viral infectivity, high-titer replication in vivo, and immune escape of HIV-infected cells. Nef lacks intrinsic biochemical activity, functioning instead through interactions with diverse host cell signaling proteins and intracellular trafficking pathways. Previous studies have established an essential role for Nef homodimer formation at the plasma membrane for most if not all its functions. Here we combined neutron reflectometry of full-length myristoylated Nef bound to model lipid bilayers with molecular simulations based on previous X-ray crystal structures of Nef homodimers. This integrated approach provides direct evidence that Nef associates with the membrane as a homodimer with its structured core region displaced from the membrane for partner protein engagement. Parallel studies of a dimerization-defective mutant, Nef-L112D, demonstrate that the helical dimerization interface present in previous crystal structures stabilizes the membrane-bound dimer. X-ray crystallography of the Nef-L112D mutant in complex with the SH3 domain of the Nef-associated host cell kinase Hck revealed a monomeric 1:1 complex instead of the 2:2 dimer complex formed with wild-type Nef. Importantly, the crystal structure of the Nef-L112D core and SH3 interface are virtually identical to the wild-type complex, indicating that this mutation does not affect the overall Nef fold. These findings support the intrinsic capacity of Nef to homodimerize at lipid bilayers using structural features present in X-ray crystal structures of dimeric complexes.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Catherine E Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Rebecca Eells
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alyssa Thomas
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Mathieu Doucet
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kindra N Whitlatch
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Manish Aryal
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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7
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Duette G, Cronin S, Kelleher AD, Palmer S. Viral competition assay to assess the role of HIV-1 proteins in immune evasion. STAR Protoc 2023; 4:102025. [PMID: 36853860 PMCID: PMC9860156 DOI: 10.1016/j.xpro.2022.102025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/29/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
CD8+ T lymphocytes can recognize and eliminate cells infected by viruses. However, the human immunodeficiency virus (HIV-1) has developed mechanisms to evade CD8+ T-cell-mediated clearance. Here, we describe a protocol to assess the role of the HIV-1 protein Nef in immune evasion. The viral competition assay reveals the preferential killing of HIV-1-infected cells unable to express Nef. This methodology can be extended to study HIV-1 proteins involved in immune evasion and viral variants encoding cytotoxic T lymphocyte escape mutations. For complete details on the use and execution of this protocol, please refer to Duette et al. (2022).1.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia.
| | - Samantha Cronin
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia.
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8
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Ghaly M, Proulx J, Borgmann K, Park IW. Novel role of HIV-1 Nef in regulating the ubiquitination of cellular proteins. Front Cell Infect Microbiol 2023; 13:1106591. [PMID: 36968110 PMCID: PMC10031067 DOI: 10.3389/fcimb.2023.1106591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 03/10/2023] Open
Abstract
Our recent data established that HIV-1 Nef is pivotal in determining the fate of cellular proteins by modulating ubiquitination. However, it is unknown which proteins are ubiquitinated in the presence of Nef, a question critical for understanding the proliferation/restriction strategies of HIV-1 in infected cells. To identify cellular proteins ubiquitinated by Nef, we conducted a proteomic analysis of cellular proteins in the presence and absence of Nef. Proteomic analysis in HEK293T cells indicated that 93 proteins were upregulated and 232 were downregulated in their ubiquitination status by Nef. Computational analysis classified these proteins based on molecular function, biological process, subcellular localization, and biological pathway. Of those proteins, we found a majority of molecular functions to be involved in binding and catalytic activity. With respect to biological processes, a significant portion of the proteins identified were related to cellular and metabolic processes. Subcellular localization analysis showed the bulk of proteins to be localized to the cytosol and cytosolic compartments, which is consistent with the known function and location of Nef during HIV-1 infection. As for biological pathways, the wide range of affected proteins was denoted by the multiple modes to fulfill function, as distinguished from a strictly singular means, which was not detected. Among these ubiquitinated proteins, six were found to directly interact with Nef, wherein two were upregulated and four downregulated. We also identified 14 proteins involved in protein stability through directly participating in the Ubiquitin Proteasome System (UPS)-mediated proteasomal degradation pathway. Of those proteins, we found six upregulated and eight downregulated. Taken together, these analyses indicate that HIV-1 Nef is integral to regulating the stability of various cellular proteins via modulating ubiquitination. The molecular mechanisms directing Nef-triggered regulation of cellular protein ubiquitination are currently under investigation.
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9
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Olety B, Usami Y, Wu Y, Peters P, Göttlinger H. AP-2 Adaptor Complex-Dependent Enhancement of HIV-1 Replication by Nef in the Absence of the Nef/AP-2 Targets SERINC5 and CD4. mBio 2023; 14:e0338222. [PMID: 36622146 PMCID: PMC9973267 DOI: 10.1128/mbio.03382-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Nef hijacks the clathrin adaptor complex 2 (AP-2) to downregulate the viral receptor CD4 and the antiviral multipass transmembrane proteins SERINC3 and SERINC5, which inhibit the infectivity of progeny virions when incorporated. In Jurkat Tag T lymphoid cells lacking SERINC3 and SERINC5, Nef is no longer required for full progeny virus infectivity and for efficient viral replication. However, in MOLT-3 T lymphoid cells, HIV-1 replication remains highly dependent on Nef even in the absence of SERINC3 and SERINC5. Using a knockout (KO) approach, we now show that the Nef-mediated enhancement of HIV-1 replication in MOLT-3 cells does not depend on the Nef-interacting kinases LCK and PAK2. Furthermore, Nef substantially enhanced HIV-1 replication even in triple-KO MOLT-3 cells that simultaneously lacked the three Nef/AP-2 targets, SERINC3, SERINC5, and CD4, and were reconstituted with a Nef-resistant CD4 to permit HIV-1 entry. Nevertheless, the ability of Nef mutants to promote HIV-1 replication in the triple-KO cells correlated strictly with the ability to bind AP-2. In addition, knockdown and reconstitution experiments confirmed the involvement of AP-2. These observations raise the possibility that MOLT-3 cells express a novel antiviral factor that is downregulated by Nef in an AP-2-dependent manner. IMPORTANCE The HIV-1 Nef protein hijacks a component of the cellular endocytic machinery called AP-2 to downregulate the viral receptor CD4 and the antiviral cellular membrane proteins SERINC3 and SERINC5. In the absence of Nef, SERINC3 and SERINC5 are taken up into viral particles, which reduces their infectivity. Surprisingly, in a T cell line called MOLT-3, Nef remains crucial for HIV-1 spreading in the absence of SERINC3 and SERINC5. We now show that this effect of Nef also does not depend on the cellular signaling molecules and Nef interaction partners LCK and PAK2. Nef was required for efficient HIV-1 spreading even in triple-knockout cells that completely lacked Nef/AP-2-sensitive CD4, in addition to the Nef/AP-2 targets SERINC3 and SERINC5. Nevertheless, our results indicate that the enhancement of HIV-1 spreading by Nef in the triple-knockout cells remained AP-2 dependent, which suggests the presence of an unknown antiviral factor that is sensitive to Nef/AP-2-mediated downregulation.
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Affiliation(s)
- Balaji Olety
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Yoshiko Usami
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Yuanfei Wu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Paul Peters
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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10
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Ramirez PW, Vollbrecht T, Acosta FM, Suarez M, Angerstein AO, Wallace J, O' Connell RM, Guatelli J. Nef enhances HIV-1 replication and infectivity independently of SERINC5 in CEM T cells. Virology 2023; 578:154-162. [PMID: 36577173 PMCID: PMC10484624 DOI: 10.1016/j.virol.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022]
Abstract
A primary function of HIV-1 Nef is the enhancement of viral infectivity and replication. Whether counteraction of the antiretroviral proteins SERINC3 and SERINC5 is the cause of this positive influence on viral growth-rate and infectivity remains unclear. Here, we utilized CRISPR/Cas9 to knockout SERINC3 and SERINC5 in a leukemic CD4-positive T cell line (CEM) that displays nef-related infectivity and growth-rate phenotypes. Viral replication was attenuated in CEM cells infected with HIV-1 lacking Nef (HIV-1ΔNef). This attenuated growth-rate phenotype was observed regardless of whether the coding regions of the serinc3 or serinc5 genes were intact. Moreover, knockout of serinc5 alone or of both serinc5 and serinc3 together failed to restore the infectivity of HIV1ΔNef virions produced from infected CEM cells. Our results corroborate a similar study using another T-lymphoid cell line (MOLT-3) and indicate that the antagonism of SERINC3 and SERINC5 does not fully explain the virology of HIV-1 lacking Nef.
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Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA, USA.
| | - Thomas Vollbrecht
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
| | - Francisco M Acosta
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA, USA
| | | | - Aaron O Angerstein
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
| | - Jared Wallace
- Division of Microbiology and Immunology, Department of Pathology, The University of Utah, Salt Lake City, UT, USA
| | - Ryan M O' Connell
- Division of Microbiology and Immunology, Department of Pathology, The University of Utah, Salt Lake City, UT, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
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Nolan DJ, Rose R, Zhang R, Leong A, Fogel GB, Scholte LLS, Bethony JM, Bracci P, Lamers SL, McGrath MS. The Persistence of HIV Diversity, Transcription, and Nef Protein in Kaposi's Sarcoma Tumors during Antiretroviral Therapy. Viruses 2022; 14:v14122774. [PMID: 36560778 PMCID: PMC9782636 DOI: 10.3390/v14122774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Epidemic Kaposi's sarcoma (KS), defined by co-infection with Human Herpes Virus 8 (HHV-8) and the Human Immunodeficiency Virus (HIV), is a major cause of mortality in sub-Saharan Africa. Antiretroviral therapy (ART) significantly reduces the risk of developing KS, and for those with KS, tumors frequently resolve with ART alone. However, for unknown reasons, a significant number of KS cases do not resolve and can progress to death. To explore how HIV responds to ART in the KS tumor microenvironment, we sequenced HIV env-nef found in DNA and RNA isolated from plasma, peripheral blood mononuclear cells, and tumor biopsies, before and after ART, in four Ugandan study participants who had unresponsive or progressive KS after 180-250 days of ART. We performed immunohistochemistry experiments to detect viral proteins in matched formalin-fixed tumor biopsies. Our sequencing results showed that HIV diversity and RNA expression in KS tumors are maintained after ART, despite undetectable plasma viral loads. The presence of spliced HIV transcripts in KS tumors after ART was consistent with a transcriptionally active viral reservoir. Immunohistochemistry staining found colocalization of HIV Nef protein and tissue-resident macrophages in the KS tumors. Overall, our results demonstrated that even after ART reduced plasma HIV viral load to undetectable levels and restored immune function, HIV in KS tumors continues to be transcriptionally and translationally active, which could influence tumor maintenance and progression.
