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Protective HLA-B57: T cell and natural killer cell recognition in HIV infection. Biochem Soc Trans 2022; 50:1329-1339. [DOI: 10.1042/bst20220244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Understanding the basis of the immune determinants controlling disease outcome is critical to provide better care to patients and could be exploited for therapeutics and vaccine design. The discovery of the human immunodeficiency virus (HIV) virus as the causing agent of acquired immunodeficiency syndrome (AIDS) decades ago, led to a tremendous amount of research. Among the findings, it was discovered that some rare HIV+ individuals, called HIV controllers (HICs), had the ability to control the virus and keep a low viral load without the need of treatment. This ability allows HICs to delay or avoid progression to AIDS. HIV control is strongly associated with the expression of human leukocyte antigen (HLA) alleles in HICs. From the HIV protective HLAs described, HLA-B57 is the most frequent in HIC patients. HLA-B57 can present a large range of highly conserved Gag-derived HIV peptides to CD8+ T cells and natural killer (NK) cells, both the focus of this review. So far there are limited differences in the immune response strength, magnitude, or receptor repertoire towards HIV epitopes that could explain viral control in HICs. Interestingly, some studies revealed that during early infection the large breadth of the immune response towards HIV mutants in HLA-B57+ HIC patients, might in turn influence the disease outcome.
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A role for CD4 + helper cells in HIV control and progression. AIDS 2022; 36:1501-1510. [PMID: 35730394 DOI: 10.1097/qad.0000000000003296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE It remains unclear why HIV persists in most untreated individuals, and why a small minority of individuals can control the virus, either spontaneously or after an early treatment. Striking differences have been discovered between patient cohorts in CD4 + T-cell avidity but not in CD8 + T-cell avidity. The present work has the aim to explain the diverse outcome of infection and identify the key virological and immunological parameters predicting the outcome. DESIGN AND METHOD A mathematical model informed by these experiments and taking into account the details of HIV virology is developed. RESULTS The model predicts an arms race between viral dissemination and the proliferation of HIV-specific CD4 + helper cells leading to one of two states: a low-viremia state (controller) or a high-viremia state (progressor). Helper CD4 + cells with a higher avidity favor virus control. The parameter segregating spontaneous and posttreatment controllers is the infectivity difference between activated and resting CD4 + T cells. The model is shown to have a better connection to experiment than a previous model based on T-cell 'exhaustion'. CONCLUSION Using the model informed by patient data, the timing of antiretroviral therapy can be optimized.
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Two distinct mechanisms leading to loss of virological control in the rare group of antiretroviral therapy-naïve, transiently aviraemic children living with HIV. J Virol 2021; 96:e0153521. [PMID: 34757843 PMCID: PMC8791270 DOI: 10.1128/jvi.01535-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-specific CD8+ T-cells play a central role in immune control of adult HIV, but their contribution in paediatric infection is less well-characterised. Previously, we identified a group of ART-naïve children with persistently undetectable plasma viraemia, termed 'elite controllers', and a second group who achieved aviraemia only transiently. To investigate the mechanisms of failure to maintain aviraemia, we characterized in three transient aviraemics (TAs), each of whom expressed the disease-protective HLA-B*81:01, longitudinal HIV-specific T-cell activity and viral sequences. In two TAs, a CD8+ T-cell response targeting the immunodominant epitope TPQDLNTML ('Gag-TL9') was associated with viral control, followed by viral rebound and the emergence of escape variants with lower replicative capacity. Both TAs mounted variant-specific responses, but only at low functional avidity, resulting in immunological progression. By contrast, in TA-3, intermittent viraemic episodes followed aviraemia without virus escape or a diminished CD4+ T-cell count. High quality and magnitude of the CD8+ T-cell response was associated with aviraemia. We therefore identify two distinct mechanisms of loss of viral control. In one scenario, CD8+ T-cell responses initially cornered low replicative capacity escape variants, but with insufficient avidity to prevent viraemia and disease progression. In the other, loss of viral control was associated neither with virus escape nor progression, but with a decrease in the quality of the CD8+ T-cell response, followed by recovery of viral control in association with improved antiviral response. These data suggest the potential for a consistently strong and polyfunctional antiviral response to achieve long-term viral control without escape. IMPORTANCE Very early initiation of antiretroviral therapy (ART) in paediatric HIV infection offers a unique opportunity to limit the size and diversity of the viral reservoir. However, only exceptionally is ART alone sufficient to achieve remission. Additional interventions are therefore required that likely include contributions from host immunity. The HIV-specific T-cell response plays a central role in immune control of adult HIV, often mediated through protective alleles such as HLA-B*57/58:01/81:01. However, due to the tolerogenic and type 2 biased immune response in early life, HLA-I-mediated immune suppression of viraemia is seldom observed in children. We describe a rare group of HLA-B*81:01-positive, ART-naïve children who achieved aviraemia, albeit only transiently, and investigate the role of the CD8+ T-cell response in the establishment and loss of viral control. We identify a mechanism by which the HIV-specific response can achieve viraemic control without viral escape, that can be explored in strategies to achieve remission.
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Immunologic Control of HIV-1: What Have We Learned and Can We Induce It? Curr HIV/AIDS Rep 2021; 18:211-220. [PMID: 33709324 DOI: 10.1007/s11904-021-00545-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW A large amount of data now exists on the virus-specific immune response associated with spontaneous or induced immunologic control of lentiviruses. This review focuses on how the current understanding of HIV-specific immunity might be leveraged into induction of immunologic control and what further research is needed to accomplish this goal. RECENT FINDINGS During chronic infection, the function most robustly associated with immunologic control of HIV-1 is CD8+ T cell cytotoxic capacity. This function has proven difficult to restore in HIV-specific CD8+ T cells of chronically infected progressors in vitro and in vivo. However, progress has been made in inducing an effective CD8+ T cell response prior to lentiviral infection in the macaque model and during acute lentiviral infection in non-human primates. Further study will likely accelerate the ability to induce an effective CD8+ T cell response as part of prophylactic or therapeutic strategies.
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Kist NC, Lambert B, Campbell S, Katzourakis A, Lunn D, Lemey P, Iversen AKN. HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification. Virus Evol 2020; 6:veaa085. [PMID: 33343925 PMCID: PMC7733611 DOI: 10.1093/ve/veaa085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.
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Affiliation(s)
- Nicolaas C Kist
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ben Lambert
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, Medical School Building St Mary’s Campus, Norfolk Place, London W2 1PG, UK
| | - Samuel Campbell
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Daniel Lunn
- Department of Statistics, University of Oxford, St Giles’, Oxford OX1 3LB, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Leuven B-3000, Belgium
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Woldemeskel BA, Kwaa AK, Blankson JN. Viral reservoirs in elite controllers of HIV-1 infection: Implications for HIV cure strategies. EBioMedicine 2020; 62:103118. [PMID: 33181459 PMCID: PMC7658501 DOI: 10.1016/j.ebiom.2020.103118] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Elite controllers are HIV-1 positive subjects who control viral replication without antiretroviral therapy. Many of these subjects have replication-competent virus and thus represent a model of a functional cure. Peripheral CD4+ T cells in these subjects have small reservoirs with a low frequency of intact proviruses. Furthermore, recent studies suggest that many of these intact proviruses are disproportionally integrated at sites that have limited transcriptional activity raising the possibility that replication-competent viruses do not replicate because they are in a “blocked and locked” state. However, this feature is probably a consequence rather than a cause of elite control. Additionally, evolution of plasma virus has been detected in many elites suggesting that there continues to be ongoing viral replication in other compartments. While exceptional elite controllers with very limited viral reservoirs have recently been described, more work is needed to determine whether these patients have achieved a sterilizing cure.
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Affiliation(s)
- Bezawit A Woldemeskel
- Center for AIDS Research, Department of Medicine, Johns Hopkins Medicine, 855 N. Wolfe Street. Baltimore, MD 21205, United States
| | - Abena K Kwaa
- Center for AIDS Research, Department of Medicine, Johns Hopkins Medicine, 855 N. Wolfe Street. Baltimore, MD 21205, United States
| | - Joel N Blankson
- Center for AIDS Research, Department of Medicine, Johns Hopkins Medicine, 855 N. Wolfe Street. Baltimore, MD 21205, United States.
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Sant S, Quiñones-Parra SM, Koutsakos M, Grant EJ, Loudovaris T, Mannering SI, Crowe J, van de Sandt CE, Rimmelzwaan GF, Rossjohn J, Gras S, Loh L, Nguyen THO, Kedzierska K. HLA-B*27:05 alters immunodominance hierarchy of universal influenza-specific CD8+ T cells. PLoS Pathog 2020; 16:e1008714. [PMID: 32750095 PMCID: PMC7428290 DOI: 10.1371/journal.ppat.1008714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/14/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022] Open
Abstract
Seasonal influenza virus infections cause 290,000–650,000 deaths annually and severe morbidity in 3–5 million people. CD8+ T-cell responses towards virus-derived peptide/human leukocyte antigen (HLA) complexes provide the broadest cross-reactive immunity against human influenza viruses. Several universally-conserved CD8+ T-cell specificities that elicit prominent responses against human influenza A viruses (IAVs) have been identified. These include HLA-A*02:01-M158-66 (A2/M158), HLA-A*03:01-NP265-273, HLA-B*08:01-NP225-233, HLA-B*18:01-NP219-226, HLA-B*27:05-NP383-391 and HLA-B*57:01-NP199-207. The immunodominance hierarchies across these universal CD8+ T-cell epitopes were however unknown. Here, we probed immunodominance status of influenza-specific universal CD8+ T-cells in HLA-I heterozygote individuals expressing two or more universal HLAs for IAV. We found that while CD8+ T-cell responses directed towards A2/M158 were generally immunodominant, A2/M158+CD8+ T-cells were markedly diminished (subdominant) in HLA-A*02:01/B*27:05-expressing donors following ex vivo and in vitro analyses. A2/M158+CD8+ T-cells in non-HLA-B*27:05 individuals were immunodominant, contained optimal public TRBV19/TRAV27 TCRαβ clonotypes and displayed highly polyfunctional and proliferative capacity, while A2/M158+CD8+ T cells in HLA-B*27:05-expressing donors were subdominant, with largely distinct TCRαβ clonotypes and consequently markedly reduced avidity, proliferative and polyfunctional efficacy. Our data illustrate altered immunodominance patterns and immunodomination within human influenza-specific CD8+ T-cells. Accordingly, our work highlights the importance of understanding immunodominance hierarchies within individual donors across a spectrum of prominent virus-specific CD8+ T-cell specificities prior to designing T cell-directed vaccines and immunotherapies, for influenza and other infectious diseases. Annual influenza infections cause significant morbidity and morbidity globally. Established T-cell immunity directed at conserved viral regions provides some protection against influenza viruses and promotes rapid recovery, leading to better clinical outcomes. Killer CD8+ T-cells recognising viral peptides in a context of HLA-I glycoproteins, provide the broadest ever reported immunity across distinct influenza strains and subtypes. We asked whether the expression of certain HLA-I alleles affects CD8+ T cells responses. Our study clearly illustrates altered immunodominance hierarchies and immunodomination within broadly-cross-reactive influenza-specific CD8+ T-cells in individuals expressing two or more universal HLA-I alleles, key for T cell-directed vaccines and immunotherapies.
