1
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Özer O, Lenz TL. Unique pathogen peptidomes facilitate pathogen-specific selection and specialization of MHC alleles. Mol Biol Evol 2021; 38:4376-4387. [PMID: 34110412 PMCID: PMC8476153 DOI: 10.1093/molbev/msab176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8% of pathogen pairs shared more than 1% of their peptides. Indeed, 98.8% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants.
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Affiliation(s)
- Onur Özer
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.,Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
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2
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Lima THA, Souza AS, Porto IOP, Paz MA, Veiga-Castelli LC, Oliveira MLG, Donadi EA, Meyer D, Sabbagh A, Mendes-Junior CT, Castelli EC. HLA-A promoter, coding, and 3'UTR sequences in a Brazilian cohort, and their evolutionary aspects. HLA 2019; 93:65-79. [PMID: 30666817 DOI: 10.1111/tan.13474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/10/2019] [Accepted: 01/18/2019] [Indexed: 12/17/2022]
Abstract
HLA-A is the second most polymorphic locus of the human leucocyte antigen (HLA) complex encoding a key molecule for antigen presentation and NK cell modulation. Many studies have evaluated HLA-A variability in worldwide populations, focusing mainly on exons, but the regulatory segments have been poorly characterized. HLA-A variability is particularly high in the segment encoding the peptide-binding groove (exons 2 and 3), which is related to the antigen presentation function and the balancing selection in these segments. Here we evaluate the genetic diversity of the HLA-A gene considering a continuous segment encompassing the extended promoter (1.5 kb upstream of the first translated ATG), all exons and introns, and the entire 3' untranslated region, by using massively parallel sequencing. To achieve this goal, we used a freely available bioinformatics workflow that optimizes read mapping for HLA genes and defines complete sequences using either the phase among variable sites directly observed in sequencing data and probabilistic models. The HLA-A variability detected in a highly admixed population sample from Brazil shows that the HLA-A regulatory segments present few, but divergent sequences. The regulatory segments are in close association with the coding alleles. Both exons and introns are highly variable. Moreover, patterns of molecular diversity suggest that the promoter, in addition to the coding region, might be under the same selective pressure, but a different scenario arises when it comes to exon 4 and the 3'UTR segment.
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Affiliation(s)
- Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Audrey Sabbagh
- UMR 216 MERIT, IRD, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
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3
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de Wit J, Borghans JAM, Kesmir C, van Baarle D. Editorial: Role of HLA and KIR in Viral Infections. Front Immunol 2016; 7:286. [PMID: 27512394 PMCID: PMC4961690 DOI: 10.3389/fimmu.2016.00286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/14/2016] [Indexed: 01/28/2023] Open
Affiliation(s)
- Jelle de Wit
- Department of Immune Mechanisms, Centre for Infectious Disease Control, National Institute for Public Health and the Environment , Bilthoven , Netherlands
| | - José A M Borghans
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center , Utrecht , Netherlands
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Debbie van Baarle
- Department of Immune Mechanisms, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands; Laboratory of Translational Immunology, Department of Immunology, University Medical Center, Utrecht, Netherlands
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4
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Rao X, Hoof I, van Baarle D, Keşmir C, Textor J. HLA Preferences for Conserved Epitopes: A Potential Mechanism for Hepatitis C Clearance. Front Immunol 2015; 6:552. [PMID: 26579127 PMCID: PMC4625101 DOI: 10.3389/fimmu.2015.00552] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infections affect more than 170 million people worldwide. Most of these individuals are chronically infected, but some clear the infection rapidly. Host factors seem to play a key role in HCV clearance, among them are the human leukocyte antigen (HLA) class I molecules. Certain HLA molecules, e.g., B*27 and B*57, are associated with viral clearance. To identify potential mechanisms for these associations, we assess epitope distribution differences between HLA molecules using experimentally verified and in silico predicted HCV epitopes. Specifically, we show that the NS5B protein harbors the largest fraction of conserved regions among all HCV proteins. Such conserved regions could be good targets for cytotoxic T-cell (CTL) responses. We find that the protective HLA-B*27 molecule preferentially presents cytotoxic T-cell (CTL) epitopes from NS5B and, in general, presents the most strongly conserved epitopes among the 23 HLA molecules analyzed. In contrast, HLA molecules known to be associated with HCV persistence do not have similar preferences and appear to target the variable P7 protein. Overall, our analysis suggests that by targeting highly constrained - and thereby conserved - regions of HCV, the protective HLA molecule HLA-B*27 reduces the ability of HCV to escape the cytotoxic T-cell response of the host. For visualizing the distribution of both experimentally verified and predicted epitopes across the HCV genome, we created the HCV epitope browser, which is available at theory.bio.uu.nl/ucqi/hcv.