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Affiliation(s)
- David J. Nolan
- Bioinfoexperts, LLC, Thibodaux, LA 70301, USA
- Correspondence:
| | | | - Rongzhen Zhang
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
| | - Alan Leong
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
| | | | - Larissa L. S. Scholte
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Jeffrey M. Bethony
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Paige Bracci
- The AIDS and Cancer Specimen Resource, San Francisco, CA 94110, USA
| | | | - Michael S. McGrath
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
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12
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Stevenson EM, Terry S, Copertino D, Leyre L, Danesh A, Weiler J, Ward AR, Khadka P, McNeil E, Bernard K, Miller IG, Ellsworth GB, Johnston CD, Finkelsztein EJ, Zumbo P, Betel D, Dündar F, Duncan MC, Lapointe HR, Speckmaier S, Moran-Garcia N, Papa MP, Nicholes S, Stover CJ, Lynch RM, Caskey M, Gaebler C, Chun TW, Bosque A, Wilkin TJ, Lee GQ, Brumme ZL, Jones RB. SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8 + T-cells. Nat Commun 2022; 13:4888. [PMID: 35985993 PMCID: PMC9389512 DOI: 10.1038/s41467-022-32376-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/26/2022] [Indexed: 12/05/2022] Open
Abstract
Efforts to cure HIV have focused on reactivating latent proviruses to enable elimination by CD8+ cytotoxic T-cells. Clinical studies of latency reversing agents (LRA) in antiretroviral therapy (ART)-treated individuals have shown increases in HIV transcription, but without reductions in virologic measures, or evidence that HIV-specific CD8+ T-cells were productively engaged. Here, we show that the SARS-CoV-2 mRNA vaccine BNT162b2 activates the RIG-I/TLR - TNF - NFκb axis, resulting in transcription of HIV proviruses with minimal perturbations of T-cell activation and host transcription. T-cells specific for the early gene-product HIV-Nef uniquely increased in frequency and acquired effector function (granzyme-B) in ART-treated individuals following SARS-CoV-2 mRNA vaccination. These parameters of CD8+ T-cell induction correlated with significant decreases in cell-associated HIV mRNA, suggesting killing or suppression of cells transcribing HIV. Thus, we report the observation of an intervention-induced reduction in a measure of HIV persistence, accompanied by precise immune correlates, in ART-suppressed individuals. However, we did not observe significant depletions of intact proviruses, underscoring challenges to achieving (or measuring) HIV reservoir reductions. Overall, our results support prioritizing the measurement of granzyme-B-producing Nef-specific responses in latency reversal studies and add impetus to developing HIV-targeted mRNA therapeutic vaccines that leverage built-in LRA activity.
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Affiliation(s)
- Eva M Stevenson
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Sandra Terry
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Dennis Copertino
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Louise Leyre
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Ali Danesh
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jared Weiler
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Adam R Ward
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Pragya Khadka
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Evan McNeil
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kevin Bernard
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Itzayana G Miller
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Grant B Ellsworth
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Carrie D Johnston
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Eli J Finkelsztein
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Paul Zumbo
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
| | - Doron Betel
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
| | - Friederike Dündar
- Applied Bioinformatics Core, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hope R Lapointe
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Sarah Speckmaier
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Nadia Moran-Garcia
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Michelle Premazzi Papa
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Samuel Nicholes
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Carissa J Stover
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Rebecca M Lynch
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID, NIH, Bethesda, MD, USA
| | - Alberto Bosque
- Dept of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Timothy J Wilkin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Guinevere Q Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - R Brad Jones
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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13
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Donadoni M, Huang W, Yarandi SS, Burdo TH, Chang SL, Sariyer IK. Modulation of OPRM1 Alternative Splicing by Morphine and HIV-1 Nef. J Neuroimmune Pharmacol 2022; 17:277-288. [PMID: 34420144 PMCID: PMC8859008 DOI: 10.1007/s11481-021-10009-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/06/2021] [Indexed: 12/29/2022]
Abstract
Clinically used opioids, such as morphine, activate the mu opioid receptor (MOR) encoded by Opioid Receptor Mu 1 (OPRM1) gene. Examination of the opioid receptor genes showed that the human OPRM1 pre-mRNA undergoes extensive alternative splicing events and capable of expressing 21 isoforms. However, characterization of OPRM1 signaling is generalized, and only one isoform (MOR-1) has been extensively studied. Compounding this issue is the increasing significance of intravenous drug abuse in HIV neuropathogenesis. Here, we investigated the molecular impact of morphine and HIV-1 on regulation of OPRM1 pre-mRNA splicing in in vitro and in vivo models. Our results suggested that morphine treatment specifically induces the alternative splicing of MOR-1X isoform among the other isoforms analyzed in neuronal cells. Interestingly, alternative splicing and expression of MOR-1X isoform was also induced in postmortem brain tissues obtained from people with HIV (PWH). Additionally, treatment of control rats with morphine induced alternative splicing of MOR-1X in the brain regions involved in the reward pathways. More interestingly, HIV-1 transgenic (HIV-1Tg) rats, showed an additive induction of MOR-1X isoform with the exposure to morphine. To further assess the possible role of HIV secretory proteins in alternative splicing of OPRM1 gene, we analyzed the impact of HIV-1 Tat, gp120 and Nef proteins on alternative splicing of MOR-1X isoform. While the Tat and gp120 had no visible effects, treatment of neurons with Nef induced MOR-1X alternative splicing that was comparable to treatment with morphine. Altogether, our results suggest that HIV-1 may alter MOR isoform expression with Nef protein by amplifying the rate of MOR-1X alternative splicing induced by morphine.
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Affiliation(s)
- Martina Donadoni
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Wenfei Huang
- Institute of NeuroImmune Pharmacology and Department of Biological Sciences, Seton Hall University, South Orange, NJ, USA
| | - Shadan S Yarandi
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Tricia H Burdo
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Sulie L Chang
- Institute of NeuroImmune Pharmacology and Department of Biological Sciences, Seton Hall University, South Orange, NJ, USA.
| | - Ilker K Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA.
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Fittje P, Hœlzemer A, Garcia-Beltran WF, Vollmers S, Niehrs A, Hagemann K, Martrus G, Körner C, Kirchhoff F, Sauter D, Altfeld M. HIV-1 Nef-mediated downregulation of CD155 results in viral restriction by KIR2DL5+ NK cells. PLoS Pathog 2022; 18:e1010572. [PMID: 35749424 PMCID: PMC9231786 DOI: 10.1371/journal.ppat.1010572] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/05/2022] [Indexed: 01/02/2023] Open
Abstract
Antiviral NK cell activity is regulated through the interaction of activating and inhibitory NK cell receptors with their ligands on infected cells. HLA class I molecules serve as ligands for most killer cell immunoglobulin-like receptors (KIRs), but no HLA class I ligands for the inhibitory NK cell receptor KIR2DL5 have been identified to date. Using a NK cell receptor/ligand screening approach, we observed no strong binding of KIR2DL5 to HLA class I or class II molecules, but confirmed that KIR2DL5 binds to the poliovirus receptor (PVR, CD155). Functional studies using primary human NK cells revealed a significantly decreased degranulation of KIR2DL5+ NK cells in response to CD155-expressing target cells. We subsequently investigated the role of KIR2DL5/CD155 interactions in HIV-1 infection, and showed that multiple HIV-1 strains significantly decreased CD155 expression levels on HIV-1-infected primary human CD4+ T cells via a Nef-dependent mechanism. Co-culture of NK cells with HIV-1-infected CD4+ T cells revealed enhanced anti-viral activity of KIR2DL5+ NK cells against wild-type versus Nef-deficient viruses, indicating that HIV-1-mediated downregulation of CD155 renders infected cells more susceptible to recognition by KIR2DL5+ NK cells. These data show that CD155 suppresses the antiviral activity of KIR2DL5+ NK cells and is downmodulated by HIV-1 Nef protein as potential trade-off counteracting activating NK cell ligands, demonstrating the ability of NK cells to counteract immune escape mechanisms employed by HIV-1. HIV infection remains a global health emergency that has caused around 36 million deaths. NK cells play an important role in the control of HIV-1 infections, and are able to detect and destroy infected cells using a large array of activating and inhibitory receptors, including KIRs. Here we demonstrate that CD155 serves as a functional interaction partner for the inhibitory NK cell receptor KIR2DL5, and that KIR2DL5+ NK cells are inhibited by CD155-expressing target cells. CD155 surface expression on HIV-1-infected CD4+ T cells was downregulated by the HIV-1 Nef protein, resulting in increased anti-viral activity of KIR2DL5+ NK cells through the loss of inhibitory signals. Taken together, these studies demonstrate functional consequences of the novel interaction between KIR2DL5 and CD155 for the antiviral activity of KIR2DL5+ NK cells during HIV-1 infection.
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Affiliation(s)
- Pia Fittje
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Angelique Hœlzemer
- Leibniz Institute of Virology (LIV), Hamburg, Germany
- First Department of Internal Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Wilfredo F. Garcia-Beltran
- Leibniz Institute of Virology (LIV), Hamburg, Germany
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Annika Niehrs
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | | | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Marcus Altfeld
- Leibniz Institute of Virology (LIV), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- * E-mail:
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15
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Prévost J, Richard J, Gasser R, Medjahed H, Kirchhoff F, Hahn BH, Kappes JC, Ochsenbauer C, Duerr R, Finzi A. Detection of the HIV-1 Accessory Proteins Nef and Vpu by Flow Cytometry Represents a New Tool to Study Their Functional Interplay within a Single Infected CD4 + T Cell. J Virol 2022; 96:e0192921. [PMID: 35080425 PMCID: PMC8941894 DOI: 10.1128/jvi.01929-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/16/2022] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 Nef and Vpu accessory proteins are known to protect infected cells from antibody-dependent cellular cytotoxicity (ADCC) responses by limiting exposure of CD4-induced (CD4i) envelope (Env) epitopes at the cell surface. Although both proteins target the host receptor CD4 for degradation, the extent of their functional redundancy is unknown. Here, we developed an intracellular staining technique that permits the intracellular detection of both Nef and Vpu in primary CD4+ T cells by flow cytometry. Using this method, we show that the combined expression of Nef and Vpu predicts the susceptibility of HIV-1-infected primary CD4+ T cells to ADCC by HIV+ plasma. We also show that Vpu cannot compensate for the absence of Nef, thus providing an explanation for why some infectious molecular clones that carry a LucR reporter gene upstream of Nef render infected cells more susceptible to ADCC responses. Our method thus represents a new tool to dissect the biological activity of Nef and Vpu in the context of other host and viral proteins within single infected CD4+ T cells. IMPORTANCE HIV-1 Nef and Vpu exert several biological functions that are important for viral immune evasion, release, and replication. Here, we developed a new method allowing simultaneous detection of these accessory proteins in their native form together with some of their cellular substrates. This allowed us to show that Vpu cannot compensate for the lack of a functional Nef, which has implications for studies that use Nef-defective viruses to study ADCC responses.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Beatrice H. Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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16
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Kuniholm J, Armstrong E, Bernabe B, Coote C, Berenson A, Patalano SD, Olson A, He X, Lin NH, Fuxman Bass JI, Henderson AJ. Intragenic proviral elements support transcription of defective HIV-1 proviruses. PLoS Pathog 2021; 17:e1009982. [PMID: 34962974 PMCID: PMC8746790 DOI: 10.1371/journal.ppat.1009982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/10/2022] [Accepted: 12/07/2021] [Indexed: 11/18/2022] Open
Abstract
HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this persistent population of proviruses which include latently infected cells that upon treatment interruption can be reactivated to contribute to HIV-1 rebound. Deep sequencing of persistent HIV proviruses has revealed that greater than 90% of integrated HIV genomes are defective and unable to produce infectious virions. We hypothesized that intragenic elements in the HIV genome support transcription of aberrant HIV-1 RNAs from defective proviruses that lack long terminal repeats (LTRs). Using an intact provirus detection assay, we observed that resting CD4+ T cells and monocyte-derived macrophages (MDMs) are biased towards generating defective HIV-1 proviruses. Multiplex reverse transcription droplet digital PCR identified env and nef transcripts which lacked 5' untranslated regions (UTR) in acutely infected CD4+ T cells and MDMs indicating transcripts are generated that do not utilize the promoter within the LTR. 5'UTR-deficient env transcripts were also identified in a cohort of people living with HIV (PLWH) on ART, suggesting that these aberrant RNAs are produced in vivo. Using 5' rapid amplification of cDNA ends (RACE), we mapped the start site of these transcripts within the Env gene. This region bound several cellular transcription factors and functioned as a transcriptional regulatory element that could support transcription and translation of downstream HIV-1 RNAs. These studies provide mechanistic insights into how defective HIV-1 proviruses are persistently expressed to potentially drive inflammation in PLWH.