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Affiliation(s)
- Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Sergio M. Quiñones-Parra
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Emma J. Grant
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Stuart I. Mannering
- Immunology and Diabetes Unit, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Guus F. Rimmelzwaan
- National Influenza Center and Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Thi H. O. Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail: (THON); (KK)
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- * E-mail: (THON); (KK)
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Gomes STM, da Silva Graça Amoras E, Gomes ÉR, Queiroz MAF, Júnior ECS, de Vasconcelos Massafra JM, da Silva Lemos P, Júnior JLV, Ishak R, Vallinoto ACR. Immune escape mutations in HIV-1 controllers in the Brazilian Amazon region. BMC Infect Dis 2020; 20:546. [PMID: 32711474 PMCID: PMC7382849 DOI: 10.1186/s12879-020-05268-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV-1) infection is characterized by high viral replication and a decrease in CD4+ T cells (CD4+TC), resulting in AIDS, which can lead to death. In elite controllers and viremia controllers, viral replication is naturally controlled, with maintenance of CD4+TC levels without the use of antiretroviral therapy (ART). METHODS The aim of the present study was to describe virological and immunological risk factors among HIV-1-infected individuals according to characteristics of progression to AIDS. The sample included 30 treatment-naive patients classified into three groups based on infection duration (> 6 years), CD4+TC count and viral load: (i) 2 elite controllers (ECs), (ii) 7 viremia controllers (VCs) and (iii) 21 nonviremia controllers (NVCs). Nested PCR was employed to amplify the virus genome, which was later sequenced using the Ion PGM platform for subtyping and analysis of immune escape mutations. RESULTS Viral samples were classified as HIV-1 subtypes B and F. Greater selection pressure on mutations was observed in the group of viremia controllers, with a higher frequency of immunological escape mutations in the genes investigated, including two new mutations in gag. The viral sequences of viremia controllers and nonviremia controllers did not differ significantly regarding the presence of immune escape mutations. CONCLUSION The results suggest that progression to AIDS is not dependent on a single variable but rather on a set of characteristics and pressures exerted by virus biology and interactions with immunogenetic host factors.
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Affiliation(s)
- Samara Tatielle Monteiro Gomes
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Biological Science Institute, Federal University of Pará, Ananindeua, Brazil
| | | | - Érica Ribeiro Gomes
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
| | - Maria Alice Freitas Queiroz
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
| | - Edivaldo Costa Sousa Júnior
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Poliana da Silva Lemos
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | - João Lídio Vianez Júnior
- Health Surveillance Department, Ministry of Health (IEC-SVS/MS), Evandro Chagas Institute, Ananindeua, Brazil
| | - Ricardo Ishak
- Laboratory of Virology, Biological Science Institute, Federal University of Pará (ICB/UFPA), Ananindeua, Brazil
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Scharf L, Tauriainen J, Buggert M, Hartogensis W, Nolan DJ, Deeks SG, Salemi M, Hecht FM, Karlsson AC. Delayed Expression of PD-1 and TIGIT on HIV-Specific CD8 T Cells in Untreated HLA-B*57:01 Individuals Followed from Early Infection. J Virol 2020; 94:e02128-19. [PMID: 32350076 PMCID: PMC7343205 DOI: 10.1128/jvi.02128-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/16/2020] [Indexed: 12/21/2022] Open
Abstract
While the relationship of protective human leukocyte antigen (HLA) class I alleles and HIV progression is well defined, the interaction of HLA-mediated protection and CD8 T-cell exhaustion is less well characterized. To gain insight into the influence of HLA-B*57:01 on the deterioration of CD8 T-cell responses during HIV infection in the absence of antiretroviral treatment, we compared HLA-B*57:01-restricted HIV-specific CD8 T-cell responses to responses restricted by other HLA class I alleles longitudinally after control of peak viremia. Detailed characterization of polyfunctionality, differentiation phenotypes, transcription factor, and inhibitory receptor expression revealed progression of CD8 T-cell exhaustion over the course of the infection in both patient groups. However, early effects on the phenotype of the total CD8 T-cell population were apparent only in HLA-B*57-negative patients. The HLA-B*57:01-restricted, HIV epitope-specific CD8 T-cell responses showed beneficial functional patterns and significantly lower frequencies of inhibitory receptor expression, i.e., PD-1 and coexpression of PD-1 and TIGIT, within the first year of infection. Coexpression of PD-1 and TIGIT was correlated with clinical markers of disease progression and declining percentages of the T-bethi Eomesdim CD8 T-cell population. In accordance with clinical and immunological deterioration in the HLA-B*57:01 group, the difference in PD-1 and TIGIT receptor expression did not persist to later stages of the disease.IMPORTANCE Given the synergistic nature of TIGIT and PD-1, the coexpression of those inhibitory receptors should be considered when evaluating T-cell pathogenesis, developing immunomodulatory therapies or vaccines for HIV, and when using immunotherapy or vaccination for other causes in HIV-infected patients. HIV-mediated T-cell exhaustion influences the patient´s disease progression, immune system and subsequently non-AIDS complications, and efficacy of vaccinations against other pathogens. Consequently, the possibilities of interfering with exhaustion are numerous. Expanding the use of immunomodulatory therapies to include HIV treatment depends on information about possible targets and their role in the deterioration of the immune system. Furthermore, the rise of immunotherapies against cancer and elevated cancer incidence in HIV-infected patients together increase the need for detailed knowledge of T-cell exhaustion and possible interactions. A broader approach to counteract immune exhaustion to alleviate complications and improve efficacy of other vaccines also promises to increase patients' health and quality of life.
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Affiliation(s)
- Lydia Scharf
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Tauriainen
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wendy Hartogensis
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - David J Nolan
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
- Bioinfoexperts LLC, Alachua, Florida, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Frederick M Hecht
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Annika C Karlsson
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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10
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A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PLoS Pathog 2020; 16:e1008171. [PMID: 32492061 PMCID: PMC7295245 DOI: 10.1371/journal.ppat.1008171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/15/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mutations. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from the p24 and gp41 regions of HIV-1 collected from 34 patients with long-term untreated HIV-1 infection. We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in most cases were have previously been associated with either CTL escape in p24 or neutralising antibody escape in gp41. We also identified a putative new CTL escape site (residue 286 in gag), and a region of gp41 (including residues 644, 648, 655 in env) likely to be associated with immune escape. Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity although not all sites with high between-host diversity were inferred to be under selection at the within-host level. Our identification of selection at sites associated with resistance to broadly neutralising antibodies (bNAbs) highlights the need to fully understand the role of selection in untreated individuals when designing bNAb based therapies.
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Jin SW, Markle TJ, Anmole G, Rahimi A, Kuang XT, Brumme ZL, Brockman MA. Modulation of TCR-dependent NFAT signaling is impaired in HIV-1 Nef isolates from elite controllers. Virology 2019; 530:39-50. [PMID: 30780124 DOI: 10.1016/j.virol.2019.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/09/2019] [Accepted: 02/10/2019] [Indexed: 12/24/2022]
Abstract
HIV-1 Nef modulates the activation state of CD4+ T cells by altering signaling events elicited by the T cell receptor (TCR). Primary nef sequences exhibit extensive inter-individual diversity that influences their ability to downregulate CD4 and HLA class I; however, the impact of nef variation on modulation of T cell signaling is poorly characterized. Here, we measured TCR-mediated activation of NFAT transcription factor in the presence of nef alleles isolated from 45 elite controllers (EC) and 46 chronic progressors (CP). EC Nef clones displayed lower ability to inhibit NFAT signaling (median 87 [IQR 75-93]% relative to SF2 Nef) compared to CP clones (94 [IQR 89-98]%) (p < 0.001). Polymorphisms in Nef's N-terminal domain impaired its ability to inhibit NFAT signaling. Results indicate that primary nef alleles exhibit a range of abilities to modulate TCR-dependent NFAT signaling, implicating natural variation in this function as a potential contributor to differential HIV-1 pathogenesis.
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Affiliation(s)
- Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Tristan J Markle
- Dept. of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Gursev Anmole
- Dept. of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Asa Rahimi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Xiaomei T Kuang
- Dept. of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; Dept. of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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12
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Veenhuis RT, Kwaa AK, Garliss CC, Latanich R, Salgado M, Pohlmeyer CW, Nobles CL, Gregg J, Scully EP, Bailey JR, Bushman FD, Blankson JN. Long-term remission despite clonal expansion of replication-competent HIV-1 isolates. JCI Insight 2018; 3:122795. [PMID: 30232278 DOI: 10.1172/jci.insight.122795] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
Clonal expansion of T cells harboring replication-competent virus has recently been demonstrated in patients on suppressive antiretroviral therapy (ART) regimens. However, there has not been direct evidence of this phenomenon in settings of natural control, including in posttreatment controllers who maintain control of viral replication after treatment when ART is discontinued. We present a case of an individual who has had undetectable viral loads for more than 15 years following the cessation of ART. Using near-full-genome sequence analysis, we demonstrate that 9 of 12 replication-competent isolates cultured from this subject were identical and that this identity was maintained 6 months later. A similar pattern of replication-competent virus clonality was seen in a treatment-naive HLA-B*57 elite controller. In both cases, we show that CD8+ T cells are capable of suppressing the replication of the clonally expanded viruses in vitro. Our data suggest that, while clonal expansion of replication-competent virus can present a barrier to viral eradication, these viral isolates remain susceptible to HIV-specific immune responses and can be controlled in patients with long-term suppression of viral replication.
