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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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San D, Lei J, Liu Y, Jing B, Ye X, Wei P, Paek C, Yang Y, Zhou J, Chen P, Wang H, Chen Y, Yin L. Structural basis of the TCR-pHLA complex provides insights into the unconventional recognition of CDR3β in TCR cross-reactivity and alloreactivity. CELL INSIGHT 2023; 2:100076. [PMID: 37192909 PMCID: PMC10120306 DOI: 10.1016/j.cellin.2022.100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/17/2022] [Accepted: 12/18/2022] [Indexed: 05/18/2023]
Abstract
Evidence shows that some class I human leucocyte antigen (HLA) alleles are related to durable HIV controls. The T18A TCR, which has the alloreactivity between HLA-B∗42:01 and HLA-B∗81:01 and the cross-reactivity with different antigen mutants, can sustain long-term HIV controls. Here the structural basis of the T18A TCR binding to the immunodominant HIV epitope TL9 (TPQDLNTML180-188) presented by HLA-B∗42:01 was determined and compared to T18A TCR binding to the TL9 presented by the allo-HLA-B∗81:01. For differences between HLA-B∗42:01 and HLA-B∗81:01, the CDR1α and CDR3α loops adopt a small rearrangement to accommodate them. For different conformations of the TL9 presented by different HLA alleles, not like the conventional recognition of CDR3s to interact with peptide antigens, CDR3β of the T18A TCR shifts to avoid the peptide antigen but intensively recognizes the HLA only, which is different with other conventional TCR structures. Featured sequence pairs of CDR3β and HLA might account for this and were additionally found in multiple other diseases indicating the popularity of the unconventional recognition pattern which would give insights into the control of diseases with epitope mutating such as HIV.
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Affiliation(s)
| | | | | | - Baowei Jing
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiang Ye
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Pengcheng Wei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chonil Paek
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yi Yang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jin Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Peng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Hongjian Wang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yongshun Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
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3
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Immunological Control of HIV-1 Disease Progression by Rare Protective HLA Allele. J Virol 2022; 96:e0124822. [DOI: 10.1128/jvi.01248-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HLA-B57 is a relatively rare allele around world and the strongest protective HLA allele in Caucasians and African black individuals infected with HIV-1. Previous studies suggested that the advantage of this allele in HIV-1 disease progression is due to a strong functional ability of HLA-B57-restricted Gag-specific T cells and lower fitness of mutant viruses selected by the T cells.
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4
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Adaptive Immune Responses, Immune Escape and Immune-Mediated Pathogenesis during HDV Infection. Viruses 2022; 14:v14020198. [PMID: 35215790 PMCID: PMC8880046 DOI: 10.3390/v14020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/13/2022] Open
Abstract
The hepatitis delta virus (HDV) is the smallest known human virus, yet it causes great harm to patients co-infected with hepatitis B virus (HBV). As a satellite virus of HBV, HDV requires the surface antigen of HBV (HBsAg) for sufficient viral packaging and spread. The special circumstance of co-infection, albeit only one partner depends on the other, raises many virological, immunological, and pathophysiological questions. In the last years, breakthroughs were made in understanding the adaptive immune response, in particular, virus-specific CD4+ and CD8+ T cells, in self-limited versus persistent HBV/HDV co-infection. Indeed, the mechanisms of CD8+ T cell failure in persistent HBV/HDV co-infection include viral escape and T cell exhaustion, and mimic those in other persistent human viral infections, such as hepatitis C virus (HCV), human immunodeficiency virus (HIV), and HBV mono-infection. However, compared to these larger viruses, the small HDV has perfectly adapted to evade recognition by CD8+ T cells restricted by common human leukocyte antigen (HLA) class I alleles. Furthermore, accelerated progression towards liver cirrhosis in persistent HBV/HDV co-infection was attributed to an increased immune-mediated pathology, either caused by innate pathways initiated by the interferon (IFN) system or triggered by misguided and dysfunctional T cells. These new insights into HDV-specific adaptive immunity will be discussed in this review and put into context with known well-described aspects in HBV, HCV, and HIV infections.