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Affiliation(s)
- Jeffrey Kuniholm
- Boston University School of Medicine, Department of Microbiology, Boston, Massachusetts, United States of America
| | - Elise Armstrong
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Brandy Bernabe
- Boston University School of Medicine Graduate Medical Sciences, Boston, Massachusetts, United States of America
| | - Carolyn Coote
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Anna Berenson
- Boston University, Department of Biology, Boston, Massachusetts, United States of America
| | - Samantha D. Patalano
- Boston University, Department of Biology, Boston, Massachusetts, United States of America
| | - Alex Olson
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Xianbao He
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Nina H. Lin
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
| | - Juan I. Fuxman Bass
- Boston University, Department of Biology, Boston, Massachusetts, United States of America
| | - Andrew J. Henderson
- Boston University School of Medicine, Department of Microbiology, Boston, Massachusetts, United States of America
- Boston University School of Medicine, Department of Medicine, Section of Infectious Diseases; Boston, Massachusetts, United States of America
- Boston University School of Medicine Graduate Medical Sciences, Boston, Massachusetts, United States of America
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17
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Rivera-Ortiz J, Pla-Tenorio J, Cruz ML, Colon K, Perez-Morales J, Rodriguez JA, Martinez-Sicari J, Noel RJ. Blockade of beta adrenergic receptors protects the blood brain barrier and reduces systemic pathology caused by HIV-1 Nef protein. PLoS One 2021; 16:e0259446. [PMID: 34784367 PMCID: PMC8594844 DOI: 10.1371/journal.pone.0259446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
Combination antiretroviral therapy (cART) targets viral replication, but early viral protein production by astrocytes may still occur and contribute to the progression of HIV-1 associated neurocognitive disorders and secondary complications seen in patients receiving cART. In prior work with our model, astrocytic HIV-1 Nef expression exhibits neurotoxic effects leading to neurological damage, learning impairment, and immune upregulation that induces inflammation in the lungs and small intestine (SI). In this follow-up study, we focus on the sympathetic nervous system (SNS) as the important branch for peripheral inflammation resulting from astrocytic Nef expression. Male and female Sprague Dawley rats were infused with transfected astrocytes to produce Nef. The rats were divided in four groups: Nef, Nef + propranolol, propranolol and naïve. The beta-adrenergic blocker, propranolol, was administered for 3 consecutive days, starting one day prior to surgery. Two days after the surgery, the rats were sacrificed, and then blood, brain, small intestine (SI), and lung tissues were collected. Levels of IL-1β were higher in both male and female rats, and treatment with propranolol restored IL-1β to basal levels. We observed that Nef expression decreased staining of the tight junction protein claudin-5 in brain tissue while animals co-treated with propranolol restored claudin-5 expression. Lungs and SI of rats in the Nef group showed histological signs of damage including larger Peyer's Patches, increased tissue thickness, and infiltration of immune cells; these findings were abrogated by propranolol co-treatment. Results suggest that interruption of the beta adrenergic signaling reduces the peripheral organ inflammation caused after Nef expression in astrocytes of the brain.
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Affiliation(s)
- Jocelyn Rivera-Ortiz
- HIV-1 Immunopathogenesis Laboratory, The Wistar Institute, Philadelphia, PA, United States of America
| | - Jessalyn Pla-Tenorio
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Myrella L. Cruz
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Krystal Colon
- HIV-1 Immunopathogenesis Laboratory, The Wistar Institute, Philadelphia, PA, United States of America
| | - Jaileene Perez-Morales
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Julio A. Rodriguez
- Cooper University Hospital Department of Orthopaedic Surgery, Camden, NJ, United States of America
| | - Jorge Martinez-Sicari
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Richard J. Noel
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
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18
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Zhao Z, Fagerlund R, Tossavainen H, Hopfensperger K, Lotke R, Srinivasachar Badarinarayan S, Kirchhoff F, Permi P, Sato K, Sauter D, Saksela K. Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage. PLoS Pathog 2021; 17:e1009728. [PMID: 34780577 PMCID: PMC8629392 DOI: 10.1371/journal.ppat.1009728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/29/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy—termed the "R-clamp”—that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpzP.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpzP.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution. Viral replication depends on interactions with a plethora of host cell proteins. Cellular protein interactions are typically mediated by specialized binding modules, such as the SH3 domain. To gain access to host cell regulation viruses have evolved to contain SH3 domain binding sites in their proteins, a notable example of which is the HIV-1 Nef protein. Here we show that during the primate lentivirus evolution the structural strategy that underlies the avid binding of Nef to cellular SH3 domains, which we have dubbed the R-clamp, has been generated via alternative but functionally interchangeable molecular designs. These patterns of SH3 recognition depend on the amino acid combinations at the positions corresponding to residues 83 and 120 in the consensus HIV-1 Nef sequence, and are distinctly different in Nef proteins from SIVs of Eastern and Central chimpanzees, gorillas, and the four groups of HIV-1 that have independently originated from the latter two. These results highlight the evolutionary plasticity of viral proteins, and have implications on therapeutic development aiming to interfere with SH3 binding of Nef.
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Affiliation(s)
- Zhe Zhao
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Riku Fagerlund
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Kristina Hopfensperger
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Rishikesh Lotke
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- * E-mail:
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19
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Kruize Z, van Nuenen AC, van Wijk SW, Girigorie AF, van Dort KA, Booiman T, Kootstra NA. Nef Obtained from Individuals with HIV-1 Vary in Their Ability to Antagonize SERINC3- and SERINC5-Mediated HIV-1 Restriction. Viruses 2021; 13:v13030423. [PMID: 33800773 PMCID: PMC8000780 DOI: 10.3390/v13030423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/14/2022] Open
Abstract
Nef is a multifunctional viral protein that has the ability to downregulate cell surface molecules, including CD4 and major histocompatibility complex class I (MHC-I) and, as recently shown, also members of the serine incorporator family (SERINC). Here, we analyzed the impact of naturally occurring mutations in HIV-1 Nef on its ability to counteract SERINC restriction and the clinical course of infection. HIV-1 Nef sequences were obtained from 123 participants of the Amsterdam Cohort Studies and showed multiple amino acid variations and mutations. Most of the primary Nef proteins showed increased activity to counteract SERINC3 and SERINC5 as compared to NL4-3 Nef. Several mutations in Nef were associated with either an increased or decreased infectivity of Bal26-pseudotyped HIV-1 produced in the presence of SERINC3 or SERINC5. The 8R, 157N and R178G Nef mutations were shown to have an effect on disease progression. Survival analysis showed an accelerated disease progression of individuals infected with HIV-1 carrying arginine or asparagine at position 8 or 157 in Nef, respectively, or the R178G Nef mutation. Here, we observed that naturally occurring mutations in Nef affect the ability of Nef to counteract SERINC3- and SERINC5-mediated inhibition of viral infectivity. The majority of these Nef mutations had no significant effect on HIV-1 pathogenesis and only the 8R, 157N and R178G mutations were associated with disease course.
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20
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Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung’u T, Brumme ZL, Brockman MA. Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. PLoS Pathog 2020; 16:e1008813. [PMID: 32925973 PMCID: PMC7515180 DOI: 10.1371/journal.ppat.1008813] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis.
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Affiliation(s)
- Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mwebesa Bosco Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q. Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter W. Hunt
- School of Medicine, University of California, San Francisco, United States of America
| | - Jeff N. Martin
- School of Medicine, University of California, San Francisco, United States of America
| | - David R. Bangsberg
- School of Public Health, Oregon Health Science University, Portland, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, United States of America
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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21
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Stoneham CA, Ramirez PW, Singh R, Suarez M, Debray A, Lim C, Jia X, Xiong Y, Guatelli J. A Conserved Acidic-Cluster Motif in SERINC5 Confers Partial Resistance to Antagonism by HIV-1 Nef. J Virol 2020; 94:e01554-19. [PMID: 31941773 PMCID: PMC7081897 DOI: 10.1128/jvi.01554-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/12/2020] [Indexed: 12/15/2022] Open
Abstract
The cellular protein SERINC5 inhibits the infectivity of diverse retroviruses, and its activity is counteracted by the glycosylated Gag (glycoGag) protein of murine leukemia virus (MLV), the S2 protein of equine infectious anemia virus (EIAV), and the Nef protein of human immunodeficiency virus type 1 (HIV-1). Determining the regions within SERINC5 that provide restrictive activity or Nef sensitivity should inform mechanistic models of the SERINC5/HIV-1 relationship. Here, we report that deletion of the conserved sequence EDTEE, which is located within a cytoplasmic loop of SERINC5 and which is reminiscent of an acidic-cluster membrane trafficking signal, increases the sensitivity of SERINC5 to antagonism by Nef, while it has no effect on the intrinsic activity of the protein as an inhibitor of infectivity. These effects correlated with enhanced removal of the ΔEDTEE mutant relative to that of wild-type SERINC5 from the cell surface and with enhanced exclusion of the mutant protein from virions by Nef. Mutational analysis indicated that the acidic residues, but not the threonine, within the EDTEE motif are important for the relative resistance to Nef. Deletion of the EDTEE sequence did not increase the sensitivity of SERINC5 to antagonism by the glycoGag protein of MLV, suggesting that its virologic role is Nef specific. These results are consistent with the reported mapping of the cytoplasmic loop that contains the EDTEE sequence as a general determinant of Nef responsiveness, but they further indicate that sequences inhibitory to as well as supportive of Nef activity reside in this region. We speculate that the EDTEE motif might have evolved to mediate resistance against retroviruses that use Nef-like proteins to antagonize SERINC5.IMPORTANCE Cellular membrane proteins in the SERINC family, especially SERINC5, inhibit the infectivity of retroviral virions. This inhibition is counteracted by retroviral proteins, specifically, HIV-1 Nef, MLV glycoGag, and EIAV S2. One consequence of such a host-pathogen "arms race" is a compensatory change in the host antiviral protein as it evolves to escape the effects of viral antagonists. This is often reflected in a genetic signature, positive selection, which is conspicuously missing in SERINC5 Here we show that despite this lack of genetic evidence, a sequence in SERINC5 nonetheless provides relative resistance to antagonism by HIV-1 Nef.
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Affiliation(s)
- Charlotte A Stoneham
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- The VA San Diego Healthcare System, San Diego, California, USA
| | - Peter W Ramirez
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rajendra Singh
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- The VA San Diego Healthcare System, San Diego, California, USA
| | - Marissa Suarez
- The VA San Diego Healthcare System, San Diego, California, USA
| | - Andrew Debray
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Xiaofei Jia
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- The VA San Diego Healthcare System, San Diego, California, USA
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Rahimi P, Aghasadeghi MR, Arefian E, Mobarakeh VI, Kamalzare S, SajadianFard FS, Amiran MR. Molecular Approach for HIV-1 Replication Inhibition: Assessment of Different siRNAs Targeting Tat and Nef Genes to Effectively Suppress their Expression. Clin Lab 2020; 65. [PMID: 31414741 DOI: 10.7754/clin.lab.2019.181230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Inhibition of viral genes through siRNA seems to be promising for treatment of complicated viral infections like human immunodeficiency virus (HIV-1). HIV-1 Tat (Trans Activator of Transcription) and Nef (Negative regulatory Factor) proteins are very interesting targets for designing siRNAs. METHODS The effectiveness of suppressing Tat and Nef was investigated using three specific siTATs and three siNEFs. They were used to transfect the developed stable and infected Human Embryonic Kidney cells (HEK293) as an ex-vivo model. Both stable and virus infected HEK293 cells were transfected with each siTAT and siNEF. The inhibitory effect was evaluated using qRT-PCR, western blot analysis, and HIV P24 ELISA. RESULTS siTAT-100, siTAT-162, and siNEF-136 and at a concentration of 100 nM/mL showed the most inhibitory effect on their target genes. CONCLUSIONS Utilization of more developed molecular inhibition strategies such as RNAi or even a combination of different molecular approaches could be promising to overcome emerging HIV escape mutants.
