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Paes W, Leonov G, Partridge T, Chikata T, Murakoshi H, Frangou A, Brackenridge S, Nicastri A, Smith AG, Learn GH, Li Y, Parker R, Oka S, Pellegrino P, Williams I, Haynes BF, McMichael AJ, Shaw GM, Hahn BH, Takiguchi M, Ternette N, Borrow P. Contribution of proteasome-catalyzed peptide cis-splicing to viral targeting by CD8 + T cells in HIV-1 infection. Proc Natl Acad Sci U S A 2019; 116:24748-24759. [PMID: 31748275 PMCID: PMC6900506 DOI: 10.1073/pnas.1911622116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Peptides generated by proteasome-catalyzed splicing of noncontiguous amino acid sequences have been shown to constitute a source of nontemplated human leukocyte antigen class I (HLA-I) epitopes, but their role in pathogen-specific immunity remains unknown. CD8+ T cells are key mediators of HIV type 1 (HIV-1) control, and identification of novel epitopes to enhance targeting of infected cells is a priority for prophylactic and therapeutic strategies. To explore the contribution of proteasome-catalyzed peptide splicing (PCPS) to HIV-1 epitope generation, we developed a broadly applicable mass spectrometry-based discovery workflow that we employed to identify spliced HLA-I-bound peptides on HIV-infected cells. We demonstrate that HIV-1-derived spliced peptides comprise a relatively minor component of the HLA-I-bound viral immunopeptidome. Although spliced HIV-1 peptides may elicit CD8+ T cell responses relatively infrequently during infection, CD8+ T cells primed by partially overlapping contiguous epitopes in HIV-infected individuals were able to cross-recognize spliced viral peptides, suggesting a potential role for PCPS in restricting HIV-1 escape pathways. Vaccine-mediated priming of responses to spliced HIV-1 epitopes could thus provide a novel means of exploiting epitope targets typically underutilized during natural infection.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
| | - German Leonov
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Takayuki Chikata
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hayato Murakoshi
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Anna Frangou
- Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Andrew G Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert Parker
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Shinichi Oka
- Centre for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
- AIDS Clinical Centre, National Centre for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Pierre Pellegrino
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Ian Williams
- Centre for Sexual Health and HIV Research, University College London, London WC1E 6JB, United Kingdom
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom;
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Abstract
A complex relationship exists between HIV and its cellular targets. The lethal effect of HIV on circulating CD4(+) helper T lymphocytes parallels the degree of the infected individual's immunodeficiency and ultimately the transition to AIDS and death. However, as with other members of the Lentivirus family of retroviruses, the ubiquitous, mobile macrophage is also a prime target for HIV infection, and apparently, in most instances, is the initial infected cell, since most people are infected with a CCR5 chemokine-tropic virus. Unlike the lymphocyte, the macrophage is apparently a more stable viral host, capable of a long infected life as an HIV reservoir and a chronic source of infectious virus. Published in vitro studies have indicated that whereas lymphocytes replicate HIV solely on their plasma membrane, macrophages have been envisaged to predominantly replicate HIV within cytoplasmic vacuoles, and thus have been likened to a "Trojan horse," when it comes to the immune system. Recent studies have revealed an ingenious way by which the cultured monocyte-derived macrophage (MDM) replicates HIV and releases it into the medium. The key macrophage organelle appears to be what is alternatively referred to as the "late endosome" (LE) or the "multivesicular body" (MVB), which have a short and a long history, respectively. Proof of the association is that chemically, LE/MVB and their vesicles possess several pathopneumonic membrane markers (e.g., CD63) that are found on released HIV particles. The hypothesis is that HIV usurps this vesicle-forming mechanism and employs it for its own replication. Release of the intravacuolar virus from the cell is hypothesized to occur by a process referred to as exocytosis, resulting from the fusion of virus-laden LE/MVB with the plasma membrane of the macrophage. Interestingly, LE/MVB are also involved in the infection stage of MDM by HIV. Close review of the literature reveals that along with the Golgi, which contributes to the formation of LE/MVB, the MVB was first identified as a site of HIV replication by macrophages many years ago, but the full implication of this observation was not appreciated at the time. As in many other areas of HIV research, what has been totally lacking is an in vivo confirmation of the in vitro phenomenon. Herein, the ultrastructure of HIV interaction with cells in vitro and in vivo is explored. It is shown that while HIV is regularly found in LE/MVB in vitro, it is infrequently the case in vivo. Therefore, the results challenge the "Trojan horse" concept.
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Affiliation(s)
- Jan Marc Orenstein
- Department of Pathology, George Washington University Medical Center, Washington, DC 20037-2336, USA.
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Ongrádi J, Laird HM, Szilágyi JF, Horváth A, Bendinelli M. Unique morphological alterations of the HTLV-I transformed C8166 cells by infection with HIV-1. Pathol Oncol Res 2000; 6:27-37. [PMID: 10749585 DOI: 10.1007/bf03032655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
C8166 cells express T lymphocyte markers, a monocyte-specific esterase, taxpolypeptide of HTLV-I. In spite of this transactivator, their HIV-1 yield is low. Their culture conditions were modified, and infected cells were immobilized on a poly-L-lysine sheet under semisolid overlays to study their phenotypic alterations and HIV-1 production by microscopy and electron microscopy. Another lymphoid cultures (MT-4, CEM, CEM-ss, AdCEM) similarly treated were infected with either HIV-1/RF or IIIB. Specificity of HIV-1 was compared to the effects of vesicular stomatitis virus (VSV). Unlike other cultures, HIV-1/RF infected C8166 cells in Eagle s MEM exhibited surface projections resembling hairy leukemia cells, which was followed by balloon degeneration and apoptosis. Immobilized HIV-1 infected cultures formed flat syncytia with several interdigitating dendritic projections. Syncytia shrunk with condensed nuclear material and axon-like filaments characteristic for infected macrophages. VSV induced enlargement and necrotic lysis of all cell types. Early postinfection with HIV-1, electron microscopy revealed irreversible membrane fusion above cell nuclei, and transient fusion between filaments. Transient presence of coated vesicles containing intact HIV-1 particles, Birbeck granule-like structures of Langerhans cells, fibrillar-lamellar structures resembling hairy leukemia or Sézary cells were detected. Late postinfection, high proportion of HIV-1 bud from polarized cytoplasm was empty particle, while that bud and entrapped in cytoplasmic vacuoles contained two or multiple cores in a fused envelope. The effect of early gene products of HIV-1 on HTLV-I and C8166 cells might elicit their latent potentials for monocyte or interdigitating dendritic cells, while in the later phase HTLV-I products might alter HIV-1 virion assembly.
