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Ternette N, Adamopoulou E, Purcell AW. How mass spectrometric interrogation of MHC class I ligandomes has advanced our understanding of immune responses to viruses. Semin Immunol 2023; 68:101780. [PMID: 37276649 DOI: 10.1016/j.smim.2023.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK.
| | - Eleni Adamopoulou
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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de Azevedo SSD, Côrtes FH, Villela LM, Hoagland B, Grinsztejn B, Veloso VG, Morgado MG, Bello G. Ongoing HIV-1 evolution and reservoir reseeding in two elite controllers with genetically diverse peripheral proviral quasispecies. Mem Inst Oswaldo Cruz 2023; 118:e230066. [PMID: 37283423 DOI: 10.1590/0074-02760230066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Elite controllers (EC) are human immunodeficiency virus (HIV)-positive individuals who can maintain low viral loads for extended periods without antiretroviral therapy due to multifactorial and individual characteristics. Most have a small HIV-1 reservoir composed of identical proviral sequences maintained by clonal expansion of infected CD4+ T cells. However, some have a more diverse peripheral blood mononuclear cell (PBMC)-associated HIV-1 reservoir with unique sequences. OBJECTIVES To understand the turnover dynamics of the PBMC-associated viral quasispecies in ECs with relatively diverse circulating proviral reservoirs. METHODS We performed single genome amplification of the env gene at three time points during six years in two EC with high intra-host HIV DNA diversity. FINDINGS Both EC displayed quite diverse PBMCs-associated viral quasispecies (mean env diversity = 1.9-4.1%) across all time-points comprising both identical proviruses that are probably clonally expanded and unique proviruses with evidence of ongoing evolution. HIV-1 env glycosylation pattern suggests that ancestral and evolving proviruses may display different phenotypes of resistance to broadly neutralising antibodies consistent with persistent immune pressure. Evolving viruses may progressively replace the ancestral ones or may remain as minor variants in the circulating proviral population. MAIN CONCLUSIONS These findings support that the high intra-host HIV-1 diversity of some EC resulted from long-term persistence of archival proviruses combined with the continuous reservoir's reseeding and low, but measurable, viral evolution despite undetectable viremia.
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Affiliation(s)
| | - Fernanda Heloise Côrtes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Larissa M Villela
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Brenda Hoagland
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Beatriz Grinsztejn
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Valdilea Gonçalvez Veloso
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Mariza G Morgado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
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Moyano A, Ndlovu B, Mbele M, Naidoo K, Khan N, Mann JK, Ndung'u T. Differing natural killer cell, T cell and antibody profiles in antiretroviral-naive HIV-1 viraemic controllers with and without protective HLA alleles. PLoS One 2023; 18:e0286507. [PMID: 37267224 DOI: 10.1371/journal.pone.0286507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
Previous work suggests that HIV controllers with protective human leukocyte antigen class I alleles (VC+) possess a high breadth of Gag-specific CD8+ T cell responses, while controllers without protective alleles (VC-) have a different unknown mechanism of control. We aimed to gain further insight into potential mechanisms of control in VC+ and VC-. We studied 15 VC+, 12 VC- and 4 healthy uninfected individuals (UI). CD8+ T cell responses were measured by ELISpot. Flow cytometry was performed to analyse surface markers for activation, maturation, and exhaustion on natural killer (NK) cell and T cells, as well as cytokine secretion from stimulated NK cells. We measured plasma neutralization activity against a panel of 18 Env-pseudotyped viruses using the TZM-bl neutralization assay. We found no significant differences in the magnitude and breadth of CD8+ T cell responses between VC+ and VC-. However, NK cells from VC- had higher levels of activation markers (HLA-DR and CD38) (p = 0.03), and lower cytokine expression (MIP-1β and TNF-α) (p = 0.05 and p = 0.04, respectively) than NK cells from VC+. T cells from VC- had higher levels of activation (CD38 and HLA-DR co-expression) (p = 0.05), as well as a trend towards higher expression of the terminal differentiation marker CD57 (p = 0.09) when compared to VC+. There was no difference in overall neutralization breadth between VC+ and VC- groups, although there was a trend for higher neutralization potency in the VC- group (p = 0.09). Altogether, these results suggest that VC- have a more activated NK cell profile with lower cytokine expression, and a more terminally differentiated and activated T cell profile than VC+. VC- also showed a trend of more potent neutralizing antibody responses that may enhance viral clearance. Further studies are required to understand how these NK, T cell and antibody profiles may contribute to differing mechanisms of control in VC+ and VC-.
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Affiliation(s)
- Ana Moyano
- Africa Health Research Institute, KwaZulu-Natal, South Africa, Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Bongiwe Ndlovu
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Msizi Mbele
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kewreshini Naidoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nasreen Khan
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, KwaZulu-Natal, South Africa, Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States of America
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Mokaleng B, Choga WT, Bareng OT, Maruapula D, Ditshwanelo D, Kelentse N, Mokgethi P, Moraka NO, Motswaledi MS, Tawe L, Koofhethile CK, Moyo S, Zachariah M, Gaseitsiwe S. No Difference in the Prevalence of HIV-1 gag Cytotoxic T-Lymphocyte-Associated Escape Mutations in Viral Sequences from Early and Late Parts of the HIV-1 Subtype C Pandemic in Botswana. Vaccines (Basel) 2023; 11:1000. [PMID: 37243104 PMCID: PMC10221913 DOI: 10.3390/vaccines11051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
HIV is known to accumulate escape mutations in the gag gene in response to the immune response from cytotoxic T lymphocytes (CTLs). These mutations can occur within an individual as well as at a population level. The population of Botswana exhibits a high prevalence of HLA*B57 and HLA*B58, which are associated with effective immune control of HIV. In this retrospective cross-sectional investigation, HIV-1 gag gene sequences were analyzed from recently infected participants across two time periods which were 10 years apart: the early time point (ETP) and late time point (LTP). The prevalence of CTL escape mutations was relatively similar between the two time points-ETP (10.6%) and LTP (9.7%). The P17 protein had the most mutations (9.4%) out of the 36 mutations that were identified. Three mutations (A83T, K18R, Y79H) in P17 and T190A in P24 were unique to the ETP sequences at a prevalence of 2.4%, 4.9%, 7.3%, and 5%, respectively. Mutations unique to the LTP sequences were all in the P24 protein, including T190V (3%), E177D (6%), R264K (3%), G248D (1%), and M228L (11%). Mutation K331R was statistically higher in the ETP (10%) compared to the LTP (1%) sequences (p < 0.01), while H219Q was higher in the LTP (21%) compared to the ETP (5%) (p < 0.01). Phylogenetically, the gag sequences clustered dependently on the time points. We observed a slower adaptation of HIV-1C to CTL immune pressure at a population level in Botswana. These insights into the genetic diversity and sequence clustering of HIV-1C can aid in the design of future vaccine strategies.
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Affiliation(s)
- Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Wonderful Tatenda Choga
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Ontlametse Thato Bareng
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Patrick Mokgethi
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone 999106, Botswana
| | - Natasha Onalenna Moraka
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Modisa Sekhamo Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Leabaneng Tawe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Catherine Kegakilwe Koofhethile
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Matshediso Zachariah
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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Impaired protective role of HLA-B*57:01/58:01 in HIV-1 CRF01_AE infection: a cohort study in Vietnam. Int J Infect Dis 2023; 128:20-31. [PMID: 36549550 DOI: 10.1016/j.ijid.2022.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Human Leukocyte Antigen HLA-B*57:01 and B*58:01 are considered anti-HIV-1 protective alleles. HLA-B*57:01/58:01-restricted HIV-1 Gag TW10 (TSTLQEQIGW, Gag residues 240-249) epitope-specific CD8+ T cell responses that frequently select for a Gag escape mutation, T242N, with viral fitness cost are crucial for HIV-1 control. Although this finding has been observed in cohorts where HIV-1 subtype B or C predominates, the protective impact of HLA-B*57:01/58:01 has not been reported in Southeast Asian countries where HIV-1 CRF01_AE is the major circulating strain. Here, the effect of HLA-B*57:01/58:01 on CRF01_AE infection was investigated. METHODS The correlation of HLA-B*57:01/58:01 with viral load and CD4 counts were analyzed in the CRF01_AE-infected Vietnamese cohort (N = 280). The impact of the T242N mutation on CRF01_AE replication capacity was assessed. RESULTS HLA-B*57:01/58:01-positive individuals mostly had HIV-1 with T242N (62/63) but showed neither a significant reduction in viral load nor increased CD4 counts relative to B*57:01/58:01-negative participants. In vitro and in vivo analyses revealed a significant reduction in viral fitness of CRF01_AE with T242N. In silico analysis indicated reduced presentation of epitopes in the context of CRF01_AE compared to subtype B or C in 10/16 HLA-B*57:01/58:01-restricted HIV-1 epitopes. CONCLUSION The protective impact of HLA-B*57:01/58:01 on CRF01_AE infection is impaired despite strong suppressive pressure by TW10-specific CD8+ T cells.
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Han L, Wu S, Zhang T, Peng W, Zhao M, Yue C, Wen W, Cai W, Li M, Wallny HJ, Avila DW, Mwangi W, Nair V, Ternette N, Guo Y, Zhao Y, Chai Y, Qi J, Liang H, Gao GF, Kaufman J, Liu WJ. A Wider and Deeper Peptide-Binding Groove for the Class I Molecules from B15 Compared with B19 Chickens Correlates with Relative Resistance to Marek's Disease. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:668-680. [PMID: 36695776 PMCID: PMC7614295 DOI: 10.4049/jimmunol.2200211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023]
Abstract
The chicken MHC is known to confer decisive resistance or susceptibility to various economically important pathogens, including the iconic oncogenic herpesvirus that causes Marek's disease (MD). Only one classical class I gene, BF2, is expressed at a high level in chickens, so it was relatively easy to discern a hierarchy from well-expressed thermostable fastidious specialist alleles to promiscuous generalist alleles that are less stable and expressed less on the cell surface. The class I molecule BF2*1901 is better expressed and more thermostable than the closely related BF2*1501, but the peptide motif was not simpler as expected. In this study, we confirm for newly developed chicken lines that the chicken MHC haplotype B15 confers resistance to MD compared with B19. Using gas phase sequencing and immunopeptidomics, we find that BF2*1901 binds a greater variety of amino acids in some anchor positions than does BF2*1501. However, by x-ray crystallography, we find that the peptide-binding groove of BF2*1901 is narrower and shallower. Although the self-peptides that bound to BF2*1901 may appear more various than those of BF2*1501, the structures show that the wider and deeper peptide-binding groove of BF2*1501 allows stronger binding and thus more peptides overall, correlating with the expected hierarchies for expression level, thermostability, and MD resistance. Our study provides a reasonable explanation for greater promiscuity for BF2*1501 compared with BF2*1901, corresponding to the difference in resistance to MD.