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Rivera J, Isidro RA, Loucil-Alicea RY, Cruz ML, Appleyard CB, Isidro AA, Chompre G, Colon-Rivera K, Noel RJ. Infusion of HIV-1 Nef-expressing astrocytes into the rat hippocampus induces enteropathy and interstitial pneumonitis and increases blood-brain-barrier permeability. PLoS One 2019; 14:e0225760. [PMID: 31774879 PMCID: PMC6881014 DOI: 10.1371/journal.pone.0225760] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/12/2019] [Indexed: 12/16/2022] Open
Abstract
Even though HIV-1 replication can be suppressed by combination antiretroviral therapy (cART) inflammatory processes still occur, contributing to comorbidities. Comorbidities are attributed to variety of factors, including HIV-1 mediated inflammation. Several HIV-1 proteins mediate central nervous system (CNS) inflammation, including Nef. Nef is an early HIV-1 protein, toxic to neurons and glia and is sufficient to cause learning impairment similar to some deficits observed in HIV-1 associated neurocognitive disorders. To determine whether hippocampal Nef expression by astrocytes contributes to comorbidities, specifically peripheral inflammation, we infused Sprague Dawley rats with GFP- (control) or Nef-transfected astrocytes into the right hippocampus. Brain, lung, and ileum were collected postmortem for the measurement of inflammatory markers. Increased blood-brain-barrier permeability and serum IL-1β levels were detected in the Nef-treated rats. The lungs of Nef-treated rats demonstrated leukocyte infiltration, macrophage upregulation, and enhanced vascular permeability. Ileal tissue showed reactive follicular lymphoid hyperplasia, increased permeability and macrophage infiltration. The intracerebroventricular application of IL-1 receptor antagonist reduced infiltration of immune cells into ileum and lung, indicating the important role of IL-1β in mediating the spread of inflammation from the brain to other tissues. This suggests that localized expression of a single viral protein, HIV-1 Nef, can contribute to a broader inflammatory response by upregulation of IL-1β. Further, these results suggest that Nef contributes to the chronic inflammation seen in HIV patients, even in those whose viremia is controlled by cART.
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Affiliation(s)
- Jocelyn Rivera
- HIV-1 Immunopathogenesis Laboratory, The Wistar Institute, Philadelphia, PA, United States of America
| | - Raymond A. Isidro
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Raisa Y. Loucil-Alicea
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Myrella L. Cruz
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Caroline B. Appleyard
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Angel A. Isidro
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico, United States of America
| | - Gladys Chompre
- Department of Biology, Pontifical Catholic University of Puerto Rico, Ponce, Puerto Rico, United States of America
| | - Krystal Colon-Rivera
- HIV-1 Immunopathogenesis Laboratory, The Wistar Institute, Philadelphia, PA, United States of America
| | - Richard J. Noel
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico, United States of America
- * E-mail:
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24
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Pyeon D, Rojas VK, Price L, Kim S, Singh M, Park IW. HIV-1 Impairment via UBE3A and HIV-1 Nef Interactions Utilizing the Ubiquitin Proteasome System. Viruses 2019; 11:v11121098. [PMID: 31783587 PMCID: PMC6950590 DOI: 10.3390/v11121098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/30/2022] Open
Abstract
Molecular basis of HIV-1 life cycle regulation has thus far focused on viral gene stage-specificity, despite the quintessence of post-function protein elimination processes in the virus life cycle and consequent pathogenesis. Our studies demonstrated that a key pathogenic HIV-1 viral protein, Nef, interacted with ubiquitin (Ub)-protein ligase E3A (UBE3A/E6AP), suggesting that interaction between Nef and UBE3A is integral to regulation of viral and cellular protein decay and thereby the competing HIV-1 and host cell survivals. In fact, Nef and UBE3A degraded reciprocally, and UBE3A-mediated degradation of Nef was significantly more potent than Nef-triggered degradation of UBE3A. Further, UBE3A degraded not only Nef but also HIV-1 structural proteins, Gag, thus significantly inhibiting HIV-1 replication in Jurkat T cells only in the presence of Nef, indicating that interaction between Nef and UBE3Awas pivotal for UBE3A-mediated degradation of the viral proteins. Mechanistic study showed that Nef and UBE3A were specific and antagonistic to each other in regulating proteasome activity and ubiquitination of cellular proteins in general, wherein specific domains of Nef overlapping with the long terminal repeat (LTR) were essential for the observed actions. Further, Nef itself reduced the level of intracellular Gag by degrading a cardinal transcription regulator, Tat, demonstrating a broad role for Nef in the regulation of the HIV-1 life cycle. Taken together, these data demonstrated that the Nef and UBE3A complex plays a crucial role in coordinating viral protein degradation and hence HIV-1 replication, providing insights as to the nature of pathobiologic and defense strategies of HIV-1 and HIV-infected host cells.
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Affiliation(s)
- Dohun Pyeon
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Vivian K. Rojas
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (V.K.R.); (L.P.)
| | - Lenore Price
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (V.K.R.); (L.P.)
| | - Seongcheol Kim
- Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA (M.S.)
| | - Meharvan Singh
- Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA (M.S.)
| | - In-Woo Park
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (V.K.R.); (L.P.)
- Correspondence: ; Tel.: +(817)-735-5115; Fax: +(817)-735-2610
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van Stigt Thans T, Akko JI, Niehrs A, Garcia-Beltran WF, Richert L, Stürzel CM, Ford CT, Li H, Ochsenbauer C, Kappes JC, Hahn BH, Kirchhoff F, Martrus G, Sauter D, Altfeld M, Hölzemer A. Primary HIV-1 Strains Use Nef To Downmodulate HLA-E Surface Expression. J Virol 2019; 93:e00719-19. [PMID: 31375574 PMCID: PMC6798123 DOI: 10.1128/jvi.00719-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/19/2019] [Indexed: 02/08/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) has evolved elaborate ways to evade immune cell recognition, including downregulation of classical HLA class I (HLA-I) from the surfaces of infected cells. Recent evidence identified HLA-E, a nonclassical HLA-I, as an important part of the antiviral immune response to HIV-1. Changes in HLA-E surface levels and peptide presentation can prompt both CD8+ T-cell and natural killer (NK) cell responses to viral infections. Previous studies reported unchanged or increased HLA-E levels on HIV-1-infected cells. Here, we examined HLA-E surface levels following infection of CD4+ T cells with primary HIV-1 strains and observed that a subset downregulated HLA-E. Two primary strains of HIV-1 that induced the strongest reduction in surface HLA-E expression were chosen for further testing. Expression of single Nef or Vpu proteins in a T-cell line, as well as tail swap experiments exchanging the cytoplasmic tail of HLA-A2 with that of HLA-E, demonstrated that Nef modulated HLA-E surface levels and targeted the cytoplasmic tail of HLA-E. Furthermore, infection of primary CD4+ T cells with HIV-1 mutants showed that a lack of functional Nef (and Vpu to some extent) impaired HLA-E downmodulation. Taken together, the results of this study demonstrate for the first time that HIV-1 can downregulate HLA-E surface levels on infected primary CD4+ T cells, potentially rendering them less vulnerable to CD8+ T-cell recognition but at increased risk of NKG2A+ NK cell killing.IMPORTANCE For almost two decades, it was thought that HIV-1 selectively downregulated the highly expressed HLA-I molecules HLA-A and HLA-B from the cell surface in order to evade cytotoxic-T-cell recognition, while leaving HLA-C and HLA-E molecules unaltered. It was stipulated that HIV-1 infection thereby maintained inhibition of NK cells via inhibitory receptors that bind HLA-C and HLA-E. This concept was recently revised when a study showed that primary HIV-1 strains reduce HLA-C surface levels, whereas the cell line-adapted HIV-1 strain NL4-3 lacks this ability. Here, we demonstrate that infection with distinct primary HIV-1 strains results in significant downregulation of surface HLA-E levels. Given the increasing evidence for HLA-E as an important modulator of CD8+ T-cell and NKG2A+ NK cell functions, this finding has substantial implications for future immunomodulatory approaches aimed at harnessing cytotoxic cellular immunity against HIV.
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Affiliation(s)
| | - Janet I Akko
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Annika Niehrs
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Germany
| | | | - Laura Richert
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Université Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Inria SISTM, Bordeaux, France
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Christopher T Ford
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christina Ochsenbauer
- Department of Medicine, Division of Hematology and Oncology, and CFAR, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - John C Kappes
- Department of Medicine, Division of Hematology and Oncology, and CFAR, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Glòria Martrus
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marcus Altfeld
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Germany
- Institute for Immunology, University Medical Center Eppendorf, Hamburg, Germany
| | - Angelique Hölzemer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Germany
- First Department of Internal Medicine, University Medical Center Eppendorf, Hamburg, Germany
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Mailler E, Waheed AA, Park SY, Gershlick DC, Freed EO, Bonifacino JS. The autophagy protein ATG9A promotes HIV-1 infectivity. Retrovirology 2019; 16:18. [PMID: 31269971 PMCID: PMC6607583 DOI: 10.1186/s12977-019-0480-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Nef is a multifunctional accessory protein encoded by HIV-1, HIV-2 and SIV that plays critical roles in viral pathogenesis, contributing to viral replication, assembly, budding, infectivity and immune evasion, through engagement of various host cell pathways. RESULTS To gain a better understanding of the role of host proteins in the functions of Nef, we carried out tandem affinity purification-mass spectrometry analysis, and identified over 70 HIV-1 Nef-interacting proteins, including the autophagy-related 9A (ATG9A) protein. ATG9A is a transmembrane component of the machinery for autophagy, a catabolic process in which cytoplasmic components are degraded in lysosomal compartments. Pulldown experiments demonstrated that ATG9A interacts with Nef from not only HIV-1 and but also SIV (cpz, smm and mac). However, expression of HIV-1 Nef had no effect on the levels and localization of ATG9A, and on autophagy, in the host cells. To investigate a possible role for ATG9A in virus replication, we knocked out ATG9A in HeLa cervical carcinoma and Jurkat T cells, and analyzed virus release and infectivity. We observed that ATG9A knockout (KO) had no effect on the release of wild-type (WT) or Nef-defective HIV-1 in these cells. However, the infectivity of WT virus produced from ATG9A-KO HeLa and Jurkat cells was reduced by ~ fourfold and eightfold, respectively, relative to virus produced from WT cells. This reduction in infectivity was independent of the interaction of Nef with ATG9A, and was not due to reduced incorporation of the viral envelope (Env) glycoprotein into the virus. The loss of HIV-1 infectivity was rescued by pseudotyping HIV-1 virions with the vesicular stomatitis virus G glycoprotein. CONCLUSIONS These studies indicate that ATG9A promotes HIV-1 infectivity in an Env-dependent manner. The interaction of Nef with ATG9A, however, is not required for Nef to enhance HIV-1 infectivity. We speculate that ATG9A could promote infectivity by participating in either the removal of a factor that inhibits infectivity or the incorporation of a factor that enhances infectivity of the viral particles. These studies thus identify a novel host cell factor implicated in HIV-1 infectivity, which may be amenable to pharmacologic manipulation for treatment of HIV-1 infection.