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Affiliation(s)
- Xiangyu Rao
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Ilka Hoof
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Debbie van Baarle
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
| | - Johannes Textor
- Theoretical Biology and Bioinformatics, Utrecht University , Utrecht , Netherlands
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5
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Characterization of the Protective HIV-1 CTL Epitopes and the Corresponding HLA Class I Alleles: A Step towards Designing CTL Based HIV-1 Vaccine. Adv Virol 2014; 2014:321974. [PMID: 24744786 PMCID: PMC3976937 DOI: 10.1155/2014/321974] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 01/18/2014] [Indexed: 01/28/2023] Open
Abstract
Human immunodeficiency virus (HIV) possesses a major threat to the human life largely due to the unavailability of an efficacious vaccine and poor access to the antiretroviral drugs against this deadly virus. High mutation rate in the viral genome underlying the antigenic variability of the viral proteome is the major hindrance as far as the antibody based vaccine development is concerned. Although the exact mechanism by which CTL epitopes and the restricting HLA alleles mediate their action towards slow disease progression is still not clear, the important CTL restricted epitopes for controlling viral infections can be utilized in future vaccine design. This study was designed for the characterization the HIV-1 optimal CTL epitopes and their corresponding HLA alleles. CTL epitope cluster distribution analysis revealed only two HIV-1 proteins, namely, Nef and Gag, which have significant cluster forming capacity. We have found the role of specific HLA supertypes such as HLA B∗07, HLA B∗58, and HLA A∗03 in selecting the hydrophobic and conserved amino acid positions within Nef and Gag proteins, to be presented as epitopes. The analyses revealed that the clusters of optimal epitopes for Nef and p24 proteins of HIV-1 could potentially serve as a source of vaccine.
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6
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Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, Hertz T, Yu X, Horton H. Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design. PLoS One 2013; 8:e64405. [PMID: 23741326 PMCID: PMC3669284 DOI: 10.1371/journal.pone.0064405] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/12/2013] [Indexed: 12/21/2022] Open
Abstract
A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8+ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8+ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8+ T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8+ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r = - 0.65, p = 0.009). Moreover, subjects possessing CD8+ T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p = 0.021). The association between viral control and the breadth of conserved CD8+ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p = 0.215). The associations with viral control were independent of functional avidity of CD8+ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that can elicit CD8+ T cell responses to multiple conserved epitopes of HIV-1.
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Affiliation(s)
- Pratima Kunwar
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Natalie Hawkins
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Warren L. Dinges
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Polyclinic Infectious Disease, Seattle, Washington, United States of America
| | - Yi Liu
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Erin E. Gabriel
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David A. Swan
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Claire E. Stevens
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Janine Maenza
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ann C. Collier
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Tomer Hertz
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Xuesong Yu
- Statistical Center for HIV Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Helen Horton
- Viral Vaccine Program, Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Global Health, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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7
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Sanjuán R, Nebot MR, Peris JB, Alcamí J. Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1. PLoS Biol 2013; 11:e1001523. [PMID: 23565057 PMCID: PMC3614509 DOI: 10.1371/journal.pbio.1001523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/14/2013] [Indexed: 01/06/2023] Open
Abstract
HIV, unlike other viruses, may benefit from immune recognition by preserving the sequence of its T cell epitopes, thereby enhancing transmission between cells. The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4+ helper T lymphocytes (TH cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient level can promote either T-cell epitope conservation or escape. We predict greater conservation for epitopes contributing significantly to total immune activation levels (immunodominance), and when TH cell infection is concomitant to epitope recognition (trans-infection). We suggest that HIV-driven immune activation in the lymph nodes during the chronic stage of the disease may offer a favorable scenario for epitope conservation. Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved TH epitopes may be counterproductive. A key component of the immune response against viruses and other pathogens is the recognition of short foreign protein sequences called epitopes. However, viruses can escape the immune system by mutating, so epitopes should accumulate high levels of genetic variability. This has been documented in several human viruses, but in HIV, unexpectedly, epitopes tend to be relatively conserved. Here, we propose that this is a consequence of the peculiar interactions that occur between HIV and the immune system. As with other viruses, recognition of HIV epitopes promotes the activation of cytotoxic and helper T lymphocytes, which then orchestrate a cellular immune response. However, HIV infects helper T lymphocytes as their target cell in the body and does so more efficiently when these cells have been activated to participate in an immune response. Mathematical modeling showed that, in some cases, HIV may take advantage of immune activation, thus favoring epitope conservation. This should be more likely to occur with epitopes that trigger more vigorous T-cell responses, and during the process known as “trans-infection,” in which helper T lymphocytes are infected while being activated. Our results highlight the potential advantages of an HIV vaccination strategy based on epitopes that stimulate cytotoxic T lymphocytes without specifically stimulating helper T lymphocytes.
