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Spottiswoode CN, Busch R. Vive la difference! Self/non-self recognition and the evolution of signatures of identity in arms races with parasites. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180206. [PMID: 30967089 PMCID: PMC6388040 DOI: 10.1098/rstb.2018.0206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
In arms races with parasites, hosts can evolve defences exhibiting extensive variability within populations, which signals individual identity ('signatures'). However, few such systems have evolved, suggesting that the conditions for their evolution are uncommon. We review (a) polymorphic egg markings that allow hosts of brood-parasitic birds to recognize and reject parasitic eggs, and (b) polymorphic tissue antigens encoded in the major histocompatibility complex (MHC), which present self- and pathogen-derived peptides to T cells of the immune system. Despite the profound differences between these systems, they share analogous features: (i) self/non-self discrimination by a highly specific recognition system (bird eyes and T-cell antigen receptor, respectively), which antagonists may escape by evolving evasion or mimicry; (ii) a self substrate upon which diversifying selection can act (eggs, and MHC molecules); (iii) acquired knowledge of self (resulting in acceptance of own eggs, and immune tolerance); and (iv) fitness costs associated with attack on self or lack of parasite detection. We suggest that these features comprise a set of requirements for parasites to drive the evolution of identity signatures in hosts, which diminish the likelihood of recognition errors. This may help to explain the variety of trajectories arising from arms races in different antagonistic contexts. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
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Affiliation(s)
- Claire N. Spottiswoode
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch 7701, South Africa
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Robert Busch
- Department of Life Sciences, Whitelands College, University of Roehampton, Holybourne Avenue, London SW15 4JD, UK
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Yaseen MM, Abuharfeil NM, Alqudah MA, Yaseen MM. Mechanisms and Factors That Drive Extensive Human Immunodeficiency Virus Type-1 Hypervariability: An Overview. Viral Immunol 2017; 30:708-726. [PMID: 29064351 DOI: 10.1089/vim.2017.0065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The extensive hypervariability of human immunodeficiency virus type-1 (HIV-1) populations represents a major barrier against the success of currently available antiretroviral therapy. Moreover, it is still the most important obstacle that faces the development of an effective preventive vaccine against this infectious virus. Indeed, several factors can drive such hypervariability within and between HIV-1 patients. These factors include: first, the very low fidelity nature of HIV-1 reverse transcriptase; second, the extremely high HIV-1 replication rate; and third, the high genomic recombination rate that the virus has. All these factors together with the APOBEC3 proteins family and the immune and antiviral drugs pressures drive the extensive hypervariability of HIV-1 populations. Studying these factors and the mechanisms that drive such hypervariability will provide valuable insights that may guide the development of effective therapeutic and preventive strategies against HIV-1 infection in the near future. To this end, in this review, we summarized recent advances in this area of HIV-1 research.
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Affiliation(s)
- Mahmoud Mohammad Yaseen
- 1 Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Jordan University of Science and Technology , Irbid, Jordan
| | - Nizar Mohammad Abuharfeil
- 2 Department of Applied Biological Sciences, College of Science and Arts, Jordan University of Science and Technology , Irbid, Jordan
| | - Mohammad Ali Alqudah
- 3 Department of Clinical Pharmacy, College of Pharmacy, Jordan University of Science and Technology , Irbid, Jordan
| | - Mohammad Mahmoud Yaseen
- 4 Department of Public Health, College of Medicine, Jordan University of Science and Technology , Irbid, Jordan
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Abstract
After the success of combination antiretroviral therapy (cART) to treat HIV infection, the next great frontier is to cure infected persons, a formidable challenge. HIV persists in a quiescent state in resting CD4+ T cells, where the replicative enzymes targeted by cART are not active. Although low levels of HIV transcripts are detectable in these resting cells, little to no viral protein is produced, rendering this reservoir difficult to detect by the host CD8+ T cell response. However, recent advances suggest that this state of latency might be pharmacologically reversed, resulting in viral protein expression without the adverse effects of massive cellular activation. Emerging data suggest that with this approach, infected cells will not die of viral cytopathic effects, but might be eliminated if HIV-specific CD8+ T cells can be effectively harnessed. Here, we address the antiviral properties of HIV-specific CD8+ T cells and how these cells might be harnessed to greater effect toward achieving viral eradication or a functional cure.
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Suzuki K, Hattori S, Marks K, Ahlenstiel C, Maeda Y, Ishida T, Millington M, Boyd M, Symonds G, Cooper DA, Okada S, Kelleher AD. Promoter Targeting shRNA Suppresses HIV-1 Infection In vivo Through Transcriptional Gene Silencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e137. [PMID: 24301868 PMCID: PMC3894581 DOI: 10.1038/mtna.2013.64] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
Despite prolonged and intensive application, combined antiretroviral therapy cannot eradicate human immunodeficiency virus (HIV)-1 because it is harbored as a latent infection, surviving for long periods of time. Alternative approaches are required to overcome the limitations of current therapy. We have been developing a short interfering RNA (siRNA) gene silencing approach. Certain siRNAs targeting promoter regions of genes induce transcriptional gene silencing. We previously reported substantial transcriptional gene silencing of HIV-1 replication by an siRNA targeting the HIV-1 promoter in vitro. In this study, we show that this siRNA, expressed as a short hairpin RNA (shRNA) (shPromA-JRFL) delivered by lentiviral transduction of human peripheral blood mononuclear cells (PBMCs), which are then used to reconstitute NOJ mice, is able to inhibit HIV-1 replication in vivo, whereas a three-base mismatched variant (shPromA-M2) does not. In shPromA-JRFL–treated mice, HIV-1 RNA in serum is significantly reduced, and the ratio of CD4+/CD8+ T cells is significantly elevated. Expression levels of the antisense RNA strand inversely correlates with HIV-1 RNA in serum. The silenced HIV-1 can be reactivated by T-cell activation in ex vivo cultures. HIV-1 suppression is not due to offtarget effects of shPromA-JRFL. These data provide “proof-of principle” that an shRNA targeting the HIV-1 promoter is able to suppress HIV-1 replication in vivo.
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Affiliation(s)
- Kazuo Suzuki
- St. Vincent's Centre for Applied Medical Research, Darlinghurst, New South Wales, Australia
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Mailliard RB, Smith KN, Fecek RJ, Rappocciolo G, Nascimento EJM, Marques ET, Watkins SC, Mullins JI, Rinaldo CR. Selective induction of CTL helper rather than killer activity by natural epitope variants promotes dendritic cell-mediated HIV-1 dissemination. THE JOURNAL OF IMMUNOLOGY 2013; 191:2570-80. [PMID: 23913962 DOI: 10.4049/jimmunol.1300373] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The ability of HIV-1 to rapidly accumulate mutations provides the virus with an effective means of escaping CD8(+) CTL responses. In this study, we describe how subtle alterations in CTL epitopes expressed by naturally occurring HIV-1 variants can result in an incomplete escape from CTL recognition, providing the virus with a selective advantage. Rather than paralyzing the CTL response, these epitope modifications selectively induce the CTL to produce proinflammatory cytokines in the absence of target killing. Importantly, instead of dampening the immune response through CTL elimination of variant Ag-expressing immature dendritic cells (DC), a positive CTL-to-DC immune feedback loop dominates whereby the immature DC differentiate into mature proinflammatory DC. Moreover, these CTL-programmed DC exhibit a superior capacity to mediate HIV-1 trans-infection of T cells. This discordant induction of CTL helper activity in the absence of killing most likely contributes to the chronic immune activation associated with HIV-1 infection, and can be used by HIV-1 to promote viral dissemination and persistence. Our findings highlight the need to address the detrimental potential of eliciting dysfunctional cross-reactive memory CTL responses when designing and implementing anti-HIV-1 immunotherapies.
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Affiliation(s)
- Robbie B Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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Langhammer S. Rationale for the design of an oncology trial using a generic targeted therapy multi‑drug regimen for NSCLC patients without treatment options (Review). Oncol Rep 2013; 30:1535-41. [PMID: 23877481 PMCID: PMC3810357 DOI: 10.3892/or.2013.2631] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/05/2013] [Indexed: 01/07/2023] Open
Abstract
Despite more than 70 years of research concerning medication for cancer treatment, the disease still remains one of the leading causes of mortality worldwide. Many cancer types lead to death within a period of months to years. The original class of chemotherapeutics is not selective for tumor cells and often has limited efficacy, while treated patients suffer from adverse side‑effects. To date, the concept of tumor‑specific targeted therapy drugs has not fulfilled its expectation to provide a key for a cure. Today, many oncology trials are designed using a combination of chemotherapeutics with targeted therapy drugs. However, these approaches have limited outcomes in most cancer indications. This perspective review provides a rationale to combine targeted therapy drugs for cancer treatment based on observations of evolutionary principles of tumor development and HIV infections. In both diseases, the mechanisms of immune evasion and drug resistance can be compared to some extent. However, only for HIV is a breakthrough treatment available, which is the highly active antiretroviral therapy (HAART). The principles of HAART and recent findings from cancer research were employed to construct a hypothetical model for cancer treatment with a multi‑drug regimen of targeted therapy drugs. As an example of this hypothesis, it is proposed to combine already marketed targeted therapy drugs against VEGFRs, EGFR, CXCR4 and COX2 in an oncology trial for non‑small cell lung cancer patients without further treatment options.