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Affiliation(s)
- Rebecca T Veenhuis
- Department of Medicine and.,Department of Molecular and Comparative Pathobiology, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John Gregg
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Joel N Blankson
- Department of Medicine and.,Department of Molecular and Comparative Pathobiology, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Caetano DG, Côrtes FH, Bello G, Teixeira SLM, Hoagland B, Grinsztejn B, Veloso VG, Guimarães ML, Morgado MG. Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control. Retrovirology 2018; 15:62. [PMID: 30201008 PMCID: PMC6131818 DOI: 10.1186/s12977-018-0444-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/05/2018] [Indexed: 01/10/2023] Open
Abstract
Background Despite the low level of viral replication in HIV controllers (HICs), studies have reported viral mutations related to escape from cytotoxic T-lymphocyte (CTL) response in HIV-1 plasma sequences. Thus, evaluating the dynamics of the emergence of CTL-escape mutants in HICs reservoirs is important for understanding viremia control. To analyze the HIV-1 mutational profile and dynamics of CTL-escape mutants in HICs, we selected 11 long-term non-progressor individuals and divided them into the following groups: (1) viremic controllers (VCs; n = 5) and (2) elite controllers (ECs; n = 6). For each individual, we used HIV-1 proviral DNA from PBMCs related to earliest (VE) and latest (VL) visits to obtain gag and nef sequences using the Illumina HiSeq system. The consensus of each mapped gene was used to assess viral divergence, and next-generation sequencing data were employed to identify SNPs and variations within and flanking CTL epitopes. Results Divergence analysis showed higher values for nef compared to gag among the HICs. EC and VC groups showed similar divergence rates for both genes. Analysis of the number of SNPs showed that VCs present more variability in both genes. Synonymous/non-synonymous mutation ratios were < 1 for gag among ECs and for nef among ECs and VCs, exhibiting a predominance of non-synonymous mutations. Such mutations were observed in regions encoding CTL-restricted epitopes in all individuals. All ECs presented non-synonymous mutations in CTL epitopes but generally at low frequency (< 1%); all VCs showed a high number of mutations, with significant frequency changes between VE and VL visits. A higher frequency of internal mutations was observed for gag epitopes, with significant changes across visits compared to Nef epitopes, indicating a pattern associated with differential genetic pressure. Conclusions The high genetic conservation of HIV-1 gag and nef among ECs indicates that the higher level of viremia control restricts the evolution of both genes. Although viral replication levels in HICs are low or undetectable, all individuals exhibited CTL epitope mutations in proviral gag and nef variants, indicating that potential CTL escape mutants are present in HIC reservoirs and that situations leading to a disequilibrium of the host-virus relationship can result in the spread of CTL-escape variants. Electronic supplementary material The online version of this article (10.1186/s12977-018-0444-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diogo Gama Caetano
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Fernanda Heloise Côrtes
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Gonzalo Bello
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Sylvia Lopes Maia Teixeira
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Brenda Hoagland
- Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil
| | - Valdilea Gonçalves Veloso
- Laboratório de Pesquisa Clínica em DST e Aids, Instituto Nacional de Infectologia Evandro Chagas (INI)-FIOCRUZ, Rio de Janeiro, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Mariza Gonçalves Morgado
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil.
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14
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Martin MP, Naranbhai V, Shea PR, Qi Y, Ramsuran V, Vince N, Gao X, Thomas R, Brumme ZL, Carlson JM, Wolinsky SM, Goedert JJ, Walker BD, Segal FP, Deeks SG, Haas DW, Migueles SA, Connors M, Michael N, Fellay J, Gostick E, Llewellyn-Lacey S, Price DA, Lafont BA, Pymm P, Saunders PM, Widjaja J, Wong SC, Vivian JP, Rossjohn J, Brooks AG, Carrington M. Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1. J Clin Invest 2018; 128:1903-1912. [PMID: 29461980 DOI: 10.1172/jci98463] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 01/11/2023] Open
Abstract
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.
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Affiliation(s)
- Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,ATIP-Avenir, Centre de Recherche en Transplantation et Immunologie, UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | | | - Steven G Deeks
- San Francisco General Hospital Medical Center, San Francisco, California, USA
| | - David W Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Stephen A Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nelson Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Jacques Fellay
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Emma Gostick
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - Sian Llewellyn-Lacey
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - David A Price
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Bernard A Lafont
- Viral Immunology Section, Office of the Scientific Director, NIAID, NIH, Bethesda, Maryland, USA
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Jacqueline Widjaja
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Shu Cheng Wong
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
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15
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HLA-B*14:02-Restricted Env-Specific CD8 + T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection. J Virol 2017; 91:JVI.00544-17. [PMID: 28878089 PMCID: PMC5660483 DOI: 10.1128/jvi.00544-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
Immune control of human immunodeficiency virus type 1 (HIV) infection is typically associated with effective Gag-specific CD8+ T-cell responses. We here focus on HLA-B*14, which protects against HIV disease progression, but the immunodominant HLA-B*14-restricted anti-HIV response is Env specific (ERYLKDQQL, HLA-B*14-EL9). A subdominant HLA-B*14-restricted response targets Gag (DRYFKTLRA, HLA-B*14-DA9). Using HLA-B*14/peptide-saporin-conjugated tetramers, we show that HLA-B*14-EL9 is substantially more potent at inhibiting viral replication than HLA-B*14-DA9. HLA-B*14-EL9 also has significantly higher functional avidity (P < 0.0001) and drives stronger selection pressure on the virus than HLA-B*14-DA9. However, these differences were HLA-B*14 subtype specific, applying only to HLA-B*14:02 and not to HLA-B*14:01. Furthermore, the HLA-B*14-associated protection against HIV disease progression is significantly greater for HLA-B*14:02 than for HLA-B*14:01, consistent with the superior antiviral efficacy of the HLA-B*14-EL9 response. Thus, although Gag-specific CD8+ T-cell responses may usually have greater anti-HIV efficacy, factors independent of protein specificity, including functional avidity of individual responses, are also critically important to immune control of HIV. IMPORTANCE In HIV infection, although cytotoxic T lymphocytes (CTL) play a potentially critical role in eradication of viral reservoirs, the features that constitute an effective response remain poorly defined. We focus on HLA-B*14, unique among HLAs associated with control of HIV in that the dominant CTL response is Env specific, not Gag specific. We demonstrate that Env-specific HLA-B*14-restricted activity is substantially more efficacious than the subdominant HLA-B*14-restricted Gag response. Env immunodominance over Gag and strong Env-mediated selection pressure on HIV are observed only in subjects expressing HLA-B*14:02, and not HLA-B*14:01. This reflects the increased functional avidity of the Env response over Gag, substantially more marked for HLA-B*14:02. Finally, we show that HLA-B*14:02 is significantly more strongly associated with viremic control than HLA-B*14:01. These findings indicate that, although Gag-specific CTL may usually have greater anti-HIV efficacy than Env responses, factors independent of protein specificity, including functional avidity, may carry greater weight in mediating effective control of HIV.
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16
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Sundaramurthi JC, Ashokkumar M, Swaminathan S, Hanna LE. HLA based selection of epitopes offers a potential window of opportunity for vaccine design against HIV. Vaccine 2017; 35:5568-5575. [PMID: 28888341 DOI: 10.1016/j.vaccine.2017.08.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
The pace of progression to AIDS after HIV infection varies from individual to individual. While some individuals develop AIDS quickly, others are protected from the onset of disease for more than a decade (elite controllers and long term non-progressors). The mechanisms of protection are not yet clearly understood, though various factors including host genetics, immune components and virus attenuation have been elucidated partly. The influence of HLA alleles on HIV-1 infection and disease outcome has been studied extensively. Several HLA alleles are known to be associated with resistance to infection or delayed progression to AIDS after infection. Similarly, certain HLA alleles are reported to be associated with rapid progression to disease. Since HLA alleles influence the outcome of HIV infection differentially, selection of epitopes specifically recognized by protective alleles could serve asa rational means for HIV vaccine design. In this review article, we discuss existing knowledge on HLA alleles and their association with resistance/susceptibility to HIV and its relevance to vaccine design.
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Affiliation(s)
- Jagadish Chandrabose Sundaramurthi
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Manickam Ashokkumar
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Soumya Swaminathan
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India.
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17
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Gonzalo-Gil E, Ikediobi U, Sutton RE. Mechanisms of Virologic Control and Clinical Characteristics of HIV+ Elite/Viremic Controllers. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:245-259. [PMID: 28656011 PMCID: PMC5482301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) disease is pandemic, with approximately 36 million infected individuals world-wide. For the vast majority of these individuals, untreated HIV eventually causes CD4+ T cell depletion and profound immunodeficiency, resulting in morbidity and mortality. But for a remarkable few (0.2 to 0.5 percent), termed elite controllers (ECs), viral loads (VLs) remain suppressed to undetectable levels (< 50 copies/ml) and peripheral CD4+ T cell counts remain high (200 to 1000/μl), all in the absence of antiretroviral therapy (ART). Viremic controllers (VCs) are a similar but larger subset of HIV-1 infected individuals who have the ability to suppress their VLs to low levels. These patients have been intensively studied over the last 10 years in order to determine how they are able to naturally control HIV in the absence of medications, and a variety of mechanisms have been proposed. Defective HIV does not explain the clinical status of most ECs/VCs; rather these individuals appear to somehow control HIV infection, through immune or other unknown mechanisms. Over time, many ECs and VCs eventually lose the ability to control HIV, leading to CD4+ T cell depletion and immunologic dysfunction in the absence of ART. Elucidating novel mechanisms of HIV control in this group of patients will be an important step in understanding HIV infection. This will extend our knowledge of HIV-host interaction and may pave the way for the development of new therapeutic approaches and advance the cure agenda.
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Affiliation(s)
| | | | - Richard E. Sutton
- To whom all correspondence should be addressed: Richard E. Sutton, Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520,Tel (203) 737-3648, Fax (203) 737-6174, .
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18
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Kang W, Zhu W, Li Y, Jiao Y, Zhuang Y, Xie Y, Zhao K, Dang B, Liu Q, Zhang Y, Sun Y. Analysis of HIV-1c-Specific CTL Responses with HIV-1 Reservoir Size and Forms. Viral Immunol 2016; 29:184-91. [PMID: 26859257 DOI: 10.1089/vim.2015.0057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytotoxic T lymphocytes (CTL) are critical in cellular immune responses; therefore the study of CTL responses is profound in HIV-1 eradication. We aim to dissect the relationship between HIV-1 reservoir size and the magnitude and recognition of viral-specific CTL responses. An IFN-γ ELISpot assay with peptides spanning the HIV-1 clade C consensus sequences were designed to analyze HIV-1c-specific CTL responses. HIV-1 DNA, integrated HIV-1 DNA, and 2-LTR HIV-1 DNA were quantitated by real-time PCR. We observed significant increases in total HIV-1 DNA and integrated HIV-1 DNA after highly active antiretroviral treatment (HAART) compared with naive patients. Total HIV-1 DNA had a significant negative correlation with HIV-1c-specific CTL response magnitude. Baseline CD4(+) T lymphocyte counts and antiretroviral treatment affected the size of the HIV-1 reservoirs. Taken together, HIV-1-specific CTL responses correlated with the size of HIV-1 reservoir. In addition, HIV-1-specific CTL response against p17 was associated with low integral efficiency of HIV-1, which might be a biomarker to evaluate the efficacy of HAART.