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Affiliation(s)
- Rafael Sanjuán
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain.
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8
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Chakraborty S, Rahman T, Chakravorty R, Kuchta A, Rabby A, Sahiuzzaman M. HLA supertypes contribute in HIV type 1 cytotoxic T lymphocyte epitope clustering in Nef and Gag proteins. AIDS Res Hum Retroviruses 2013; 29:270-8. [PMID: 23061377 DOI: 10.1089/aid.2012.0160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Induction of HIV-1-specific cytotoxic T lymphocyte (CTL) responses largely depends upon the presentation of CTL epitopes to the CD8(+) T cells aided by a large number of different HLA class I alleles. Although several studies showed the clustering pattern of HIV-1 CTL epitopes, the underlying reason for this tendency remains unresolved. Moreover, the hypothesis that the CTL epitope clusters tend to coincide with the conserved and hydrophobic regions of HIV-1 proteins has been challenged in recent times. The present study aims to characterize and compare the HIV-1 CTL epitope clusters in terms of restricting HLA alleles, hydrophobicity, and sequence conservation in a proteome-wide manner by including a large number of experimentally validated CTL epitopes from the HIV Molecular Immunology Database. CTL epitope cluster distribution analysis in a proteome-wide manner revealed that only two HIV-1 proteins, namely Nef and Gag, have significant cluster-forming capacity where their epitope localization coincides with the hydrophobic and conserved regions. Furthermore, analyses of proteasomal cleavage sites and HLA anchoring motif frequencies in the epitope-dense regions highlighted the role of specific HLA supertypes such as HLA B*07, HLA B*58, HLA A*02, and HLA A*03 in selecting the hydrophobic and conserved amino acid positions within Nef and Gag proteins to be presented as epitopes. Based on our results, we hypothesize that the cluster-forming tendency of HIV-1 CTL epitopes is not a proteome-wide feature confined to Nef and Gag proteins. Their cluster-forming tendency largely depends on the host HLA alleles that contribute significantly in selecting functionally constrained hydrophobic regions within the HIV-1 proteome.
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Affiliation(s)
- Sajib Chakraborty
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Taibur Rahman
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Rajib Chakravorty
- Department of EEE, University of Melbourne, National ICT Australia, Victoria, Australia
| | - Alison Kuchta
- Virginia Commonwealth University, Richmond, Virginia
| | - Atai Rabby
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Munsi Sahiuzzaman
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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9
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Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response. Adv Virol 2012; 2012:508967. [PMID: 22666249 PMCID: PMC3361994 DOI: 10.1155/2012/508967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/26/2012] [Accepted: 03/11/2012] [Indexed: 11/18/2022] Open
Abstract
As of February 2012, 50 circulating recombinant forms (CRFs) have been reported for HIV-1 while one CRF for HIV-2. Also according to HIV sequence compendium 2011, the HIV sequence database is replete with 414,398 sequences. The fact that there are CRFs, which are an amalgamation of sequences derived from six or more subtypes (CRF27_cpx (cpx refers to complex) is a mosaic with sequences from 6 different subtypes besides an unclassified fragment), serves as a testimony to the continual divergent evolution of the virus with its approximate 1% per year rate of evolution, and this phenomena per se poses tremendous challenge for vaccine development against HIV/AIDS, a devastating disease that has killed 1.8 million patients in 2010. Here, we explore the interaction between HIV-1 and host genetic variation in the context of HIV/AIDS and antiretroviral therapy response.