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Affiliation(s)
- Elodie Mailler
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Abdul A Waheed
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Sang-Yoon Park
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David C Gershlick
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Eric O Freed
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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27
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Zotova A, Atemasova A, Pichugin A, Filatov A, Mazurov D. Distinct Requirements for HIV-1 Accessory Proteins during Cell Coculture and Cell-Free Infection. Viruses 2019; 11:v11050390. [PMID: 31027334 PMCID: PMC6563509 DOI: 10.3390/v11050390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022] Open
Abstract
The role of accessory proteins during cell-to-cell transmission of HIV-1 has not been explicitly defined. In part, this is related to difficulties in measuring virus replication in cell cocultures with high accuracy, as cells coexist at different stages of infection and separation of effector cells from target cells is complicated. In this study, we used replication-dependent reporter vectors to determine requirements for Vif, Vpu, Vpr, or Nef during one cycle of HIV-1 cell coculture and cell-free infection in lymphoid and nonlymphoid cells. Comparative analysis of HIV-1 replication in two cell systems showed that, irrespective of transmission way, accessory proteins were generally less required for virus replication in 293T/CD4/X4 cells than in Jurkat-to-Raji/CD4 cell cocultures. This is consistent with a well-established fact that lymphoid cells express a broad spectrum of restriction factors, while nonlymphoid cells are rather limited in this regard. Remarkably, Vpu deletion reduced the level of cell-free infection, but enhanced the level of cell coculture infection and increased the fraction of multiply infected cells. Nef deficiency did not influence or moderately reduced HIV-1 infection in nonlymphoid and lymphoid cell cocultures, respectively, but strongly affected cell-free infection. Knockout of BST2-a Vpu antagonizing restriction factor-in Jurkat producer cells abolished the enhanced replication of HIV-1 ΔVpu in cell coculture and prevented the formation of viral clusters on cell surface. Thus, BST2-tethered viral particles mediated cell coculture infection more efficiently and at a higher level of multiplicity than diffusely distributed virions. In conclusion, our results demonstrate that the mode of transmission may determine the degree of accessory protein requirements during HIV-1 infection.
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Affiliation(s)
- Anastasia Zotova
- Cell and Gene Technology Group, Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia.
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia.
| | - Anastasia Atemasova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia.
| | - Alexey Pichugin
- NRC Institute of Immunology FMBA of Russia, 24 Kashirskoe Shosse, 115472 Moscow, Russia.
| | - Alexander Filatov
- NRC Institute of Immunology FMBA of Russia, 24 Kashirskoe Shosse, 115472 Moscow, Russia.
| | - Dmitriy Mazurov
- Cell and Gene Technology Group, Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia.
- NRC Institute of Immunology FMBA of Russia, 24 Kashirskoe Shosse, 115472 Moscow, Russia.
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Naidoo L, Mzobe Z, Jin SW, Rajkoomar E, Reddy T, Brockman MA, Brumme ZL, Ndung'u T, Mann JK. Nef-mediated inhibition of NFAT following TCR stimulation differs between HIV-1 subtypes. Virology 2019; 531:192-202. [PMID: 30927712 DOI: 10.1016/j.virol.2019.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/13/2019] [Accepted: 02/16/2019] [Indexed: 01/11/2023]
Abstract
Functional characterisation of different HIV-1 subtypes may improve understanding of viral pathogenesis and spread. Here, we evaluated the ability of 345 unique HIV-1 Nef clones representing subtypes A, B, C and D to inhibit NFAT signalling following TCR stimulation. The contribution of this Nef function to disease progression was also assessed in 211 additional Nef clones isolated from unique subtype C infected individuals in early or chronic infection. On average, subtype A and C Nef clones exhibited significantly lower ability to inhibit TCR-mediated NFAT signalling compared to subtype B and D Nef clones. While this observation corroborates accumulating evidence supporting relative attenuation of subtypes A and C that may paradoxically contribute to their increased global prevalence and spread, no significant correlations between Nef-mediated NFAT inhibition activity and clinical markers of HIV-1 infection were observed, indicating that the relationship between Nef function and pathogenesis is complex.
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Affiliation(s)
- Lisa Naidoo
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Zinhle Mzobe
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
| | - Erasha Rajkoomar
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Tarylee Reddy
- Medical Research Council, Biostatistics Unit, Durban 4001, South Africa
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada V6Z 1Y6
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada V6Z 1Y6
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban 4001, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Africa Health Research Institute, Durban 4001, South Africa; Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban 4001, South Africa.
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Martínez L, Milanič M, Malaina I, Álvarez C, Pérez MB, M. de la Fuente I. Weighted lambda superstrings applied to vaccine design. PLoS One 2019; 14:e0211714. [PMID: 30735507 PMCID: PMC6368308 DOI: 10.1371/journal.pone.0211714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/19/2019] [Indexed: 11/23/2022] Open
Abstract
We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins.
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Affiliation(s)
- Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Basque Center for Applied Mathematics BCAM, Bilbao, Spain
- * E-mail:
| | - Martin Milanič
- University of Primorska, UP IAM and UP FAMNIT, Koper, Slovenia
| | - Iker Malaina
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Carmen Álvarez
- IDIVAL Valdecilla Biomedical Research Institute, Santander, Spain
| | - Martín-Blas Pérez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Ildefonso M. de la Fuente
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
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BRUMME ZL, SUDDERUDDIN H, ZIEMNIAK C, LUZURIAGA K, JONES BR, JOY JB, CUNNINGHAM CK, GREENOUGH T, PERSAUD D. Genetic complexity in the replication-competent latent HIV reservoir increases with untreated infection duration in infected youth. AIDS 2019; 33:211-218. [PMID: 30325763 PMCID: PMC6298800 DOI: 10.1097/qad.0000000000002045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Timely initiation of combination antiretroviral therapy (ART) limits latent HIV reservoir size and should also limit reservoir genetic complexity. However, the relationship between these two factors remains unclear, particularly among HIV-infected youth. DESIGN Retrospective analysis of replication-competent latent HIV clones serially isolated by limiting-dilution culture from resting CD4 T-cell reservoirs from ART-suppressed, young adult participants of a historic phase I therapeutic vaccine trial (PACTG/IMPAACT-P1059). METHODS Replication-competent latent HIV clones isolated from resting CD4 T cells of four perinatally and 10 nonperinatally infected young adults (average 22 versus 6 years uncontrolled infection, respectively) were sequenced in Pol and Nef. Within-host HIV sequence datasets were characterized with respect to their genetic diversity and inferred immune escape mutation burden. RESULTS Although participants were comparable in terms of sociodemographic and HIV sampling characteristics (e.g. on average, a mean 17 Pol sequences were recovered at five timepoints over up to 70 weeks) and the length of ART suppression at study entry (average 3 years), replication-competent HIV reservoir size, genetic diversity, immune escape mutation burden and variant complexity were significantly higher among the perinatally infected participants who experienced longer durations of uncontrolled viremia. Nevertheless, viral sequences inferred to retain susceptibility to host cellular immune responses were detected in all participants, irrespective of uncontrolled viremia duration. CONCLUSION HIV elimination in late-suppressed youth may be doubly challenged by larger and more genetically complex reservoirs. Strategies that integrate host and viral genetic complexity to achieve HIV remission or cure may merit consideration in such cases.
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Affiliation(s)
- Zabrina L. BRUMME
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
| | | | | | | | - Bradley R. JONES
- BC Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC Canada
| | - Jeffrey B. JOY
- BC Centre for Excellence in HIV/AIDS, Vancouver BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC Canada
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Chang C, Young LN, Morris KL, von Bülow S, Schöneberg J, Yamamoto-Imoto H, Oe Y, Yamamoto K, Nakamura S, Stjepanovic G, Hummer G, Yoshimori T, Hurley JH. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Mol Cell 2019; 73:339-353.e6. [PMID: 30581147 PMCID: PMC6450660 DOI: 10.1016/j.molcel.2018.10.035] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/15/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes.
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Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lindsey N Young
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kyle L Morris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hitomi Yamamoto-Imoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Yukako Oe
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Kentaro Yamamoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany; Institute of Biophysics, Goethe University, 60438 Frankfurt/M, Germany
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Vekariya U, Saxena R, Singh P, Rawat K, Kumar B, Kumari S, Agnihotri SK, Kaur S, Sachan R, Nazir A, Bhadauria S, Sachdev M, Tripathi RK. HIV-1 Nef-POTEE; A novel interaction modulates macrophage dissemination via mTORC2 signaling pathway. Life Sci 2018; 214:158-166. [PMID: 30391463 DOI: 10.1016/j.lfs.2018.10.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/29/2018] [Indexed: 12/16/2022]
Abstract
AIMS Human immunodeficiency virus -1 [HIV-1] Nef, localizes in different cellular compartments and modulates several cellular pathways. Nef promotes virus pathogenicity through alteration in cell surface receptor expression, apoptosis, protein trafficking etc. Nef regulates viral pathogenesis through interaction with different host proteins. Thus, molecular mechanisms of pathogenesis could be deciphered by identifying novel Nef interacting proteins. MAIN METHODS HIV-1 Nef interacting proteins were identified by pull down assay and MALDI-TOF analysis. The interaction was further validated through mammalian two hybrid assay. Functional role of this interaction was identified by immunoprecipitation assay, cell invasion and cell migration studies. Fold Change in mRNA levels of CD163, CD206, CCL17 and CCL18 was analyzed using qPCR. KEY FINDINGS In current study, C. elegans protein ACT4C and its human homolog POTEE was identified to be interacting with Nef. This interaction activates mTORC2 complex, which in-turn activates AKT and PKC-α. The activation of mTORC2 complex was found to be initiated by the interaction of Nef, mTORC2, Rictor to POTEE. The cellular phenotype and functions affected by Nef-POTEE interaction resulted in significant increase in cell invasion and migration of macrophages (MΦ). SIGNIFICANCE MΦ is primary target of HIV-1 infection where HIV-1 replicates and polarizes immunosuppressive M2 phenotype. Combine effect of M2 phenotype and Viral-host protein interactions compromise the MΦ associated physiological functions. Infected MΦ dissemination into other system also leads to HIV-1 induced malignancies. Therefore, targeting POTEE-Nef interaction can lead to formulating better therapeutic strategy against HIV-1.
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Affiliation(s)
- Umeshkumar Vekariya
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Reshu Saxena
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Poonam Singh
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Kavita Rawat
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Balawant Kumar
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Sushila Kumari
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | | | - Supinder Kaur
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Rekha Sachan
- Department of Obstetrics & Gynecology, King George Medical University, Lucknow, UP, India
| | - Aamir Nazir
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Smrati Bhadauria
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Monika Sachdev
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Raj Kamal Tripathi
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, UP, India.