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Tóth I, Le AQ, Hartjen P, Thomssen A, Matzat V, Lehmann C, Scheurich C, Beisel C, Busch P, Degen O, Lohse AW, Eiermann T, Fätkenheuer G, Meyer-Olson D, Bockhorn M, Hauber J, van Lunzen J, Schulze Zur Wiesch J. Decreased frequency of CD73+CD8+ T cells of HIV-infected patients correlates with immune activation and T cell exhaustion. J Leukoc Biol 2013; 94:551-61. [PMID: 23709688 DOI: 10.1189/jlb.0113018] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent studies indicate that murine Tregs highly express the ENTDP1, as well as the 5'-NT and thereby, suppress Teff function by extracellular adenosine production. Furthermore, CD73 seems to play a role as costimulatory molecule for T cell differentiation. In this study, we analyzed the expression of CD73 on peripheral and lymph nodal Teffs and Tregs in a cohort of 95 HIV patients at different stages of disease, including LTNP and ECs. In contrast to murine Tregs, CD73 was only expressed on a small minority (∼10%) of peripheral Tregs. In contrast, we see high expression of CD73 on peripheral CD8(+) T cells. In HIV infection, CD73 is markedly reduced on all Teffs and Tregs, regardless of the memory subtype. On CD8(+) T cells, a positive correlation between CD73 expression and CD4 counts (P=0.0003) was detected. CD73 expression on CD8(+) T cells negatively correlated with HLA-DR (<0.0001) and PD1 (P=0.0457) expression. The lower CD73 expression on CD8(+) T cells was partially reversible after initiation of ART (P=0.0016). Functionally, we observed that CD8(+)CD73(+) T cells produce more IL-2 upon HIV-specific and unspecific stimulation than their CD73(-) counterparts and show a higher proliferative capacity. These data indicate that down-regulation of CD73 on CD8(+) T cells correlates with immune activation and leads to functional deficits in HIV infection.
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Affiliation(s)
- Ilona Tóth
- 1.Section Infectious Diseases, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany.
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Lin YT, Yen CH, Chen HL, Liao YJ, Lin IF, Chen M, Lan YC, Chuang SY, Hsieh SL, Chen YMA. The serologic decoy receptor 3 (DcR3) levels are associated with slower disease progression in HIV-1/AIDS patients. J Formos Med Assoc 2013; 114:498-503. [PMID: 26062966 DOI: 10.1016/j.jfma.2013.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/15/2013] [Accepted: 01/22/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND/PURPOSE The decoy receptor 3 (DcR3) is a member of the tumor necrosis factor receptor (TNFR) super-family. It counteracts the biological effects of Fas ligands and inhibits apoptosis. The goals of this study were to understand the associations between serologic DcR3 (sDcR3) levels and different human immunodeficiency virus type 1 (HIV-1) subtypes, as well as the AIDS disease progression. METHODS Serum samples from 61 HIV/AIDS patients, who had been followed up every 6 months for 3 years, were collected. sDcR3 levels were quantified using an enzyme immunoassay (EIA). RESULTS The sDcR3 levels in patients with HIV-1 subtype B were significantly higher than those in patients infected with subtype CRF01_AE (p < 0.001). In addition, multivariable linear mixed model analysis demonstrated that HIV-1 subtype B and slow disease progression were associated with higher levels of sDcR3, adjusting for potential predictors (p = 0.0008 and 0.0455, respectively). CONCLUSION HIV-1-infected cells may gain a survival advantage by activating DcR3, which prevents infected cell detection by the host immune system. These data indicate that the sDcR3 level is a biomarker for AIDS disease progression.
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Affiliation(s)
- Yu-Ting Lin
- AIDS Prevention and Research Centre, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chia-Hung Yen
- AIDS Prevention and Research Centre, National Yang-Ming University, Taipei 11221, Taiwan
| | - Heng-Li Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Jen Liao
- AIDS Prevention and Research Centre, National Yang-Ming University, Taipei 11221, Taiwan; School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei 11031, Taiwan
| | - I-Feng Lin
- Institute of Public Health, National Yang-Ming University, Taipei 11221, Taiwan
| | - Marcelo Chen
- AIDS Prevention and Research Centre, National Yang-Ming University, Taipei 11221, Taiwan; Department of Urology, Mackay Memorial Hospital, Taipei 10449, Taiwan; School of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Yu-Ching Lan
- AIDS Prevention and Research Centre, National Yang-Ming University, Taipei 11221, Taiwan; Department of Health Risk Management, China Medical University, Taichung 40402, Taiwan
| | - Shao-Yuan Chuang
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 35053, Taiwan
| | - Shie-Liang Hsieh
- Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan; Department and Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 11221, Taiwan; Infection and Immunity Research Centre, National Yang-Ming University, Taipei 11221, Taiwan; Immunology Centre, Taipei Veterans General Hospital, Taipei 11221, Taiwan
| | - Yi-Ming Arthur Chen
- AIDS Prevention and Research Centre, National Yang-Ming University, Taipei 11221, Taiwan; Department of Microbiology, School of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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Abstract
PURPOSE OF REVIEW Much of the current HIV-1 vaccine research focuses on harnessing the cytotoxic T-lymphocyte arm of the immune response. However, HIV-1 appears to have an unerring ability to evade cytotoxic T-lymphocyte responses, through the process of escape mutation, and thus the potential benefit of a cytotoxic T-lymphocyte-based vaccine remains uncertain. This review focuses on several recent studies that question whether escape mutation is always detrimental to the host, and may provide new hope for the success of a cytotoxic T-lymphocyte-based vaccine against HIV. RECENT FINDINGS Several recent studies, in both natural HIV-1 infection and the SIV model, have identified examples of cytotoxic T-lymphocyte escape mutants that revert on transmission to individuals lacking the selecting major histocompatibility complex alleles. The obvious implication of these data is that some cytotoxic T-lymphocyte responses can only be evaded through escape mutations that actually reduce the replicative fitness of the virus. In addition, a recent vaccine study in macaques found that the control of immunodeficiency virus to undetectable levels was only achieved in animals that were able to force the virus to make such detrimental escape mutations. These data raise the intriguing possibility that, rather than undermining cytotoxic T-lymphocyte vaccines, escape mutation may be one of the keys to their success. SUMMARY Clearly, not all escape mutations help to control viral replication. We discuss how these new data may assist in the struggle to develop a successful cytotoxic T-lymphocyte-based HIV vaccine, and what they tell us about the responses such a vaccine should aim to elicit.
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Blacklaws BA. Small ruminant lentiviruses: immunopathogenesis of visna-maedi and caprine arthritis and encephalitis virus. Comp Immunol Microbiol Infect Dis 2012; 35:259-69. [PMID: 22237012 DOI: 10.1016/j.cimid.2011.12.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
Abstract
The small ruminant lentiviruses include the prototype for the genus, visna-maedi virus (VMV) as well as caprine arthritis encephalitis virus (CAEV). Infection of sheep or goats with these viruses causes slow, progressive, inflammatory pathology in many tissues, but the most common clinical signs result from pathology in the lung, mammary gland, central nervous system and joints. This review examines replication, immunity to and pathogenesis of these viruses and highlights major differences from and similarities to some of the other lentiviruses.
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Affiliation(s)
- Barbara A Blacklaws
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
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Février M, Dorgham K, Rebollo A. CD4+ T cell depletion in human immunodeficiency virus (HIV) infection: role of apoptosis. Viruses 2011; 3:586-612. [PMID: 21994747 PMCID: PMC3185763 DOI: 10.3390/v3050586] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 02/07/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection is principally a mucosal disease and the gastrointestinal (GI) tract is the major site of HIV replication. Loss of CD4+ T cells and systemic immune hyperactivation are the hallmarks of HIV infection. The end of acute infection is associated with the emergence of specific CD4+ and CD8+ T cell responses and the establishment of a chronic phase of infection. Abnormal levels of immune activation and inflammation persist despite a low steady state level of viremia. Although the causes of persistent immune hyperactivation remain incompletely characterized, physiological alterations of gastrointestinal tract probably play a major role. Failure to restore Th17 cells in gut-associated lymphoid tissues (GALT) might impair the recovery of the gut mucosal barrier. This review discusses recent advances on understanding the contribution of CD4+ T cell depletion to HIV pathogenesis.
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Affiliation(s)
- Michèle Février
- Unité Génomique Virale et Vaccination, CNRS URA3015, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France.
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Irausquin SJ, Hughes AL. Conflicting selection pressures on T-cell epitopes in HIV-1 subtype B. INFECTION GENETICS AND EVOLUTION 2011; 11:483-8. [PMID: 21232634 DOI: 10.1016/j.meegid.2010.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 12/20/2010] [Accepted: 12/23/2010] [Indexed: 12/26/2022]
Abstract
Analysis of population-level polymorphism in eight coding genes of human immunodeficiency virus type 1 (HIV-1) subtype B revealed evidence not only of past purifying selection, but also of abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection. Both CD4 and CTL epitopes showed an excess of nonsynonymous variants that were singletons (occurring in just one sequence) in our dataset. Overall, median gene diversities at polymorphic nonsynonymous sites were highest at sites located in neither CD4 nor CTL epitopes, while polymorphic nonsynonymous sites in CD4 epitopes revealed the lowest median gene diversity. Our results support the hypothesis that there is an evolutionary conflict between immune escape and functional constraint on epitopes recognized by host T-cells, and suggest that amino acid sequences of CD4 epitopes are subject to particularly strong functional constraint.