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10
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Mostowy R, Kouyos RD, Hoof I, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Keşmir C, Bonhoeffer S. Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase. PLoS Comput Biol 2012; 8:e1002525. [PMID: 22654656 PMCID: PMC3359966 DOI: 10.1371/journal.pcbi.1002525] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 04/03/2012] [Indexed: 12/11/2022] Open
Abstract
Human immunodeficiency virus (HIV-1) is, like most pathogens, under selective pressure to escape the immune system of its host. In particular, HIV-1 can avoid recognition by cytotoxic T lymphocytes (CTLs) by altering the binding affinity of viral peptides to human leukocyte antigen (HLA) molecules, the role of which is to present those peptides to the immune system. It is generally assumed that HLA escape mutations carry a replicative fitness cost, but these costs have not been quantified. In this study, we assess the replicative cost of mutations which are likely to escape presentation by HLA molecules in the region of HIV-1 protease and reverse transcriptase. Specifically, we combine computational approaches for prediction of in vitro replicative fitness and peptide binding affinity to HLA molecules. We find that mutations which impair binding to HLA-A molecules tend to have lower in vitro replicative fitness than mutations which do not impair binding to HLA-A molecules, suggesting that HLA-A escape mutations carry higher fitness costs than non-escape mutations. We argue that the association between fitness and HLA-A binding impairment is probably due to an intrinsic cost of escape from HLA-A molecules, and these costs are particularly strong for HLA-A alleles associated with efficient virus control. Counter-intuitively, we do not observe a significant effect in the case of HLA-B, but, as discussed, this does not argue against the relevance of HLA-B in virus control. Overall, this article points to the intriguing possibility that HLA-A molecules preferentially target more conserved regions of HIV-1, emphasizing the importance of HLA-A genes in the evolution of HIV-1 and RNA viruses in general. Our immune system can recognize and kill virus-infected cells by distinguishing between self and virus-derived protein fragments, called peptides, displayed on the surface of each cell. One requirement for a successful recognition is that those peptides bind to the human leukocyte antigen (HLA) class I molecules, which present them to the immune system. As a counter-strategy, human immunodeficiency virus type 1 (HIV-1) can acquire mutations that prevent this binding, thereby helping the virus to escape the surveillance of T-lymphocytes. It is likely that the virus pays a replicative cost for such escape mutations, but the magnitude of this cost has remained elusive. Here, we quantified this fitness cost in HIV-1 protease and reverse transcriptase by combining two computational systems biology approaches: one for prediction of in vitro replicative fitness, and one for the prediction of the efficiency of peptide binding to HLA. We found that in viral proteins targeted by HLA-A molecules, mutations which disrupt binding to those molecules carry a lower replicative fitness than mutations which do not have such an effect. We argue that these results are consistent with the hypothesis that our immune systems might have evolved to target genetic regions of RNA viruses which are costly for the pathogen to alter.
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Affiliation(s)
- Rafal Mostowy
- Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland.
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11
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Immunodominance: a pivotal principle in host response to viral infections. Clin Immunol 2012; 143:99-115. [PMID: 22391152 DOI: 10.1016/j.clim.2012.01.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 11/24/2022]
Abstract
We encounter pathogens on a daily basis and our immune system has evolved to mount an immune response following an infection. An interesting phenomenon that has evolved in response to clearing bacterial and viral infections is called immunodominance. Immunodominance refers to the phenomenon that, despite co-expression of multiple major histocompatibility complex class I alleles by host cells and the potential generation of hundreds of distinct antigenic peptides for recognition following an infection, a large portion of the anti-viral cytotoxic T lymphocyte population targets only some peptide/MHC class I complexes. Here we review the main factors contributing to immunodominance in relation to influenza A and HIV infection. Of special interest are the factors contributing to immunodominance in humans and rodents following influenza A infection. By critically reviewing these findings, we hope to improve understanding of the challenges facing the discovery of new factors enabling better anti-viral vaccine strategies in the future.