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Kaseke C, Park RJ, Singh NK, Koundakjian D, Bashirova A, Garcia Beltran WF, Takou Mbah OC, Ma J, Senjobe F, Urbach JM, Nathan A, Rossin EJ, Tano-Menka R, Khatri A, Piechocka-Trocha A, Waring MT, Birnbaum ME, Baker BM, Carrington M, Walker BD, Gaiha GD. HLA class-I-peptide stability mediates CD8 + T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Rep 2021; 36:109378. [PMID: 34260940 PMCID: PMC8293625 DOI: 10.1016/j.celrep.2021.109378] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/24/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
Defining factors that govern CD8+ T cell immunodominance is critical for the rational design of vaccines for viral pathogens. Here, we assess the contribution of human leukocyte antigen (HLA) class-I-peptide stability for 186 optimal HIV epitopes across 18 HLA alleles using transporter associated with antigen processing (TAP)-deficient mono-allelic HLA-expressing cell lines. We find that immunodominant HIV epitopes increase surface stabilization of HLA class-I molecules in comparison to subdominant epitopes. HLA class-I-peptide stability is also strongly correlated with overall immunodominance hierarchies, particularly for epitopes from high-abundance proteins (e.g., Gag). Moreover, HLA alleles associated with HIV protection are preferentially stabilized by epitopes derived from topologically important viral regions at a greater frequency than neutral and risk alleles. These findings indicate that relative stabilization of HLA class-I is a key factor for CD8+ T cell epitope immunodominance hierarchies, with implications for HIV control and the design of T-cell-based vaccines.
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Affiliation(s)
- Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ryan J Park
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Harvard Radiation Oncology Program, Boston, MA 02114, USA
| | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wilfredo F Garcia Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Jiaqi Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Virology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth J Rossin
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA 02114, USA; The Broad Institute, Cambridge, MA 02142, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Unit and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael E Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; The Broad Institute, Cambridge, MA 02142, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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6
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Mohamed YS, Borthwick NJ, Moyo N, Murakoshi H, Akahoshi T, Siliquini F, Hannoun Z, Crook A, Hayes P, Fast PE, Mutua G, Jaoko W, Silva-Arrieta S, Llano A, Brander C, Takiguchi M, Hanke T. Specificity of CD8 + T-Cell Responses Following Vaccination with Conserved Regions of HIV-1 in Nairobi, Kenya. Vaccines (Basel) 2020; 8:E260. [PMID: 32485938 PMCID: PMC7349992 DOI: 10.3390/vaccines8020260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023] Open
Abstract
Sub-Saharan Africa carries the biggest burden of the human immunodeficiency virus type 1 (HIV-1)/AIDS epidemic and is in an urgent need of an effective vaccine. CD8+ T cells are an important component of the host immune response to HIV-1 and may need to be harnessed if a vaccine is to be effective. CD8+ T cells recognize human leukocyte antigen (HLA)-associated viral epitopes and the HLA alleles vary significantly among different ethnic groups. It follows that definition of HIV-1-derived peptides recognized by CD8+ T cells in the geographically relevant regions will critically guide vaccine development. Here, we study fine details of CD8+ T-cell responses elicited in HIV-1/2-uninfected individuals in Nairobi, Kenya, who received a candidate vaccine delivering conserved regions of HIV-1 proteins called HIVconsv. Using 10-day cell lines established by in vitro peptide restimulation of cryopreserved PBMC and stably HLA-transfected 721.221/C1R cell lines, we confirm experimentally many already defined epitopes, for a number of epitopes we define the restricting HLA molecule(s) and describe four novel HLA-epitope pairs. We also identify specific dominance patterns, a promiscuous T-cell epitope and a rescue of suboptimal T-cell epitope induction in vivo by its functional variant, which all together inform vaccine design.
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Affiliation(s)
- Yehia S. Mohamed
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11823, Egypt
| | - Nicola J. Borthwick
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Nathifa Moyo
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Hayato Murakoshi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Tomohiro Akahoshi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Francesca Siliquini
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Zara Hannoun
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Alison Crook
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
| | - Peter Hayes
- International AIDS Vaccine Initiative IAVI-Human Immunology Laboratory, Imperial College London, London SW10 9NH, UK;
| | - Patricia E. Fast
- International AIDS Vaccine Initiative-New York, New York, NY 10004, USA;
| | - Gaudensia Mutua
- KAVI-Institute of Clinical Research, University of Nairobi, Nairobi 19676 00202, Kenya; (G.M.); (W.J.)
| | - Walter Jaoko
- KAVI-Institute of Clinical Research, University of Nairobi, Nairobi 19676 00202, Kenya; (G.M.); (W.J.)
| | - Sandra Silva-Arrieta
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
| | - Christian Brander
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Barcelona, Spain; (S.S.-A.); (A.L.); (C.B.)
- Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; (Y.S.M.); (N.J.B.); (N.M.); (F.S.); (Z.H.); (A.C.)
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan; (H.M.); (T.A.); (M.T.)