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Murakoshi H, Koyanagi M, Akahoshi T, Chikata T, Kuse N, Gatanaga H, Rowland-Jones SL, Oka S, Takiguchi M. Impact of a single HLA-A*24:02-associated escape mutation on the detrimental effect of HLA-B*35:01 in HIV-1 control. EBioMedicine 2018; 36:103-112. [PMID: 30249546 PMCID: PMC6197679 DOI: 10.1016/j.ebiom.2018.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 01/06/2023] Open
Abstract
Background HLA-B*35 is an HLA allele associated with rapid progression to AIDS. However, a mechanism underlying the detrimental effect of HLA-B*35 on disease outcome remains unknown. Recent studies demonstrated that most prevalent subtype HLA-B*35:01 is a detrimental allele in HIV-1 clade B-infected individuals. We here investigated the effect of mutations within the epitopes on HLA-B*35:01-restricted CD8+ T cells having abilities to suppress HIV-1 replication. Methods We analyzed 16 HLA-B*35:01-restricted epitope-specific T cells in 63 HIV-1 clade B-infected Japanese B*35:01+ individuals and identified HLA-B*35:01-restricted CD8+ T cells having abilities to suppress HIV-1 replication. We further analyzed the effect of HLA-associated mutations on the ability of these T cells. Findings The breadth of T cell responses to 4 epitopes was inversely associated with plasma viral load (pVL). However, the accumulation of an Y135F mutation in NefYF9 out of the 4 epitopes, which is selected by HLA-A*24:02-restricted T cells, affected the ability of YF9-specific T cells to suppress HIV-1 replication. HLA-B*35:01+ individuals harboring this mutation had much higher pVL than those without it. YF9-specific T cells failed to suppress replication of the Y135F mutant in vitro. These results indicate that this mutation impairs suppression of HIV-1 replication by YF9-specific T cells. Interpretation These findings indicate that the Y135F mutation is a key factor underlying the detrimental effect of HLA-B*35:01 on disease outcomes in HIV-1 clade B-infected individuals. Fund Grants-in-aid for AIDS Research from AMED and for scientific research from the Ministry of Education, Science, Sports, and Culture, Japan. T cells specific for 4 HLA-B*35:01-restricted epitopes have abilities to suppress HIV-1 replication in vivo. An Y135F mutation selected by HLA-A*24:02-restricted T cells affected HIV-1 control by NefYF9-specific T cells in vivo. The NefY135F mutation impaired suppression of HIV-1 replication by NefYF9-specific T cells in vitro.
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Affiliation(s)
- Hayato Murakoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Madoka Koyanagi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Tomohiro Akahoshi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Sarah L Rowland-Jones
- IRCMS, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, Japan; Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK.
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Joas S, Parrish EH, Gnanadurai CW, Lump E, Stürzel CM, Parrish NF, Learn GH, Sauermann U, Neumann B, Rensing KM, Fuchs D, Billingsley JM, Bosinger SE, Silvestri G, Apetrei C, Huot N, Garcia-Tellez T, Müller-Trutwin M, Hotter D, Sauter D, Stahl-Hennig C, Hahn BH, Kirchhoff F. Species-specific host factors rather than virus-intrinsic virulence determine primate lentiviral pathogenicity. Nat Commun 2018; 9:1371. [PMID: 29636452 PMCID: PMC5893559 DOI: 10.1038/s41467-018-03762-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/07/2018] [Indexed: 12/23/2022] Open
Abstract
HIV-1 causes chronic inflammation and AIDS in humans, whereas related simian immunodeficiency viruses (SIVs) replicate efficiently in their natural hosts without causing disease. It is currently unknown to what extent virus-specific properties are responsible for these different clinical outcomes. Here, we incorporate two putative HIV-1 virulence determinants, i.e., a Vpu protein that antagonizes tetherin and blocks NF-κB activation and a Nef protein that fails to suppress T cell activation via downmodulation of CD3, into a non-pathogenic SIVagm strain and test their impact on viral replication and pathogenicity in African green monkeys. Despite sustained high-level viremia over more than 4 years, moderately increased immune activation and transcriptional signatures of inflammation, the HIV-1-like SIVagm does not cause immunodeficiency or any other disease. These data indicate that species-specific host factors rather than intrinsic viral virulence factors determine the pathogenicity of primate lentiviruses.
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Affiliation(s)
- Simone Joas
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Erica H Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 372327, USA
| | - Clement W Gnanadurai
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
- Department of Veterinary Pathology, University of Georgia, Athens, GA, 30602, USA
| | - Edina Lump
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Nicholas F Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | | | - Dietmar Fuchs
- Division of Biological Chemistry, Biocenter Innsbruck Medical University, Center for Chemistry and Biomedicine, A-6020, Innsbruck, Austria
| | - James M Billingsley
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Steven E Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Cristian Apetrei
- WA Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nicolas Huot
- Institut Pasteur, Unité HIV, Inflammation and Persistence, Paris, 75015, France
- Vaccine Research Institute, Hôpital Henri Mondor, Créteil, 94010, France
| | | | | | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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Dai W, Usami Y, Wu Y, Göttlinger H. A Long Cytoplasmic Loop Governs the Sensitivity of the Anti-viral Host Protein SERINC5 to HIV-1 Nef. Cell Rep 2018; 22:869-875. [PMID: 29386131 PMCID: PMC5810964 DOI: 10.1016/j.celrep.2017.12.082] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/05/2017] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
We recently identified the multipass transmembrane protein SERINC5 as an antiviral protein that can potently inhibit HIV-1 infectivity and is counteracted by HIV-1 Nef. We now report that the anti-HIV-1 activity, but not the sensitivity to Nef, is conserved among vertebrate SERINC5 proteins. However, a Nef-resistant SERINC5 became Nef sensitive when its intracellular loop 4 (ICL4) was replaced by that of Nef-sensitive human SERINC5. Conversely, human SERINC5 became resistant to Nef when its ICL4 was replaced by that of a Nef-resistant SERINC5. In general, ICL4 regions from SERINCs that exhibited resistance to a given Nef conferred resistance to the same Nef when transferred to a sensitive SERINC, and vice versa. Our results establish that human SERINC5 can be modified to restrict HIV-1 infectivity even in the presence of Nef.
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Affiliation(s)
- Weiwei Dai
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yoshiko Usami
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Yuanfei Wu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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36
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Milani A, Bolhassani A, Heshmati M. Delivery of HIV-1 Nef linked to heat shock protein 27 using a cationic polymer is more effective than cationic lipid in mammalian cells. ACTA ACUST UNITED AC 2017; 118:334-338. [PMID: 28664742 DOI: 10.4149/bll_2017_064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Different adjuvants and delivery systems have been used to enhance the potency of DNA vaccines against viral diseases. Among them, heat shock proteins (HSPs) are stress proteins that have multiple roles such as chaperon activity and anti-apoptotic and adjuvant properties. The goal of this study was to compare the expression of HIV-1 Nef, Hsp27 and Hsp27-Nef genes transfected in HEK-293T mammalian cells by TurboFect and Lipofectamine as a cationic polymer and lipid, respectively. METHODS At first, the pEGFP eukaryotic vectors encoding HIV-1 Nef, Hsp27 and Hsp27-Nef genes were generated and transfected in HEK-293T using TurboFect and Lipofectamine delivery systems. Then, the expression of proteins was evaluated and compared using fluorescent microscopy, flow cytometry and western blotting 48 hr after transfection. RESULTS The accuracy of the DNA constructs was confirmed on agarose gel electrophoresis to be ~ 720 bp, ~ 648 bp, and ~ 1368 bp bands for Hsp27, Nef, and Hsp-Nef, respectively. The expression analysis in the transfected cells showed that the delivery of genes using TurboFect was significantly higher than that using Lipofectamine. Furthermore, transfection of Hsp27 gene was more effective than that of Nef gene using both delivery systems. Hsp27 linked to Nef could also increase its delivery and expression in HEK-293T cells. CONCLUSION Generally, Hsp27 can be used as a suitable carrier in DNA vaccine design against HIV-1 infections (Fig. 5, Ref. 28).
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Lamers SL, Fogel GB, Liu ES, Barbier AE, Rodriguez CW, Singer EJ, Nolan DJ, Rose R, McGrath MS. Brain-specific HIV Nef identified in multiple patients with neurological disease. J Neurovirol 2017; 24:1-15. [PMID: 29063512 DOI: 10.1007/s13365-017-0586-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/28/2017] [Accepted: 10/03/2017] [Indexed: 12/11/2022]
Abstract
HIV-1 Nef is a flexible, multifunctional protein with several cellular targets that is required for pathogenicity of the virus. This protein maintains a high degree of genetic variation among intra- and inter-host isolates. HIV Nef is relevant to HIV-associated neurological diseases (HAND) in patients treated with combined antiretroviral therapy because of the protein's role in promoting survival and migration of infected brain macrophages. In this study, we analyzed 2020 HIV Nef sequences derived from 22 different tissues and 31 subjects using a novel computational approach. This approach combines statistical regression and evolved neural networks (ENNs) to classify brain sequences based on the physical and chemical characteristics of functional Nef domains. Based on training, testing, and validation data, the method successfully classified brain Nef sequences at 84.5% and provided informative features for further examination. These included physicochemical features associated with the Src-homology-3 binding domain, the Nef loop (including the AP-2 Binding region), and a cytokine-binding domain. Non-brain sequences from patients with HIV-associated neurological disease were frequently classified as brain, suggesting that the approach could indicate neurological risk using blood-derived virus or for the development of biomarkers for use in assay systems aimed at drug efficacy studies for the treatment of HIV-associated neurological diseases.
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Abstract
The development of an efficient prophylactic HIV vaccine has been one of the major challenges in infectious disease research during the last three decades. Here, we present a mini review on strategies employed for the development of HIV vaccines with an emphasis on a well-established vaccine technology, the killed whole-virus vaccine approach. Recently, we reported an evaluation of the safety and the immunogenicity of a genetically modified and killed whole-HIV-1 vaccine designated as SAV001 [1]. HIV-1 Clade B NL4-3 was genetically modified by deleting the nef and vpu genes and substituting the coding sequence of the Env signal peptide with that of honeybee melittin to produce an avirulent and replication efficient HIV-1. This genetically modified virus (gmHIV-1 NL4-3 ) was propagated in a human T cell line followed by virus purification and inactivation by aldrithiol-2 and γ-irradiation. We found that SAV001 was well tolerated with no serious adverse events. HIV-1 NL4-3 -specific polymerase chain reaction showed no evidence of vaccine virus replication in participants receiving SAV001 and in human T cells infected in vitro. Furthermore, SAV001 with an adjuvant significantly increased the antibody response to HIV-1 structural proteins. Moreover, antibodies in the plasma from these vaccinations neutralized tier I and tier II of HIV-1 B, A, and D subtypes. These results indicated that the killed whole-HIV vaccine is safe and may trigger appropriate immune responses to prevent HIV infection. Utilization of this killed whole-HIV vaccine strategy may pave the way to develop an effective HIV vaccine.
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MESH Headings
- AIDS Vaccines/administration & dosage
- AIDS Vaccines/adverse effects
- AIDS Vaccines/genetics
- AIDS Vaccines/immunology
- Clinical Trials as Topic
- HIV Antibodies/blood
- HIV Antibodies/immunology
- HIV Infections/immunology
- HIV Infections/prevention & control
- HIV-1/genetics
- HIV-1/immunology
- HIV-1/physiology
- Humans
- Vaccines, Inactivated/administration & dosage
- Vaccines, Inactivated/adverse effects
- Vaccines, Inactivated/genetics
- Vaccines, Inactivated/immunology
- Virus Replication
- env Gene Products, Human Immunodeficiency Virus/genetics
- env Gene Products, Human Immunodeficiency Virus/immunology
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/immunology
- nef Gene Products, Human Immunodeficiency Virus/genetics
- nef Gene Products, Human Immunodeficiency Virus/immunology
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Affiliation(s)
- C. Yong Kang
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6G 2V4 Canada
| | - Yong Gao
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6G 2V4 Canada
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Navarro Negredo P, Edgar JR, Wrobel AG, Zaccai NR, Antrobus R, Owen DJ, Robinson MS. Contribution of the clathrin adaptor AP-1 subunit µ1 to acidic cluster protein sorting. J Cell Biol 2017; 216:2927-2943. [PMID: 28743825 PMCID: PMC5584140 DOI: 10.1083/jcb.201602058] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
Acidic clusters act as sorting signals for packaging cargo into clathrin-coated vesicles (CCVs), and also facilitate down-regulation of MHC-I by HIV-1 Nef. To find acidic cluster sorting machinery, we performed a gene-trap screen and identified the medium subunit (µ1) of the clathrin adaptor AP-1 as a top hit. In µ1 knockout cells, intracellular CCVs still form, but acidic cluster proteins are depleted, although several other CCV components were either unaffected or increased, indicating that cells can compensate for long-term loss of AP-1. In vitro experiments showed that the basic patch on µ1 that interacts with the Nef acidic cluster also contributes to the binding of endogenous acidic cluster proteins. Surprisingly, µ1 mutant proteins lacking the basic patch and/or the tyrosine-based motif binding pocket could rescue the µ1 knockout phenotype completely. In contrast, these mutants failed to rescue Nef-induced down-regulation of MHC class I, suggesting a possible mechanism for attacking the virus while sparing the host cell.