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Affiliation(s)
- Wenzhen Kang
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Weijun Zhu
- 2 AIDS Research Center, MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology , Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yuan Li
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Yanmei Jiao
- 3 Center for Infectious Diseases, Beijing You-An Hospital, Capital Medical University , Beijing, People's Republic of China
| | - Yan Zhuang
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Yumei Xie
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Ke Zhao
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Bianli Dang
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Qingquan Liu
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Ye Zhang
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
| | - Yongtao Sun
- 1 Department of Infectious Diseases, Tangdu Hospital Affiliated to the Fourth Military Medical University , Xi'an, People's Republic of China
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19
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Success and failure of the cellular immune response against HIV-1. Nat Immunol 2015; 16:563-70. [PMID: 25988888 DOI: 10.1038/ni.3161] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/27/2015] [Indexed: 02/07/2023]
Abstract
The cellular immune response to HIV-1 has now been studied in extraordinary detail. A very large body of data provides the most likely reasons that the HIV-specific cellular immune response succeeds in a small number of people but fails in most. Understanding the success and failure of the HIV-specific cellular immune response has implications that extend not only to immunotherapies and vaccines for HIV-1 but also to the cellular immune response in other disease states. This Review focuses on the mechanisms that are most likely responsible for durable and potent immunologic control of HIV-1. Although we now have a detailed picture of the cellular immune responses to HIV-1, important questions remain regarding the nature of these responses and how they arise.
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20
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CD8(+) T-cell Cytotoxic Capacity Associated with Human Immunodeficiency Virus-1 Control Can Be Mediated through Various Epitopes and Human Leukocyte Antigen Types. EBioMedicine 2014; 2:46-58. [PMID: 26137533 PMCID: PMC4485486 DOI: 10.1016/j.ebiom.2014.12.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 12/16/2022] Open
Abstract
Understanding natural immunologic control over Human Immunodeficiency Virus (HIV)-1 replication, as occurs in rare long-term nonprogressors/elite controllers (LTNP/EC), should inform the design of efficacious HIV vaccines and immunotherapies. Durable control in LTNP/EC is likely mediated by highly functional virus-specific CD8+ T-cells. Protective Human Leukocyte Antigen (HLA) class I alleles, like B*27 and B*57, are present in most, but not all LTNP/EC, providing an opportunity to investigate features shared by their HIV-specific immune responses. To better understand the contribution of epitope targeting and conservation to immune control, we compared the CD8+ T-cell specificity and function of B*27/57neg LTNP/EC (n = 23), B*27/57pos LTNP/EC (n = 23) and B*27/57neg progressors (n = 13). Fine mapping revealed 11 previously unreported immunodominant responses. Although B*27/57neg LTNP/EC did not target more highly conserved epitopes, their CD8+ T-cell cytotoxic capacity was significantly higher than progressors. Similar to B*27/57pos LTNP/EC, this superior cytotoxicity was mediated by preferential expansion of immunodominant responses and lysis through the predicted HLA. These findings suggest that increased CD8+ T-cell cytotoxic capacity is a common mechanism of control in most LTNP/EC regardless of HLA type. They also suggest that potent cytotoxicity can be mediated through various epitopes and HLA molecules and could, in theory, be induced in most people. HIV-specific cytotoxicity associated with control can be mediated across a wide variety of epitopes and HLA types. Targeting of conserved epitopes does not differentiate patients with immunologic control of HIV-1. High level cytotoxic capacity is a feature shared among LTNP/EC across HLA types.
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21
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Moroni M, Ghezzi S, Baroli P, Heltai S, De Battista D, Pensieroso S, Cavarelli M, Dispinseri S, Vanni I, Pastori C, Zerbi P, Tosoni A, Vicenzi E, Nebuloni M, Wong K, Zhao H, McHugh S, Poli G, Lopalco L, Scarlatti G, Biassoni R, Mullins JI, Malnati MS, Alfano M. Spontaneous control of HIV-1 viremia in a subject with protective HLA-B plus HLA-C alleles and HLA-C associated single nucleotide polymorphisms. J Transl Med 2014; 12:335. [PMID: 25477316 PMCID: PMC4272524 DOI: 10.1186/s12967-014-0335-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 11/20/2014] [Indexed: 01/10/2023] Open
Abstract
Introduction Understanding the mechanisms by which some individuals are able to naturally control HIV-1 infection is an important goal of AIDS research. We here describe the case of an HIV-1+ woman, CASE1, who has spontaneously controlled her viremia for the last 14 of her 20 years of infection. Methods CASE1 has been clinically monitored since 1993. Detailed immunological, virological and histological analyses were performed on samples obtained between 2009 and 2011. Results As for other Elite Controllers, CASE1 is characterized by low to undetectable levels of plasma HIV-1 RNA, peripheral blood mononuclear cell (PBMC) associated HIV-1 DNA and reduced in vitro susceptibility of target cells to HIV-1 infection. Furthermore, a slow rate of virus evolution was demonstrated in spite the lack of assumption of any antiretroviral agent. CASE1 failed to transmit HIV-1 to either her sexual male partner or to her child born by vaginal delivery. Normal values and ratios of T and B cells were observed, along with normal histology of the intestinal mucosa. Attempts to isolate HIV-1 from her PBMC and gut-derived cells were unsuccessful, despite expression of normal cell surface levels of CD4, CCRC5 and CXCR4. CASE1 did not produce detectable anti-HIV neutralizing antibodies in her serum or genital mucosal fluid although she displayed potent T cell responses against HIV-1 Gag and Nef. CASE1 also possessed multiple genetic polymorphisms, including HLA alleles (B*14, B*57, C*06 and C*08.02) and HLA-C single nucleotide polymorphisms (SNPs, rs9264942 C/C and rs67384697 del/del), that have been previously individually associated with spontaneous control of plasma viremia, maintenance of high CD4+ T cell counts and delayed disease progression. Conclusions CASE1 has controlled her HIV-1 viremia below the limit of detection in the absence of antiretroviral therapy for more than 14 years and has not shown any sign of immunologic deterioration or disease progression. Co-expression of multiple protective HLA alleles, HLA-C SNPs and strong T cell responses against HIV-1 proteins are the most likely explanation of this very benign case of spontaneous control of HIV-1 disease progression. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0335-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Moroni
- Infectious Disease Unit, Busto Arsizio Public Hospital, P.le Solaro n. 3, Busto Arsizio, 21052, Varese, Italy.
| | - Silvia Ghezzi
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Paolo Baroli
- Service Lab Fleming Research, Busto Arsizio, Varese, Italy.
| | - Silvia Heltai
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Davide De Battista
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Simone Pensieroso
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Mariangela Cavarelli
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Stefania Dispinseri
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Irene Vanni
- Department of Translational Research, Istituto Giannina Gaslini, Genoa, Italy.
| | - Claudia Pastori
- Immunobiology of HIV Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Pietro Zerbi
- Pathology Unit, Luigi Sacco Hospital, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
| | - Antonella Tosoni
- Pathology Unit, Luigi Sacco Hospital, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
| | - Elisa Vicenzi
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Manuela Nebuloni
- Pathology Unit, Luigi Sacco Hospital, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
| | - Kim Wong
- Departments of Microbiology, Medicine and Laboratory Medicine, University of Washington, Seattle, WA, USA.
| | - Hong Zhao
- Departments of Microbiology, Medicine and Laboratory Medicine, University of Washington, Seattle, WA, USA.
| | - Sarah McHugh
- Departments of Microbiology, Medicine and Laboratory Medicine, University of Washington, Seattle, WA, USA.
| | - Guido Poli
- AIDS Immunopathogenesis Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Via Olgettina n. 58, Milan, 20132, Italy. .,School of Medicine, Vita-Salute San Raffaele University, Milan, Italy.
| | - Lucia Lopalco
- Immunobiology of HIV Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Roberto Biassoni
- Department of Translational Research, Istituto Giannina Gaslini, Genoa, Italy.
| | - James I Mullins
- Departments of Microbiology, Medicine and Laboratory Medicine, University of Washington, Seattle, WA, USA.
| | - Mauro S Malnati
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy.
| | - Massimo Alfano
- AIDS Immunopathogenesis Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Via Olgettina n. 58, Milan, 20132, Italy. .,Present address; Division of Experimental Oncology, Unit of Urology, URI; IRCCS Ospedale San Raffaele, Via Olgettina n. 60, Milan, 20132, Italy.
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Tomescu C, Liu Q, Ross BN, Yin X, Lynn K, Mounzer KC, Kostman JR, Montaner LJ. A correlate of HIV-1 control consisting of both innate and adaptive immune parameters best predicts viral load by multivariable analysis in HIV-1 infected viremic controllers and chronically-infected non-controllers. PLoS One 2014; 9:e103209. [PMID: 25078947 PMCID: PMC4117509 DOI: 10.1371/journal.pone.0103209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infected viremic controllers maintain durable viral suppression below 2000 copies viral RNA/ml without anti-retroviral therapy (ART), and the immunological factor(s) associated with host control in presence of low but detectable viral replication are of considerable interest. Here, we utilized a multivariable analysis to identify which innate and adaptive immune parameters best correlated with viral control utilizing a cohort of viremic controllers (median 704 viral RNA/ml) and non-controllers (median 21,932 viral RNA/ml) that were matched for similar CD4+ T cell counts in the absence of ART. We observed that HIV-1 Gag-specific CD8+ T cell responses were preferentially targeted over Pol-specific responses in viremic controllers (p = 0.0137), while Pol-specific responses were positively associated with viral load (rho = 0.7753, p = 0.0001, n = 23). Viremic controllers exhibited significantly higher NK and plasmacytoid dendritic cells (pDC) frequency as well as retained expression of the NK CD16 receptor and strong target cell-induced NK cell IFN-gamma production compared to non-controllers (p<0.05). Despite differences in innate and adaptive immune function however, both viremic controllers (p<0.05) and non-controller subjects (p<0.001) exhibited significantly increased CD8+ T cell activation and spontaneous NK cell degranulation compared to uninfected donors. Overall, we identified that a combination of innate (pDC frequency) and adaptive (Pol-specific CD8+ T cell responses) immune parameters best predicted viral load (R2 = 0.5864, p = 0.0021, n = 17) by a multivariable analysis. Together, this data indicates that preferential Gag-specific over Pol-specific CD8+ T cell responses along with a retention of functional innate subsets best predict host control over viral replication in HIV-1 infected viremic controllers compared to chronically-infected non-controllers.
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Affiliation(s)
- Costin Tomescu
- The Wistar Institute, HIV Immunopathogenesis Laboratory, Philadelphia, Pennsylvania, United States of America
| | - Qin Liu
- The Wistar Institute, Biostatistics Laboratory, Philadelphia, Pennsylvania, United States of America
| | - Brian N. Ross
- The Wistar Institute, HIV Immunopathogenesis Laboratory, Philadelphia, Pennsylvania, United States of America
| | - Xiangfan Yin
- The Wistar Institute, Biostatistics Laboratory, Philadelphia, Pennsylvania, United States of America
| | - Kenneth Lynn
- UPENN-Presbyterian Medical Center, Philadelphia, Pennsylvania, United States of America
| | - Karam C. Mounzer
- Philadelphia FIGHT, The Jonathan Lax Treatment Center, Philadelphia, Pennsylvania, United States of America
| | - Jay R. Kostman
- UPENN-Presbyterian Medical Center, Philadelphia, Pennsylvania, United States of America
| | - Luis J. Montaner
- The Wistar Institute, HIV Immunopathogenesis Laboratory, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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23
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Dynamic regulation of host restriction factor expression over the course of HIV-1 infection in vivo. J Virol 2014; 88:11624-9. [PMID: 25031350 DOI: 10.1128/jvi.01771-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In this study, we investigated the expression levels of host restriction factors in six untreated HIV-1-positive patients over the course of infection. We found that the host restriction factor gene expression profile consistently increased over time and was significantly associated with CD4+ T cell activation and viral load. Our data are among the first to demonstrate the dynamic nature of host restriction factors in vivo over time.