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Affiliation(s)
- Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- National Poultry Laboratory Animal Resource Center, Harbin 150001, China
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin 150069, China
| | - Shaolian Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Zhang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Weiyu Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Min Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Can Yue
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanxin Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Wenbo Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Min Li
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | | | - David W. Avila
- The Basel Institute for Immunology, Basel CH4001, Switzerland
| | - William Mwangi
- The Pirbright Institute, Pirbright GU24 0NF, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute, Pirbright GU24 0NF, United Kingdom
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Headington OX37BN, United Kingdom
| | - Yaxin Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Liang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Jim Kaufman
- The Basel Institute for Immunology, Basel CH4001, Switzerland
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Department of Veterinary Science, University of Cambridge, Cambridge CB3 0ES, United Kingdom
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - William J. Liu
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
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Definition of a New HLA B*52-Restricted Rev CTL Epitope Targeted by an HIV-1-Infected Controller. Viruses 2023; 15:v15020567. [PMID: 36851781 PMCID: PMC9959870 DOI: 10.3390/v15020567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/05/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The analysis of T-cell responses in HIV-1-infected controllers may contribute to a better understanding of the protective components of the immune system. Here, we analyzed the HIV-1-specific T-cell response in a 59-year-old HIV-1-infected controller, infected for at least seven years, who presented with low viral loads ranging from <20 copies/mL to 200 copies/mL and normal CD4 counts of >800 cells/µL. In γ-IFN-ELISpot assays using freshly isolated PBMCs, he displayed a very strong polyclonal T-cell response to eight epitopes in Gag, Nef and Rev; with the dominant responses directed against the HLA-B*57-epitope AISPRTLNAW and against a so-far-unknown epitope within Rev. Further analyses using peptide-stimulated T-cell lines in γ-IFN-ELISpot assays delineated the peptide RQRQIRSI (Rev-RI8) as a newly defined HLA-B*52-restricted epitope located within a functionally important region of Rev. Peptide-stimulation assays in 15 HLA-B*52-positive HIV-1-infected subjects, including the controller, demonstrated recognition of the Rev-RI8 epitope in 6/15 subjects. CD4 counts before the start of antiviral therapy were significantly higher in subjects with recognition of the Rev-RI8 epitope. Targeting of the Rev-RI8 epitope in Rev by CTL could contribute to the positive association of HLA-B*52 with a more favorable course of HIV-1-infection.
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Yuan X, Lai Y. Bibliometric and visualized analysis of elite controllers based on CiteSpace: landscapes, hotspots, and frontiers. Front Cell Infect Microbiol 2023; 13:1147265. [PMID: 37124043 PMCID: PMC10130382 DOI: 10.3389/fcimb.2023.1147265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Background A unique subset of people living with HIV, known as elite controllers, possess spontaneous and consistent control over viral replication and disease progression in the absence of antiviral intervention. In-depth research on elite controllers is conducive to designing better treatment strategies for HIV. However, comprehensive and illuminating bibliometric reports on elite controllers are rare. Methods Articles on elite controllers were retrieved from the Web of Science Core Collection. A visualized analysis of this domain was conducted by CiteSpace software. Taking count, betweenness centrality, and burst value as criteria, we interpreted the visualization results and predicted future new directions and emerging trends. Results By December 31, 2022, 843 articles related to elite controllers had been published. The largest contributors in terms of country, institution, and author were the United States (485), Univ Calif San Francisco (87), and Walker B.D. (65), respectively. Migueles S.A. (325) and Journal of Virology (770) were the most cocited author and journal, respectively. Additionally, by summarizing the results of our CiteSpace software analysis on references and keywords, we considered that the research hotspots and frontiers on elite controllers mainly focus on three aspects: deciphering the mechanisms of durable control, delineating the implications for the development of treatments for HIV infection, and highlighting the clinical risks faced by elite controllers and coping strategies. Conclusion This study performed a bibliometric and visual analysis of elite controllers, identified the main characteristics and emerging trends, and provided insightful references for further development of this rapidly evolving and complex field.
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Affiliation(s)
- Xingyue Yuan
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu Lai
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Yu Lai,
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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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10
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Abstract
PURPOSE OF REVIEW The quest for HIV-1 cure could take advantage of the study of rare individuals that control viral replication spontaneously (elite controllers) or after an initial course of antiretroviral therapy (posttreatment controllers, PTCs). In this review, we will compare back-to-back the immunological and virological features underlying viral suppression in elite controllers and PTCs, and explore their possible contributions to the HIV-1 cure research. RECENT FINDINGS HIV-1 control in elite controllers shows hallmarks of an effective antiviral response, favored by genetic background and possibly associated to residual immune activation. The immune pressure in elite controllers might select against actively transcribing intact proviruses, allowing the persistence of a small and poorly inducible reservoir. Evidence on PTCs is less abundant but preliminary data suggest that antiviral immune responses may be less pronounced. Therefore, these patients may rely on distinct mechanisms, not completely elucidated to date, suppressing HIV-1 transcription and replication. SUMMARY PTCs and elite controllers may control HIV replication using distinct pathways, the elucidation of which may contribute to design future interventional strategies aiming to achieve a functional cure.
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11
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Halabi S, Kaufman J. New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system. Front Immunol 2022; 13:886672. [PMID: 35967451 PMCID: PMC9372762 DOI: 10.3389/fimmu.2022.886672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022] Open
Abstract
The functions of a wide variety of molecules with structures similar to the classical class I and class II molecules encoded by the major histocompatibility complex (MHC) have been studied by biochemical and structural studies over decades, with many aspects for humans and mice now enshrined in textbooks as dogma. However, there is much variation of the MHC and MHC molecules among the other jawed vertebrates, understood in the most detail for the domestic chicken. Among the many unexpected features in chickens is the co-evolution between polymorphic TAP and tapasin genes with a dominantly-expressed class I gene based on a different genomic arrangement compared to typical mammals. Another important discovery was the hierarchy of class I alleles for a suite of properties including size of peptide repertoire, stability and cell surface expression level, which is also found in humans although not as extreme, and which led to the concept of generalists and specialists in response to infectious pathogens. Structural studies of chicken class I molecules have provided molecular explanations for the differences in peptide binding compared to typical mammals. These unexpected phenomena include the stringent binding with three anchor residues and acidic residues at the peptide C-terminus for fastidious alleles, and the remodelling binding sites, relaxed binding of anchor residues in broad hydrophobic pockets and extension at the peptide C-terminus for promiscuous alleles. The first few studies for chicken class II molecules have already uncovered unanticipated structural features, including an allele that binds peptides by a decamer core. It seems likely that the understanding of how MHC molecules bind and present peptides to lymphocytes will broaden considerably with further unexpected discoveries through biochemical and structural studies for chickens and other non-mammalian vertebrates.
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Affiliation(s)
- Samer Halabi
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Jim Kaufman,
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12
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Mechanism of Viral Suppression among HIV Elite Controllers and Long-Term Nonprogressors in Nigeria and South Africa. Viruses 2022; 14:v14061270. [PMID: 35746741 PMCID: PMC9228396 DOI: 10.3390/v14061270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022] Open
Abstract
A subgroup among people living with HIV (PLHIV) experience viral suppression, sometimes to an undetectable level in the blood and/or are able to maintain a healthy CD4+ T-cell count without the influence of antiretroviral (ARV) therapy. One out of three hundred PLHIV fall into this category, and a large sample of this group can be found in areas with a high prevalence of HIV infection such as Nigeria and South Africa. Understanding the mechanism underpinning the nonprogressive phenotype in this subgroup may provide insights into the control of the global HIV epidemic. This work provides mechanisms of the elite control and nonprogressive phenotype among PLHIV in Nigeria and South Africa and identifies research gaps that will contribute to a better understanding on HIV controllers among PLHIV.
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13
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Gaebler C, Nogueira L, Stoffel E, Oliveira TY, Breton G, Millard KG, Turroja M, Butler A, Ramos V, Seaman MS, Reeves JD, Petroupoulos CJ, Shimeliovich I, Gazumyan A, Jiang CS, Jilg N, Scheid JF, Gandhi R, Walker BD, Sneller MC, Fauci A, Chun TW, Caskey M, Nussenzweig MC. Prolonged viral suppression with anti-HIV-1 antibody therapy. Nature 2022; 606:368-374. [PMID: 35418681 PMCID: PMC9177424 DOI: 10.1038/s41586-022-04597-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/28/2022] [Indexed: 01/26/2023]
Abstract
HIV-1 infection remains a public health problem with no cure. Anti-retroviral therapy (ART) is effective but requires lifelong drug administration owing to a stable reservoir of latent proviruses integrated into the genome of CD4+ T cells1. Immunotherapy with anti-HIV-1 antibodies has the potential to suppress infection and increase the rate of clearance of infected cells2,3. Here we report on a clinical study in which people living with HIV received seven doses of a combination of two broadly neutralizing antibodies over 20 weeks in the presence or absence of ART. Without pre-screening for antibody sensitivity, 76% (13 out of 17) of the volunteers maintained virologic suppression for at least 20 weeks off ART. Post hoc sensitivity analyses were not predictive of the time to viral rebound. Individuals in whom virus remained suppressed for more than 20 weeks showed rebound viraemia after one of the antibodies reached serum concentrations below 10 µg ml-1. Two of the individuals who received all seven antibody doses maintained suppression after one year. Reservoir analysis performed after six months of antibody therapy revealed changes in the size and composition of the intact proviral reservoir. By contrast, there was no measurable decrease in the defective reservoir in the same individuals. These data suggest that antibody administration affects the HIV-1 reservoir, but additional larger and longer studies will be required to define the precise effect of antibody immunotherapy on the reservoir.