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Affiliation(s)
- Stephanie Jiménez Irausquin
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter St., Columbia, SC 29208, USA
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Epitope mapping of HIV-specific CD8+ T cell responses by multiple immunological readouts reveals distinct specificities defined by function. J Virol 2010; 85:1275-86. [PMID: 21084478 DOI: 10.1128/jvi.01707-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The limited success of HIV vaccine candidates to date highlights our need to better characterize protective cell-mediated immunity (CMI). While HIV-specific CD8(+) T cell responses have been defined largely by measuring gamma interferon (IFN-γ), these responses are not always protective, and it is unclear whether the same epitopes would predominate if other functional parameters were examined. Here, we assessed the epitope specificity of HIV-specific CD8(+) T cell responses by multiparametric flow cytometry, measuring five CD8(+) T cell functions (IFN-γ, macrophage inflammatory protein 1β [MIP-1β], tumor necrosis factor alpha [TNF-α], interleukin-2 [IL-2], and proliferative capacity) in 24 chronically HIV-infected individuals. Sixty-nine epitope-specific responses to 50 epitopes within p24 were measured. Surprisingly, most epitope-specific responses were IFN-γ negative (50/69 responses). Many responses had polyfunctional (33%) and proliferative (19%) components. An inverse association between IL-2 and proliferation responses was also observed, contrary to what was described previously. We confirm that long-term nonprogressors (LTNP) have more polyfunctional responses and also have higher-magnitude and broader p24-specific proliferation and higher levels of IL-2 and TNF-α production than do progressing controls. Together, these data suggest that the specificity of CD8(+) T cell responses differs depending on the immunological readout, with a 3.5-fold increase in breadth detected by including multiple parameters. Furthermore, the identification of epitopes that elicit polyfunctional responses reinforces the need for the comprehensive evaluation of HIV vaccine candidates, and these epitopes may represent novel targets for CMI-based vaccines.
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Zhang C, Ding N, Chen K, Yang R. Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1204-14. [PMID: 20953943 PMCID: PMC7089306 DOI: 10.1007/s11427-010-4066-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 08/01/2010] [Indexed: 11/26/2022]
Abstract
HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtypes B and C. The results showed that R5 and X4 variants experienced differential evolutionary patterns and different HIV-1 genes encountered various positive selection pressures, suggesting that complex selection pressures are driving HIV-1 evolution. Compared with other hypervariable regions of Gp120, significantly more positively selected sites were detected in the V3 region of subtype B X4 variants, V2 region of subtype B R5 variants, and V1 and V4 regions of subtype C X4 variants, indicating an association of positive selection with co-receptor recognition/binding. Intriguingly, a significantly higher proportion (33.3% and 55.6%, P<0.05) of positively selected sites were identified in the C3 region than other conserved regions of Gp120 in all the analyzed HIV-1 variants, indicating that the C3 region might be more important to HIV-1 adaptation than previously thought. Approximately half of the positively selected sites identified in the env gene were identical between R5 and X4 variants. There were three common positively selected sites (96, 113 and 281) identified in Gp41 of all X4 and R5 variants from subtypes B and C. These sites might not only suggest a functional importance in viral survival and adaptation, but also imply a potential cross-immunogenicity between HIV-1 R5 and X4 variants, which has important implications for AIDS vaccine development.
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Affiliation(s)
- ChiYu Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013 China
| | - Na Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013 China
| | - KePing Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013 China
| | - RongGe Yang
- HIV Molecular Epidemiology and Virology Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
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Paul S, Piontkivska H. Discovery of novel targets for multi-epitope vaccines: screening of HIV-1 genomes using association rule mining. Retrovirology 2009; 6:62. [PMID: 19580659 PMCID: PMC2716299 DOI: 10.1186/1742-4690-6-62] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 07/06/2009] [Indexed: 11/24/2022] Open
Abstract
Background Studies have shown that in the genome of human immunodeficiency virus (HIV-1) regions responsible for interactions with the host's immune system, namely, cytotoxic T-lymphocyte (CTL) epitopes tend to cluster together in relatively conserved regions. On the other hand, "epitope-less" regions or regions with relatively low density of epitopes tend to be more variable. However, very little is known about relationships among epitopes from different genes, in other words, whether particular epitopes from different genes would occur together in the same viral genome. To identify CTL epitopes in different genes that co-occur in HIV genomes, association rule mining was used. Results Using a set of 189 best-defined HIV-1 CTL/CD8+ epitopes from 9 different protein-coding genes, as described by Frahm, Linde & Brander (2007), we examined the complete genomic sequences of 62 reference HIV sequences (including 13 subtypes and sub-subtypes with approximately 4 representative sequences for each subtype or sub-subtype, and 18 circulating recombinant forms). The results showed that despite inclusion of recombinant sequences that would be expected to break-up associations of epitopes in different genes when two different genomes are recombined, there exist particular combinations of epitopes (epitope associations) that occur repeatedly across the world-wide population of HIV-1. For example, Pol epitope LFLDGIDKA is found to be significantly associated with epitopes GHQAAMQML and FLKEKGGL from Gag and Nef, respectively, and this association rule is observed even among circulating recombinant forms. Conclusion We have identified CTL epitope combinations co-occurring in HIV-1 genomes including different subtypes and recombinant forms. Such co-occurrence has important implications for design of complex vaccines (multi-epitope vaccines) and/or drugs that would target multiple HIV-1 regions at once and, thus, may be expected to overcome challenges associated with viral escape.
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Affiliation(s)
- Sinu Paul
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA.
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Duda A, Lee-Turner L, Fox J, Robinson N, Dustan S, Kaye S, Fryer H, Carrington M, McClure M, McLean AR, Fidler S, Weber J, Phillips RE, Frater AJ. HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection. J Virol 2009; 83:1228-39. [PMID: 19019964 PMCID: PMC2620910 DOI: 10.1128/jvi.01545-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 10/21/2008] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) can evade immunity shortly after transmission to a new host but the clinical significance of this early viral adaptation in HIV infection is not clear. We present an analysis of sequence variation from a longitudinal cohort study of HIV adaptation in 189 acute seroconverters followed for up to 3 years. We measured the rates of variation within well-defined epitopes to determine associations with the HLA-linked hazard of disease progression. We found early reversion across both the gag and pol genes, with a 10-fold faster rate of escape in gag (2.2 versus 0.27 forward mutations/1,000 amino acid sites). For most epitopes (23/34), variation in the HLA-matched and HLA-unmatched controls was similar. For a minority of epitopes (8/34, and generally associated with HLA class I alleles that confer clinical benefit), new variants appeared early and consistently over the first 3 years of infection. Reversion occurred early at a rate which was HLA-dependent and correlated with the HLA class 1-associated relative hazard of disease progression and death (P = 0.0008), reinforcing the association between strong cytotoxic T-lymphocyte responses, viral fitness, and disease status. These data provide a comprehensive overview of viral adaptation in the first 3 years of infection. Our findings of HLA-dependent reversion suggest that costs are borne by some escape variants which may benefit the host, a finding contrary to a simple immune evasion paradigm. These epitopes, which are both strongly and frequently recognized, and for which escape involves a high cost to the virus, have the potential to optimize vaccine design.
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Affiliation(s)
- A Duda
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, Oxford University, South Parks Road, Oxford OX1 3SY, United Kingdom
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18
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Napolitano LA, Schmidt D, Gotway MB, Ameli N, Filbert EL, Ng MM, Clor JL, Epling L, Sinclair E, Baum PD, Li K, Killian ML, Bacchetti P, McCune JM. Growth hormone enhances thymic function in HIV-1-infected adults. J Clin Invest 2008; 118:1085-98. [PMID: 18292808 DOI: 10.1172/jci32830] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 01/02/2008] [Indexed: 01/05/2023] Open
Abstract
Growth hormone (GH) is an underappreciated but important regulator of T cell development that can reverse age-related declines in thymopoiesis in rodents. Here, we report findings of a prospective randomized study examining the effects of GH on the immune system of HIV-1-infected adults. GH treatment was associated with increased thymic mass. In addition, GH treatment enhanced thymic output, as measured by both the frequency of T cell receptor rearrangement excision circles in circulating T cells and the numbers of circulating naive and total CD4(+) T cells. These findings provide compelling evidence that GH induces de novo T cell production and may, accordingly, facilitate CD4(+) T cell recovery in HIV-1-infected adults. Further, these randomized, prospective data have shown that thymic involution can be pharmacologically reversed in humans, suggesting that immune-based therapies could be used to enhance thymopoiesis in immunodeficient individuals.
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Affiliation(s)
- Laura A Napolitano
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, USA.
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19
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Holtappels R, Janda J, Thomas D, Schenk S, Reddehase MJ, Geginat G. Adoptive CD8 T cell control of pathogens cannot be improved by combining protective epitope specificities. J Infect Dis 2008; 197:622-9. [PMID: 18240950 DOI: 10.1086/526791] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Adoptive transfer of CD8 T cells has the potential to cure infectious or malignant diseases that are refractory to conventional chemotherapy. A practically important but still unanswered question is whether mixtures of protective CD8 T cells with different epitope specificities mediate more efficient effector cell functions than do the monospecific individual CD8 T cell populations. In this study, we have addressed this issue for models of viral and bacterial infection. CD8 T cell-mediated cytotoxicity in vitro and protection in vivo were assessed to test whether CD8 T cell lines cooperate in target cell lysis and control of infection, respectively. Our data clearly show that mixtures of cytolytic T cell lines specific for different epitopes of either murine cytomegalovirus or Listeria monocytogenes do not act synergistically. An efficient anti-infectious protection thus proved to be dependent primarily on the number of transferred protective CD8 T cells rather than on the cooperative effects of multiple specificities.