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Affiliation(s)
- J Ongrádi
- National Institute of Dermato-Venerology Mária utca 41., Budapest, 1085, Hungary.
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Abstract
The life-cycle of human immunodeficiency virus type 1 (HIV-1) has been studied using several techniques including immunoelectron microscopy and cryomicroscopy. The HIV-1 particle consists of an envelope, a core and the region between the core and the envelope (matrix). Virus particles in the extracellular space are observed as having various profiles: a central or an eccentric round electron-dense core, a bar-shaped electron-dense core, and immature doughnut-shaped particle. HIV-1 particles in the hydrated state were observed by high-resolution electron cryomicroscopy to be spherical and the lipid membrane was clearly resolved as a bilayer. Projections around the circumference were seen to be knob-like. The shapes and sizes of the projections, especially the head parts, were found to vary with each projection. HIV-1 cores were isolated with a mixture of Nonidet P40 and glutaraldehyde, and were confirmed to consist of HIV-1 Gag p24 protein by immunogold labelling. On infection, the HIV-1 virus was found to enter the cell in two ways: membrane fusion and endocytosis. After viral entry, no structures resembling virus particles could be seen in the cytoplasm. In the infected cells, positive reactions by immunolabelling suggest that HIV-1 Gag is produced in membrane-bound structures and transported to the cell surface by the cytoskeletons. A crescent electron-dense layer is then formed underneath the cell membrane. Finally, the virus particle is released from the cell surface and found extracellularly to be a complete virus particle with an electron-dense core. However, several cell clones producing defective mature, doughnut-shaped (immature) or teardrop-shaped particles were found to be produced in the extracellular space. In the doughnut-shaped particles, Gag p17 and p24 proteins exist facing each other against an inner electron-dense ring, suggesting that the inner ring consists of a precursor Gag protein showing a defect at the viral proteinase.
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Affiliation(s)
- T Goto
- Department of Microbiology, Osaka Medical College, Japan.
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Yu QC, Matsuda Z, Yu X, Ito S, Essex M, Lee TH. An electron-lucent region within the virion distinguishes HIV-1 from HIV-2 and simian immunodeficiency virus. AIDS Res Hum Retroviruses 1994; 10:757-61. [PMID: 8074937 DOI: 10.1089/aid.1994.10.757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Ultrastructural comparisons of immature or budding particles of human immunodeficiency virus (HIV) types 1 and 2 and simian immunodeficiency virus of macaques (SIVmac) revealed no significant difference between these genetically distinct, but related, viruses. However, a region encompassing the core of mature HIV-1 virions was found to be more electron lucent than that observed in HIV-2 and SIVmac. This ultrastructural distinction cannot be attributed to HIV-1-specific vpu, HIV-2/SIV-specific vpx, or virion-associated vpr gene products.
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Affiliation(s)
- Q C Yu
- Department of Cancer Biology, Harvard School of Public Health, Boston, Massachusetts 02115
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Abstract
The electron microscope has been used with great skill in many aspects of the acquired immunodeficiency syndrome. It has played a critical role in classifying the human immunodeficiency virus, in characterizing the morphogenesis and gene products of the virus, and in elucidating the host cell targets and interactions. With the aid of the electron microscope, new opportunistic pathogens are being identified, and particularly difficult diagnoses are being made. Extrapolations from observations made at the ultrastructural level to the light microscopic level have provided criteria for the diagnosis of several infectious agents. As with any powerful scientific tool, observations must be interpreted with great care by scientists experienced in electron microscopy.
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Affiliation(s)
- J M Orenstein
- Department of Pathology, George Washington University Medical Center, Washington, DC 20037
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Kiernan R, Marshall J, Bowers R, Doherty R, McPhee D. Kinetics of HIV-1 replication and intracellular accumulation of particles in HTLV-I-transformed cells. AIDS Res Hum Retroviruses 1990; 6:743-52. [PMID: 2364017 DOI: 10.1089/aid.1990.6.743] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The replication kinetics of HIV were examined in HTLV-I-transformed MT-2 cells. The duration of the initial replication cycle was 20 hours, determined by the first detection of infectious progeny virus, development of syncytia, and production of viral RNA and protein. A phase of exponential virus production followed until 62 h postinfection. Cell death occurred in the final phase of infection during which infectious virus production remained constant even though viral RNA and protein production increased at an exponential rate. Accumulations of HIV particles were observed within cytoplasmic vacuoles of infected MT-2 cells. Although cell lysates contained high titers of infectious virus, our data show that an increasing proportion of particles produced late in infection were not infectious.
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Affiliation(s)
- R Kiernan
- NHMRC Special Unit for AIDS Virology, Macfarlane Burnet Centre for Medical Research, Fairfield, Victoria, Australia
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