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7
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Bunsuz A, Serçinoğlu O, Ozbek P. Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles. Comput Biol Chem 2019; 84:107195. [PMID: 31877499 DOI: 10.1016/j.compbiolchem.2019.107195] [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: 06/21/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 11/27/2022]
Abstract
Major Histocompatibility Complex (MHC) is a cell surface glycoprotein that binds to foreign antigens and presents them to T lymphocyte cells on the surface of Antigen Presenting Cells (APCs) for appropriate immune recognition. Recently, studies focusing on peptide-based vaccine design have allowed a better understanding of peptide immunogenicity mechanisms, which is defined as the ability of a peptide to stimulate CTL-mediated immune response. Peptide immunogenicity is also known to be related to the stability of peptide-loaded MHC (pMHC) complex. In this study, ENCoM server was used for structure-based estimation of the impact of single point mutations on pMHC complex stabilities. For this purpose, two human MHC molecules from the HLA-B*27 group (HLA-B*27:05 and HLA-B*27:09) in complex with four different peptides (GRFAAAIAK, RRKWRRWHL, RRRWRRLTV and IRAAPPPLF) and three HLA-B*44 molecules (HLA-B*44:02, HLA-B*44:03 and HLA-B*44:05) in complex with two different peptides (EEYLQAFTY and EEYLKAWTF) were analyzed. We found that the stability of pMHC complexes is dependent on both peptide sequence and MHC allele. Furthermore, we demonstrate that allele-specific peptide-binding preferences can be accurately revealed using structure-based computational methods predicting the effect of mutations on protein stability.
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Affiliation(s)
- Asuman Bunsuz
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, Istanbul, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Recep Tayyip Erdogan University, Rize, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey.
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8
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Barton JP, Rajkoomar E, Mann JK, Murakowski DK, Toyoda M, Mahiti M, Mwimanzi P, Ueno T, Chakraborty AK, Ndung'u T. Modelling and in vitro testing of the HIV-1 Nef fitness landscape. Virus Evol 2019; 5:vez029. [PMID: 31392033 PMCID: PMC6680064 DOI: 10.1093/ve/vez029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An effective vaccine is urgently required to curb the HIV-1 epidemic. We have previously described an approach to model the fitness landscape of several HIV-1 proteins, and have validated the results against experimental and clinical data. The fitness landscape may be used to identify mutation patterns harmful to virus viability, and consequently inform the design of immunogens that can target such regions for immunological control. Here we apply such an analysis and complementary experiments to HIV-1 Nef, a multifunctional protein which plays a key role in HIV-1 pathogenesis. We measured Nef-driven replication capacities as well as Nef-mediated CD4 and HLA-I down-modulation capacities of thirty-two different Nef mutants, and tested model predictions against these results. Furthermore, we evaluated the models using 448 patient-derived Nef sequences for which several Nef activities were previously measured. Model predictions correlated significantly with Nef-driven replication and CD4 down-modulation capacities, but not HLA-I down-modulation capacities, of the various Nef mutants. Similarly, in our analysis of patient-derived Nef sequences, CD4 down-modulation capacity correlated the most significantly with model predictions, suggesting that of the tested Nef functions, this is the most important in vivo. Overall, our results highlight how the fitness landscape inferred from patient-derived sequences captures, at least in part, the in vivo functional effects of mutations to Nef. However, the correlation between predictions of the fitness landscape and measured parameters of Nef function is not as accurate as the correlation observed in past studies for other proteins. This may be because of the additional complexity associated with inferring the cost of mutations on the diverse functions of Nef.