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Affiliation(s)
- Rafaela Holtappels
- Institut für Virologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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20
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Ridolfi B, Genovese D, Argentini C, Maggiorella MT, Sernicola L, Buttò S, Titti F, Borsetti A, Ensoli B. Tat protein vaccination of cynomolgus macaques influences SHIV-89.6Pcy243 epitope variability. Virus Genes 2007; 36:105-15. [DOI: 10.1007/s11262-007-0179-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Accepted: 11/16/2007] [Indexed: 10/22/2022]
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21
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Létourneau S, Im EJ, Mashishi T, Brereton C, Bridgeman A, Yang H, Dorrell L, Dong T, Korber B, McMichael AJ, Hanke T. Design and pre-clinical evaluation of a universal HIV-1 vaccine. PLoS One 2007; 2:e984. [PMID: 17912361 PMCID: PMC1991584 DOI: 10.1371/journal.pone.0000984] [Citation(s) in RCA: 229] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 09/13/2007] [Indexed: 02/08/2023] Open
Abstract
Background One of the big roadblocks in development of HIV-1/AIDS vaccines is the enormous diversity of HIV-1, which could limit the value of any HIV-1 vaccine candidate currently under test. Methodology and Findings To address the HIV-1 variation, we designed a novel T cell immunogen, designated HIVCONSV, by assembling the 14 most conserved regions of the HIV-1 proteome into one chimaeric protein. Each segment is a consensus sequence from one of the four major HIV-1 clades A, B, C and D, which alternate to ensure equal clade coverage. The gene coding for the HIVCONSV protein was inserted into the three most studied vaccine vectors, plasmid DNA, human adenovirus serotype 5 and modified vaccine virus Ankara (MVA), and induced HIV-1-specific T cell responses in mice. We also demonstrated that these conserved regions prime CD8+ and CD4+ T cell to highly conserved epitopes in humans and that these epitopes, although usually subdominant, generate memory T cells in patients during natural HIV-1 infection. Significance Therefore, this vaccine approach provides an attractive and testable alternative for overcoming the HIV-1 variability, while focusing T cell responses on regions of the virus that are less likely to mutate and escape. Furthermore, this approach has merit in the simplicity of design and delivery, requiring only a single immunogen to provide extensive coverage of global HIV-1 population diversity.
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Affiliation(s)
- Sven Létourneau
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Eung-Jun Im
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Tumelo Mashishi
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Choechoe Brereton
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Hongbing Yang
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Lucy Dorrell
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Tao Dong
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Bette Korber
- Los Alamo National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, United States of America
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Andrew J. McMichael
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Tomáš Hanke
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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22
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Schaubert KL, Price DA, Frahm N, Li J, Ng HL, Joseph A, Paul E, Majumder B, Ayyavoo V, Gostick E, Adams S, Marincola FM, Sewell AK, Altfeld M, Brenchley JM, Douek DC, Yang OO, Brander C, Goldstein H, Kan-Mitchell J. Availability of a diversely avid CD8+ T cell repertoire specific for the subdominant HLA-A2-restricted HIV-1 Gag p2419-27 epitope. THE JOURNAL OF IMMUNOLOGY 2007; 178:7756-66. [PMID: 17548613 PMCID: PMC2365726 DOI: 10.4049/jimmunol.178.12.7756] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
HLA-A2-restricted CTL responses to immunodominant HIV-1 epitopes do not appear to be very effective in the control of viral replication in vivo. In this study, we studied human CD8+ T cell responses to the subdominant HLA-A2-restricted epitope TV9 (Gag p24(19-27), TLNAWVKVV) to explore the possibility of increasing its immune recognition. We confirmed in a cohort of 313 patients, infected by clade B or clade C viruses, that TV9 is rarely recognized. Of interest, the functional sensitivity of the TV9 response can be relatively high. The potential T cell repertoires for TV9 and the characteristics of constituent clonotypes were assessed by ex vivo priming of circulating CD8+ T cells from healthy seronegative donors. TV9-specific CTLs capable of suppressing viral replication in vitro were readily generated, suggesting that the cognate T cell repertoire is not limiting. However, these cultures contained multiple discrete populations with a range of binding avidities for the TV9 tetramer and correspondingly distinct functional dependencies on the CD8 coreceptor. The lack of dominant clonotypes was not affected by the stage of maturation of the priming dendritic cells. Cultures primed by dendritic cells transduced to present endogenous TV9 were also incapable of clonal maturation. Thus, a diffuse TCR repertoire appeared to be an intrinsic characteristic of TV9-specific responses. These data indicate that subdominance is not a function of poor immunogenicity, cognate TCR repertoire availability, or the potential avidity properties thereof, but rather suggest that useful responses to this epitope are suppressed by competing CD8+ T cell populations during HIV-1 infection.
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Affiliation(s)
- Keri L. Schaubert
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201
- Department of Biological Sciences, University of Texas, El Paso, TX 79968
| | - David A. Price
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
- Weatherall Institute of Molecular Medicine, University of Oxford, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicole Frahm
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charles-town, MA 02192
| | - Jinzhu Li
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201
| | - Hwee L. Ng
- Department of Medicine and AIDS Institute, Center for Health Sciences, University of California, Los Angeles, CA 90095
| | - Aviva Joseph
- Department of Micro-biology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Elyse Paul
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201
| | - Biswanath Majumder
- Department of Infectious Diseases and Micro-biology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Micro-biology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Emma Gostick
- Weatherall Institute of Molecular Medicine, University of Oxford, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sharon Adams
- Section of Immunogenetics, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892
| | - Francesco M. Marincola
- Section of Immunogenetics, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892
| | - Andrew K. Sewell
- Department of Medical Biochemistry and Immunology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Marcus Altfeld
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charles-town, MA 02192
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Otto O. Yang
- Department of Medicine and AIDS Institute, Center for Health Sciences, University of California, Los Angeles, CA 90095
| | - Christian Brander
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charles-town, MA 02192
| | - Harris Goldstein
- Department of Micro-biology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - June Kan-Mitchell
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201
- Department of Biological Sciences, University of Texas, El Paso, TX 79968
- Address correspondence and reprint requests to Dr. June Kan-Mitchell, Biological Sciences Building, University of Texas, 500 West University Avenue, El Paso, TX 79968. E-mail address:
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23
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Semmo N, Krashias G, Willberg C, Klenerman P. Analysis of the relationship between cytokine secretion and proliferative capacity in hepatitis C virus infection. J Viral Hepat 2007; 14:492-502. [PMID: 17576391 DOI: 10.1111/j.1365-2893.2007.00842.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CD4(+) T-cell responses are important for the outcome of hepatitis C virus (HCV) infection. However, the functional status of HCV-specific CD4(+) T cells in persistent infection is poorly understood. It is generally recognized that proliferative capacity of HCV-specific CD4(+) T cells is weak or absent in persistent infection, but whether this results from deletion of antigen-specific cells or represents maintenance of antigen-specific but poorly proliferative populations is not defined. We used a set of ex vivo assays to evaluate the functionality of HCV specific CD4(+) T cells in persistent and resolved infection. Peripheral blood mononuclear cells (PBMC) from 24 prospectively recruited HCV polymerase chain reaction (PCR) positive individuals, 12 spontaneously resolved individuals (i.e. anti-HCV+, PCR-) and 11 healthy controls were analysed for interferon-gamma (IFN-gamma) and interleukin 2 (IL-2) secretion by enzyme linked immunospot assays (ELISpot). HCV-specific CD4(+) proliferative responses of carboxy fluorescein succinimidyl ester-labelled PBMC were assessed using a sensitive single cell flow cytometric assay. Sustained IFN-gamma ELISpot responses were observed in the PCR+ group. However, proliferation of HCV-specific CD4(+) T cells in the PCR+ group was substantially reduced on a per cell basis, in parallel to IL-2 secretion, compared with responses in the PCR- group. In PCR- individuals, a strong relationship between cytokine secretion and proliferative capacity was seen. However, in PCR+ individuals, IFN-gamma secretion far exceeded proliferative capacity. During persistent HCV infection, some CD4(+) T-cell specificities appear to be lost, as measured using a range of techniques, but others, potentially important, are maintained as IFN-gamma secretors but with low proliferative capacity even using a highly sensitive assay. Such subsets may yet play a significant role in vivo and also provide a template for modulation in immunotherapeutic interventions.
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Affiliation(s)
- N Semmo
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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24
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Frater AJ, Brown H, Oxenius A, Günthard HF, Hirschel B, Robinson N, Leslie AJ, Payne R, Crawford H, Prendergast A, Brander C, Kiepiela P, Walker BD, Goulder PJR, McLean A, Phillips RE. Effective T-cell responses select human immunodeficiency virus mutants and slow disease progression. J Virol 2007; 81:6742-51. [PMID: 17409157 PMCID: PMC1900110 DOI: 10.1128/jvi.00022-07] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The possession of some HLA class I molecules is associated with delayed progression to AIDS. The mechanism behind this beneficial effect is unclear. We tested the idea that cytotoxic T-cell responses restricted by advantageous HLA class I molecules impose stronger selection pressures than those restricted by other HLA class I alleles. As a measure of the selection pressure imposed by HLA class I alleles, we determined the extent of HLA class I-associated epitope variation in a cohort of European human immunodeficiency virus (HIV)-positive individuals (n=84). We validated our findings in a second, distinct cohort of African patients (n=516). We found that key HIV epitopes restricted by advantageous HLA molecules (B27, B57, and B51 in European patients and B5703, B5801, and B8101 in African patients) were more frequently mutated in individuals bearing the restricting HLA than in those who lacked the restricting HLA class I molecule. HLA alleles associated with clinical benefit restricted certain epitopes for which the consensus peptides were frequently recognized by the immune response despite the circulating virus's being highly polymorphic. We found a significant inverse correlation between the HLA-associated hazard of disease progression and the mean HLA-associated prevalence of mutations within epitopes (P=0.028; R2=0.34). We conclude that beneficial HLA class I alleles impose strong selection at key epitopes. This is revealed by the frequent association between effective T-cell responses and circulating viral escape mutants and the rarity of these variants in patients who lack these favorable HLA class I molecules, suggesting a significant pressure to revert.