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12
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Gijsbers EF, Schuitemaker H, Kootstra NA. HIV-1 transmission and viral adaptation to the host. Future Virol 2012. [DOI: 10.2217/fvl.11.134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
HIV-1 transmission predominantly occurs via mucosal transmission and blood–blood contact. In most newly infected individuals, outgrowth of a single virus variant has been described. This indicates that HIV-1 transmission is a very inefficient process and is restricted by an extensive transmission bottleneck. The transmission rate is directly correlated to the viral load in the donor and the susceptibility of the recipient, which is influenced by factors such as the integrity of mucosal barriers, target cell availability and genetic host factors. After establishment of infection in the new host, the viral population remains very homogenous until the host immune response drives evolution of the viral quasispecies. This review describes our current knowledge on HIV-1 transmission and recent insights in viral adaption to its host.
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Affiliation(s)
- Esther F Gijsbers
- Department of Experimental Immunology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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13
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Berger CT, Frahm N, Price DA, Mothe B, Ghebremichael M, Hartman KL, Henry LM, Brenchley JM, Ruff LE, Venturi V, Pereyra F, Sidney J, Sette A, Douek DC, Walker BD, Kaufmann DE, Brander C. High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control. J Virol 2011; 85:9334-45. [PMID: 21752903 PMCID: PMC3165743 DOI: 10.1128/jvi.00460-11] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/30/2011] [Indexed: 12/20/2022] Open
Abstract
Virus-specific cytotoxic T lymphocytes (CTL) with high levels of functional avidity have been associated with viral clearance in hepatitis C virus infection and with enhanced antiviral protective immunity in animal models. However, the role of functional avidity as a determinant of HIV-specific CTL efficacy remains to be assessed. Here we measured the functional avidities of HIV-specific CTL responses targeting 20 different, optimally defined CTL epitopes restricted by 13 different HLA class I alleles in a cohort comprising 44 HIV controllers and 68 HIV noncontrollers. Responses restricted by HLA-B alleles and responses targeting epitopes located in HIV Gag exhibited significantly higher functional avidities than responses restricted by HLA-A or HLA-C molecules (P = 0.0003) or responses targeting epitopes outside Gag (P < 0.0001). The functional avidities of Gag-specific and HLA-B-restricted responses were higher in HIV controllers than in noncontrollers (P = 0.014 and P = 0.018) and were not restored in HIV noncontrollers initiating antiretroviral therapy. T-cell receptor (TCR) analyses revealed narrower TCR repertoires in higher-avidity CTL populations, which were dominated by public TCR sequences in HIV controllers. Together, these data link the presence of high-avidity Gag-specific and HLA-B-restricted CTL responses with viral suppression in vivo and provide new insights into the immune parameters that mediate spontaneous control of HIV infection.
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Affiliation(s)
- Christoph T. Berger
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Nicole Frahm
- Fred Hutchinson Cancer Research Center/NIAID HIV Vaccine Trials Network (HVTN), Seattle, Washington
| | - David A. Price
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
- Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
| | - Beatriz Mothe
- Lluita contra la Sida Foundation, Hospital Germans Trias i Pujol, Universitat Autònoma de Badalona, Barcelona, Spain
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Musie Ghebremichael
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kari L. Hartman
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Leah M. Henry
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Laura E. Ruff
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Daniel E. Kaufmann
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Christian Brander
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
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14
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Sowmya G, Shamini G, Anita S, Sakharkar M, Mathura V, Rodriguez H, Levine AJ, Singer E, Commins D, Somboonwit C, Sinnott JT, Sidhu HS, Rajaseger G, Pushparaj PN, Kangueane P, Shapshak P. HIV-1 envelope accessible surface and polarity: clade, blood, and brain. Bioinformation 2011; 6:48-56. [PMID: 21544164 PMCID: PMC3082861 DOI: 10.6026/97320630006048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 03/11/2011] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The human immunodeficiency virus type-1 (HIV-1) gp160 (gp120-gp41 complex) trimer envelope (ENV) protein is a potential vaccine candidate for HIV/AIDS. HIV-1 vaccine development has been problematic and charge polarity as well as sequence variation across clades may relate to the