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24
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Pohlmeyer CW, Buckheit RW, Siliciano RF, Blankson JN. CD8+ T cells from HLA-B*57 elite suppressors effectively suppress replication of HIV-1 escape mutants. Retrovirology 2013; 10:152. [PMID: 24330837 PMCID: PMC3878989 DOI: 10.1186/1742-4690-10-152] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/03/2013] [Indexed: 11/30/2022] Open
Abstract
Background Elite Controllers or Suppressors (ES) are HIV-1 positive individuals who maintain plasma viral loads below the limit of detection of standard clinical assays without antiretroviral therapy. Multiple lines of evidence suggest that the control of viral replication in these patients is due to a strong and specific cytotoxic T lymphocyte (CTL) response. The ability of CD8+ T cells to control HIV-1 replication is believed to be impaired by the development of escape mutations. Surprisingly, viruses amplified from the plasma of ES have been shown to contain multiple escape mutations, and it is not clear how immunologic control is maintained in the face of virologic escape. Results We investigated the effect of escape mutations within HLA*B-57-restricted Gag epitopes on the CD8+ T cell mediated suppression of HIV-1 replication. Using site directed mutagenesis, we constructed six NL4-3 based viruses with canonical escape mutations in one to three HLA*B-57-restricted Gag epitopes. Interestingly, similar levels of CTL-mediated suppression of replication in autologous primary CD4+ T cells were observed for all of the escape mutants. Intracellular cytokine staining was performed in order to determine the mechanisms involved in the suppression of the escape variants. While low baseline CD8+ T cells responses to wild type and escape variant peptides were seen, stimulation of PBMC with either wild type or escape variant peptides resulted in increased IFN-γ and perforin expression. Conclusions These data presented demonstrate that CD8+ T cells from ES are capable of suppressing replication of virus harboring escape mutations in HLA-B*57-restricted Gag epitopes. Additionally, our data suggest that ES CD8+ T cells are capable of generating effective de novo responses to escape mutants.
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Affiliation(s)
| | | | | | - Joel N Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, 733 N, Broadway, BRB 880, Baltimore, MD 21205, USA.
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25
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Abdel-Mohsen M, Raposo RAS, Deng X, Li M, Liegler T, Sinclair E, Salama MS, Ghanem HEDA, Hoh R, Wong JK, David M, Nixon DF, Deeks SG, Pillai SK. Expression profile of host restriction factors in HIV-1 elite controllers. Retrovirology 2013; 10:106. [PMID: 24131498 PMCID: PMC3827935 DOI: 10.1186/1742-4690-10-106] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/10/2013] [Indexed: 11/10/2022] Open
Abstract
Background Several host-encoded antiviral factors suppress HIV-1 replication in a cell-autonomous fashion in vitro. The relevance of these defenses to the control of HIV-1 in vivo remains to be elucidated. We hypothesized that cellular restriction of HIV-1 replication plays a significant role in the observed suppression of HIV-1 in "elite controllers", individuals who maintain undetectable levels of viremia in the absence of antiretroviral therapy (ART). We comprehensively compared the expression levels of 34 host restriction factors and cellular activation levels in CD4+ T cells and sorted T cell subsets between elite controllers, HIV-1-infected (untreated) non-controllers, ART-suppressed, and uninfected individuals. Results Expression of schlafen 11, a codon usage-based inhibitor of HIV-1 protein synthesis, was significantly elevated in CD4+ T cells from elite controllers as compared to both non-controllers (p = 0.048) and ART-suppressed individuals (p = 0.024), with this effect most apparent in central memory CD4+ T cells. Schlafen 11 expression levels were comparable between controllers and uninfected individuals. Cumulative restriction factor expression was positively correlated with CD4+ T cell activation (r2 = 0.597, p < 0.0001), viral load (r2 = 0.34, p = 0.015), and expression of ISG15 (r2 = 0.73, p < 0.0001), a marker of interferon exposure. APOBEC3C, APOBEC3D, CTR9, TRIM26, and TRIM32 were elevated in elite controllers with respect to ART-suppressed individuals, while levels were comparable to uninfected individuals and non-controllers. Conclusions Host restriction factor expression typically scales with cellular activation levels. However, the elevated mRNA and protein expression of schlafen 11, despite low activation and viral load, violates the global pattern and may be a signature characteristic of HIV-1 elite control.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Satish K Pillai
- Department of Medicine, University of California San Francisco, San Francisco, California, USA.
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26
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Raposo RAS, Abdel-Mohsen M, Holditch SJ, Kuebler PJ, Cheng RG, Eriksson EM, Liao W, Pillai SK, Nixon DF. Increased expression of intrinsic antiviral genes in HLA-B*57-positive individuals. J Leukoc Biol 2013; 94:1051-9. [PMID: 23929683 DOI: 10.1189/jlb.0313150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genetic background of HIV-1-infected subjects, particularly the HLA class I haplotype, appears to be critical in determining disease progression rates, thought to be a result of the role of HIV-1-specific CD8(+) T cell responses. The HLA-B*57 allele is strongly associated with viremic suppression and slower disease progression. However, there is considerable heterogeneity in HIV-1 disease progression rates among HLA-B*57-positive subjects, suggesting that additional factors may help to contain viral replication. In this report, we investigated the association between host restriction factors, other established immunological parameters, and HLA type in HIV-1-seronegative individuals. Our results demonstrate that healthy, uninfected HLA-B*57-positive individuals exhibit significantly higher gene-expression levels of host restriction factors, such as APOBEC3A, APOBEC3B, BST-2/tetherin, and ISG15. Interestingly, HLA-B*57 individuals have significantly lower CD4(+) T cell frequencies but harbor slightly more activated CD4(+) T cells compared with their HLA-B*35 counterparts. We detected significant correlations between CD4(+) T cell activation and expression of several APOBEC3 family members, BST-2/tetherin, SAMHD1, and TRIM5α in HLA-B*57-positive individuals. To our knowledge, this is the first report showing distinct associations between host restriction factors and HLA class I genotype. Our results provide insights into natural protection mechanisms and immunity against HIV-1 that fall outside of classical HLA-mediated effects.
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Affiliation(s)
- Rui André Saraiva Raposo
- 2.Division of Experimental Medicine, 1001 Potrero Ave., Bldg. 3, Room 603, Box 1234, San Francisco, CA 94110, USA.
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27
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Pressure from TRIM5α contributes to control of HIV-1 replication by individuals expressing protective HLA-B alleles. J Virol 2013; 87:10368-80. [PMID: 23864638 DOI: 10.1128/jvi.01313-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The expression of certain HLA class I alleles, including HLA-B*27 and HLA-B*57, is associated with better control of human immunodeficiency virus type 1 (HIV-1) infection, but the mechanisms responsible are not fully understood. We sought evidence that pressure from the human restriction factor TRIM5α (hTRIM5α) could contribute to viral control. The hTRIM5α sensitivity of viruses from both HLA-B*57-positive (HLA-B*57(+)) and HLA-B*27(+) patients who spontaneously controlled viral replication, but not viruses from viremic patients expressing these alleles, was significantly greater than that of viruses from patients not expressing these protective HLA-B alleles. Overall, a significant negative correlation between hTRIM5α sensitivity and viral load was observed. In HLA-B*57(+) patients, the T242N mutation in the HLA-B*57-restricted TW10 CD8(+) T lymphocyte (CTL) epitope was strongly associated with hTRIM5α sensitivity. In HLA-B*27(+) controllers, hTRIM5α sensitivity was associated with a significant reduction in emergence of key CTL mutations. In several patients, viral evolution to avoid hTRIM5α sensitivity was observed but could be associated with reduced viral replicative capacity. Thus, in individuals expressing protective HLA-B alleles, the combined pressures exerted by CTL, hTRIM5α, and capsid structural constraints can prevent viral escape both by impeding the selection of necessary resistance/compensatory mutations and forcing the selection of escape mutations that increase hTRIM5α sensitivity or impair viral replicative capacity.
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28
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Viganò S, Bellutti Enders F, Miconnet I, Cellerai C, Savoye AL, Rozot V, Perreau M, Faouzi M, Ohmiti K, Cavassini M, Bart PA, Pantaleo G, Harari A. Rapid perturbation in viremia levels drives increases in functional avidity of HIV-specific CD8 T cells. PLoS Pathog 2013; 9:e1003423. [PMID: 23853580 PMCID: PMC3701695 DOI: 10.1371/journal.ppat.1003423] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/30/2013] [Indexed: 01/16/2023] Open
Abstract
The factors determining the functional avidity and its relationship with the broad heterogeneity of antiviral T cell responses remain partially understood. We investigated HIV-specific CD8 T cell responses in 85 patients with primary HIV infection (PHI) or chronic (progressive and non-progressive) infection. The functional avidity of HIV-specific CD8 T cells was not different between patients with progressive and non-progressive chronic infection. However, it was significantly lower in PHI patients at the time of diagnosis of acute infection and after control of virus replication following one year of successful antiretroviral therapy. High-avidity HIV-specific CD8 T cells expressed lower levels of CD27 and CD28 and were enriched in cells with an exhausted phenotype, i.e. co-expressing PD-1/2B4/CD160. Of note, a significant increase in the functional avidity of HIV-specific CD8 T cells occurred in early-treated PHI patients experiencing a virus rebound after spontaneous treatment interruption. This increase in functional avidity was associated with the accumulation of PD-1/2B4/CD160 positive cells, loss of polyfunctionality and increased TCR renewal. The increased TCR renewal may provide the mechanistic basis for the generation of high-avidity HIV-specific CD8 T cells. These results provide insights on the relationships between functional avidity, viremia, T-cell exhaustion and TCR renewal of antiviral CD8 T cell responses. CD8 T cells directed against virus are complex and functionally heterogeneous. One relevant component of CD8 T cells is their functional avidity which reflects their sensitivity to cognate antigens, i.e. how prone T cells are to respond when they encounter low doses of antigens. In patients with chronic and established HIV infection, we observed that the sensitivity of HIV-specific CD8 T cells was not different between patients with progressive or non-progressive disease. In contrast, the sensitivity of HIV-specific CD8 T cells was significantly lower in patients with early and recent HIV infection. Furthermore, CD8 T cells of high avidity were preferentially associated with a state of functional impairment known as exhaustion. Of interest, some patients treated with antiretroviral therapy during acute infection spontaneously interrupted their treatment and experienced a rebound of virus. In these patients, the avidity of HIV-specific CD8 T cells increased and this increase was associated to stronger cell exhaustion and greater renewal of the population of antiviral CD8 T cells, thus potentially providing the mechanistic basis for the generation of high-avidity CD8 T cells. Overall, our data suggest that rapid perturbation in viremia levels drove increases in the functional avidity of HIV-specific CD8 T cells.