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Affiliation(s)
- Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Elina Stoffel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Columbia University Irving Medical Center, New York, NY, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Allison Butler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Caroline S Jiang
- Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA
| | - Nikolaus Jilg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Johannes F Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Rajesh Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael C Sneller
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anthony Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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14
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Zhang H, He C, Jiang F, Cao S, Zhao B, Ding H, Dong T, Han X, Shang H. A longitudinal analysis of immune escapes from HLA-B*13-restricted T-cell responses at early stage of CRF01_AE subtype HIV-1 infection and implications for vaccine design. BMC Immunol 2022; 23:15. [PMID: 35366796 PMCID: PMC8976269 DOI: 10.1186/s12865-022-00491-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying immunogens which can elicit effective T cell responses against human immunodeficiency virus type 1 (HIV-1) is important for developing a T-cell based vaccine. It has been reported that human leukocyte antigen (HLA)-B*13-restricted T-cell responses contributed to HIV control in subtype B' and C infected individuals. However, the kinetics of B*13-restricted T-cell responses, viral evolution within epitopes, and the impact on disease progression in CRF01_AE subtype HIV-1-infected men who have sex with men (MSM) are not known. RESULTS Interferon-γ ELISPOT assays and deep sequencing of viral RNAs were done in 14 early HLA-B*13-positive CRF01_AE subtype HIV-1-infected MSM. We found that responses to RQEILDLWV (Nef106-114, RV9), GQMREPRGSDI (Gag226-236, GI11), GQDQWTYQI (Pol487-498, GI9), and VQNAQGQMV (Gag135-143, VV9) were dominant. A higher relative magnitude of Gag-specific T-cell responses, contributed to viral control, whereas Nef-specific T-cell responses were associated with rapid disease progression. GI11 (Gag) was conserved and strong GI11 (Gag)-specific T-cell responses showed cross-reactivity with a dominant variant, M228I, found in 3/12 patients; GI11 (Gag)-specific T-cell responses were positively associated with CD4 T-cell counts (R = 0.716, P = 0.046). Interestingly, the GI9 (Pol) epitope was also conserved, but GI9 (Pol)-specific T-cell responses did not influence disease progression (P > 0.05), while a D490G variant identified in one patient did not affect CD4 T-cell counts. All the other epitopes studied [VV9 (Gag), RQYDQILIEI (Pol113-122, RI10), HQSLSPRTL (Gag144-152, HL9), and RQANFLGRL (Gag429-437, RL9)] developed escape mutations within 1 year of infection, which may have contributed to overall disease progression. Intriguingly, we found early RV9 (Nef)-specific T-cell responses were associated with rapid disease progression, likely due to escape mutations. CONCLUSIONS Our study strongly suggested the inclusion of GI11 (Gag) and exclusion of RV9 (Nef) for T-cell-based vaccine design for B*13-positive CRF01_AE subtype HIV-1-infected MSM and high-risk individuals.
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Affiliation(s)
- Hui Zhang
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Chuan He
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China ,grid.412636.40000 0004 1757 9485Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001 China
| | - Fanming Jiang
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China ,grid.412636.40000 0004 1757 9485Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001 China
| | - Shuang Cao
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China ,grid.412449.e0000 0000 9678 1884Department of Laboratory Medicine, China Medical University Shengjing Hospital Nanhu Branch, Shenyang, 110001 China
| | - Bin Zhao
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Haibo Ding
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Tao Dong
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, Oxford University, Oxford, UK ,grid.4991.50000 0004 1936 8948Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK
| | - Xiaoxu Han
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Hong Shang
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
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15
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Pérez-Yanes S, Pernas M, Marfil S, Cabrera-Rodríguez R, Ortiz R, Urrea V, Rovirosa C, Estévez-Herrera J, Olivares I, Casado C, Lopez-Galindez C, Blanco J, Valenzuela-Fernández A. The Characteristics of the HIV-1 Env Glycoprotein Are Linked With Viral Pathogenesis. Front Microbiol 2022; 13:763039. [PMID: 35401460 PMCID: PMC8988142 DOI: 10.3389/fmicb.2022.763039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/31/2022] [Indexed: 12/17/2022] Open
Abstract
The understanding of HIV-1 pathogenesis and clinical progression is incomplete due to the variable contribution of host, immune, and viral factors. The involvement of viral factors has been investigated in extreme clinical phenotypes from rapid progressors to long-term non-progressors (LTNPs). Among HIV-1 proteins, the envelope glycoprotein complex (Env) has been concentrated on in many studies for its important role in the immune response and in the first steps of viral replication. In this study, we analyzed the contribution of 41 Envs from 24 patients with different clinical progression rates and viral loads (VLs), LTNP-Elite Controllers (LTNP-ECs); Viremic LTNPs (vLTNPs), and non-controller individuals contemporary to LTNPs or recent, named Old and Modern progressors. We studied the Env expression, the fusion and cell-to-cell transfer capacities, as well as viral infectivity. The sequence and phylogenetic analysis of Envs were also performed. In every functional characteristic, the Envs from subjects with viral control (LTNP-ECs and vLTNPs) showed significant lower performance compared to those from the progressor individuals (Old and Modern). Regarding sequence analysis, the variable loops of the gp120 subunit of the Env (i.e., V2, V4, and mainly V5) of the progressor individuals showed longer and more glycosylated sequences than controller subjects. Therefore, HIV-1 Envs from virus of patients presenting viremic control and the non-progressor clinical phenotype showed poor viral functions and shorter sequences, whereas functional Envs were associated with virus of patients lacking virological control and with progressor clinical phenotypes. These correlations support the role of Env genotypic and phenotypic characteristics in the in vivo HIV-1 infection and pathogenesis.
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Affiliation(s)
- Silvia Pérez-Yanes
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - María Pernas
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Marfil
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Romina Cabrera-Rodríguez
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Raquel Ortiz
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Víctor Urrea
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Carla Rovirosa
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Judith Estévez-Herrera
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Isabel Olivares
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción Casado
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
- Concepción Casado,
| | - Cecilio Lopez-Galindez
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
- Cecilio Lopez-Galindez,
| | - Julià Blanco
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
- Chair of Infectious Diseases and Immunity, Faculty of Medicine, Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Barcelona, Spain
- Julià Blanco,
| | - Agustín Valenzuela-Fernández
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
- *Correspondence: Agustín Valenzuela-Fernández,
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16
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Distinct Plasma Concentrations of Acyl-CoA-Binding Protein (ACBP) in HIV Progressors and Elite Controllers. Viruses 2022; 14:v14030453. [PMID: 35336860 PMCID: PMC8949460 DOI: 10.3390/v14030453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/28/2022] Open
Abstract
HIV elite controllers (ECs) are characterized by the spontaneous control of viral replication, and by metabolic and autophagic profiles which favor anti-HIV CD4 and CD8 T-cell responses. Extracellular acyl coenzyme A binding protein (ACBP) acts as a feedback inhibitor of autophagy. Herein, we assessed the circulating ACBP levels in ECs, compared to people living with HIV (PLWH) receiving antiretroviral therapy (ART) or not. We found lower ACBP levels in ECs compared to ART-naïve or ART-treated PLWH (p < 0.01 for both comparisons), independently of age and sex. ACBP levels were similar in ECs and HIV-uninfected controls. The expression of the protective HLA alleles HLA-B*27, *57, or *58 did not influence ACBP levels in ECs. ACBP levels were not associated with CD4 or CD8 T-cell counts, CD4 loss over time, inflammatory cytokines, or anti-CMV IgG titers in ECs. In ART-treated PLWH, ACBP levels were correlated with interleukin (IL)-1β levels, but not with other inflammatory cytokines such as IL-6, IL-8, IL-32, or TNF-α. In conclusion, ECs are characterized by low ACBP plasma levels compared to ART-naïve or ART-treated PLWH. As autophagy is key to anti-HIV CD4 and CD8 T-cell responses, the ACBP pathway constitutes an interesting target in HIV cure strategies.
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17
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Vieira VA, Millar J, Adland E, Muenchhoff M, Roider J, Guash CF, Peluso D, Thomé B, Garcia-Guerrero MC, Puertas MC, Bamford A, Brander C, Carrington M, Martinez-Picado J, Frater J, Tudor-Williams G, Goulder P. Robust HIV-specific CD4+ and CD8+ T-cell responses distinguish elite control in adolescents living with HIV from viremic nonprogressors. AIDS 2022; 36:95-105. [PMID: 34581306 PMCID: PMC8654249 DOI: 10.1097/qad.0000000000003078] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Elite controllers are therapy-naive individuals living with HIV capable of spontaneous control of plasma viraemia for at least a year. Although viremic nonprogressors are more common in vertical HIV-infection than in adults' infection, elite control has been rarely characterized in the pediatric population. DESIGN We analyzed the T-cell immunophenotype and the HIV-specific response by flow cytometry in four pediatric elite controllers (PECs) compared with age-matched nonprogressors (PNPs), progressors and HIV-exposed uninfected (HEUs) adolescents. RESULTS PECs T-cell populations had lower immune activation and exhaustion levels when compared with progressors, reflected by a more sustained and preserved effector function. The HIV-specific T-cell responses among PECs were characterized by high-frequency Gag-specific CD4+ T-cell activity, and markedly more polyfunctional Gag-specific CD8+ activity, compared with PNPs and progressors. These findings were consistently observed even in the absence of protective HLA-I molecules such as HLA-B∗27/57/81. CONCLUSION Pediatric elite control is normally achieved after years of infection, and low immune activation in PNPs precedes the increasing ability of CD8+ T-cell responses to achieve immune control of viraemia over the course of childhood, whereas in adults, high immune activation in acute infection predicts subsequent CD8+ T-cell mediated immune control of viremia, and in adult elite controllers, low immune activation is therefore the consequence of the rapid CD8+ T-cell mediated immune control generated after acute infection. This distinct strategy adopted by PECs may help identify pathways that facilitate remission in posttreatment controllers, in whom protective HLA-I molecules are not the main factor.