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Affiliation(s)
- A J Frater
- Nuffield Department of Medicine, John Radcliffe Hospital and Peter Medawar Building for Pathogen Research, Oxford University, OX1 3SY, United Kingdom
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25
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Mylin LM, Schell TD, Epler M, Kusuma C, Assis D, Matsko C, Smith A, Allebach A, Tevethia SS. Diversity of escape variant mutations in Simian virus 40 large tumor antigen (SV40 Tag) epitopes selected by cytotoxic T lymphocyte (CTL) clones. Virology 2007; 364:155-68. [PMID: 17368499 PMCID: PMC3866617 DOI: 10.1016/j.virol.2007.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 01/23/2007] [Accepted: 02/11/2007] [Indexed: 01/22/2023]
Abstract
To better understand the relationship between epitope variation and tumor escape from immune surveillance, SV40 T antigen-transformed B6/K-0 cells were subjected to selection with individual CTL clones specific for the SV40 T antigen H-2D(b)-restricted epitopes I or V. CTL-resistant populations were isolated from a majority of the selection cultures and substituted epitope sequences were identified within most of the resistant populations. Tag sequences deleted of all or portions of the selection-targeted epitope were identified, but in lower numbers compared to epitope sequences bearing single residue substitutions. Relatively few flanking residue substitutions were identified, and only in epitope I-targeted selections. The diversity (numbers and epitope residue locations) of substituted epitope residue positions varied between selections. These findings suggest that the scope of spontaneously occurring mutations that could allow for escape from individual CD8+ T cell clones is large.
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Affiliation(s)
- Lawrence M. Mylin
- Department of Microbiology and Immunology H107, The Pennsylvania State University College of Medicine, Hershey, PA 17033
- Department of Biological Sciences, Box 3030, Messiah College, Grantham, PA 17027
| | - Todd D. Schell
- Department of Microbiology and Immunology H107, The Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Melanie Epler
- Department of Microbiology and Immunology H107, The Pennsylvania State University College of Medicine, Hershey, PA 17033
| | - Carolyn Kusuma
- Department of Biological Sciences, Box 3030, Messiah College, Grantham, PA 17027
| | - David Assis
- Department of Biological Sciences, Box 3030, Messiah College, Grantham, PA 17027
| | - Chelsea Matsko
- Department of Biological Sciences, Box 3030, Messiah College, Grantham, PA 17027
| | - Alexandra Smith
- Department of Biological Sciences, Box 3030, Messiah College, Grantham, PA 17027
| | - April Allebach
- Department of Biological Sciences, Box 3030, Messiah College, Grantham, PA 17027
| | - Satvir S. Tevethia
- Department of Microbiology and Immunology H107, The Pennsylvania State University College of Medicine, Hershey, PA 17033
- Corresponding author. Tele: (717) 531-8872; Fax: (717) 531-6522; E-mail:
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26
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Northfield JW, Loo CP, Barbour JD, Spotts G, Hecht FM, Klenerman P, Nixon DF, Michaëlsson J. Human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T(EMRA) cells in early infection are linked to control of HIV-1 viremia and predict the subsequent viral load set point. J Virol 2007; 81:5759-65. [PMID: 17376902 PMCID: PMC1900265 DOI: 10.1128/jvi.00045-07] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD8(+) T cells are believed to play an important role in the control of human immunodeficiency virus type 1 (HIV-1) infection. However, despite intensive efforts, it has not been possible to consistently link the overall magnitude of the CD8(+) T-cell response with control of HIV-1. Here, we have investigated the association of different CD8(+) memory T-cell subsets responding to HIV-1 in early infection with future control of HIV-1 viremia. Our results demonstrate that both a larger proportion and an absolute number of HIV-1-specific CD8(+) CCR7(-) CD45RA(+) effector memory T cells (T(EMRA) cells) were associated with a lower future viral load set point. In contrast, a larger absolute number of HIV-1-specific CD8(+) CCR7(-) CD45RA(-) effector memory T cells (T(EM)) was not related to the viral load set point. Overall, the findings suggest that CD8(+) T(EMRA) cells have superior antiviral activity and indicate that both qualitative and quantitative aspects of the CD8(+) T-cell response need to be considered when defining the characteristics of protective immunity to HIV-1.
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Affiliation(s)
- John W Northfield
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, United Kingdom
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27
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Boulet S, Ndongala ML, Peretz Y, Boisvert MP, Boulassel MR, Tremblay C, Routy JP, Sekaly RP, Bernard NF. A dual color ELISPOT method for the simultaneous detection of IL-2 and IFN-gamma HIV-specific immune responses. J Immunol Methods 2006; 320:18-29. [PMID: 17222422 PMCID: PMC3627477 DOI: 10.1016/j.jim.2006.11.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 09/20/2006] [Accepted: 11/27/2006] [Indexed: 01/17/2023]
Abstract
The single color IFN-gamma ELISPOT assay has become a standard for assessing HIV-specific immune responses in HIV-infected subjects. However, recent data suggests that single cytokine detection for immune monitoring of HIV-infected individuals may not be sufficient to fully describe virus-specific immune responses. Here, we have designed and validated a dual color ELISPOT assay capable of detecting both IL-2 and IFN-gamma secreting cells simultaneously in response to HIV antigens. We found that a cell input number of 200,000 cells/well provided a good balance between limited availability of cells due to blood volume restrictions and ability to detect all cytokine secretion patterns. The simultaneous detection of IL-2 and IFN-gamma resulted in a decreased magnitude of IFN-gamma but not IL-2 responses. Measures of intra- and inter-assay variability for the dual color ELISPOT assay were comparable to that seen for single cytokine ELISPOT assay with coefficients of variation below 20% for IL-2, IFN-gamma and dual secretion. Although CD8+ T cells mediated most HIV-specific responses in infected subjects, CD4+ T cells mediated responses to HIV were also detected. Features of this assay such as high throughput, cell number requirement and cytokine choice should make this assay a valuable tool for screening for HIV-specific immune responses in several clinically relevant settings.
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Affiliation(s)
- Salix Boulet
- Research Institute of the McGill University Health Center, Montreal, Canada
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28
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Zinkernagel RM, Hengartner H. Protective 'immunity' by pre-existent neutralizing antibody titers and preactivated T cells but not by so-called 'immunological memory'. Immunol Rev 2006; 211:310-9. [PMID: 16824138 DOI: 10.1111/j.0105-2896.2006.00402.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The idea of immunological memory originally arose from the observation that survivors of infections were subsequently resistant to disease caused by the same infection. While most immunologists accept a special 'remembering' memory quality, we have argued previously and document here that increased resistance against re-infection, i.e. immunity, reflects low-level antigen-driven T- and B-cell responses, resulting in elevated serum or mucosal titers of protective antibodies or of activated T cells, respectively. Periodic antigen re-exposure is from within, by persisting infection (long-term) or by immune complexes (short-term), or from without, by low-level re-infections. This simple concept is supported by clinical evidence and model experiments but is often ignored, although this concept, but not so-called 'immunological memory', as defined in textbooks (i.e. earlier and better responses of a primed host), is compatible with evolutionary maternal antibody transfer of protection as well as immunity against existing infections. The concept of 'immunity without immunological remembering memory' explains why it is easy to generate vaccines against acute cytopathic infections, particularly those of early childhood, where neutralizing antibodies are the key to protection, because it has been validated by adoptive transfer of maternal antibodies. It also explains why we have not succeeded (yet?) to generate truly protective vaccines against persisting infections, because we cannot imitate 'infection immunity' that is long-lasting, generating protective T- and B-cell stimulation against variable infections without causing disease by either immunopathology or tolerance.
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Affiliation(s)
- Rolf M Zinkernagel
- University Hospital Zürich, Institute of Experimental Immunology, Zürich, Switzerland.
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29
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Leslie A, Price DA, Mkhize P, Bishop K, Rathod A, Day C, Crawford H, Honeyborne I, Asher TE, Luzzi G, Edwards A, Rousseau CM, Rosseau CM, Mullins JI, Tudor-Williams G, Novelli V, Brander C, Douek DC, Kiepiela P, Walker BD, Goulder PJR. Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype. THE JOURNAL OF IMMUNOLOGY 2006; 177:4699-708. [PMID: 16982909 DOI: 10.4049/jimmunol.177.7.4699] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
HLA diversity is seen as a major challenge to CTL vaccines against HIV. One current approach focuses on "promiscuous" epitopes, presented by multiple HLA alleles from within the same HLA supertype. However, the effectiveness of such supertype vaccines depends upon the functional equivalence of CTL targeting a particular epitope, irrespective of the restricting HLA. In this study, we describe the promiscuous HIV-specific CTL epitopes presented by alleles within the B7 supertype. Substantial differences were observed in the ability of CTL to select for escape mutation when targeting the same epitope but restricted by different HLA. This observation was common to all six promiscuous B7 epitopes identified. Moreover, with one exception, there were no significant differences in the frequency, magnitude, or immunodominance of the CTL responses restricted by different HLA alleles to explain these discrepancies. This suggests that the unique peptide/MHC complexes generated by even closely related HLA induce CTL responses that are qualitatively different. This hypothesis is supported by additional differences observed between CTL targeting identical epitopes but restricted by different HLA: first, the occurrence of distinct, HLA-specific escape mutation; second, the recruitment of distinct TCR repertoires by particular peptide/MHC complexes; and, third, significant differences in the functional avidity of CTL. Taken together, these data indicate that significant functional differences exist between CTL targeting identical epitopes but restricted by different, albeit closely related HLA. These findings are of relevance to vaccine approaches that seek to exploit HLA supertypes to overcome the problem of HLA diversity.
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Affiliation(s)
- Alasdair Leslie
- Department of Paediatrics, Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom.