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Affiliation(s)
- Selena Viganò
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Felicitas Bellutti Enders
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Isabelle Miconnet
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Cristina Cellerai
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Anne-Laure Savoye
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Virginie Rozot
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Matthieu Perreau
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Mohamed Faouzi
- The Center of Clinical Epidemiology, Institut de Médecine Sociale et Préventive, Lausanne University Hospital, Lausanne, Switzerland
| | - Khalid Ohmiti
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
- The Center of Clinical Epidemiology, Institut de Médecine Sociale et Préventive, Lausanne University Hospital, Lausanne, Switzerland
| | - Matthias Cavassini
- Service of Infectious Diseases, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Pierre-Alexandre Bart
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
- Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Alexandre Harari
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
- Swiss Vaccine Research Institute, Lausanne, Switzerland
- * E-mail:
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Abstract
Host genetic factors are a major contributing factor to the inter-individual variation observed in response to human immunodeficiency virus (HIV) infection and are linked to resistance to HIV infection among exposed individuals, as well as rate of disease progression and the likelihood of viral transmission. Of the genetic variants that have been shown to affect the natural history of HIV infection, the human leukocyte antigen (HLA) class I genes exhibit the strongest and most consistent association, underscoring a central role for CD8(+) T cells in resistance to the virus. HLA proteins play important roles in T-cell-mediated adaptive immunity by presenting immunodominant HIV epitopes to cytotoxic T lymphocytes (CTLs) and CD4(+) T cells. Genetic and functional data also indicate a function for HLA in natural killer cell-mediated innate immunity against HIV by interacting with killer cell immunoglobulin-like receptors (KIR). We review the HLA and KIR associations with HIV disease and discuss the mechanisms underlying these associations.
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Affiliation(s)
- Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
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30
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Genovese L, Nebuloni M, Alfano M. Cell-Mediated Immunity in Elite Controllers Naturally Controlling HIV Viral Load. Front Immunol 2013; 4:86. [PMID: 23577012 PMCID: PMC3620550 DOI: 10.3389/fimmu.2013.00086] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/26/2013] [Indexed: 12/26/2022] Open
Abstract
The natural course of human immunodeficiency virus (HIV) infection is characterized by high viral load, depletion of immune cells, and immunodeficiency, ultimately leading to acquired immunodeficiency syndrome phase and the occurrence of opportunistic infections and diseases. Since the discovery of HIV in the early 1980s a naturally selected population of infected individuals has been emerged in the last years, characterized by being infected for many years, with viremia constantly below detectable level and poor depletion of immune cells. These individuals are classified as “elite controllers (EC) or suppressors” and do not develop disease in the absence of anti-retroviral therapy. Unveiling host factors and immune responses responsible for the elite status will likely provide clues for the design of therapeutic vaccines and functional cures. Scope of this review was to examine and discuss differences of the cell-mediated immune responses between HIV+ individuals with disease progression and EC.
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Affiliation(s)
- Luca Genovese
- AIDS Immunopathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute Milan, Italy
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31
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Abstract
Two human leukocyte antigen (HLA) variants, HLA-B*57 and -B*81, are consistently known as favorable host factors in human immunodeficiency virus type 1 (HIV-1)-infected Africans and African-Americans. In our analyses of prospective data from 538 recent HIV-1 seroconverters and cross-sectional data from 292 subjects with unknown duration of infection, HLA-B*57 (mostly B*57:03) and -B*81 (exclusively B*81:01) had mostly discordant associations with virologic and immunologic manifestations before antiretroviral therapy. Specifically, relatively low viral load (VL) in HLA-B*57-positive subjects (P ≤ 0.03 in various models) did not translate to early advantage in CD4(+) T-cell (CD4) counts (P ≥ 0.37). In contrast, individuals with HLA-B*81 showed little deviation from the normal set point VL (P > 0.18) while maintaining high CD4 count during early and chronic infection (P = 0.01). These observations suggest that discordance between VL and CD4 count can occur in the presence of certain HLA alleles and that effective control of HIV-1 viremia is not always a prerequisite for favorable prognosis (delayed immunodeficiency). Of note, steady CD4 count associated with HLA-B*81 in HIV-1-infected Africans may depend on the country of origin, as observations differed slightly between subgroups enrolled in southern Africa (Zambia) and eastern Africa (Kenya, Rwanda, and Uganda).
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High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control. Blood 2012; 121:801-11. [PMID: 23233659 DOI: 10.1182/blood-2012-06-436295] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED The development of immunomonitoring models to determine HIV-1 vaccine efficacy is a major challenge. Studies suggest that HIV-1–specific CD8 T cells play a critical role in subjects achieving spontaneous viral control (HIV-1 controllers) and that they will be important in immune interventions. However, no single CD8 T-cell function is uniquely associated with controller status and the heterogeneity of responses targeting different epitopes further complicates the discovery of determinants of protective immunity. In the present study, we describe immunomonitoring models integrating multiple functions of epitope-specific CD8 T cells that distinguish controllers from subjects with treated or untreated progressive infection. Models integrating higher numbers of variables and trained with the least absolute shrinkage and selection operator (LASSO) variant of logistic regression and 10-fold cross-validation produce “diagnostic tests” that display an excellent capacity to delineate subject categories. The test accuracy reaches 75% area under the receiving operating characteristic curve in cohorts matched for prevalence of protective alleles. Linear mixed-effects model analyses show that the proliferative capacity, cytokine production, and kinetics of cytokine secretion are associated with HIV-1 control. Although proliferative capacity is the strongest single discriminant, integrated modeling of different dimensions of data leverages individual associations. This strategy may have important applications in predictive model development and immune monitoring of HIV-1 vaccine trials. KEY POINTS Immune monitoring models integrating multiple functions of HIV-1-specific CD8 T cells distinguish controllers from subjects with progressive HIV-1 infection. This strategy may have important applications in predictive model development and immune monitoring of HIV-1 vaccine trials.
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Functional avidity: a measure to predict the efficacy of effector T cells? Clin Dev Immunol 2012; 2012:153863. [PMID: 23227083 PMCID: PMC3511839 DOI: 10.1155/2012/153863] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/22/2012] [Indexed: 01/30/2023]
Abstract
The functional avidity is determined by exposing T-cell populations in vitro to different amounts of cognate antigen. T-cells with high functional avidity respond to low antigen doses. This in vitro measure is thought to correlate well with the in vivo effector capacity of T-cells. We here present the multifaceted factors determining and influencing the functional avidity of T-cells. We outline how changes in the functional avidity can occur over the course of an infection. This process, known as avidity maturation, can occur despite the fact that T-cells express a fixed TCR. Furthermore, examples are provided illustrating the importance of generating T-cell populations that exhibit a high functional avidity when responding to an infection or tumors. Furthermore, we discuss whether criteria based on which we evaluate an effective T-cell response to acute infections can also be applied to chronic infections such as HIV. Finally, we also focus on observations that high-avidity T-cells show higher signs of exhaustion and facilitate the emergence of virus escape variants. The review summarizes our current understanding of how this may occur as well as how T-cells of different functional avidity contribute to antiviral and anti-tumor immunity. Enhancing our knowledge in this field is relevant for tumor immunotherapy and vaccines design.
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The potential role of epitope-specific T-cell receptor diversity in the control of HIV replication. Curr Opin HIV AIDS 2012; 2:177-82. [PMID: 19372884 DOI: 10.1097/coh.0b013e3280ef692f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to assess the influence of T-cell receptor clonotype diversity on the recognition and control of chronic viral infections, and specifically in the case of HIV infection. RECENT FINDINGS The latest publications have examined the role of T-cell receptor repertoires specific for dominant epitopes in the ability to recognize variants and control viremia in chronic viral infections. In the hepatitis C virus and SIV models, diverse T-cell receptor repertoires appear to limit immune escape. In HIV infection, circulating clonotypes may have different functional abilities, showing another potential advantage of diverse clonotypic repertoires. A recent study suggests that at times narrow repertoires against a conserved epitope may be effective, perhaps through the ability to cross-recognize potential epitope variants. SUMMARY The studies discussed in this review have identified T-cell receptor diversity as an important factor for understanding the immune recognition of highly variable viruses. Further studies are needed to determine whether T-cell receptor repertoire analysis of HIV epitope-specific immune responses will provide a more accurate correlate for the control of viremia than conventional immune function assays.
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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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Qualitative host factors associated with immunological control of HIV infection by CD8 T cells. Curr Opin HIV AIDS 2012; 1:28-33. [PMID: 19372780 DOI: 10.1097/01.coh.0000194108.14601.69] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Despite significant technical advances that have permitted an increasingly more quantitative and detailed study of virus-specific cellular immunity over the past few years, our understanding of the nature of immunological control in rare cases of non-progressive HIV infection and diminished control in the majority of untreated chronically infected patients remains incomplete. This review will summarize recent findings and points of controversy within areas of active investigation of the cellular immune response to HIV. RECENT FINDINGS It is now appreciated that high frequencies of virus-specific CD8 T cells are readily detectable in chronic HIV infection, but do not restrict viral replication. For this reason, attention has shifted to qualitative features of the host immune response that might accurately determine the restriction of viral replication. A number of qualitative changes in the phenotype, cytokine secretion, and proliferative capacity of HIV-specific CD8 T cells of progressors have recently been described. SUMMARY Given that the desired response to the majority of vaccines in pre-clinical or clinical testing is to stimulate cellular immunity in an attempt to alter disease progression, understanding these qualitative features is of particular relevance. Further study will probably yield critical information for the means to stimulate effective immunity in vaccinees, prevent the loss of control of viral replication upon infection of vaccinees, or induce durable immunological control in humans already infected with HIV.
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Impact of protective killer inhibitory receptor/human leukocyte antigen genotypes on natural killer cell and T-cell function in HIV-1-infected controllers. AIDS 2012; 26:1869-78. [PMID: 22874514 DOI: 10.1097/qad.0b013e32835861b0] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Both protective T-cell genotypes and natural killer (NK) cell genotypes have been associated with delayed progression to AIDS and shown to be co-inherited in HIV-1-infected individuals who limit viral replication in absence of antiretroviral therapy ('controllers'). However, a comparative analysis of the genotype and function of the innate and adaptive immune compartments in HIV-1-infected controller individuals has been understudied to date. DESIGN Here, we simultaneously tested NK and T-cell function in controllers to investigate the mechanism(s) that might account for host immune control over viral replication. METHODS We measured CD8 T-cell responses against HIV-1 utilizing overlapping 15-mer peptides spanning the HIV-1 consensus clade B Gag protein and tested NK cell degranulation and cytokine secretion against tumor target cells following interferon-α (IFNα) stimulation. RESULTS Among a cohort of 37 controllers, the presence of protective major histocompatibility complex class I human leukocyte antigen (HLA) alleles (such as HLA-B*57) was not correlated with HIV-specific CD8 responses. In contrast, the inheritance of a protective killer inhibitory receptor KIR3DL1*h/*y receptor genotype along with the corresponding HLA-Bw4*80I ligand was associated with significantly heightened target cell-induced NK degranulation and cytokine secretion following IFNα stimulation (P = 0.0201, n = 13). Interestingly, we observed a significant inverse association between the IFNα stimulated NK response to K562 cells and the HIV-specific CD8 T-cell response to Gag among elite controllers (rho = -0.8321, P = 0.0010, n = 12). CONCLUSION Together, these results suggest that heightened NK responses can be evidenced independently of HIV-specific T-cell responses in HIV-1-infected elite controllers.