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Affiliation(s)
| | - Jane Millar
- Department of Paediatrics, University of Oxford, Oxford, UK
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Maximilian Muenchhoff
- Max von Pettenkofer-Institute, Department of Virology, Ludwig-Maximilians-University
- German Center for Infection Research (DZIF)
| | - Julia Roider
- German Center for Infection Research (DZIF)
- Department of Infectious Diseases, Ludwig-Maximilians-University, Munich, Germany
| | - Claudia Fortuny Guash
- Unidad de Enfermedades Infecciosas, Servicio de Pediatría, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | | | - Beatriz Thomé
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Medicina Preventiva, São Paulo, Brazil
| | | | | | - Alasdair Bamford
- Great Ormond Street Hospital for Children NHS Foundation Trust
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Christian Brander
- IrsiCaixa - AIDS Research Institute, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, Maryland, USA
| | - Javier Martinez-Picado
- IrsiCaixa - AIDS Research Institute, Badalona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - John Frater
- Nuffield Department of Medicine, University of Oxford
- Oxford NIHR Biomedical Research Centre, Oxford
| | | | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, UK
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal (UKZN), Durban, South Africa
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18
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HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy. mBio 2021; 12:e0249021. [PMID: 34781741 PMCID: PMC8693448 DOI: 10.1128/mbio.02490-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Curing HIV will require eliminating the reservoir of integrated, replication-competent proviruses that persist despite antiretroviral therapy (ART). Understanding the burden, genetic diversity, and longevity of persisting proviruses in diverse individuals with HIV is critical to this goal, but these characteristics remain understudied in some groups. Among them are viremic controllers—individuals who naturally suppress HIV to low levels but for whom therapy is nevertheless recommended. We reconstructed within-host HIV evolutionary histories from longitudinal single-genome amplified viral sequences in four viremic controllers who eventually initiated ART and used this information to characterize the age and diversity of proviruses persisting on therapy. We further leveraged these within-host proviral age distributions to estimate rates of proviral turnover prior to ART. This is an important yet understudied metric, since pre-ART proviral turnover dictates reservoir composition at ART initiation (and thereafter), which is when curative interventions, once developed, would be administered. Despite natural viremic control, all participants displayed significant within-host HIV evolution pretherapy, where overall on-ART proviral burden and diversity broadly reflected the extent of viral replication and diversity pre-ART. Consistent with recent studies of noncontrollers, the proviral pools of two participants were skewed toward sequences that integrated near ART initiation, suggesting dynamic proviral turnover during untreated infection. In contrast, proviruses recovered from the other two participants dated to time points that were more evenly spread throughout infection, suggesting slow or negligible proviral decay following deposition. HIV cure strategies will need to overcome within-host proviral diversity, even in individuals who naturally controlled HIV replication before therapy.
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19
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Currenti J, Law BM, Qin K, John M, Pilkinton MA, Bansal A, Leary S, Ram R, Chopra A, Gangula R, Yue L, Warren C, Barnett L, Alves E, McDonnell WJ, Sooda A, Heath SL, Mallal S, Goepfert P, Kalams SA, Gaudieri S. Cross-Reactivity to Mutated Viral Immune Targets Can Influence CD8 + T Cell Functionality: An Alternative Viral Adaptation Strategy. Front Immunol 2021; 12:746986. [PMID: 34764960 PMCID: PMC8577586 DOI: 10.3389/fimmu.2021.746986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022] Open
Abstract
Loss of T cell immunogenicity due to mutations in virally encoded epitopes is a well-described adaptation strategy to limit host anti-viral immunity. Another described, but less understood, adaptation strategy involves the selection of mutations within epitopes that retain immune recognition, suggesting a benefit for the virus despite continued immune pressure (termed non-classical adaptation). To understand this adaptation strategy, we utilized a single cell transcriptomic approach to identify features of the HIV-specific CD8+ T cell responses targeting non-adapted (NAE) and adapted (AE) forms of epitopes containing a non-classical adaptation. T cell receptor (TCR) repertoire and transcriptome were obtained from antigen-specific CD8+ T cells of chronic (n=7) and acute (n=4) HIV-infected subjects identified by either HLA class I tetramers or upregulation of activation markers following peptide stimulation. CD8+ T cells were predominantly dual tetramer+, confirming a large proportion of cross-reactive TCR clonotypes capable of recognizing the NAE and AE form. However, single-reactive CD8+ T cells were identified in acute HIV-infected subjects only, providing the potential for the selection of T cell clones over time. The transcriptomic profile of CD8+ T cells was dependent on the autologous virus: subjects whose virus encoded the NAE form of the epitope (and who transitioned to the AE form at a later timepoint) exhibited an 'effective' immune response, as indicated by expression of transcripts associated with polyfunctionality, cytotoxicity and apoptosis (largely driven by the genes GZMB, IFNɣ, CCL3, CCL4 and CCL5). These data suggest that viral adaptation at a single amino acid residue can provide an alternative strategy for viral survival by modulating the transcriptome of CD8+ T cells and potentially selecting for less effective T cell clones from the acute to chronic phase.
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Affiliation(s)
- Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Becker M.P. Law
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Kai Qin
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, WA, Australia
| | - Mark A. Pilkinton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Rama Gangula
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Christian Warren
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Louise Barnett
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Wyatt J. McDonnell
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Anuradha Sooda
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Sonya L. Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Spyros A. Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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20
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Tregaskes CA, Kaufman J. Chickens as a simple system for scientific discovery: The example of the MHC. Mol Immunol 2021; 135:12-20. [PMID: 33845329 PMCID: PMC7611830 DOI: 10.1016/j.molimm.2021.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 01/07/2023]
Abstract
Chickens have played many roles in human societies over thousands of years, most recently as an important model species for scientific discovery, particularly for embryology, virology and immunology. In the last few decades, biomedical models like mice have become the most important model organism for understanding the mechanisms of disease, but for the study of outbred populations, they have many limitations. Research on humans directly addresses many questions about disease, but frank experiments into mechanisms are limited by practicality and ethics. For research into all levels of disease simultaneously, chickens combine many of the advantages of humans and of mice, and could provide an independent, integrated and overarching system to validate and/or challenge the dogmas that have arisen from current biomedical research. Moreover, some important systems are simpler in chickens than in typical mammals. An example is the major histocompatibility complex (MHC) that encodes the classical MHC molecules, which play crucial roles in the innate and adaptive immune systems. Compared to the large and complex MHCs of typical mammals, the chicken MHC is compact and simple, with single dominantly-expressed MHC molecules that can determine the response to infectious pathogens. As a result, some fundamental principles have been easier to discover in chickens, with the importance of generalist and specialist MHC alleles being the latest example.
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Affiliation(s)
- Clive A Tregaskes
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; University of Edinburgh, Institute for Immunology and Infection Research, Ashworth Laboratories, Kings Buildings, Edinburgh, EH9 3FL, United Kingdom.
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21
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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: 5] [Impact Index Per Article: 1.7] [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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22
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Abstract
Neutralizing antibodies are the basis of almost all approved prophylactic vaccines and the foundation of effective protection from pathogens, including the recently emerging SARS Coronavirus 2 (SARS-CoV-2). However, the contribution of antibodies to protection and to the course of the disease during first-time exposure to a pathogen is unknown. We analyzed the antibodies and B cell responses in severe and mild COVID-19 patients. Despite our primary assumption that high antibody titers contribute to a mild disease, we found that severe COVID-19 illness, and not mild infection, correlates with strong anti-viral antibody and memory B cell responses. This phenomenon was also demonstrated for anti-Mycobacterium tuberculosis inhibiting antibodies that we recently isolated from an actively infected Tuberculosis-sick donor. This correlation between disease severity and antibody responses can be explained by the fact that high viral loads drive B cell stimulation and generation of high-affinity antibodies that will be protective upon future encounter with the particular pathogen.
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Affiliation(s)
- Natalia T Freund
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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23
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McCann CD, van Dorp CH, Danesh A, Ward AR, Dilling TR, Mota TM, Zale E, Stevenson EM, Patel S, Brumme CJ, Dong W, Jones DS, Andresen TL, Walker BD, Brumme ZL, Bollard CM, Perelson AS, Irvine DJ, Jones RB. A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies. J Exp Med 2021; 218:212105. [PMID: 33988715 PMCID: PMC8129803 DOI: 10.1084/jem.20201908] [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] [Received: 09/02/2020] [Revised: 02/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
HIV-specific CD8+ T cells partially control viral replication and delay disease progression, but they rarely provide lasting protection, largely due to immune escape. Here, we show that engrafting mice with memory CD4+ T cells from HIV+ donors uniquely allows for the in vivo evaluation of autologous T cell responses while avoiding graft-versus-host disease and the need for human fetal tissues that limit other models. Treating HIV-infected mice with clinically relevant HIV-specific T cell products resulted in substantial reductions in viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an IL-15 superagonist, but it was ultimately limited by the pervasive selection of a diverse array of escape mutations, recapitulating patterns seen in humans. By applying mathematical modeling, we show that the kinetics of the CD8+ T cell response have a profound impact on the emergence and persistence of escape mutations. This “participant-derived xenograft” model of HIV provides a powerful tool for studying HIV-specific immunological responses and facilitating the development of effective cell-based therapies.
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Affiliation(s)
- Chase D McCann
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | | | - Ali Danesh
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Adam R Ward
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC.,PhD Program in Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Thomas R Dilling
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Talia M Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Elizabeth Zale
- Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Eva M Stevenson
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Shabnum Patel
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | | | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA.,Institute for Medical and Engineering Sciences, Massachusetts Institute of Technology, Cambridge, MA.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM
| | - Darrell J Irvine
- Howard Hughes Medical Institute, Chevy Chase, MD.,Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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24
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Yang H, Llano A, Cedeño S, von Delft A, Corcuera A, Gillespie GM, Knox A, Leneghan DB, Frater J, Stöhr W, Fidler S, Mothe B, Mak J, Brander C, Ternette N, Dorrell L. Incoming HIV virion-derived Gag Spacer Peptide 2 (p1) is a target of effective CD8 + T cell antiviral responses. Cell Rep 2021; 35:109103. [PMID: 33979627 DOI: 10.1016/j.celrep.2021.109103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/20/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022] Open
Abstract
Persistence of HIV through integration into host DNA in CD4+ T cells presents a major barrier to virus eradication. Viral integration may be curtailed when CD8+ T cells are triggered to kill infected CD4+ T cells through recognition of histocompatibility leukocyte antigen (HLA) class I-bound peptides derived from incoming virions. However, this has been reported only in individuals with "beneficial" HLA alleles that are associated with superior HIV control. Through interrogation of the pre-integration immunopeptidome, we obtain proof of early presentation of a virion-derived HLA-A∗02:01-restricted epitope, FLGKIWPSH (FH9), located in Gag Spacer Peptide 2 (SP2). FH9-specific CD8+ T cell responses are detectable in individuals with primary HIV infection and eliminate HIV-infected CD4+ T cells prior to virus production in vitro. Our data show that non-beneficial HLA class I alleles can elicit an effective antiviral response through early presentation of HIV virion-derived epitopes and also demonstrate the importance of SP2 as an immune target.