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30
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López M, Soriano V, Lozano S, Martinez P, Sempere J, González-Lahoz J, Benito J. Impact of Gag sequence variability on level, phenotype, and function of anti-HIV Gag-specific CD8(+) cytotoxic T lymphocytes in untreated chronically HIV-infected patients. AIDS Res Hum Retroviruses 2006; 22:884-92. [PMID: 16989614 DOI: 10.1089/aid.2006.22.884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The role of cytotoxic T lymphocyte responses in controlling viral replication during chronic HIV infection remains controversial. Viral escape mutations driven by immune pressure have been postulated to be an important mechanism contributing to the evasion of CD8(+) T cell responses. To explore this issue in more detail, HIV-1 p17 sequence variability was examined in chronically HIV-infected patients, in parallel with the level, phenotype, and function of HIV-SL9-specific CD8(+) T cell. Thirty-one HLA-A*0201(+) (A2(+)) and 10 HLAA* 02() (A2()) patients were included. The phenotype of SL9-specific CD8(+) T cell and their ability to produce IFN-gamma were analyzed by multiparameter flow cytometry. The HIV Gag p17 was sequenced and the mean variability score for each residue within SL9 and the two epitope flanking regions were calculated using Shannon entropy. The mean variability of SL9 and the proportion of patients with amino acid changes within SL9 were similar in A2(+) and A2() patients. Patients without Tet(+) cells had a significantly higher prevalence of aminoacid changes in SL9 than patients with Tet(+) cells. Interestingly, in patients with Tet(+) cells, the Y79F mutation within SL9 tended to be associated with lower levels of Tet(+) cells. We did not find any association between amino acid changes within SL9 and the differentiation stage of Tet(+) cells, or with IFN-gamma production. A similar analysis within the epitope flanking sequences did not reveal differences in the variability of these regions. These results suggest that viral mutations driven by immune selection pressure may play an important role in evading the immunological response in chronically HIV-infected individuals.
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Affiliation(s)
- Mariola López
- Infectious Diseases and Haematology Unit, Hospital Carlos III, 28029 Madrid, Spain
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31
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Asquith B, Edwards CTT, Lipsitch M, McLean AR. Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo. PLoS Biol 2006; 4:e90. [PMID: 16515366 PMCID: PMC1395353 DOI: 10.1371/journal.pbio.0040090] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 01/23/2006] [Indexed: 12/17/2022] Open
Abstract
Understanding the role of cytotoxic T lymphocytes (CTLs) in controlling HIV-1 infection is vital for vaccine design. However, it is difficult to assess the importance of CTLs in natural infection. Different human leukocyte antigen (HLA) class I alleles are associated with different rates of progression to AIDS, indicating that CTLs play a protective role. Yet virus clearance rates following antiretroviral therapy are not impaired in individuals with advanced HIV disease, suggesting that weakening of the CTL response is not the major underlying cause of disease progression and that CTLs do not have an important protective role. Here we reconcile these apparently conflicting studies. We estimate the selection pressure exerted by CTL responses that drive the emergence of immune escape variants, thereby directly quantifying the efficiency of HIV-1–specific CTLs in vivo. We estimate that only 2% of productively infected CD4
+ cell death is attributable to CTLs recognising a single epitope. We suggest that CTLs kill a large number of infected cells (about 10
7) per day but are not responsible for the majority of infected cell death.
Although cytotoxic T lymphocytes (CTLs) kill a large number of HIV-infected cells every day, they may not be responsible for the majority of infected cell death.
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Affiliation(s)
- Becca Asquith
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
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32
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Komatsu H, Lauer G, Pybus OG, Ouchi K, Wong D, Ward S, Walker B, Klenerman P. Do antiviral CD8+ T cells select hepatitis C virus escape mutants? Analysis in diverse epitopes targeted by human intrahepatic CD8+ T lymphocytes. J Viral Hepat 2006; 13:121-30. [PMID: 16436130 DOI: 10.1111/j.1365-2893.2005.00676.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Hepatitis C virus (HCV) is a variable RNA virus that can readily establish persistent infection. Cellular immune responses are important in the early control of the virus. Evidence from animal models suggests that mutation in epitopes recognized by CD8+ T lymphocytes may play an important role in the establishment of persistence but in human persistent infection, equivalent evidence is lacking. We investigated this by analysing a unique resource: viruses from a set of chronically HCV-infected individuals in whom the CD8+ T-cell responses in liver had previously been accurately mapped. Virus was sequenced in seven individuals at 10 epitopes restricted by 10 human leucocyte antigen (HLA) molecules. Two main patterns emerged: in the majority of epitopes sequenced, no variation was seen. In three epitopes, mutations were identified which were compatible with immune escape as assessed using phylogenetic and/or functional studies. These data suggest that - even where specific intrahepatic T cells are detectable - many epitopes do not undergo mutation in chronic human infection. On the contrary, virus may escape from intrahepatic CD8+ T-cell responses in a 'patchy' manner in certain specific epitopes. Furthermore, longitudinal studies to identify the differences between 'selecting' and 'nonselecting' intrahepatic CD8+ T-cell responses are needed in HCV infection.
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Affiliation(s)
- H Komatsu
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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33
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Allen TM, Yu XG, Kalife ET, Reyor LL, Lichterfeld M, John M, Cheng M, Allgaier RL, Mui S, Frahm N, Alter G, Brown NV, Johnston MN, Rosenberg ES, Mallal SA, Brander C, Walker BD, Altfeld M. De novo generation of escape variant-specific CD8+ T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 infection. J Virol 2005; 79:12952-60. [PMID: 16188997 PMCID: PMC1235830 DOI: 10.1128/jvi.79.20.12952-12960.2005] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) evades CD8(+) T-cell responses through mutations within targeted epitopes, but little is known regarding its ability to generate de novo CD8(+) T-cell responses to such mutants. Here we examined gamma interferon-positive, HIV-1-specific CD8(+) T-cell responses and autologous viral sequences in an HIV-1-infected individual for more than 6 years following acute infection. Fourteen optimal HIV-1 T-cell epitopes were targeted by CD8(+) T cells, four of which underwent mutation associated with dramatic loss of the original CD8(+) response. However, following the G(357)S escape in the HLA-A11-restricted Gag(349-359) epitope and the decline of wild-type-specific CD8(+) T-cell responses, a novel CD8(+) T-cell response equal in magnitude to the original response was generated against the variant epitope. CD8(+) T cells targeting the variant epitope did not exhibit cross-reactivity against the wild-type epitope but rather utilized a distinct T-cell receptor Vbeta repertoire. Additional studies of chronically HIV-1-infected individuals expressing HLA-A11 demonstrated that the majority of the subjects targeted the G(357)S escape variant of the Gag(349-359) epitope, while the wild-type consensus sequence was significantly less frequently recognized. These data demonstrate that de novo responses against escape variants of CD8(+) T-cell epitopes can be generated in chronic HIV-1 infection and provide the rationale for developing vaccines to induce CD8(+) T-cell responses directed against both the wild-type and variant forms of CD8 epitopes to prevent the emergence of cytotoxic T-lymphocyte escape variants.
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Affiliation(s)
- Todd M Allen
- Partners AIDS Research Center, Massachusetts General Hospital, Boston, 02129, USA
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34
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Burgers WA, Williamson C. The challenges of HIV vaccine development and testing. Best Pract Res Clin Obstet Gynaecol 2005; 19:277-91. [PMID: 15778116 DOI: 10.1016/j.bpobgyn.2004.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A vaccine against HIV remains the best hope for bringing the epidemic under control. An intensive global effort is underway to develop such a vaccine; however, the challenges are considerable. Several new vaccine technologies that have been developed and shown promise in animal models are now being tested in early phase safety trials in humans. Because there is no laboratory assay that will predict whether an HIV vaccine can protect humans from infection, clinical trials involving thousands of volunteers will need to be conducted to determine the efficacy of HIV vaccines. These trials need to take place in the developing countries that bear the burden of the epidemic, requiring a substantial amount of infrastructure development and capacity building.
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Affiliation(s)
- Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, Cape Town, South Africa.
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35
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Abstract
Viral fitness is defined by the ability of an individual genotype to produce infectious progeny in a specific environment. For HIV the environment is never constant but rather fluctuates in time and space. For instance, environmental factors that determine viral fitness during transmission from host to host are different to the pressures from either cytotoxic T-lymphocytes (CTLs) or antiviral drugs. Consequently, viral fitness is highly dependent on the environment and the accurate determination of this value therefore depends strongly on the chosen environmental setting. This review describes how the host environment imposes selective pressures on the virus that shape its genotype and fitness. The most important environments that the virus encounters throughout its life cycle and during natural infection are discussed. In order of appearance, CTLs are discussed, followed by neutralising antibodies and antiretroviral drug treatment. It then goes on to describe receptor molecules that mediate viral entry and intracellular restriction factors, which represent selective pressures that are present directly from the start of a natural infection. It concludes by discussing the complexity of viral fitness and how an accurate measure of viral fitness eventually may, for example, contribute to the improvement of antiretroviral therapy or help in the formulation of an optimal vaccination strategy.
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Affiliation(s)
- Tim van Opijnen
- Department of Human Retrovirology, Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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36
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Abstract
HIV-1 and other retroviruses exhibit mutation rates that are 1,000,000-fold greater than their host organisms. Error-prone viral replication may place retroviruses and other RNA viruses near the threshold of "error catastrophe" or extinction due to an intolerable load of deleterious mutations. Strategies designed to drive viruses to error catastrophe have been applied to HIV-1 and a number of RNA viruses. Here, we review the concept of extinguishing HIV infection by "lethal mutagenesis" and consider the utility of this new approach in combination with conventional antiretroviral strategies.