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Affiliation(s)
- John P Barton
- Departments of Chemical Engineering, Physics, and Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Erasha Rajkoomar
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dariusz K Murakowski
- Departments of Chemical Engineering, Physics, and Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mako Toyoda
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | | | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Arup K Chakraborty
- Departments of Chemical Engineering, Physics, and Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute, Durban, South Africa.,Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany
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9
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Kinloch NN, Lee GQ, Carlson JM, Jin SW, Brumme CJ, Byakwaga H, Muzoora C, Bwana MB, Cobarrubias KD, Hunt PW, Martin JN, Carrington M, Bangsberg DR, Harrigan PR, Brockman MA, Brumme ZL. Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity. J Virol 2019; 93:e01502-18. [PMID: 30305354 PMCID: PMC6288327 DOI: 10.1128/jvi.01502-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/28/2018] [Indexed: 11/20/2022] Open
Abstract
The extent to which viral genetic context influences HIV adaptation to human leukocyte antigen (HLA) class I-restricted immune pressures remains incompletely understood. The Ugandan HIV epidemic, where major pandemic group M subtypes A1 and D cocirculate in a single host population, provides an opportunity to investigate this question. We characterized plasma HIV RNA gag, pol, and nef sequences, along with host HLA genotypes, in 464 antiretroviral-naive individuals chronically infected with HIV subtype A1 or D. Using phylogenetically informed statistical approaches, we identified HLA-associated polymorphisms and formally compared their strengths of selection between viral subtypes. A substantial number (32%) of HLA-associated polymorphisms identified in subtype A1 and/or D had previously been reported in subtype B, C, and/or circulating recombinant form 01_AE (CRF01_AE), confirming the shared nature of many HLA-driven escape pathways regardless of viral genetic context. Nevertheless, 34% of the identified HLA-associated polymorphisms were significantly differentially selected between subtypes A1 and D. Experimental investigation of select examples of subtype-specific escape revealed distinct underlying mechanisms with important implications for vaccine design: whereas some were attributable to subtype-specific sequence variation that influenced epitope-HLA binding, others were attributable to differential mutational barriers to immune escape. Overall, our results confirm that HIV genetic context is a key modulator of viral adaptation to host cellular immunity and highlight the power of combined bioinformatic and mechanistic studies, paired with knowledge of epitope immunogenicity, to identify appropriate viral regions for inclusion in subtype-specific and universal HIV vaccine strategies.IMPORTANCE The identification of HIV polymorphisms reproducibly selected under pressure by specific HLA alleles and the elucidation of their impact on viral function can help identify immunogenic viral regions where immune escape incurs a fitness cost. However, our knowledge of HLA-driven escape pathways and their functional costs is largely limited to HIV subtype B and, to a lesser extent, subtype C. Our study represents the first characterization of HLA-driven adaptation pathways in HIV subtypes A1 and D, which dominate in East Africa, and the first statistically rigorous characterization of differential HLA-driven escape across viral subtypes. The results support a considerable impact of viral genetic context on HIV adaptation to host HLA, where HIV subtype-specific sequence variation influences both epitope-HLA binding and the fitness costs of escape. Integrated bioinformatic and mechanistic characterization of these and other instances of differential escape could aid rational cytotoxic T-lymphocyte-based vaccine immunogen selection for both subtype-specific and universal HIV vaccines.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Guinevere Q Lee
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, Massachusetts, USA
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, San Francisco, California, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - P Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - 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
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10
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Xia Y, Pan W, Ke X, Skibbe K, Walker A, Hoffmann D, Lu Y, Yang X, Feng X, Tong Q, Timm J, Yang D. Differential escape of HCV from CD8 + T cell selection pressure between China and Germany depends on the presenting HLA class I molecule. J Viral Hepat 2019; 26:73-82. [PMID: 30260541 PMCID: PMC7379502 DOI: 10.1111/jvh.13011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 09/07/2018] [Indexed: 12/16/2022]
Abstract
Adaptation of hepatitis C virus (HCV) to CD8+ T cell selection pressure is well described; however, it is unclear if HCV differentially adapts in different populations. Here, we studied HLA class I-associated viral sequence polymorphisms in HCV 1b isolates in a Chinese population and compared viral substitution patterns between Chinese and German populations. We identified three HLA class I-restricted epitopes in HCV NS3 with statistical support for selection pressure and found evidence for differential escape pathways between isolates from China and Germany depending on the HLA class I molecule. The substitution patterns particularly differed in the epitope VTLTHPITK1635-1643 , which was presented by HLA-A*03 as well as HLA-A*11, two alleles with highly different frequencies in the two populations. In Germany, a substitution in position seven of the epitope was the most frequent substitution in the presence of HLA-A*03, functionally associated with immune escape and nearly absent in Chinese isolates. In contrast, the most frequent substitution in China was located at position two of the epitope and became the predominant consensus residue. Moreover, substitutions in position one of the epitope were significantly enriched in HLA-A*11-positive individuals in China and associated with different patterns of CD8+ T cell reactivity. Our study confirms the differential escape pathways selected by HCV that depended on different HLA class I alleles in Chinese and German populations, indicating that HCV differentially adapts to distinct HLA class I alleles in these populations. This result has important implications for vaccine design against highly variable and globally distributed pathogens, which may require matching antigen sequences to geographic regions for T cell-based vaccine strategies.