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Affiliation(s)
- Hongbing Yang
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; Research In Viral Eradication of Reservoirs (RIVER) trial study group.
| | - Anuska Llano
- Irsicaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Samandhy Cedeño
- Irsicaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Annette von Delft
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Angelica Corcuera
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Andrew Knox
- Immunocore Ltd, Milton, Abingdon OX14 4RY, UK
| | | | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; Research In Viral Eradication of Reservoirs (RIVER) trial study group
| | - Wolfgang Stöhr
- Medical Research Council Clinical Trials Unit, University College London, London WC1V 6LJ, UK; Research In Viral Eradication of Reservoirs (RIVER) trial study group
| | - Sarah Fidler
- Department of Infectious Disease, Imperial College London, National Institute for Health Research Imperial Biomedical Research Centre, London W2 1NY, UK; Research In Viral Eradication of Reservoirs (RIVER) trial study group
| | - Beatriz Mothe
- Irsicaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain; Fundació Lluita contra la Sida, Infectious Disease Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport QLD 4215, Australia
| | - Christian Brander
- Irsicaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain; Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford OX4 2PG, UK; Immunocore Ltd, Milton, Abingdon OX14 4RY, UK; Research In Viral Eradication of Reservoirs (RIVER) trial study group.
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25
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Cohn LB, Chomont N, Deeks SG. The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies. Cell Host Microbe 2020; 27:519-530. [PMID: 32272077 DOI: 10.1016/j.chom.2020.03.014] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Antiretroviral therapy (ART) inhibits HIV replication but is not curative. During ART, the integrated HIV genome persists indefinitely within CD4+ T cells and perhaps other cells. Here, we describe the mechanisms thought to contribute to its persistence during treatment and highlight findings from numerous recent studies describing the importance of cell proliferation in that process. Continued progress elucidating the biology will enhance our ability to develop effective curative interventions.
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Affiliation(s)
- Lillian B Cohn
- Chan Zuckerberg Biohub, San Francisco, CA; Department of Medicine, University of California, San Francisco, CA
| | - Nicolas Chomont
- Centre de recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA.
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26
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Kaufman J. From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles. Front Immunol 2020; 11:601089. [PMID: 33381122 PMCID: PMC7767893 DOI: 10.3389/fimmu.2020.601089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
In humans, killer immunoglobulin-like receptors (KIRs), expressed on natural killer (NK) and thymus-derived (T) cells, and their ligands, primarily the classical class I molecules of the major histocompatibility complex (MHC) expressed on nearly all cells, are both polymorphic. The variation of this receptor-ligand interaction, based on which alleles have been inherited, is known to play crucial roles in resistance to infectious disease, autoimmunity, and reproduction in humans. However, not all the variation in response is inherited, since KIR binding can be affected by a portion of the peptide bound to the class I molecules, with the particular peptide presented affecting the NK response. The extent to which the large multigene family of chicken immunoglobulin-like receptors (ChIRs) is involved in functions similar to KIRs is suspected but not proven. However, much is understood about the two MHC-I molecules encoded in the chicken MHC. The BF2 molecule is expressed at a high level and is thought to be the predominant ligand of cytotoxic T lymphocytes (CTLs), while the BF1 molecule is expressed at a much lower level if at all and is thought to be primarily a ligand for NK cells. Recently, a hierarchy of BF2 alleles with a suite of correlated properties has been defined, from those expressed at a high level on the cell surface but with a narrow range of bound peptides to those expressed at a lower level on the cell surface but with a very wide repertoire of bound peptides. Interestingly, there is a similar hierarchy for human class I alleles, although the hierarchy is not as wide. It is a question whether KIRs and ChIRs recognize class I molecules with bound peptide in a similar way, and whether fastidious to promiscuous hierarchy of class I molecules affect both T and NK cell function. Such effects might be different from those predicted by the similarities of peptide-binding based on peptide motifs, as enshrined in the idea of supertypes. Since the size of peptide repertoire can be very different for alleles with similar peptide motifs from the same supertype, the relative importance of these two properties may be testable.
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Affiliation(s)
- Jim Kaufman
- School of Biological Sciences, Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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27
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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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28
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Romero-López JP, Carnalla-Cortés M, Pacheco-Olvera DL, Ocampo-Godínez JM, Oliva-Ramírez J, Moreno-Manjón J, Bernal-Alferes B, López-Olmedo N, García-Latorre E, Domínguez-López ML, Reyes-Sandoval A, Jiménez-Zamudio L. A bioinformatic prediction of antigen presentation from SARS-CoV-2 spike protein revealed a theoretical correlation of HLA-DRB1*01 with COVID-19 fatality in Mexican population: An ecological approach. J Med Virol 2020; 93:2029-2038. [PMID: 32986250 PMCID: PMC7537233 DOI: 10.1002/jmv.26561] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/31/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022]
Abstract
SARS‐CoV‐2 infection is causing a pandemic disease that is reflected in challenging public health problems worldwide. Human leukocyte antigen (HLA)‐based epitope prediction and its association with disease outcomes provide an important base for treatment design. A bioinformatic prediction of T cell epitopes and their restricted HLA Class I and II alleles was performed to obtain immunogenic epitopes and HLA alleles from the spike protein of the severe acute respiratory syndrome coronavirus 2 virus. Also, a correlation with the predicted fatality rate of hospitalized patients in 28 states of Mexico was done. Here, we describe a set of 10 highly immunogenic epitopes, together with different HLA alleles that can efficiently present these epitopes to T cells. Most of these epitopes are located within the S1 subunit of the spike protein, suggesting that this area is highly immunogenic. A statistical negative correlation was found between the frequency of HLA‐DRB1*01 and the fatality rate in hospitalized patients in Mexico. First HLA association study for COVID‐19 in Mexico An epitope prediction for HLA Class I and II provided a list of highly immunogenic epitopes from the S protein of SARS‐CoV2 with potential use for vaccine development. A multi‐level approach revealed a correlation of HLA‐DRB1*01 frequency with fatality in Mexican hospitalized patients at ecological level.
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Affiliation(s)
- José Pablo Romero-López
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, UNAM, Avenida de los Barrios 1, Tlalnepantla de Baz, Estado de México, Mexico.,Laboratorio de Inmunoquímica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico
| | - Martha Carnalla-Cortés
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Diana L Pacheco-Olvera
- Laboratorio de Inmunoquímica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico.,Unidad Médica de Investigación en Inmunoquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Juan Moisés Ocampo-Godínez
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, UNAM, Avenida de los Barrios 1, Tlalnepantla de Baz, Estado de México, Mexico.,Laboratorio de Inmunoquímica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico.,Laboratorio de Ingeniería de Tejidos, Posgrado de la Facultad de Odontología, UNAM, Mexico City, Mexico
| | | | - Julia Moreno-Manjón
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, UNAM, Mexico City, Mexico.,Laboratorio de Bacteriología Médica, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico
| | - Brian Bernal-Alferes
- Laboratorio de Inmunoquímica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico.,Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Nancy López-Olmedo
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Ethel García-Latorre
- Laboratorio de Inmunoquímica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico
| | - María Lilia Domínguez-López
- Laboratorio de Inmunoquímica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala SN, Mexico City, Mexico
| | - Arturo Reyes-Sandoval
- Nuffield Department of Medicine, The Jenner Institute, The Henry Welcome Building for Molecular Physiology, University of Oxford, Oxford, UK
| | - Luis Jiménez-Zamudio
- Laboratorio de Inmunología Clínica 1, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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29
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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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30
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Nakamura-Hoshi M, Takahara Y, Matsuoka S, Ishii H, Seki S, Nomura T, Yamamoto H, Sakawaki H, Miura T, Tokusumi T, Shu T, Matano T. Therapeutic vaccine-mediated Gag-specific CD8 + T-cell induction under anti-retroviral therapy augments anti-virus efficacy of CD8 + cells in simian immunodeficiency virus-infected macaques. Sci Rep 2020; 10:11394. [PMID: 32647227 PMCID: PMC7347614 DOI: 10.1038/s41598-020-68267-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Anti-retroviral therapy (ART) can inhibit HIV proliferation but not achieve virus eradication from HIV-infected individuals. Under ART-based HIV control, virus-specific CD8+ T-cell responses are often reduced. Here, we investigated the impact of therapeutic vaccination inducing virus-specific CD8+ T-cell responses under ART on viral control in a macaque AIDS model. Twelve rhesus macaques received ART from week 12 to 32 after simian immunodeficiency virus (SIV) infection. Six of them were vaccinated with Sendai virus vectors expressing SIV Gag and Vif at weeks 26 and 32, and Gag/Vif-specific CD8+ T-cell responses were enhanced and became predominant. All macaques controlled viremia during ART but showed viremia rebound after ART cessation. Analysis of in vitro CD8+ cell ability to suppress replication of autologous lymphocytes-derived SIVs found augmentation of anti-SIV efficacy of CD8+ cells after vaccination. In the vaccinated animals, the anti-SIV efficacy of CD8+ cells at week 34 was correlated positively with Gag-specific CD8+ T-cell frequencies and inversely with rebound viral loads at week 34. These results indicate that Gag-specific CD8+ T-cell induction by therapeutic vaccination can augment anti-virus efficacy of CD8+ cells, which may be insufficient for functional cure but contribute to more stable viral control under ART.