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Affiliation(s)
- Robert A Smith
- Department of Pathology, University of Washington, Seattle, WA 18195, USA.
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37
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Jiang JQ, Patrick A, Moss RB, Rosenthal KL. CD8+ T-cell-mediated cross-clade protection in the genital tract following intranasal immunization with inactivated human immunodeficiency virus antigen plus CpG oligodeoxynucleotides. J Virol 2005; 79:393-400. [PMID: 15596832 PMCID: PMC538685 DOI: 10.1128/jvi.79.1.393-400.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a mucosally transmitted infection that rapidly targets and depletes CD4+ T cells in mucosal tissues and establishes a major reservoir for viral persistence in gut-associated lymphoid tissues. Therefore, vaccines designed to prevent HIV infections must induce potent and durable mucosal immune responses, especially in the genital tract. Here we investigated whether intranasal (i.n.) immunization with inactivated gp120-depleted HIV-1 antigen (Ag) plus CpG oligodeoxynucleotide (ODN) as an adjuvant induced local immune responses in the genital tract and cross-clade protection against intravaginal (IVAG) challenge. Lymphocytes isolated from the iliac lymph nodes (ILNs) and genital tracts of female mice i.n. immunized with HIV-1 Ag plus CpG showed significant HIV-specific proliferation and produced significantly higher levels of gamma interferon (IFN-gamma) and beta-chemokines than mice immunized with HIV-1 Ag alone or mixed with non-CpG ODN. CD8+ lymphocytes were dramatically increased in the genital tracts of mice immunized with HIV-1 Ag plus CpG, and protection following IVAG challenge with recombinant vaccinia viruses (rVVs) expressing HIV-1 gag was shown to be CD8 dependent. Finally, cross-clade protection was observed between clades A, C, and G but not B following IVAG challenge with rVVs expressing HIV-1 gag from different clades. These studies provide evidence that mucosal (i.n.) immunization induced strong local T-cell-mediated immune responses in the genital tract and cross-clade protection against IVAG challenge.
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Affiliation(s)
- Janina Q Jiang
- Centre for Gene Therapeutics, Department of Pathology & Molecular Medicine, McMaster University, McMaster University Health Sciences Center, Hamilton, Ontario, Canada
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38
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Dagarag M, Evazyan T, Rao N, Effros RB. Genetic manipulation of telomerase in HIV-specific CD8+ T cells: enhanced antiviral functions accompany the increased proliferative potential and telomere length stabilization. THE JOURNAL OF IMMUNOLOGY 2004; 173:6303-11. [PMID: 15528369 DOI: 10.4049/jimmunol.173.10.6303] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A large proportion of the CD8(+) T cell pool in persons chronically infected with HIV consists of cells that show features of replicative senescence, an end stage characterized by irreversible cell cycle arrest, multiple genetic and functional changes, and shortened telomeres. The objective of our research was to determine whether constitutive expression of the gene for the human telomerase (hTERT) can prevent senescence-induced impairments in human virus-specific CD8(+) T cells, particularly in the context of HIV-1 disease. Our results indicate that hTERT-expressing HIV-specific CD8(+) lymphocytes show both an enhanced and sustained capacity to inhibit HIV-1 replication in in vitro coculture experiments, as well as prolonged ability to produce IFN-gamma and TNF-alpha in response to stimulation with HIV-1-derived peptides, as compared with vector-transduced controls. Loss of CD28 expression, the signature change of replicative senescence in cell culture, was retarded in those CD8(+) T cell cultures that had high levels of CD28 at the time of hTERT transduction. These findings suggest that telomere shortening may be the primary driving force behind several aspects of CD8(+) T cell dysfunction associated with replicative senescence. We also demonstrate reduced accumulation of the p16(INK4a) and p21(WAF1) cell cycle inhibitors in hTERT-transduced lymphocytes, providing a possible mechanism by which stable hTERT expression is able to circumvent the senescence barrier in CD8(+) T cells. Given the key role of CD8(+) T cell function in controlling a variety of acute and latent viral infections, approaches to retard the functional decrements associated with replicative senescence may lead to novel types of immunotherapy.
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Affiliation(s)
- Mirabelle Dagarag
- Department of Pathology and Laboratory Medicine, Geffen School of Medicine, University of California-Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
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39
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Haaft PT, Verschoor EJ, Verstrepen B, Niphuis H, Dubbes R, Koornstra W, Bogers W, Rosenwirth B, Heeney JL. Readily acquired secondary infections of human and simian immunodeficiency viruses following single intravenous exposure in non-human primates. J Gen Virol 2004; 85:3735-3745. [PMID: 15557247 DOI: 10.1099/vir.0.80223-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accumulating evidence suggests that exposed individuals may acquire multiple human immunodeficiency virus (HIV) infections more frequently than originally believed. As a result, circulating recombinant forms of HIV are emerging that are of particular concern in the AIDS epidemic and HIV vaccine development efforts. The aim of this study was to determine under what conditions secondary or superinfections of HIV or simian immunodeficiency virus (SIV) may be acquired under controlled settings in well-defined, non-human primate models. Retrospective analysis of macaques that had acquired apparent immunity upon infection with a defined attenuated SIV(mac) strain revealed that eight out of eight animals that were secondarily exposed to a new virus variant became infected with the new virus strain, but at low levels. Interestingly, similarly high frequencies of secondary infections were observed after early (4 months), as well as late (5 years), exposure following primary infection. As possible causes of susceptibility to secondary infections, perturbations in the immune system associated with exacerbated infections were then investigated prospectively. Results revealed that short-term immune-suppression therapy did not increase susceptibility to secondary infections. Taken together, data suggested that neither early- nor late-exposure immune-suppressive events following primary infection accounted for the observed high incidence of secondary infections. With HIV-1, the question of whether secondary infections with very closely related viral variants could occur in the chimpanzee model was addressed. In both animal models, secondary infections were confirmed, notably with relatively closely related SIV(mac) or HIV-1 strains, following a single exposure to the secondary virus strain. These findings reveal that secondary lentiviral infections may be acquired readily during different stages of primary infection, in contrast to co-infections, which are acquired at the moment of initial infection.
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Affiliation(s)
- Peter Ten Haaft
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Babs Verstrepen
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Henk Niphuis
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Rob Dubbes
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Wim Koornstra
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Willy Bogers
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Brigitte Rosenwirth
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
| | - Jonathan L Heeney
- Department of Virology, Biomedical Primate Research Centre, PO Box 3306, 2280 GH Rijswijk, The Netherlands
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Abstract
Development of a vaccine against human immunodeficiency virus type 1 (HIV-1) is the main hope for controlling the acquired immunodeficiency syndrome pandemic. An ideal HIV vaccine should induce neutralizing antibodies, CD4+ helper T cells, and CD8+ cytotoxic T cells. While the induction of broadly neutralizing antibodies remains a highly challenging goal, there are a number of technologies capable of inducing potent cell-mediated responses in animal models, which are now starting to be tested in humans. Naked DNA immunization is one of them. This review focuses on the stimulation of HIV-specific T cells and discusses in the context of the current 'state-of-art' of DNA vaccines, the areas where this technology might assist either alone or as a part of more complex vaccine formulations in the HIV vaccine development.
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Affiliation(s)
- Marie J Estcourt
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
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41
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Piontkivska H, Hughes AL. Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisons. J Virol 2004; 78:11758-65. [PMID: 15479817 PMCID: PMC523241 DOI: 10.1128/jvi.78.21.11758-11765.2004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In human immunodeficiency virus type 1 (HIV-1), mutations that escape from cytotoxic T-lymphocyte (CTL) recognition have been documented, and sequence analyses have provided indirect support for the hypothesis that natural selection has favored CTL escape mutants within an infected host. In spite of such evidence for within-host selection by CTL, it has been more difficult to determine how natural selection by host CTL has influenced long-term evolution of HIV-1. We used statistical analysis of published HIV-1 genomic sequences to examine the role of natural selection in between-host evolution of CTL epitopes. Based on a phylogenetic analysis, we identified 21 pairs of closely related genomes isolated from different hosts and examined the pattern of nucleotide substitution in genomic regions encoding well-characterized CTL epitopes. The results revealed that certain CTL epitopes have been subject to repeated positive selection across the population, while others are generally conserved. Furthermore, evidence of positive selection was associated with divergence from the canonical epitope sequence and with an enhanced frequency of convergent amino acid sequence changes in CTL epitopes. The results support the hypothesis that CTL-driven selection has been a major factor in the long-term evolution of HIV-1.
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Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Bldg., 700 Sumter St., Columbia, SC 29208, USA
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42
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Berger G. Hypotheses on a germline origin of antibody diversity. Possible applications: improvement of the efficiency of immune response and autoimmune disease treatment. Med Hypotheses 2004; 63:847-54. [PMID: 15488659 DOI: 10.1016/j.mehy.2004.02.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2003] [Accepted: 02/26/2004] [Indexed: 10/26/2022]
Abstract
In this paper, the antibody reaction is supposed to be due to the combination of a limited number of different antibodies against the epitopes of the antigen. In addition, the efficient part of the epitopes of proteins is assumed to be the size of dipeptides. The 400 different dipeptides would be distributed in two sets, those which are foreign to the host, against which would be directed antibodies, and those which are present in the proteins of the self, which would elicit no reaction. Each chain of the antibodies would recognise one aminoacid and 40 genes would be sufficient (20 for the light chains and 20 for the heavy chains) to code for the variable parts of the immunoglobulins against proteic antigens. With these hypotheses, the combination of antibodies against at least four different epitopes of the size of dipeptides can account for the main characteristics of the antibody reaction: response against any foreign proteic antigen and specificity. In fact, the epitopes have been found to be larger than dipeptides, several additional aminoacids are involved in the antibody-binding sites. Somatic mutations and VDJ recombinations are selected to give the maximal affinity for the antigens. However, these mechanisms have not been shown to create different specificities from the same V genes. Moreover, the phenomenon of heteroclisis and the decrease, due to mutations, of antigen-binding capacity of antibodies, sometimes observed, are better explained by the model proposed here than by the classical theory. The modification of the epitope subset of the self, by intrathymic injection of antibodies against particular pathogens, is proposed to improve the immune response when microorganisms develop immune escape mechanisms. On the other hand, in the case of autoimmune diseases, the displacement of autoantibodies against self-epitopes could be carried out by the injection into the thymus of specific anti-idiotypic antibodies.