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Combination of immune and viral factors distinguishes low-risk versus high-risk HIV-1 disease progression in HLA-B*5701 subjects. J Virol 2012; 86:9802-16. [PMID: 22761389 DOI: 10.1128/jvi.01165-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HLA-B*5701 is the host factor most strongly associated with slow HIV-1 disease progression, although rates can vary within this group. Underlying mechanisms are not fully understood but likely involve both immunological and virological dynamics. The present study investigated HIV-1 in vivo evolution and epitope-specific CD8(+) T cell responses in six HLA-B*5701 patients who had not received antiretroviral treatment, monitored from early infection for up to 7 years. The subjects were classified as high-risk progressors (HRPs) or low-risk progressors (LRPs) based on baseline CD4(+) T cell counts. Dynamics of HIV-1 Gag p24 evolution and multifunctional CD8(+) T cell responses were evaluated by high-resolution phylogenetic analysis and polychromatic flow cytometry, respectively. In all subjects, substitutions occurred more frequently in flanking regions than in HLA-B*5701-restricted epitopes. In LRPs, p24 sequence diversity was significantly lower; sequences exhibited a higher degree of homoplasy and more constrained mutational patterns than HRPs. The HIV-1 intrahost evolutionary rate was also lower in LRPs and followed a strict molecular clock, suggesting neutral genetic drift rather than positive selection. Additionally, polyfunctional CD8(+) T cell responses, particularly to TW10 and QW9 epitopes, were more robust in LRPs, who also showed significantly higher interleukin-2 (IL-2) production in early infection. Overall, the findings indicate that HLA-B*5701 patients with higher CD4 counts at baseline have a lower risk of HIV-1 disease progression because of the interplay between specific HLA-linked immune responses and the rate and mode of viral evolution. The study highlights the power of a multidisciplinary approach, integrating high-resolution evolutionary and immunological data, to understand mechanisms underlying HIV-1 pathogenesis.
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Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJR, Heckerman D. Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J Virol 2012; 86:5230-43. [PMID: 22379086 PMCID: PMC3347390 DOI: 10.1128/jvi.06728-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/20/2012] [Indexed: 11/20/2022] Open
Abstract
The promiscuous presentation of epitopes by similar HLA class I alleles holds promise for a universal T-cell-based HIV-1 vaccine. However, in some instances, cytotoxic T lymphocytes (CTL) restricted by HLA alleles with similar or identical binding motifs are known to target epitopes at different frequencies, with different functional avidities and with different apparent clinical outcomes. Such differences may be illuminated by the association of similar HLA alleles with distinctive escape pathways. Using a novel computational method featuring phylogenetically corrected odds ratios, we systematically analyzed differential patterns of immune escape across all optimally defined epitopes in Gag, Pol, and Nef in 2,126 HIV-1 clade C-infected adults. Overall, we identified 301 polymorphisms in 90 epitopes associated with HLA alleles belonging to shared supertypes. We detected differential escape in 37 of 38 epitopes restricted by more than one allele, which included 278 instances of differential escape at the polymorphism level. The majority (66 to 97%) of these resulted from the selection of unique HLA-specific polymorphisms rather than differential epitope targeting rates, as confirmed by gamma interferon (IFN-γ) enzyme-linked immunosorbent spot assay (ELISPOT) data. Discordant associations between HLA alleles and viral load were frequently observed between allele pairs that selected for differential escape. Furthermore, the total number of associated polymorphisms strongly correlated with average viral load. These studies confirm that differential escape is a widespread phenomenon and may be the norm when two alleles present the same epitope. Given the clinical correlates of immune escape, such heterogeneity suggests that certain epitopes will lead to discordant outcomes if applied universally in a vaccine.
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Buckheit RW, Allen TG, Alme A, Salgado M, O’Connell KA, Huculak S, Falade-Nwulia O, Williams TM, Gallant JE, Siliciano RF, Blankson JN. Host factors dictate control of viral replication in two HIV-1 controller/chronic progressor transmission pairs. Nat Commun 2012; 3:716. [PMID: 22395607 PMCID: PMC3549550 DOI: 10.1038/ncomms1697] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 01/23/2012] [Indexed: 02/07/2023] Open
Abstract
Viremic controllers and elite controllers/suppressors maintain control over HIV-1 replication. Some studies have suggested that control is a result of infection with a defective viral strain, while others suggested host immune factors have a key role. Here we document two HIV-1 transmission pairs: one consisting of a patient with progressive disease and an individual who became an elite suppressor, and the second consisting of a patient with progressive disease and a viremic controller. In contrast to another elite suppressor transmission pair, virus isolated from all patients was fully competent. These data suggest that some viremic controllers and elite suppressors are infected with HIV-1 isolates that replicate vigorously in vitro and are able to cause progressive disease in vivo. These data suggest that host factors have a dominant role in the control of HIV-1 infection, thus it may be possible to control fully pathogenic HIV-1 isolates with therapeutic vaccination.
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Affiliation(s)
- Robert W. Buckheit
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Tracy G. Allen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Angela Alme
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Maria Salgado
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Karen A. O’Connell
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Sarah Huculak
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Oluwaseun Falade-Nwulia
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Thomas M. Williams
- Department of Pathology, School of Medicine and Tricore Reference Laboratories, University of New Mexico, Albuquerque, New Mexico
| | - Joel E. Gallant
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
- Howard Hughes Medical Institute. Johns Hopkins University School of Medicine. 733 N. Broadway, Baltimore MD 21205, USA
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 733 N. Broadway, BRB 880, Baltimore, MD 21205
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HLA B*5701-positive long-term nonprogressors/elite controllers are not distinguished from progressors by the clonal composition of HIV-specific CD8+ T cells. J Virol 2012; 86:4014-8. [PMID: 22278241 DOI: 10.1128/jvi.06982-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To better understand the qualitative features of effective human immunodeficiency virus (HIV)-specific immunity, we examined the TCR clonal composition of CD8(+) T cells recognizing conserved HIV p24-derived epitopes in HLA-B*5701-positive long-term nonprogressors/elite controllers (LTNP/EC) and HLA-matched progressors. Both groups displayed oligoclonal HLA-B5701-restricted p24-specific CD8(+) T-cell responses with similar levels of diversity and few public clonotypes. Thus, HIV-specific CD8(+) T-cell responses in LTNP/EC are not differentiated from those of progressors on the basis of clonal diversity or TCR sharing.
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Novitsky V, Wang R, Baca J, Margolin L, McLane MF, Moyo S, van Widenfelt E, Makhema J, Essex M. Evolutionary gamut of in vivo Gag substitutions during early HIV-1 subtype C infection. Virology 2011; 421:119-28. [PMID: 22014506 DOI: 10.1016/j.virol.2011.09.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/18/2011] [Accepted: 09/21/2011] [Indexed: 01/03/2023]
Abstract
Two analyses of HIV-1 subtype C Gag quasispecies were performed in a prospective cohort of 42 acutely and recently infected individuals by SGA on viral RNA/proviral DNA templates. First, in vivo Gag substitutions were assessed in relation to the HIV-1C consensus sequence, which revealed that 29.3% of detected amino acid substitutions can be classified as reversions to subtype consensus, 61.3% as forward substitutions from subtype consensus, and 9.3% as polymorphisms not associated with the subtype consensus sequence. Second, the proportion, dynamics, and relationships within individual pools of viral quasispecies were analyzed. Among reverse substitutions, 16.1% were minor, 11.0% transient, 13.6% dominant, and 59.2% fixed. In contrast, 31.6% of forward substitutions were minor, 59.3% transient, 3.8% dominant, and 5.3% fixed. The distinct patterns in the spectrum and dynamics of reverse and forward Gag substitutions suggest that these differences should be considered in HIV-1 evolutionary studies and analyses of viral mutational pathways.
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Affiliation(s)
- Vladimir Novitsky
- Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, United States
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Gag cytotoxic T lymphocyte escape mutations can increase sensitivity of HIV-1 to human TRIM5alpha, linking intrinsic and acquired immunity. J Virol 2011; 85:11846-54. [PMID: 21917976 DOI: 10.1128/jvi.05201-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although laboratory-adapted HIV-1 strains are largely resistant to the human restriction factor TRIM5α (hTRIM5α), we have recently shown that some viruses carrying capsid (CA) sequences from clinical isolates can be more sensitive to this restriction factor. In this study we evaluated the contribution to this phenotype of CA mutations known to be associated with escape from cytotoxic T lymphocyte (CTL) responses. Recombinant viruses carrying HIV-1 CA sequences from NL4-3 and three different clinical isolates were prepared, along with variants in which mutations associated with CTL resistance were modified by site-directed mutagenesis, and the infectivities of these viruses in target cells expressing hTRIM5α and cells in which TRIM5α activity had been inhibited by overexpression of TRIM5γ were compared. For both hTRIM5α-sensitive viruses studied, CTL-associated mutations were found to be responsible for this phenotype. Both CTL resistance mutations occurring within HLA-restricted CA epitopes and compensatory mutations occurring outside CTL epitopes influenced hTRIM5α sensitivity, and mutations associated with CTL resistance selected in prior hosts can contribute to this effect. The impact of CTL resistance mutations on hTRIM5α sensitivity was context dependent, because mutations shown to be responsible for the TRIM5α-sensitive phenotype in viruses from one patient could have little or no impact on this parameter when introduced into another virus. No fixed relationship between changes in hTRIM5α sensitivity and infectivity was discernible in our studies. Taken together, these findings suggest that CTL mutations may influence HIV-1 replication by modifying both viral infectivity and sensitivity to TRIM5α.