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Affiliation(s)
- Midori Nakamura-Hoshi
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yusuke Takahara
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hiroshi Ishii
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Sayuri Seki
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Takushi Nomura
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hiroyuki Yamamoto
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hiromi Sakawaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tomoyuki Miura
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | | | - Tsugumine Shu
- ID Pharma Co., Ltd., 6 Ohkubo, Tsukuba, Ibaraki, 300-2611, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan. .,The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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31
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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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32
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Impact of HLA-B*52:01-Driven Escape Mutations on Viral Replicative Capacity. J Virol 2020; 94:JVI.02025-19. [PMID: 32321820 DOI: 10.1128/jvi.02025-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
HLA-B*52:01 is strongly associated with protection against HIV disease progression. However, the mechanisms of HLA-B*52:01-mediated immune control have not been well studied. We here describe a cohort with a majority of HIV C-clade-infected individuals from Delhi, India, where HLA-B*52:01 is highly prevalent (phenotypic frequency, 22.5%). Consistent with studies of other cohorts, expression of HLA-B*52:01 was associated with high absolute CD4 counts and therefore a lack of HIV disease progression. We here examined the impact of HLA-B*52:01-associated viral polymorphisms within the immunodominant C clade Gag epitope RMTSPVSI (here, RI8; Gag residues 275 to 282) on viral replicative capacity (VRC) since HLA-mediated reduction in VRC is a central mechanism implicated in HLA-associated control of HIV. We observed in HLA-B*52:01-positive individuals a higher frequency of V280T, V280S, and V280A variants within RI8 (P = 0.0001). Each of these variants reduced viral replicative capacity in C clade viruses, particularly the V280A variant (P < 0.0001 in both the C clade consensus and in the Indian study cohort consensus p24 Gag backbone), which was also associated with significantly higher absolute CD4 counts in the donors (median, 941.5 cells/mm3; P = 0.004). A second HLA-B*52:01-associated mutation, K286R, flanking HLA-B*52:01-RI8, was also analyzed. Although selected in HLA-B*52:01-positive subjects often in combination with the V280X variants, this mutation did not act as a compensatory mutant but, indeed, further reduced VRC. These data are therefore consistent with previous work showing that HLA-B molecules that are associated with immune control of HIV principally target conserved epitopes within the capsid protein, escape from which results in a significant reduction in VRC.IMPORTANCE Few studies have addressed the mechanisms of immune control in HIV-infected subjects in India, where an estimated 2.7 million people are living with HIV. We focus here on a study cohort in Delhi on one of the most prevalent HLA-B alleles, HLA-B*52:01, present in 22.5% of infected individuals. HLA-B*52:01 has consistently been shown in other cohorts to be associated with protection against HIV disease progression, but studies have been limited by the low prevalence of this allele in North America and Europe. Among the C-clade-infected individuals, we show that HLA-B*52:01 is the most protective of all the HLA-B alleles expressed in the Indian cohort and is associated with the highest absolute CD4 counts. Further, we show that the mechanism by which HLA-B*52:01 mediates immune protection is, at least in part, related to the inability of HIV to evade the HLA-B*52:01-restricted p24 Gag-specific CD8+ T-cell response without incurring a significant loss to viral replicative capacity.
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33
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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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34
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Chan HY, Zhang J, Garliss CC, Kwaa AK, Blankson JN, Smith KN. A T Cell Receptor Sequencing-Based Assay Identifies Cross-Reactive Recall CD8 + T Cell Clonotypes Against Autologous HIV-1 Epitope Variants. Front Immunol 2020; 11:591. [PMID: 32318072 PMCID: PMC7154155 DOI: 10.3389/fimmu.2020.00591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/13/2020] [Indexed: 12/31/2022] Open
Abstract
HIV-1 positive elite controllers or suppressors control viral replication without antiretroviral therapy, likely via CTL-mediated elimination of infected cells, and therefore represent a model of an HIV-1 functional cure. Efforts to cure HIV-1 accordingly rely on the existence or generation of antigen-specific cytotoxic T lymphocytes (CTL) to eradicate infected cells upon reversal of latency. Detecting and quantifying these HIV-1-specific CTL responses will be crucial for developing vaccine and T cell-based immunotherapies. A recently developed assay, called MANAFEST, uses T cell receptor (TCR) Vβ sequencing of peptide-stimulated cultures followed by a bioinformatic pipeline to identify neoantigen-specific T cells in cancer patients. This assay is more sensitive than conventional immune assays and therefore has the possibility to identify HIV-1 antigenic targets that have not been previously explored for vaccine or T cell immunotherapeutic strategies. Here we show that a modified version of the MANAFEST assay, called ViraFEST, can identify memory CD8+ T cell responses against autologous HIV-1 Gag and Nef epitope variants in an elite suppressor. Nine TCR Vβ clonotypes were identified and 6 of these were cross-reactive for autologous variants or known escape variants. Our findings are a proof of principle that the ViraFEST assay can be used to detect and monitor these responses for downstream use in immunotherapeutic treatment approaches.
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Affiliation(s)
- Hok Yee Chan
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Jiajia Zhang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Caroline C Garliss
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Abena K Kwaa
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Kellie N Smith
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
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35
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Debebe BJ, Boelen L, Lee JC, Thio CL, Astemborski J, Kirk G, Khakoo SI, Donfield SM, Goedert JJ, Asquith B. Identifying the immune interactions underlying HLA class I disease associations. eLife 2020; 9:54558. [PMID: 32238263 PMCID: PMC7253178 DOI: 10.7554/elife.54558] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/06/2020] [Indexed: 12/11/2022] Open
Abstract
Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8+ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8+ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.
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Affiliation(s)
- Bisrat J Debebe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - James C Lee
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | -
- Johns Hopkins University, Baltimore, United States.,Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chloe L Thio
- Johns Hopkins University, Baltimore, United States
| | | | - Gregory Kirk
- Johns Hopkins University, Baltimore, United States
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, United States
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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36
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Wang C, Liu D, Zuo T, Hora B, Cai F, Ding H, Kappes J, Ochsenbauer C, Kong W, Yu X, Bhattacharya T, Perelson AS, Gao F. Accumulated mutations by 6 months of infection collectively render transmitted/founder HIV-1 significantly less fit. J Infect 2019; 80:210-218. [PMID: 31812703 DOI: 10.1016/j.jinf.2019.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/22/2019] [Accepted: 12/01/2019] [Indexed: 01/16/2023]
Abstract
OBJECTIVE Viral fitness plays an important role in HIV-1 evolution, transmission and pathogenesis. However, how mutations accumulated during early infection affect viral fitness has not been well studied. METHODS Paired infectious molecular clones (IMCs) for transmitted/founder (T/F) and 6-month (6-mo) viruses post infection were generated from 10 infected individuals to investigate the impact of accumulated mutations on viral fitness by comparing 6-mo viruses to their cognate T/F viruses. RESULTS All ten 6-mo viruses were less fit than their cognate T/F viruses. Moreover, the fitness losses of the 6-mo viruses correlated with the decrease in viral loads from the peak of viremia. CONCLUSION These results show that the mutations accumulated during half a year post infection collectively reduce viral fitness and thereby contribute to lowering viral loads.
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Affiliation(s)
- Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Donglai Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Division of the Second in Vitro Diagnostic, National Institute for Food and Drug Control, Beijing 100050, China
| | - Tao Zuo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Bhavna Hora
- Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Fangping Cai
- Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - John Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Alan S Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
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Abstract
The accessory protein Nef of human immunodeficiency virus (HIV) is a primary determinant of viral pathogenesis. Nef is abundantly expressed during infection and reroutes a variety of cell surface proteins to disrupt host immunity and promote the viral replication cycle. Nef counteracts host defenses by sequestering and/or degrading its targets via the endocytic and secretory pathways. Nef does this by physically engaging a number of host trafficking proteins. Substantial progress has been achieved in identifying the targets of Nef, and a structural and mechanistic understanding of Nef's ability to command the protein trafficking machinery has recently started to coalesce. Comparative analysis of HIV and simian immunodeficiency virus (SIV) Nef proteins in the context of recent structural advances sheds further light on both viral evolution and the mechanisms whereby trafficking is hijacked. This review describes how advances in cell and structural biology are uncovering in growing detail how Nef subverts the host immune system, facilitates virus release, and enhances viral infectivity.
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López-Galíndez C. HIV long-term non-progressors elite controllers: an interplay between host, immune and viral factors. Future Virol 2019. [DOI: 10.2217/fvl-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There is a rare group of HIV-1-infected individuals who show permanent control of clinical progression for over 10 years, maintain CD4+ cells >500 μl and have undetectable viral loads; they are designated long-term non-progressors elite controllers (LTNPs ECs). Multiple studies have demonstrated the necessary contribution of at least two of host, immune and viral factors to the LTNP phenotype. This group of individuals is not homogenous because of the different involvement of these factors. We will review the role of each of these and their combinations to the LTNP EC phenotype. LTNP EC individuals offer an opportunity for the investigation into the mechanisms for the spontaneous control of HIV infection.
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Affiliation(s)
- Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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High polymorphism rates in well-known T cell epitopes restricted by protective HLA alleles during HIV infection are associated with rapid disease progression in early-infected MSM in China. Med Microbiol Immunol 2019; 208:239-251. [PMID: 30848362 DOI: 10.1007/s00430-019-00585-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/21/2019] [Indexed: 11/26/2022]
Abstract
T cell epitopes restricted by several protective HLA alleles, such as B*57, B*5801, B*27, B*51 and B*13, have been very well defined over the past two decades. We investigated 32 well-known T cell epitopes restricted by protective HLA molecules among 54 Chinese men who have sex with men (MSM) at the early stage of HIV-1 infection. Subjects in our cohort carrying protective HLA types did not exhibit slow CD4 T cell count decline (P = 0.489) or low viral load set points (P = 0.500). Variations occurred in 96.88% (31/32) of the known wild-type epitopes (rate 1.85-100%), and the variation rates of the strains of two CRF01_AE lineages were significantly higher than those of non-CRF01_AE strains (76.82% vs. 48.96%, P = 0.004; 71.27% vs. 8.96%, P = 0.025). Subjects infected with CRF01_AE exhibited relatively rapid disease progression (P = 0.035). Therefore, the lack of wild-type protective T cell epitopes restricted by classic protective HLA alleles in CRF01_AE HIV-1 strains may be one of the reasons why rapid disease progression is observed in Chinese MSM with HIV-1 infection.