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Affiliation(s)
- Youchen Xia
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gastroenterology and HepatologyShanghai General HospitalShanghai Jiao Tong University School of Medicine (originally named “Shanghai First People's Hospital”)ShanghaiChina
| | - Wen Pan
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiaoyu Ke
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of EmergencyTongji Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Kathrin Skibbe
- Institute of VirologyUniversity Hospital DüsseldorfHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Andreas Walker
- Institute of VirologyUniversity Hospital DüsseldorfHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Daniel Hoffmann
- Bioinformatics and Computational BiophysicsFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Yinping Lu
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xuecheng Yang
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xuemei Feng
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Qiaoxia Tong
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jörg Timm
- Institute of VirologyUniversity Hospital DüsseldorfHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Dongliang Yang
- Department of Infectious DiseasesUnion Hospital of Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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11
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Bhaskaran M, ArunKumar G. A meta-analysis of association of Human Leukocyte Antigens A, B, C, DR and DQ with Human Papillomavirus 16 infection. INFECTION GENETICS AND EVOLUTION 2018; 68:194-202. [PMID: 30590170 DOI: 10.1016/j.meegid.2018.12.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/23/2018] [Accepted: 12/23/2018] [Indexed: 12/30/2022]
Abstract
Human Papillomavirus (HPV) induced cervical cancer (CaCx) is a major health problem in women from both developing and developed regions of the world. This virus accounts for >95% of the CaCx cases with a preponderance of HPV type -16 (65%). Paradoxically HPV-16 is prevalent even in the cervix of healthier women and anti HPV-16 T-cell response is considered critical for the viral clearance. Studies on HLA association with HPV-16 infection and cervical cancer have yielded varied HLA associations in different epidemiological settings. To validate these associations, we performed a meta-analysis of HLA-A, B, C, DR and DQ association with HPV-16 infection. Of the 1409 studies retrieved, 26 qualified for meta-analysis based on stringent inclusion and exclusion criteria. HLA-B*47, B*57, DRB1*10, DRB1*15 and DQB1*0303 were significantly associated with HPV-16 infection (OR = 3.4, 1.8, 1.5, 1.1 and 1.5 respectively). HLA-B*49, B*39, A28 (serotype), C*04 and DRB1*13 were negatively associated with HPV-16 (OR = 0.5, 0.6, 0.7, 0.7, and 0.7 respectively). Certain HLA alleles such as B*07, DRB1*15, DRB1*11 and DRB1*07 showed weakly positive associations. A comprehensive analysis coupling HPV-16 antigenic diversity and the HLA variation in various global populations shall provide further insights into the immunogenetic predisposition to HPV-16 and shall help identify host-parasite co-evolution.
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Affiliation(s)
- Muthumeenakshi Bhaskaran
- Human Genomics Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur-613 401, India
| | - GaneshPrasad ArunKumar
- Human Genomics Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur-613 401, India.
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12
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Ogunshola F, Anmole G, Miller RL, Goering E, Nkosi T, Muema D, Mann J, Ismail N, Chopera D, Ndung'u T, Brockman MA, Ndhlovu ZM. Dual HLA B*42 and B*81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants. Nat Commun 2018; 9:5023. [PMID: 30479346 PMCID: PMC6258674 DOI: 10.1038/s41467-018-07209-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Some closely related human leukocyte antigen (HLA) alleles are associated with variable clinical outcomes following HIV-1 infection despite presenting the same viral epitopes. Mechanisms underlying these differences remain unclear but may be due to intrinsic characteristics of the HLA alleles or responding T cell repertoires. Here we examine CD8+ T cell responses against the immunodominant HIV-1 Gag epitope TL9 (TPQDLNTML180–188) in the context of the protective allele B*81:01 and the less protective allele B*42:01. We observe a population of dual-reactive T cells that recognize TL9 presented by both B*81:01 and B*42:01 in individuals lacking one allele. The presence of dual-reactive T cells is associated with lower plasma viremia, suggesting a clinical benefit. In B*42:01 expressing individuals, the dual-reactive phenotype defines public T cell receptor (TCR) clones that recognize a wider range of TL9 escape variants, consistent with enhanced control of viral infection through containment of HIV-1 sequence adaptation. Closely related HLA alleles presenting similar HIV-1 epitopes can be associated with variable clinical outcome. Here the authors report their findings on CD8+ T cell responses to the HIV-1 Gag-p24 TL9 immunodominant epitope in the context of closely related protective and less protective HLA alleles, and their differential effect on viral control
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Affiliation(s)
- Funsho Ogunshola
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Gursev Anmole
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Rachel L Miller
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Emily Goering
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Thandeka Nkosi
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel Muema
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Nasreen Ismail
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Denis Chopera
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Mark A Brockman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada.