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43
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Feeney ME, Tang Y, Roosevelt KA, Leslie AJ, McIntosh K, Karthas N, Walker BD, Goulder PJR. Immune escape precedes breakthrough human immunodeficiency virus type 1 viremia and broadening of the cytotoxic T-lymphocyte response in an HLA-B27-positive long-term-nonprogressing child. J Virol 2004; 78:8927-30. [PMID: 15280502 PMCID: PMC479057 DOI: 10.1128/jvi.78.16.8927-8930.2004] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of cytotoxic T-lymphocyte (CTL) escape mutations in human immunodeficiency virus type 1 (HIV-1) proteins has been anecdotally associated with progression to AIDS, but it has been difficult to determine whether viral mutation is the cause or the result of increased viral replication. Here we describe a perinatally HIV-infected child who maintained a plasma viral load of <400 copies/ml for almost a decade until a nonbinding escape mutation emerged within the immunodominant CTL epitope. The child subsequently experienced a reemergence of HIV-1 viremia accompanied by a marked increase in the number of CTL epitopes targeted. This temporal pattern suggests that CD8 escape can play a causal role in the loss of immune control.
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Affiliation(s)
- M E Feeney
- Partners AIDS Research Center, 5th Floor, 149 13th St., Charlestown, MA 02129, USA.
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44
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Zafiropoulos A, Barnes E, Piggott C, Klenerman P. Analysis of 'driver' and 'passenger' CD8+ T-cell responses against variable viruses. Proc Biol Sci 2004; 271 Suppl 3:S53-6. [PMID: 15101418 PMCID: PMC1809984 DOI: 10.1098/rsbl.2003.0088] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Variable viruses, such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV), persist despite host immune responses directed against them. Numerous lines of evidence have suggested that antiviral CD8+ T-cell responses are key among these immune responses, but these vary widely in their ability to contain virus. We propose that only a proportion of responses may exert significant antiviral pressure ('driver' responses), leading to control over viral replication (protection) and/or, ultimately, selection of escape mutants. Another set of responses may exert only weak pressure on the virus ('passenger' responses): these neither protect nor select. To examine this we have analysed (using established databases of HIV and HCV sequences and cytotoxic T-lymphocyte (CTL) epitopes, and published experimental datasets) two important features--predicted binding of the epitope to major histocompatibility complex molecule and observed variability of the epitope--that might distinguish such responses. We find that a high predicted binding estimate could only explain a limited set of 'driver' responses associated with protection or selection. There is statistical evidence that readily defined (and non-protective) CTL responses target regions associated with lower levels of viral variability. Taken together, this suggests that a large number of well-documented responses may represent 'passengers' and we propose a mechanism that might explain their presence.
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Affiliation(s)
- Andreas Zafiropoulos
- Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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45
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Abstract
Recent data have established the HIV-1 and SIV escape CTL through epitope mutation. However, three novel studies prove that such escape comes at a "cost" to overall viral fitness. Understanding how HIV-1/SIV escape CTL and the impact of the escape mutations has tremendous importance in developing CTL based vaccines. Further, a CTL based HIV-1 vaccine is likely to have long-term protective effect against disease only if the escape virus is significantly weakened compared with wild type.
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Affiliation(s)
- Stephen M Smith
- Saint Michael's Medical Center and The New Jersey Medical School, Newark, New Jersey 07102, USA.
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Velloso LM, Michaëlsson J, Ljunggren HG, Schneider G, Achour A. Determination of Structural Principles Underlying Three Different Modes of Lymphocytic Choriomeningitis Virus Escape from CTL Recognition. THE JOURNAL OF IMMUNOLOGY 2004; 172:5504-11. [PMID: 15100292 DOI: 10.4049/jimmunol.172.9.5504] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lymphocytic choriomeningitis virus infection of H-2(b) mice generates a strong CD8(+) CTL response mainly directed toward three immunodominant epitopes, one of which, gp33, is presented by both H-2D(b) and H-2K(b) MHC class I molecules. This CTL response acts as a selective agent for the emergence of viral escape variants. These variants generate altered peptide ligands (APLs) that, when presented by class I MHC molecules, antagonize CTL recognition and ultimately allow the virus to evade the cellular immune response. The emergence of APLs of the gp33 epitope is particularly advantageous for LCMV, as it allows viral escape in the context of both H-2D(b) and H-2K(b) MHC class I molecules. We have determined crystal structures of three different APLs of gp33 in complex with both H-2D(b) and H-2K(b). Comparison between these APL/MHC structures and those of the index gp33 peptide/MHC reveals the structural basis for three different strategies used by LCMV viral escape mutations: 1) conformational changes in peptide and MHC residues that are potential TCR contacts, 2) impairment of APL binding to the MHC peptide binding cleft, and 3) introduction of subtle changes at the TCR/pMHC interface, such as the removal of a single hydroxyl group.
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MESH Headings
- Amino Acid Substitution/genetics
- Animals
- Antigen Presentation/genetics
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Glycoproteins/chemistry
- Glycoproteins/genetics
- Glycoproteins/immunology
- H-2 Antigens/chemistry
- H-2 Antigens/genetics
- H-2 Antigens/immunology
- Leucine/genetics
- Lymphocytic choriomeningitis virus/genetics
- Lymphocytic choriomeningitis virus/immunology
- Mice
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Phenylalanine/genetics
- Protein Binding/genetics
- Protein Binding/immunology
- Protein Conformation
- Protein Structure, Tertiary/genetics
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Structure-Activity Relationship
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- T-Lymphocytes, Cytotoxic/virology
- Tyrosine/genetics
- Valine/genetics
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Lucas Malard Velloso
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Mastroianni CM, d'Ettorre G, Forcina G, Vullo V. Teaching tired T cells to fight HIV: time to test IL-15 for immunotherapy? Trends Immunol 2004; 25:121-5. [PMID: 15036038 DOI: 10.1016/j.it.2004.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Claudio M Mastroianni
- Department of Infectious and Tropical Diseases, La Sapienza University, Viale del Policlinico 155, 00161 Rome, Italy.
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49
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Nikolich-Zugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immunol 2004; 4:123-32. [PMID: 15040585 DOI: 10.1038/nri1292] [Citation(s) in RCA: 450] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the thymus, a diverse and polymorphic T-cell repertoire is generated by random recombination of discrete T-cell receptor (TCR)-alphabeta gene segments. This repertoire is then shaped by intrathymic selection events to generate a peripheral T-cell pool of self-MHC restricted, non-autoaggressive T cells. It has long been postulated that some optimal level of TCR diversity allows efficient protection against pathogens. This article focuses on several recent advances that address the required diversity for the generation of an optimal immune response.
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Affiliation(s)
- Janko Nikolich-Zugich
- Vaccine and Gene Therapy Institute, Department of Molecular Microbiology and Immunology and the Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon 97006, USA.
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50
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Frahm N, Korber BT, Adams CM, Szinger JJ, Draenert R, Addo MM, Feeney ME, Yusim K, Sango K, Brown NV, SenGupta D, Piechocka-Trocha A, Simonis T, Marincola FM, Wurcel AG, Stone DR, Russell CJ, Adolf P, Cohen D, Roach T, StJohn A, Khatri A, Davis K, Mullins J, Goulder PJR, Walker BD, Brander C. Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities. J Virol 2004; 78:2187-200. [PMID: 14963115 PMCID: PMC369231 DOI: 10.1128/jvi.78.5.2187-2200.2004] [Citation(s) in RCA: 234] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although there is increasing evidence that virus-specific cytotoxic-T-lymphocyte (CTL) responses play an important role in the control of human immunodeficiency virus (HIV) replication in vivo, only scarce CTL data are available for the ethnic populations currently most affected by the epidemic. In this study, we examined the CD8(+)-T-cell responses in African-American, Caucasian, Hispanic, and Caribbean populations in which clade B virus dominates and analyzed the potential factors influencing immune recognition. Total HIV-specific CD8(+)-T-cell responses were determined by enzyme-linked immunospot assays in 150 HIV-infected individuals by using a clade B consensus sequence peptide set spanning all HIV proteins. A total of 88% of the 410 tested peptides were recognized, and Nef- and Gag-specific responses dominated the total response for each ethnicity in terms of both breadth and magnitude. Three dominantly targeted regions within these proteins that were recognized by >90% of individuals in each ethnicity were identified. Overall, the total breadth and magnitude of CD8(+)-T-cell responses correlated with individuals' CD4 counts but not with viral loads. The frequency of recognition for each peptide was highly correlated with the relative conservation of the peptide sequence, the presence of predicted immunoproteasomal cleavage sites within the C-terminal half of the peptide, and a reduced frequency of amino acids that impair binding of optimal epitopes to the restricting class I molecules. The present study thus identifies factors that contribute to the immunogenicity of these highly targeted and relatively conserved sequences in HIV that may represent promising vaccine candidates for ethnically heterogeneous populations.
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Affiliation(s)
- Nicole Frahm
- Partners AIDS Research Center, Endocrine Unit, Massachusetts General Hospital, Charlestown, Massachusetts 02129-2000, USA
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