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Affiliation(s)
- Paloma Navarro Negredo
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Antoni G Wrobel
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Nathan R Zaccai
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - David J Owen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
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Wales TE, Poe JA, Emert-Sedlak L, Morgan CR, Smithgall TE, Engen JR. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants. J Am Soc Mass Spectrom 2016; 27:1048-61. [PMID: 27032648 PMCID: PMC4865444 DOI: 10.1007/s13361-016-1365-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 05/16/2023]
Abstract
Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS. Graphical Abstract ᅟ.
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Affiliation(s)
- Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Jerrod A Poe
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Lori Emert-Sedlak
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Christopher R Morgan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
- Genzyme Corporation, Framingham, MA, 01701-9322, USA
| | - Thomas E Smithgall
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
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Katoh J, Kawana-Tachikawa A, Shimizu A, Zhu D, Han C, Nakamura H, Koga M, Kikuchi T, Adachi E, Koibuchi T, Gao GF, Brumme ZL, Iwamoto A. Rapid HIV-1 Disease Progression in Individuals Infected with a Virus Adapted to Its Host Population. PLoS One 2016; 11:e0150397. [PMID: 26953793 PMCID: PMC4783116 DOI: 10.1371/journal.pone.0150397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
HIV-1 escape from CTL is predictable based on the Human Leukocyte Antigen (HLA) class I alleles expressed by the host. As such, HIV-1 sequences circulating in a population of hosts will harbor escape mutations specific to the HLA alleles of that population. In theory, this should increase the frequency of escape mutation transmission to persons expressing the restricting HLA allele, thereby compromising host immunity to the incoming HIV-1 strain. However, the clinical impact of infection with HIV-1 containing immune escape mutations has not conclusively been demonstrated. Japan’s population features limited HLA diversity which is driving population-level HIV adaptation: for example, >60% of Japanese express HLA-A*24:02 and its associated Nef-Y135F escape mutation represents the population consensus. As such, Japan is an ideal population in which to examine this phenomenon. Here, we combine genetic and immunological analyses to identify A*24:02-positive individuals likely to have been infected with Y135F-containing HIV-1. Over a ~5 year follow-up, these individuals exhibited significantly lower CD4 counts compared to individuals inferred to have been infected with wild-type HIV-1. Our results support a significant negative clinical impact of pathogen adaptation to host pressures at the population level.
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Affiliation(s)
- Jiro Katoh
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo. Kashiwa-shi, Chiba, Japan
| | - Ai Kawana-Tachikawa
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Akihisa Shimizu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Dayong Zhu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Chungyong Han
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Hitomi Nakamura
- Department of Infectious Disease Control, the International Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - George F. Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Aikichi Iwamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo. Kashiwa-shi, Chiba, Japan
- Department of Infectious Disease Control, the International Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Asian Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- * E-mail:
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Gandhi RT, Kwon DS, Macklin EA, Shopis JR, McLean AP, McBrine N, Flynn T, Peter L, Sbrolla A, Kaufmann DE, Porichis F, Walker BD, Bhardwaj N, Barouch DH, Kavanagh DG. Immunization of HIV-1-Infected Persons With Autologous Dendritic Cells Transfected With mRNA Encoding HIV-1 Gag and Nef: Results of a Randomized, Placebo-Controlled Clinical Trial. J Acquir Immune Defic Syndr 2016; 71:246-53. [PMID: 26379068 PMCID: PMC4752409 DOI: 10.1097/qai.0000000000000852] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 08/31/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-1 eradication may require reactivation of latent virus along with stimulation of HIV-1-specific immune responses to clear infected cells. Immunization with autologous dendritic cells (DCs) transfected with viral mRNA is a promising strategy for eliciting HIV-1-specific immune responses. We performed a randomized controlled clinical trial to evaluate the immunogenicity of this approach in HIV-1-infected persons on antiretroviral therapy. METHODS Fifteen participants were randomized 2:1 to receive intradermal immunization with HIV-1 Gag- and Nef-transfected DCs (vaccine) or mock-transfected DCs (placebo) at weeks 0, 2, 6, and 10. All participants also received DCs pulsed with keyhole limpet hemocyanin (KLH) to assess whether responses to a neo-antigen could be induced. RESULTS After immunization, there were no differences in interferon-gamma enzyme-linked immunospot responses to HIV-1 Gag or Nef in the vaccine or placebo group. CD4 proliferative responses to KLH increased 2.4-fold (P = 0.026) and CD8 proliferative responses to KLH increased 2.5-fold (P = 0.053) after vaccination. There were increases in CD4 proliferative responses to HIV-1 Gag (2.5-fold vs. baseline, 3.4-fold vs. placebo, P = 0.054) and HIV-1 Nef (2.3-fold vs. baseline, 6.3-fold vs. placebo, P = 0.009) among vaccine recipients, but these responses were short-lived. CONCLUSION Immunization with DCs transfected with mRNA encoding HIV-1 Gag and Nef did not induce significant interferon-gamma enzyme-linked immunospot responses. There were increases in proliferative responses to HIV-1 antigens and to a neo-antigen, KLH, but the effects were transient. Dendritic cell vaccination should be optimized to elicit stronger and long-lasting immune responses for this strategy to be effective as an HIV-1 therapeutic vaccine.
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Affiliation(s)
- Rajesh T. Gandhi
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
| | - Douglas S. Kwon
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
| | - Eric A. Macklin
- Biostatistics Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Janet R. Shopis
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA
| | - Anna P. McLean
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
| | - Nicole McBrine
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
| | - Theresa Flynn
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Amy Sbrolla
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA
| | - Daniel E. Kaufmann
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and University of Montreal, Montréal, QC, Canada
| | - Filippos Porichis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
| | - Bruce D. Walker
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Nina Bhardwaj
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY; and
| | - Dan H. Barouch
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Daniel G. Kavanagh
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA
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Martínez-Bonet M, Palladino C, Briz V, Rudolph JM, Fackler OT, Relloso M, Muñoz-Fernandez MA, Madrid R. A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities. PLoS One 2015; 10:e0145239. [PMID: 26700863 PMCID: PMC4689412 DOI: 10.1371/journal.pone.0145239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121–137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection.
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Affiliation(s)
- Marta Martínez-Bonet
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Claudia Palladino
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Veronica Briz
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Jochen M. Rudolph
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Miguel Relloso
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Maria Angeles Muñoz-Fernandez
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Ricardo Madrid
- Departament of Virology. Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Madrid, Spain
- * E-mail:
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van der Velden YU, Kleibeuker W, Harwig A, Klaver B, Siteur-van Rijnstra E, Frankin E, Berkhout B, Das AT. Construction of Nef-positive doxycycline-dependent HIV-1 variants using bicistronic expression elements. Virology 2015; 488:96-107. [PMID: 26615334 DOI: 10.1016/j.virol.2015.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/14/2015] [Accepted: 11/06/2015] [Indexed: 11/19/2022]
Abstract
Conditionally replicating HIV-1 variants that can be switched on and off at will are attractive tools for HIV research. We previously developed a genetically modified HIV-1 variant that replicates exclusively when doxycycline (dox) is administered. The nef gene in this HIV-rtTA variant was replaced with the gene encoding the dox-dependent rtTA transcriptional activator. Because loss of Nef expression compromises virus replication in primary cells and precludes studies on Nef function, we tested different approaches to restore Nef production in HIV-rtTA. Strategies that involved translation via an EMCV or synthetic internal ribosome entry site (IRES) failed because these elements were incompatible with efficient virus replication. Fusion protein approaches with the FMDV 2A peptide and human ubiquitin were successful and resulted in genetically-stable Nef-expressing HIV-rtTA strains that replicate more efficiently in primary T-cells and human immune system (HIS) mice than Nef-deficient variants, thus confirming the positive effect of Nef on in vivo virus replication.
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Affiliation(s)
- Yme U van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Wendy Kleibeuker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther Siteur-van Rijnstra
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Esmay Frankin
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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Choma MK, Lumb J, Kozik P, Robinson MS. A Genome-Wide Screen for Machinery Involved in Downregulation of MHC Class I by HIV-1 Nef. PLoS One 2015; 10:e0140404. [PMID: 26466362 PMCID: PMC4605695 DOI: 10.1371/journal.pone.0140404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/24/2015] [Indexed: 12/02/2022] Open
Abstract
The HIV-1-encoded protein, Nef, plays a key role in the development of AIDS. One of Nef’s functions is to keep MHC class I off the surface of infected cells, a process that requires the host proteins clathrin and AP-1. To identify other proteins involved in this pathway, we carried out a genome-wide siRNA library screen on HeLa cells co-expressing HLA-A2 and an inducible form of Nef. Out of 21,121 siRNA pools, 100 were selected for further analysis, based on their ability to either inhibit or enhance downregulation of MHC-I by Nef. When cells were treated with the same siRNA pools as those used in the screen, 79% produced a similar phenotype. However, when the cells were treated with different siRNA reagents targeting the same genes, only 16% produced a similar phenotype. This indicates that most of the hits found in the original screen are likely to have been off-target, an important concern that is often not taken into account in siRNA screening studies. Nevertheless, we identified novel host factors involved in Nef-induced downregulation of MHC-I, including four genes, MIIP, CAMSAP3, SLC6A3, and KCTD19, where multiple reagents produced a strong inhibitory effect on Nef activity. Other hits slightly below our very high stringency cutoff point may also deserve further study. Thus, our dataset is a valuable resource for scientists investigating the pathogenesis of HIV.