| | - Zaza M Ndhlovu
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa. .,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa. .,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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13
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Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection. J Virol 2018; 92:JVI.00811-18. [PMID: 29997209 DOI: 10.1128/jvi.00811-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/20/2018] [Indexed: 01/31/2023] Open
Abstract
CD8+ T cell-mediated escape mutations in Gag can reduce HIV-1 replication capacity (RC) and alter disease progression, but less is known about immune-mediated attenuation in other HIV-1 proteins. We generated 487 recombinant viruses encoding RT-integrase from individuals with chronic (n = 406) and recent (n = 81) HIV-1 subtype C infection and measured their in vitro RC using a green fluorescent protein (GFP) reporter T cell assay. In recently infected individuals, reverse transcriptase (RT)-integrase-driven RC correlated significantly with viral load set point (r = 0.25; P = 0.03) and CD4+ T cell decline (P = 0.013). Moreover, significant associations between RT integrase-driven RC and viral load (r = 0.28; P < 0.0001) and CD4+ T cell count (r = -0.29; P < 0.0001) remained in chronic infection. In early HIV infection, host expression of the protective HLA-B*81 allele was associated with lower RC (P = 0.05), as was expression of HLA-B*07 (P = 0.02), suggesting early immune-driven attenuation of RT-integrase by these alleles. In chronic infection, HLA-A*30:09 (in linkage disequilibrium with HLA-B*81) was significantly associated with lower RC (P = 0.05), and all 6 HLA-B alleles with the lowest RC measurements represented protective alleles, consistent with long-term effects of host immune pressures on lowering RT-integrase RC. The polymorphisms V241I, I257V, P272K, and E297K in reverse transcriptase and I201V in integrase, all relatively uncommon polymorphisms occurring in or adjacent to optimally described HLA-restricted cytotoxic T-lymphocyte epitopes, were associated with reduced RC. Together, our data suggest that RT-integrase-driven RC is clinically relevant and provide evidence that immune-driven selection of mutations in RT-integrase can compromise RC.IMPORTANCE Identification of viral mutations that compromise HIV's ability to replicate may aid rational vaccine design. However, while certain escape mutations in Gag have been shown to reduce HIV replication and influence clinical progression, less is known about the consequences of mutations that naturally arise in other HIV proteins. Pol is a highly conserved protein, but the impact of Pol function on HIV disease progression is not well defined. Here, we generated recombinant viruses using the RT-integrase region of Pol derived from HIV-1C-infected individuals with recent and chronic infection and measured their ability to replicate in vitro We demonstrate that RT-integrase-driven replication ability significantly impacts HIV disease progression. We further show evidence of immune-mediated attenuation in RT-integrase and identify specific polymorphisms in RT-integrase that significantly decrease HIV-1 replication ability, suggesting which Pol epitopes could be explored in vaccine development.
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14
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Potential immune escape mutations under inferred selection pressure in HIV-1 strains circulating in Medellín, Colombia. INFECTION GENETICS AND EVOLUTION 2018; 69:267-278. [PMID: 30808498 DOI: 10.1016/j.meegid.2018.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/22/2018] [Accepted: 07/02/2018] [Indexed: 11/20/2022]
Abstract
The introduction of highly active antiretroviral therapy (HAART) has significantly improved life expectancy of HIV-infected patients; nevertheless, it does not eliminate the virus from hosts, so a cure for this infection is crucial. Some strategies have employed the induction of anti-HIV CD8+ T cells. However, the high genetic variability of HIV-1 represents the biggest obstacle for these strategies, since immune escape mutations within epitopes restricted by Human Leukocyte Antigen class I molecules (HLA-I) abrogate the antiviral activity of these cells. We used a bioinformatics pipeline for the determination of such mutations, based on selection pressure and docking/refinement analyses. Fifty HIV-1 infected patients were recruited; HLA-A and HLA-B alleles were typified using sequence-specific oligonucleotide approach, and viral RNA was extracted for the amplification of HIV-1 gag, which was bulk sequenced and aligned to perform selection pressure analysis, using Single Likelihood Ancestor Counting (SLAC) and Fast Unconstrained Bayesian Approximation (FUBAR) algorithms. Positively selected sites were mapped into HLA-I-specific epitopes, and both mutated and wild type epitopes were modelled using PEP-FOLD. Molecular docking and refinement assays were carried out using AutoDock Vina 4 and FlexPepDock. Five positively selected sites were found: S54 at HLA-A*02 GC9, T84 at HLA-A*02 SL9, S125 at HLA-B*35 HY9, S173 at HLA-A*02/B*57 KS12 and I223 at HLA-B*35 HA9. Although some mutations have been previously described as immune escape mutations, the majority of them have not been reported. Molecular docking/refinement analysis showed that one combination of mutations at GC9, one at SL9, and eight at HY9 epitopes could act as immune escape mutations. Moreover, HLA-A*02-positive patients harbouring mutations at KS12, and HLA-B*35-positive patients with mutations at HY9 have significantly higher plasma viral loads than patients lacking such mutations. Thus, HLA-A and -B alleles could be shaping the genetic diversity of HIV-1 through the selection of potential immune escape mutations.