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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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Avettand‐Fenoel V, Bayan T, Gardiennet E, Boufassa F, Lopez P, Lecuroux C, Noel N, Trémeaux P, Monceaux V, Autran B, Meyer L, Saez‐Cirion A, Lambotte O, Rouzioux C. Dynamics in HIV-DNA levels over time in HIV controllers. J Int AIDS Soc 2019; 22:e25221. [PMID: 30629340 PMCID: PMC6327944 DOI: 10.1002/jia2.25221] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/03/2018] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION HIV controllers (HIC) maintain viraemia at low levels without antiretroviral treatment and have small HIV reservoirs. Nevertheless, they are heterogeneous regarding their risk of infection progression. The study of reservoirs can help elucidate this control. This study aimed to explore the factors implicated in the pathogenesis of HIV infection that are potentially associated with HIV reservoirs and their dynamics in HIC. METHODS Individuals living with HIV included in the ANRS-CODEX cohort with at least two HIV-DNA measurements between 2009 and 2016 were selected. The total HIV-DNA levels had been quantified prospectively from blood samples. Mixed-effect linear models estimated the HIV-DNA dynamics over time. RESULTS The median (interquartile range (IQR)) HIV-DNA level was 1.5 (1.3 to 1.9) log copies/million peripheral blood mononuclear cells at inclusion (n = 202 individuals). These low levels showed heterogeneity among HIC. Lower levels were then associated with the protective HLA-B*27/B*57 alleles and/or lower HIV-RNA level at inclusion, negative hepatitis C virus serology, lower HIV-suppressive capacity of specific CD8 T cells and lower levels of immune activation and inflammation. Interestingly, mathematical modelling of the dynamics of HIV-DNA over time (840 measurements) showed that the number of infected cells decreased in 46% of HIC (follow-up: 47.6 months) and increased in 54% of HIC. A multivariate analysis indicated that HLA-B*27/B*57 alleles, a low level of HIV-RNA and a low level of HIV-DNA at inclusion were markers independently associated with this decrease. CONCLUSIONS These results offer new insights into the mechanisms of long-term control in HIC. In half of HIC, the decrease in HIV-DNA level could be linked to tighter viral control and progressive loss of infected cells. These findings allow the identification of HIC with a low risk of progression who may not need treatment.
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Affiliation(s)
- Véronique Avettand‐Fenoel
- Université Paris DescartesSorbonne Paris CitéParisFrance
- AP‐HPLaboratoire de VirologieCHU Necker‐Enfants MaladesParisFrance
| | - Tatiana Bayan
- INSERM CESP U1018Université Paris SudLe Kremlin BicêtreFrance
| | | | | | - Pauline Lopez
- Université Paris DescartesSorbonne Paris CitéParisFrance
| | - Camille Lecuroux
- INSERM UMR 1184Immunologie des Maladies Virales et Autoimmunes (IMVA)Université Paris SudLe Kremlin BicêtreFrance
- CEADSV/iMETIDivision of Immuno‐VirologyIDMITFontenay aux RosesFrance
| | - Nicolas Noel
- INSERM UMR 1184Immunologie des Maladies Virales et Autoimmunes (IMVA)Université Paris SudLe Kremlin BicêtreFrance
- CEADSV/iMETIDivision of Immuno‐VirologyIDMITFontenay aux RosesFrance
| | - Pauline Trémeaux
- Université Paris DescartesSorbonne Paris CitéParisFrance
- AP‐HPLaboratoire de VirologieCHU CochinParisFrance
| | - Valérie Monceaux
- Institut PasteurUnité HIV inflammation et persistanceParisFrance
| | - Brigitte Autran
- Cellular Immunology LaboratoryUniversité Pierre and Marie CurieINSERMUMRS 945ParisFrance
| | - Laurence Meyer
- INSERM CESP U1018Université Paris SudLe Kremlin BicêtreFrance
| | | | - Olivier Lambotte
- INSERM UMR 1184Immunologie des Maladies Virales et Autoimmunes (IMVA)Université Paris SudLe Kremlin BicêtreFrance
- CEADSV/iMETIDivision of Immuno‐VirologyIDMITFontenay aux RosesFrance
- AP‐HP, CHU BicêtreService de Médecine Interne et Immunologie CliniqueLe Kremlin‐BicêtreFrance
- Université Paris SudUMR 1184Le Kremlin‐BicêtreFrance
| | - Christine Rouzioux
- Université Paris DescartesSorbonne Paris CitéParisFrance
- AP‐HPLaboratoire de VirologieCHU Necker‐Enfants MaladesParisFrance
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42
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Broad Recognition of Circulating HIV-1 by HIV-1-Specific Cytotoxic T-Lymphocytes with Strong Ability to Suppress HIV-1 Replication. J Virol 2018; 93:JVI.01480-18. [PMID: 30333175 DOI: 10.1128/jvi.01480-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
HIV-1-specific cytotoxic T-lymphocytes (CTLs) with strong abilities to suppress HIV-1 replication and recognize most circulating HIV-1 strains are candidates for effector T cells for cure treatment and prophylactic AIDS vaccine. Previous studies demonstrated that the existence of CTLs specific for 11 epitopes was significantly associated with good clinical outcomes in Japan, although CTLs specific for one of these epitopes select for escape mutations. However, it remains unknown whether the CTLs specific for the remaining 10 epitopes suppress HIV-1 replication in vitro and recognize circulating HIV-1. Here, we investigated the abilities of these CTLs to suppress HIV-1 replication and to recognize variants in circulating HIV-1. CTL clones specific for 10 epitopes had strong abilities to suppress HIV-1 replication in vitro The ex vivo and in vitro analyses of T-cell responses to variant epitope peptides showed that the T cells specific for 10 epitopes recognized mutant peptides which are detected in 84.1% to 98.8% of the circulating HIV-1 strains found in HIV-1-infected Japanese individuals. In addition, the T cells specific for 5 epitopes well recognized target cells infected with 7 mutant viruses that had been detected in >5% of tested individuals. Taken together, these results suggest that CTLs specific for the 10 epitopes effectively suppress HIV-1 replication and broadly recognize the circulating HIV-1 strains in the HIV-1-infected individuals. This study suggests the use of these T cells in clinical trials.IMPORTANCE In recent T-cell AIDS vaccine trials, the vaccines did not prevent HIV-1 infection, although HIV-1-specific T cells were induced in the vaccinated individuals, suggesting that the T cells have a weak ability to suppress HIV-1 replication and fail to recognize circulating HIV-1. We previously demonstrated that the T-cell responses to 10 epitopes were significantly associated with good clinical outcome. However, there is no direct evidence that these T cells have strong abilities to suppress HIV-1 replication and recognize circulating HIV-1. Here, we demonstrated that the T cells specific for the 10 epitopes had strong abilities to suppress HIV-1 replication in vitro Moreover, the T cells cross-recognized most of the circulating HIV-1 in HIV-1-infected individuals. This study suggests the use of T cells specific for these 10 epitopes in clinical trials of T-cell vaccines as a cure treatment.
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Takahashi N, Matsuoka S, Thi Minh TT, Ba HP, Naruse TK, Kimura A, Shiino T, Kawana-Tachikawa A, Ishikawa K, Matano T, Nguyen Thi LA. Human leukocyte antigen-associated gag and nef polymorphisms in HIV-1 subtype A/E-infected individuals in Vietnam. Microbes Infect 2018; 21:113-118. [PMID: 30385305 DOI: 10.1016/j.micinf.2018.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
Abstract
Numbers of HLA-associated polymorphisms have been reported on HIV-1 subtypes B and C, but few on other subtypes. Here, we analyzed HLA-associated gag and nef polymorphisms in HIV-1 subtype A/E prevalent in Vietnam. We determined HLA-A, B and C genotypes in 179 HIV-1-infected Vietnamese by next generation sequencing and analyzed proviral genome sequences in 144 of them, showing that 142 of the 144 were subtype A/E. Analysis revealed HLA-associated subtype A/E gag and nef polymorphisms at nineteen residues including those newly determined. Accumulation of these data would contribute to our understanding of HIV-1 subtype A/E and host immune interaction.
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Affiliation(s)
- Naofumi Takahashi
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Saori Matsuoka
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tam Tran Thi Minh
- Center of BioMedical Research, National Institute of Hygiene and Epidemiology, No.1 Yersin Street, Hanoi, Viet Nam
| | - Hien Pham Ba
- Dong Da General Hospital, No. 192, Nguyen Luong Bang Street, Hanoi, Viet Nam
| | - Taeko K Naruse
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akinori Kimura
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Teiichiro Shiino
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Koichi Ishikawa
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Lan Anh Nguyen Thi
- Center of BioMedical Research, National Institute of Hygiene and Epidemiology, No.1 Yersin Street, Hanoi, Viet Nam.
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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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Clutton GT, Jones RB. Diverse Impacts of HIV Latency-Reversing Agents on CD8+ T-Cell Function: Implications for HIV Cure. Front Immunol 2018; 9:1452. [PMID: 29988382 PMCID: PMC6023971 DOI: 10.3389/fimmu.2018.01452] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral therapy regimens durably suppress HIV replication, but do not cure infection. This is partially attributable to the persistence of long-lived pools of resting CD4+ T-cells harboring latent replication-competent virus. Substantial clinical and pre-clinical research is currently being directed at purging this viral reservoir by combining pharmacological latency reversal with immune effectors, such as HIV-specific CD8+ T-cells, capable of eliminating reactivated targets-the so-called "shock-and-kill" approach. However, several studies indicate that the latency-reversing agents (LRAs) may affect CD8+ T-cell function. The current review aims to frame recent advances, and ongoing challenges, in implementing "shock-and-kill" strategies from the perspective of effectively harnessing CD8+ T-cells. We review and contextualize findings indicating that LRAs often have unintended impacts on CD8+ T-cell function, both detrimental and beneficial. We identify and attempt to bridge the gap between viral reactivation, as measured by the detection of RNA or protein, and bona fide presentation of viral antigens to CD8+ T-cells. Finally, we highlight factors on the effector (CD8+) and target (CD4+) cell sides that contribute to whether or not infected-cell recognition results in killing/elimination. These perspectives may contribute to an integrated view of "shock-and-kill," with implications for therapeutic development.