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Affiliation(s)
- Maja K. Choma
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
| | - Jennifer Lumb
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
| | - Patrycja Kozik
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
| | - Margaret S. Robinson
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
- * E-mail:
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Huang Y, Follmann D, Nason M, Zhang L, Huang Y, Mehrotra DV, Moodie Z, Metch B, Janes H, Keefer MC, Churchyard G, Robb ML, Fast PE, Duerr A, McElrath MJ, Corey L, Mascola JR, Graham BS, Sobieszczyk ME, Kublin JG, Robertson M, Hammer SM, Gray GE, Buchbinder SP, Gilbert PB. Effect of rAd5-Vector HIV-1 Preventive Vaccines on HIV-1 Acquisition: A Participant-Level Meta-Analysis of Randomized Trials. PLoS One 2015; 10:e0136626. [PMID: 26332672 PMCID: PMC4558095 DOI: 10.1371/journal.pone.0136626] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022] Open
Abstract
Background Three phase 2b, double-blind, placebo-controlled, randomized efficacy trials have tested recombinant Adenovirus serotype-5 (rAd5)-vector preventive HIV-1 vaccines: MRKAd5 HIV-1 gag/pol/nef in Step and Phambili, and DNA/rAd5 HIV-1 env/gag/pol in HVTN505. Due to efficacy futility observed at the first interim analysis in Step and HVTN505, participants of all three studies were unblinded to their vaccination assignments during the study but continued follow–up. Rigorous meta-analysis can provide crucial information to advise the future utility of rAd5-vector vaccines. Methods We included participant-level data from all three efficacy trials, and three Phase 1–2 trials evaluating the HVTN505 vaccine regimen. We predefined two co-primary analysis cohorts for assessing the vaccine effect on HIV-1 acquisition. The modified-intention-to-treat (MITT) cohort included all randomly assigned participants HIV-1 uninfected at study entry, who received at least the first vaccine/placebo, and the Ad5 cohort included MITT participants who received at least one dose of rAd5-HIV vaccine or rAd5-placebo. Multivariable Cox regression models were used to estimate hazard ratios (HRs) of HIV-1 infection (vaccine vs. placebo) and evaluate HR variation across vaccine regimens, time since vaccination, and subgroups using interaction tests. Findings Results are similar for the MITT and Ad5 cohorts; we summarize MITT cohort results. Pooled across the efficacy trials, over all follow-up time 403 (n = 224 vaccine; n = 179 placebo) of 6266 MITT participants acquired HIV-1, with a non-significantly higher incidence in vaccine recipients (HR 1.21, 95% CI 0.99–1.48, P = 0.06). The HRs significantly differed by vaccine regimen (interaction P = 0.03; MRKAd5 HR 1.41, 95% CI 1.11–1.78, P = 0.005 vs. DNA/rAd5 HR 0.88, 95% CI 0.61–1.26, P = 0.48). Results were similar when including the Phase 1–2 trials. Exploratory analyses based on the efficacy trials supported that the MRKAd5 vaccine-increased risk was concentrated in Ad5-positive or uncircumcised men early in follow-up, and in Ad5-negative or circumcised men later. Overall, MRKAd5 vaccine-increased risk was evident across subgroups except in circumcised Ad5-negative men (HR 0.97, 95% CI 0.58−1.63, P = 0.91); there was little evidence that the DNA/rAd5 vaccine, that was tested in this subgroup, increased risk (HR 0.88, 95% CI 0.61–1.26, P = 0.48). When restricting the analysis of Step and Phambili to follow-up time before unblinding, 114 (n = 65 vaccine; n = 49 placebo) of 3770 MITT participants acquired HIV-1, with a non-significantly higher incidence in MRKAd5 vaccine recipients (HR 1.30, 95% CI 0.89–1.14, P = 0.18). Interpretation and Significance The data support increased risk of HIV-1 infection by MRKAd5 over all follow-up time, but do not support increased risk of HIV-1 infection by DNA/rAd5. This study provides a rationale for including monitoring plans enabling detection of increased susceptibility to infection in HIV-1 at-risk populations.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Dean Follmann
- National Institute of Allergy and Infectious Diseases and Biostatistics Research Branch, National Institutes of Health, Bethesda, MD, United States of America
| | - Martha Nason
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Lily Zhang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ying Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Devan V. Mehrotra
- Merck Research Laboratories, North Wales, PA, United States of America
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara Metch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael C. Keefer
- Infectious Disease Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| | | | - Merlin L. Robb
- HJF HIV Program, US Military HIV Research Program, Bethesda, MD, United States of America
| | - Patricia E. Fast
- Research and Development, International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Ann Duerr
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Barney S. Graham
- Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States of America
| | - Magdalena E. Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Robertson
- Infectious Disease Clinical Research, Merck, Philadelphia, Pennsylvania, United States of America
| | - Scott M. Hammer
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, New York, United States of America
| | - Glenda E. Gray
- University of the Witwatersrand, Johannesburg, South Africa
| | - Susan P. Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, United States of America
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Adegoke A, Gladney K, Gallant M, Grant M. Heteroclitic Peptides Increase Proliferation and Reduce Evidence of Human Immunodeficiency Virus-Specific CD8⁺ T Cell Dysfunction. Viral Immunol 2015; 28:455-63. [PMID: 26230145 DOI: 10.1089/vim.2015.0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus (HIV)-specific CD8(+) T cell dysfunction parallels disease progression; therefore, restoring potent HIV-specific CD8(+) T cell responses is a key therapeutic goal. Certain CD8(+) T cell peptide epitope variants, termed heteroclitic, enhance cytokine production by the HIV-specific CD8(+) T cells of some individuals. In this study, we investigated whether heteroclitic peptides that enhance cytokine production by HIV-specific CD8(+) T cells also reduce functional and phenotypic evidence of HIV-specific CD8(+) T cell exhaustion in those instances. Twenty-four variant peptides of human histocompatibility-linked leukocyte antigen (HLA)-A2-restricted reference HIV peptide epitopes designated as A2-7; Nef 83→91, A2-8; Nef 135→143, A2-Gag; Gag 77→85 and A2-9; Gag 433→440 were synthesized with conservative and semiconservative amino acid substitutions at positions 3, 5, and 7 or 3, 5, and 8 of Gag 433→440. Variants that enhanced interferon-gamma (IFN-γ) and/or interleukin-2 (IL-2) production in enzyme-linked immunospot assays (29 cases overall) were subsequently tested by 7-day in vitro peptide stimulation for their effects on HIV-specific CD8(+) T cell proliferation and programmed death-1 (PD-1) expression. Heteroclitic variants enhanced HIV-specific CD8(+) T cell proliferation by >20% in 13/29 cases tested, reduced PD-1 expression on proliferating cells by 15-50% in 10 cases, and reduced PD-1 expression on proliferating cells by >50% in 3 cases. In five cases, the same heteroclitic peptide increased proliferation by >20% and reduced PD-1 expression by >15%. These data demonstrate that heteroclitic peptides can alter the magnitude and character of HIV-specific CD8(+) cell responses relative to reference peptides and may have a unique immunotherapeutic value in therapeutic vaccines.
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Affiliation(s)
- Adeolu Adegoke
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada
| | - Krista Gladney
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada
| | - Maureen Gallant
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada
| | - Michael Grant
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland , St. John's, Newfoundland and Labrador, Canada
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Pirrone GF, Emert-Sedlak LA, Wales TE, Smithgall TE, Kent MS, Engen JR. Membrane-Associated Conformation of HIV-1 Nef Investigated with Hydrogen Exchange Mass Spectrometry at a Langmuir Monolayer. Anal Chem 2015; 87:7030-5. [PMID: 26133569 PMCID: PMC4509969 DOI: 10.1021/acs.analchem.5b01725] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the companion paper to this work, we described development of a new type of hydrogen exchange (HX) mass spectrometry (MS) measurement that integrates Langmuir monolayers. With Langmuir monolayers, the lipid packing density can be reproducibly controlled and changed as desired. Analysis of HX in proteins that may undergo conformational changes as a function of lipid packing (for example, conformational rearrangements after insertion into a lipid layer) are then possible. We previously used neutron reflection to characterize just such a conformational change in the myristoylated HIV-1 Nef protein (myrNef): at high lipid packing density, myrNef could not insert into the lipids and maintained a compact conformation adjacent to the monolayer, whereas at lower lipid packing density, myrNef was able to insert N-terminal arm residues, causing displacement of the core domain away from the monolayer. In order to locate where conformation may have been altered by lipid association, we applied the HX MS Langmuir monolayer method to myrNef associated with monolayers of packing densities identical to those used for the prior neutron reflection measurements. The results show that the N-terminal region and the C-terminal unstructured loop undergo conformational changes when associated with a low density lipid monolayer. The results are not consistent with the hypothesis of myrNef dimerization upon membrane association in the absence of other myrNef binding partners. The HX MS Langmuir monolayer method provides new and meaningful information for myrNef that helps explain necessary conformational changes required for function at the membrane.
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Affiliation(s)
- Gregory F. Pirrone
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
| | - Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - Michael S. Kent
- Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, NM 87185
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115
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Emadpour M, Karcher D, Bock R. Boosting riboswitch efficiency by RNA amplification. Nucleic Acids Res 2015; 43:e66. [PMID: 25824954 PMCID: PMC4446413 DOI: 10.1093/nar/gkv165] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 01/17/2023] Open
Abstract
Riboswitches are RNA sensors that regulate gene expression in response to binding of small molecules. Although they conceptually represent simple on/off switches and, therefore, hold great promise for biotechnology and future synthetic biology applications, the induction of gene expression by natural riboswitches after ligand addition or removal is often only moderate and, consequently, the achievable expression levels are not very high. Here, we have designed an RNA amplification-based system that strongly improves the efficiency of riboswitches. We have successfully implemented the method in a biological system for which currently no efficient endogenous tools for inducible (trans)gene expression are available: the chloroplasts of higher plants. We further show that an HIV antigen whose constitutive expression from the chloroplast genome is deleterious to the plant can be inducibly expressed under the control of the RNA amplification-enhanced riboswitch (RAmpER) without causing a mutant phenotype, demonstrating the potential of the method for the production of proteins and metabolites that are toxic to the host cell.
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Affiliation(s)
- Masoumeh Emadpour
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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Saxena R, Gupta S, Singh K, Mitra K, Tripathi AK, Tripathi RK. Proteomic profiling of SupT1 cells reveal modulation of host proteins by HIV-1 Nef variants. PLoS One 2015; 10:e0122994. [PMID: 25874870 PMCID: PMC4395413 DOI: 10.1371/journal.pone.0122994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 02/26/2015] [Indexed: 01/14/2023] Open
Abstract
Nef is an accessory viral protein that promotes HIV-1 replication, facilitating alterations in cellular pathways via multiple protein-protein interactions. The advent of proteomics has expanded the focus on better identification of novel molecular pathways regulating disease progression. In this study, nef was sequenced from randomly selected patients, however, sequence variability identified did not elicited any specific mutation that could have segregated HIV-1 patients in different stages of disease progression. To explore the difference in Nef functionality based on sequence variability we used proteomics approach. Proteomic profiling was done to compare the effect of Nef variants in host cell protein expression. 2DGE in control and Nef transfected SupT1 cells demonstrated several differentially expressed proteins. Fourteen protein spots were detected with more than 1.5 fold difference. Significant down regulation was seen in six unique protein spots in the Nef treated cells. Proteins were identified as Cyclophilin A, EIF5A-1 isoform B, Rho GDI 1 isoform a, VDAC1, OTUB1 and α-enolase isoform 1 (ENO1) through LC-MS/MS. The differential expression of the 6 proteins was analyzed by Real time PCR, Western blotting and Immunofluorescence studies with two Nef variants (RP14 and RP01) in SupT1 cells. There was contrasting difference between the effect of these Nef variants upon the expression of these six proteins. Downregulation of α-enolase (ENO1), VDAC1 and OTUB1 was more significant by Nef RP01 whereas Cyclophilin A and RhoGDI were found to be more downregulated by Nef RP14. This difference in Nef variants upon host protein expression was also studied through a site directed mutant of Nef RP01 (55AAAAAAA61) and the effect was found to be reversed. Deciphering the role of these proteins mediated by Nef variants will open a new avenue of research in understanding Nef mediated pathogenesis. Overall study determines modulation of cellular protein expression in T cells by HIV-1 Nef variants.
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Affiliation(s)
- Reshu Saxena
- Toxicology division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Sudipti Gupta
- Toxicology division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Kavita Singh
- Electron Microscopy Lab, Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Kalyan Mitra
- Electron Microscopy Lab, Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
| | - Anil Kumar Tripathi
- Department of Medicine, King George’s Medical University, Chowk, Lucknow, India
| | - Raj Kamal Tripathi
- Toxicology division, CSIR-Central Drug Research Institute, Sector-10, Janakipuram Extension, Sitapur Road, Lucknow, India
- * E-mail:
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