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15
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Malik A, Adland E, Laker L, Kløverpris H, Fardoos R, Roider J, Severinsen MC, Chen F, Riddell L, Edwards A, Buus S, Jooste P, Matthews PC, Goulder PJR. Immunodominant cytomegalovirus-specific CD8+ T-cell responses in sub-Saharan African populations. PLoS One 2017; 12:e0189612. [PMID: 29232408 PMCID: PMC5726643 DOI: 10.1371/journal.pone.0189612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 11/29/2017] [Indexed: 01/14/2023] Open
Abstract
More than 90% of children in Africa are infected with cytomegalovirus (CMV) by the age of 12 months. However, the high-frequency, immunodominant CD8+ T-cell responses that control CMV infection have not been well studied in African populations. We therefore sought to define the immunodominant CMV-specific CD8+ T-cell responses within sub-Saharan African study subjects. Among 257 subjects, we determined the CD8+ T-cell responses to overlapping peptides spanning three of the most immunogenic CMV proteins, pp65, IE-1 and IE-2, using IFN-γ ELISpot assays. A bioinformatics tool was used to predict optimal epitopes within overlapping peptides whose recognition was statistically associated with expression of particular HLA class I molecules. Using this approach, we identified 16 predicted novel CMV-specific epitopes within CMV-pp65, IE-1 and IE-2. The immunodominant pp65-specific, IE-1, IE-2 responses were all either previously well characterised or were confirmed using peptide-MHC tetramers. The novel epitopes identified included an IE-2-specific epitope restricted by HLA*B*44:03 that induced high-frequency CD8+ T-cell responses (mean 3.4% of CD8+ T-cells) in 95% of HLA-B*44:03-positive subjects tested, in one individual accounting for 18.8% of all CD8+ T-cells. These predicted novel CMV-specific CD8+ T-cell epitopes identified in an African cohort will facilitate future analyses of immune responses in African populations where CMV infection is almost universal during infancy.
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Affiliation(s)
- Amna Malik
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Leana Laker
- Kimberley General Hospital, Kimberley, South Africa
| | - Henrik Kløverpris
- Africa Health Research Institute, AHRI, Durban, South Africa
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- University College London, Department of Infection and Immunity, London, United Kingdom
| | - Rabiah Fardoos
- Africa Health Research Institute, AHRI, Durban, South Africa
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julia Roider
- Africa Health Research Institute, AHRI, Durban, South Africa
| | - Mai C. Severinsen
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Lynn Riddell
- Department of Genitourinary Medicine, Northamptonshire Healthcare NHS Trust, Northampton General Hospital, Northampton, United Kingdom
| | - Anne Edwards
- Oxford Department of Genitourinary Medicine, the Churchill Hospital, Oxford, United Kingdom
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Philip J. R. Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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16
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Leitman EM, Thobakgale CF, Adland E, Ansari MA, Raghwani J, Prendergast AJ, Tudor-Williams G, Kiepiela P, Hemelaar J, Brener J, Tsai MH, Mori M, Riddell L, Luzzi G, Jooste P, Ndung'u T, Walker BD, Pybus OG, Kellam P, Naranbhai V, Matthews PC, Gall A, Goulder PJR. Role of HIV-specific CD8 + T cells in pediatric HIV cure strategies after widespread early viral escape. J Exp Med 2017; 214:3239-3261. [PMID: 28983013 PMCID: PMC5679167 DOI: 10.1084/jem.20162123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 06/22/2017] [Accepted: 08/30/2017] [Indexed: 11/04/2022] Open
Abstract
Recent studies have suggested greater HIV cure potential among infected children than adults. A major obstacle to HIV eradication in adults is that the viral reservoir is largely comprised of HIV-specific cytotoxic T lymphocyte (CTL) escape variants. We here evaluate the potential for CTL in HIV-infected slow-progressor children to play an effective role in "shock-and-kill" cure strategies. Two distinct subgroups of children were identified on the basis of viral load. Unexpectedly, in both groups, as in adults, HIV-specific CTL drove the selection of escape variants across a range of epitopes within the first weeks of infection. However, in HIV-infected children, but not adults, de novo autologous variant-specific CTL responses were generated, enabling the pediatric immune system to "corner" the virus. Thus, even when escape variants are selected in early infection, the capacity in children to generate variant-specific anti-HIV CTL responses maintains the potential for CTL to contribute to effective shock-and-kill cure strategies in pediatric HIV infection.