difficulties. Further obstacles are caused by sequence variation between blood and brain-derived sequences, since the brain is a separate compartment for HIV-1 infection. We utilize a threedimensional residue measure of solvent exposure, accessible surface area (ASA), which shows that major segments of gp120 and gp41 known structures are solvent exposed across clades. We demonstrate a large percent sequence polarity for solvent exposed residues in gp120 and gp41. The range of sequence polarity varies across clades, blood, and brain from different geographical locations. Regression analysis shows that blood and brain gp120 and gp41 percent sequence polarity range correlate with mean Shannon entropy. These results point to the use of protein modifications to enhance HIV-1 ENV vaccines across multiple clades, blood, and brain. It should be noted that we do not address the issue of protein glycosylation here; however, this is an important issue for vaccine design and development. ABBREVIATIONS HIV-1 - human immunodeficiency virus type 1, AIDS - acquired immunodeficiency syndrome, ENV - envelope, gp160 - 160,000d glycoprotein, gp120 - 120,000d glycoprotein, gp41 - 41,000d glycoprotein, LANL - Los Alamos National Laboratories, PDB - Protein Data Bank, HVTN - STEP HIV vaccine trial, AA - amino acids, MSA - multiple sequence alignment, ASA - accessible surface area, SNPs- single nucleotide polymorphisms, HAART - Highly Active Antiretroviral Therapy, CCR5 - C-C chemokine receptor type 5, CNS - central nervous system, HIVE - HIV encephalitis, P - polarity, NP - non-polarity, CTL - cytotoxic T lymphocyte, NIAID - National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Gopichandran Sowmya
- Biomedical Informatics, Pondicherry 607402, India
- Aimst University, 08100 Semeling, Malaysia
| | - Gunasagaran Shamini
- Biomedical Informatics, Pondicherry 607402, India
- Aimst University, 08100 Semeling, Malaysia
| | | | - Meena Sakharkar
- Graduate School of Life and Environmental Sciences University of Tsukuba, Japan
| | - Venkat Mathura
- Archer Pharmaceuticals, Sarasota, Florida, USA
- Roskamp Institute, 2040 Whitfield Avenue, Sarasota, FL 34243, US
| | - Hector Rodriguez
- Department of Biology, University of Miami, Coral Gables, FL 33146
| | - Andrew J Levine
- National Neurological AIDS Bank, UCLA School of Medicine, Westwood, CA 90095
- Department of Neurology, UCLA School of Medicine, Westwood, CA 90095
| | - Elyse Singer
- National Neurological AIDS Bank, UCLA School of Medicine, Westwood, CA 90095
- Department of Neurology, UCLA School of Medicine, Westwood, CA 90095
| | - Deborah Commins
- National Neurological AIDS Bank, UCLA School of Medicine, Westwood, CA 90095
- Department of Neuropathology, USC Keck School of Medicine, Los Angeles, CA90089
| | - Charurut Somboonwit
- Clinical Research Unit, Hillsborough Health Department, Tampa, Florida 33602
- Division of Infectious Disease and International Medicine, Tampa General Hospital, USF Health, Tampa, FL 33601
| | - John T Sinnott
- Clinical Research Unit, Hillsborough Health Department, Tampa, Florida 33602
- Division of Infectious Disease and International Medicine, Tampa General Hospital, USF Health, Tampa, FL 33601
| | | | | | | | | | - Paul Shapshak
- Division of Infectious Disease and International Medicine, Tampa General Hospital, USF Health, Tampa, FL 33601
- Department of Psychiatry & Behavioral Medicine, University of South Florida, College of Medicine, Tampa, FL 33613
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15
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Ferrari G, Korber B, Goonetilleke N, Liu MKP, Turnbull EL, Salazar-Gonzalez JF, Hawkins N, Self S, Watson S, Betts MR, Gay C, McGhee K, Pellegrino P, Williams I, Tomaras GD, Haynes BF, Gray CM, Borrow P, Roederer M, McMichael AJ, Weinhold KJ. Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection. PLoS Pathog 2011; 7:e1001273. [PMID: 21347345 PMCID: PMC3037354 DOI: 10.1371/journal.ppat.1001273] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 01/06/2011] [Indexed: 01/09/2023] Open
Abstract
In the present study, we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection, and examined whether multifunctionality is required for selection of virus escape mutations. Seven anti-retroviral therapy-naïve subjects were studied in detail between 1 and 87 weeks following onset of symptoms of acute HIV-1 infection. Synthetic peptides representing the autologous transmitted/founder HIV-1 sequences were used in multiparameter flow cytometry assays to determine the functionality of HIV-1-specific CD8+ T memory cells. In all seven patients, the earliest T cell responses were predominantly oligofunctional, although the relative contribution of multifunctional cell responses increased significantly with time from infection. Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants. However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection. Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants.
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Affiliation(s)
- Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America.
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