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Affiliation(s)
- Genevieve Tyndale Clutton
- Department of Microbiology and Immunology, UNC Chapel Hill School of Medicine, Chapel Hill, NC, United States
| | - R. Brad Jones
- Department of Microbiology Immunology and Tropical Medicine, The George Washington University, Washington, DC, United States
- Infectious Disease Division, Weill Cornell Medical College, New York, NY, United States
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Control of HIV-1 Pathogenesis in Viremic Nonprogressors Is Independent of Gag-Specific Cytotoxic T Lymphocyte Responses. J Virol 2018; 92:JVI.00346-18. [PMID: 29593044 PMCID: PMC5974496 DOI: 10.1128/jvi.00346-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/21/2018] [Indexed: 01/01/2023] Open
Abstract
Viremic nonprogressors (VNPs) constitute a very scarce group of untreated human immunodeficiency virus type 1 (HIV-1)-infected individuals who maintain stable CD4+ T cell counts despite high levels of HIV-1 replication. The specific factors associated with this atypical control of the HIV infection have been poorly described. Since specific T cell responses seem to be one of the main causes of HIV-1 control in elite controllers, we studied whether HIV-1 Gag-specific cytotoxic T lymphocyte (CTL) responses could also modulate disease control in VNPs. We characterized the immune responses from four VNPs compared to those of five standard progressors (SPs) during the first years of HIV-1 infection. We observed no differences in the breadth and frequency of Gag-specific cellular responses. Furthermore, we obtained 217 HIV-1Gag clonal sequences in which the viral variability of Gag increased over 3 years of infection for synonymous and nonsynonymous mutations in both VNPs and SPs. VNPs evolution rates in gag were comparable to SPs. This observation is in line with a similar accumulation of CTL putative escape mutations in Gag epitopes targeted by CTL responses. Altogether, the absence of viral pathogenesis in VNP individuals seems to be independent of HIV-Gag-specific CTL responses. This novel information guides to the study of alternative mechanism of HIV-1 pathogenesis control. IMPORTANCE Control of HIV infection has been widely studied in elite controllers or long-term nonprogressor models. However, there is a less-known group of individuals, termed viremic nonprogressors (VNPs), who maintain stable CD4+ T cell counts despite high plasma viremia. The mechanisms involved in this remarkable control of HIV-1 pathogenesis clearly have implications for the development of new drugs and vaccines. We show here for the first time that VNPs have immune responses and HIV-gag evolution similar to those of standard progressors. Remarkably, we demonstrate that the mechanism of pathogenesis control in these individuals differs from some elite controllers that are reported to have improved immune control. This is noteworthy since it opens the door to new, as-yet-unknown mechanisms for HIV control. Our novel results advance the understanding of mechanisms involved in viremic nonprogression and suggest that there are alternative mechanisms to the adaptive immune responses for an effective control of viral pathogenesis.
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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 PMCID: PMC5919796 DOI: 10.1172/jci98463] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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48
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Ramarathinam SH, Gras S, Alcantara S, Yeung AWS, Mifsud NA, Sonza S, Illing PT, Glaros EN, Center RJ, Thomas SR, Kent SJ, Ternette N, Purcell DFJ, Rossjohn J, Purcell AW. Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics. Proteomics 2018; 18:e1700253. [PMID: 29437277 DOI: 10.1002/pmic.201700253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/29/2018] [Indexed: 12/20/2022]
Abstract
The recognition of pathogen-derived peptides by T lymphocytes is the cornerstone of adaptive immunity, whereby intracellular antigens are degraded in the cytosol and short peptides assemble with class I human leukocyte antigen (HLA) molecules in the ER. These peptide-HLA complexes egress to the cell surface and are scrutinized by cytotoxic CD8+ T-cells leading to the eradication of the infected cell. Here, naturally presented HLA-B*57:01 bound peptides derived from the envelope protein of the human immunodeficiency virus (HIVenv) are identified. HIVenv peptides are present at a very small percentage of the overall HLA-B*57:01 peptidome (<0.1%) and both native and posttranslationally modified forms of two distinct HIV peptides are identified. Notably, a peptide bearing a natively encoded C-terminal tryptophan residue is also present in a modified form containing a kynurenine residue. Kynurenine is a major product of tryptophan catabolism and is abundant during inflammation and infection. Binding of these peptides at a molecular level and their immunogenicity in preliminary functional studies are examined. Modest immune responses are observed to the modified HIVenv peptide, highlighting a potential role for kynurenine-modified peptides in the immune response to HIV and other viral infections.
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Affiliation(s)
- Sri H Ramarathinam
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Stephanie Gras
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Amanda W S Yeung
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Secondo Sonza
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Patricia T Illing
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Elias N Glaros
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Robert J Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.,Burnet Institute, Melbourne, Australia
| | - Shane R Thomas
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.,Melbourne Sexual Health Centre, Central Clinical School, Monash University, Melbourne, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Australia
| | - Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, UK
| | - Damian F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Anthony W Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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49
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High-Resolution Sequencing of Viral Populations during Early Simian Immunodeficiency Virus Infection Reveals Evolutionary Strategies for Rapid Escape from Emerging Env-Specific Antibody Responses. J Virol 2018; 92:JVI.01574-17. [PMID: 29343575 DOI: 10.1128/jvi.01574-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/08/2018] [Indexed: 01/01/2023] Open
Abstract
Primate lentiviruses, including the human and simian immunodeficiency viruses (HIV and SIV), produce infections marked by persistent, ongoing viral replication. This occurs despite the presence of virus-specific adaptive immune responses, including antibodies targeting the viral envelope glycoprotein (Env), and evolution of antibody-escape variants is a well-documented feature of lentiviral infection. Here, we examined the evolutionary dynamics of the SIV env gene during early infection (≤29 weeks postinfection) in a cohort of four SIVmac251-infected rhesus macaques. We tracked env evolution during acute and early infection using frequent sampling and ultradeep sequencing of viral populations, capturing a transmission bottleneck and the subsequent reestablishment of Env diversity. A majority of changes in the gp120 subunit mapped to two short clusters, one in the first variable region (V1) and one in V4, while most changes in the gp41 subunit appeared in the cytoplasmic domain. Variation in V1 was dominated by short duplications and deletions of repetitive sequence, while variation in V4 was marked by short in-frame deletions and closely overlapping substitutions. The most common substitutions in both patches did not alter viral replicative fitness when tested using a highly sensitive, deep-sequencing-based competition assay. Our results, together with the observation that very similar or identical patterns of sequence evolution also occur in different macaque species infected with related but divergent strains of SIV, suggest that resistance to early, strain-specific anti-Env antibodies is the result of temporally and mutationally predictable pathways of escape that occur during the early stages of infection.IMPORTANCE The envelope glycoprotein (Env) of primate lentiviruses mediates entry by binding to host cell receptors followed by fusion of the viral membrane with the cell membrane. The exposure of Env complexes on the surface of the virion results in targeting by antibodies, leading to selection for virus escape mutations. We used the SIV/rhesus macaque model to track in vivo evolution of variation in Env during acute/early infection in animals with and without antibody responses to Env, uncovering remarkable variation in animals with antibody responses within weeks of infection. Using a deep-sequencing-based fitness assay, we found substitutions associated with antibody escape had little to no effect on inherent replicative capacity. The ability to readily propagate advantageous changes that incur little to no replicative fitness costs may be a mechanism to maintain continuous replication under constant immune selection, allowing the virus to persist for months to years in the infected host.
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50
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Freund NT, Wang H, Scharf L, Nogueira L, Horwitz JA, Bar-On Y, Golijanin J, Sievers SA, Sok D, Cai H, Cesar Lorenzi JC, Halper-Stromberg A, Toth I, Piechocka-Trocha A, Gristick HB, van Gils MJ, Sanders RW, Wang LX, Seaman MS, Burton DR, Gazumyan A, Walker BD, West AP, Bjorkman PJ, Nussenzweig MC. Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller. Sci Transl Med 2018; 9:9/373/eaal2144. [PMID: 28100831 DOI: 10.1126/scitranslmed.aal2144] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/14/2016] [Accepted: 12/08/2016] [Indexed: 12/13/2022]
Abstract
Some HIV-1-infected patients develop broad and potent HIV-1 neutralizing antibodies (bNAbs) that when passively transferred to mice or macaques can treat or prevent infection. However, bNAbs typically fail to neutralize coexisting autologous viruses due to antibody-mediated selection against sensitive viral strains. We describe an HIV-1 controller expressing HLA-B57*01 and HLA-B27*05 who maintained low viral loads for 30 years after infection and developed broad and potent serologic activity against HIV-1. Neutralization was attributed to three different bNAbs targeting nonoverlapping sites on the HIV-1 envelope trimer (Env). One of the three, BG18, an antibody directed against the glycan-V3 portion of Env, is the most potent member of this class reported to date and, as revealed by crystallography and electron microscopy, recognizes HIV-1 Env in a manner that is distinct from other bNAbs in this class. Single-genome sequencing of HIV-1 from serum samples obtained over a period of 9 years showed a diverse group of circulating viruses, 88.5% (31 of 35) of which remained sensitive to at least one of the temporally coincident autologous bNAbs and the individual's serum. Thus, bNAb-sensitive strains of HIV-1 coexist with potent neutralizing antibodies that target the virus and may contribute to control in this individual. When administered as a mix, the three bNAbs controlled viremia in HIV-1YU2-infected humanized mice. Our finding suggests that combinations of bNAbs may contribute to control of HIV-1 infection.
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Affiliation(s)
- Natalia T Freund
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Louise Scharf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Joshua A Horwitz
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Yotam Bar-On
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Stuart A Sievers
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, and International AIDS Vaccine Initiative Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hui Cai
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742, USA
| | | | | | - Ildiko Toth
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, and International AIDS Vaccine Initiative Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Rockefeller University, New York, NY 10065, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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