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Compensatory mutations restore the replication defects caused by cytotoxic T lymphocyte escape mutations in hepatitis C virus polymerase. J Virol 2011; 85:11883-90. [PMID: 21880756 DOI: 10.1128/jvi.00779-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
While human leukocyte antigen B57 (HLA-B57) is associated with the spontaneous clearance of hepatitis C virus (HCV), the mechanisms behind this control remain unclear. Immunodominant CD8(+) T cell responses against the B57-restricted epitopes comprised of residues 2629 to 2637 of nonstructural protein 5B (NS5B(2629-2637)) (KSKKTPMGF) and E2(541-549) (NTRPPLGNW) were recently shown to be crucial in the control of HCV infection. Here, we investigated whether the selection of deleterious cytotoxic T lymphocyte (CTL) escape mutations in the NS5B KSKKTPMGF epitope might impair viral replication and contribute to the B57-mediated control of HCV. Common CTL escape mutations in this epitope were identified from a cohort of 374 HCV genotype 1a-infected subjects, and their impact on HCV replication assessed using a transient HCV replicon system. We demonstrate that while escape mutations at residue 2633 (position 5) of the epitope had little or no impact on HCV replication in vitro, mutations at residue 2629 (position 1) substantially impaired replication. Notably, the deleterious mutations at position 2629 were tightly linked in vivo to upstream mutations at residue 2626, which functioned to restore the replicative defects imparted by the deleterious escape mutations. These data suggest that the selection of costly escape mutations within the immunodominant NS5B KSKKTPMGF epitope may contribute in part to the control of HCV replication in B57-positive individuals and that persistence of HCV in B57-positive individuals may involve the development of specific secondary compensatory mutations. These findings are reminiscent of the selection of deleterious CTL escape and compensatory mutations by HLA-B57 in HIV-1 infection and, thus, may suggest a common mechanism by which alleles like HLA-B57 mediate protection against these highly variable pathogens.
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O'Connell KA, Hegarty RW, Siliciano RF, Blankson JN. Viral suppression of multiple escape mutants by de novo CD8(+) T cell responses in a human immunodeficiency virus-1 infected elite suppressor. Retrovirology 2011; 8:63. [PMID: 21812985 PMCID: PMC3173334 DOI: 10.1186/1742-4690-8-63] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 08/03/2011] [Indexed: 11/10/2022] Open
Abstract
Elite suppressors or controllers (ES) are HIV-1 infected patients who maintain undetectable viral loads without treatment. While HLA-B*57-positive ES are usually infected with virus that is unmutated at CTL epitopes, a single, dominant variant containing CTL escape mutations is typically seen in plasma during chronic infection. We describe an ES who developed seven distinct and rare escape variants at an HLA-B*57-restricted Gag epitope over a five year period. Interestingly, he developed proliferative, de novo CTL responses that suppressed replication of each of these variants. These responses, in combination with low viral fitness of each variant, may contribute to sustained elite control in this ES.
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Affiliation(s)
- Karen A O'Connell
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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46
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Sharp ER, Willberg CB, Kuebler PJ, Abadi J, Fennelly GJ, Dobroszycki J, Wiznia AA, Rosenberg MG, Nixon DF. Immunodominance of HIV-1 specific CD8+ T-cell responses is related to disease progression rate in vertically infected adolescents. PLoS One 2011; 6:e21135. [PMID: 21818255 PMCID: PMC3139570 DOI: 10.1371/journal.pone.0021135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 05/20/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND HIV-1 vertically infected children in the USA are living into adolescence and beyond with the widespread use of antiretroviral drugs. These patients exhibit striking differences in the rate of HIV-1 disease progression which could provide insights into mechanisms of control. We hypothesized that differences in the pattern of immunodomination including breadth, magnitude and polyfunctionality of HIV-1 specific CD8+ T cell response could partially explain differences in progression rate. METHODOLOGY/PRINCIPAL FINDINGS In this study, we mapped, quantified, and assessed the functionality of these responses against individual HIV-1 Gag peptides in 58 HIV-1 vertically infected adolescents. Subjects were divided into two groups depending upon the rate of disease progression: adolescents with a sustained CD4%≥25 were categorized as having no immune suppression (NS), and those with CD4%≤15 categorized as having severe immune suppression (SS). We observed differences in the area of HIV-1-Gag to which the two groups made responses. In addition, subjects who expressed the HLA- B*57 or B*42 alleles were highly likely to restrict their immunodominant response through these alleles. There was a significantly higher frequency of naïve CD8+ T cells in the NS subjects (p = 0.0066) compared to the SS subjects. In contrast, there were no statistically significant differences in any other CD8+ T cell subsets. The differentiation profiles and multifunctionality of Gag-specific CD8+ T cells, regardless of immunodominance, also failed to demonstrate meaningful differences between the two groups. CONCLUSIONS/SIGNIFICANCE Together, these data suggest that, at least in vertically infected adolescents, the region of HIV-1-Gag targeted by CD8+ T cells and the magnitude of that response relative to other responses may have more importance on the rate of disease progression than their qualitative effector functions.
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Affiliation(s)
- Elizabeth R. Sharp
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Christian B. Willberg
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Peter J. Kuebler
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jacob Abadi
- Jacobi Medical Center, Bronx, New York, United States of America
| | | | | | - Andrew A. Wiznia
- Jacobi Medical Center, Bronx, New York, United States of America
| | | | - Douglas F. Nixon
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
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Abstract
Multiple epidemiological studies have demonstrated associations between the human leukocyte antigen (HLA) loci and human immunodeficiency virus (HIV) disease, and more recently the killer cell immunoglobulin-like (KIR) locus has been implicated in differential responses to the virus. Genome-wide association studies have convincingly shown that the HLA class I locus is the most significant host genetic contributor to the variation in HIV control, underscoring a central role for CD8 T cells in resistance to the virus. However, both genetic and functional data indicate that part of the HLA effect on HIV is due to interactions between KIR and HLA genes, also implicating natural killer cells in defense against viral infection and viral expansion prior to initiation of an adaptive response. We review the HLA and KIR associations with HIV disease and the progress that has been made in understanding the mechanisms that explain these associations.
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Affiliation(s)
- Arman A Bashirova
- Ragon Institute of Massachusetts General Hospital, MIT, Boston, Massachusetts 02129, USA.
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Hersperger AR, Migueles SA, Betts MR, Connors M. Qualitative features of the HIV-specific CD8+ T-cell response associated with immunologic control. Curr Opin HIV AIDS 2011; 6:169-73. [PMID: 21399496 PMCID: PMC4309378 DOI: 10.1097/coh.0b013e3283454c39] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Over the past 2 years, a clearer picture has emerged regarding the properties of HIV-specific CD8+ T cells associated with immunologic control of HIV replication. These properties represent a potential mechanism by which rare patients might control HIV replication in the absence of antiretroviral therapy. This review addresses the background and recent findings that have lead to our current understanding of these mechanism(s). RECENT FINDINGS Patients with immunologic control of HIV are not distinguished by targeted specificities, or greater numbers or breadth of their HIV-specific CD8+ T-cell response. For this reason, recent work has focused greater attention on qualitative features of this response. The qualitative features most closely associated with immunologic control of HIV are related to the granule-exocytosis-mediated elimination of HIV-infected CD4 T cells. The ability of HIV-specific CD8+ T cells to increase their contents of proteins known to mediate cytotoxicity, such as granzyme B and perforin, appears to be a critical means by which HIV-specific cytotoxic capacity is regulated. SUMMARY Investigation from multiple groups has now focused upon HIV-specific CD8+ T-cell granule-exocytosis-mediated cytotoxicity as a correlate of immunologic control of HIV. In the near future, a more detailed understanding of the qualities associated with immunologic control may provide critical insights regarding the necessary features of a response that should be stimulated by immunotherapies or T-cell-based vaccines.
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Affiliation(s)
- Adam R. Hersperger
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen A. Migueles
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michael R. Betts
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark Connors
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Graf EH, Mexas AM, Yu JJ, Shaheen F, Liszewski MK, Di Mascio M, Migueles SA, Connors M, O'Doherty U. Elite suppressors harbor low levels of integrated HIV DNA and high levels of 2-LTR circular HIV DNA compared to HIV+ patients on and off HAART. PLoS Pathog 2011; 7:e1001300. [PMID: 21383972 PMCID: PMC3044690 DOI: 10.1371/journal.ppat.1001300] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/19/2011] [Indexed: 12/22/2022] Open
Abstract
Elite suppressors (ES) are a rare population of HIV-infected individuals that are capable of naturally controlling the infection without the use of highly active anti-retroviral therapy (HAART). Patients on HAART often achieve viral control to similar (undetectable) levels. Accurate and sensitive methods to measure viral burden are needed to elucidate important differences between these two patient populations in order to better understand their mechanisms of control. Viral burden quantification in ES patients has been limited to measurements of total DNA in PBMC, and estimates of Infectious Units per Million cells (IUPM). There appears to be no significant difference in the level of total HIV DNA between cells from ES patients and patients on HAART. However, recovering infectious virus from ES patient samples is much more difficult, suggesting their reservoir size should be much smaller than that in patients on HAART. Here we find that there is a significant difference in the level of integrated HIV DNA in ES patients compared to patients on HAART, providing an explanation for the previous results. When comparing the level of total to integrated HIV DNA in these samples we find ES patients have large excesses of unintegrated HIV DNA. To determine the composition of unintegrated HIV DNA in these samples, we measured circular 2-LTR HIV DNA forms and found ES patients frequently have high levels of 2-LTR circles in PBMC. We further show that these high levels of 2-LTR circles are not the result of inefficient integration in ES cells, since HIV integrates with similar efficiency in ES and normal donor cells. Our findings suggest that measuring integration provides a better surrogate of viral burden than total HIV DNA in ES patients. Moreover, they add significantly to our understanding of the mechanisms that allow viral control and reservoir maintenance in this unique patient population.
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Affiliation(s)
- Erin H. Graf
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Angela M. Mexas
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jianqing J. Yu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Farida Shaheen
- The Center for Aids Research, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Megan K. Liszewski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michele Di Mascio
- Biostatistics Research Branch and NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen A. Migueles
- Laboratory of Immunoregulation, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Connors
- Laboratory of Immunoregulation, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Salgado M, Brennan TP, O'Connell KA, Bailey JR, Ray SC, Siliciano RF, Blankson JN. Evolution of the HIV-1 nef gene in HLA-B*57 positive elite suppressors. Retrovirology 2010; 7:94. [PMID: 21059238 PMCID: PMC2993647 DOI: 10.1186/1742-4690-7-94] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 11/08/2010] [Indexed: 12/29/2022] Open
Abstract
Elite controllers or suppressors (ES) are HIV-1 infected patients who maintain viral loads of < 50 copies/ml without antiretroviral therapy. CD8+ T cells are thought to play a key role in the control of viral replication and exert selective pressure on gag and nef in HLA-B*57 positive ES. We previously showed evolution in the gag gene of ES which surprisingly was mostly due to synonymous mutations rather than non-synonymous mutation in targeted CTL epitopes. This finding could be the result of structural constraints on Gag, and we therefore examined the less conserved nef gene. We found slow evolution of nef in plasma virus in some ES. This evolution is mostly due to synonymous mutations and occurs at a rate similar to that seen in the gag gene in the same patients. The results provide further evidence of ongoing viral replication in ES and suggest that the nef and gag genes in these patients respond similarly to selective pressure from the host.
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Affiliation(s)
- Maria Salgado
- Department of Medicine, Johns Hopkins University School of Medicine, 733 N, Broadway, Baltimore, MD 21205, USA
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