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Affiliation(s)
- Ellen M Leitman
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - Christina F Thobakgale
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - M Azim Ansari
- Oxford Martin School, University of Oxford, Oxford, England, UK
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford, England, UK
| | - Andrew J Prendergast
- Blizard Institute, Queen Mary University of London, London, England, UK.,Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Gareth Tudor-Williams
- Division of Medicine, Department of Paediatrics, Imperial College London, London, England, UK
| | - Photini Kiepiela
- Medical Research Council, Durban, South Africa.,Witwatersrand Health Consortium, Johannesburg, South Africa
| | - Joris Hemelaar
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford, England, UK.,Linacre Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Jacqui Brener
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - Ming-Han Tsai
- Department of Paediatrics, University of Oxford, Oxford, England, UK
| | - Masahiko Mori
- Department of Paediatrics, University of Oxford, Oxford, England, UK.,Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Lynn Riddell
- Northampton Healthcare NHS Foundation Trust, Cliftonville, England, UK
| | - Graz Luzzi
- Buckinghampshire Healthcare NHS Foundation Trust, High Wycombe, England, UK
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, England, UK
| | - Paul Kellam
- Kymab Ltd., Babraham Research Campus, Babraham, England, UK.,Department of Medicine, Division of Infectious Diseases, Imperial College Faculty of Medicine, London, England, UK
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA.,Centre for the AIDS Programme of Research in South Africa, University of KwaZulu Natal, Durban, South Africa
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, England, UK
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Hinxton, England, UK
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, Oxford, England, UK .,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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17
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John M, Gaudieri S, Mallal S. Immunogenetics and Vaccination. HUMAN VACCINES 2017. [DOI: 10.1016/b978-0-12-802302-0.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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CD8+ T Cell Breadth and Ex Vivo Virus Inhibition Capacity Distinguish between Viremic Controllers with and without Protective HLA Class I Alleles. J Virol 2016; 90:6818-6831. [PMID: 27194762 DOI: 10.1128/jvi.00276-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/11/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The mechanisms of viral control and loss of viral control in chronically infected individuals with or without protective HLA class I alleles are not fully understood. We therefore characterized longitudinally the immunological and virological features that may explain divergence in disease outcome in 70 HIV-1 C-clade-infected antiretroviral therapy (ART)-naive South African adults, 35 of whom possessed protective HLA class I alleles. We demonstrate that, over 5 years of longitudinal study, 35% of individuals with protective HLA class I alleles lost viral control compared to none of the individuals without protective HLA class I alleles (P = 0.06). Sustained HIV-1 control in patients with protective HLA class I alleles was characteristically related to the breadth of HIV-1 CD8(+) T cell responses against Gag and enhanced ability of CD8(+) T cells to suppress viral replication ex vivo In some cases, loss of virological control was associated with reduction in the total breadth of CD8(+) T cell responses in the absence of differences in HIV-1-specific CD8(+) T cell polyfunctionality or proliferation. In contrast, viremic controllers without protective HLA class I alleles possessed reduced breadth of HIV-1-specific CD8(+) T cell responses characterized by reduced ability to suppress viral replication ex vivo These data suggest that the control of HIV-1 in individuals with protective HLA class I alleles may be driven by broad CD8(+) T cell responses with potent viral inhibitory capacity while control among individuals without protective HLA class I alleles may be more durable and mediated by CD8(+) T cell-independent mechanisms. IMPORTANCE Host mechanisms of natural HIV-1 control are not fully understood. In a longitudinal study of antiretroviral therapy (ART)-naive individuals, we show that those with protective HLA class I alleles subsequently experienced virologic failure compared to those without protective alleles. Among individuals with protective HLA class I alleles, viremic control was associated with broad CD8(+) T cells that targeted the Gag protein, and CD8(+) T cells from these individuals exhibited superior virus inhibition capacity. In individuals without protective HLA class I alleles, HIV-1-specific CD8(+) T cell responses were narrow and poorly inhibited virus replication. These results suggest that broad, highly functional cytotoxic T cells (cytotoxic T lymphocytes [CTLs]) against the HIV-1 Gag protein are associated with control among those with protective HLA class I alleles and that loss of these responses eventually leads to viremia. A subset of individuals appears to have alternative, non-CTL mechanisms of viral control. These controllers may hold the key to an effective HIV vaccine.
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19
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Abstract
Human leukocyte antigen class I (HLA)-restricted CD8(+) T lymphocyte (CTL) responses are crucial to HIV-1 control. Although HIV can evade these responses, the longer-term impact of viral escape mutants remains unclear, as these variants can also reduce intrinsic viral fitness. To address this, we here developed a metric to determine the degree of HIV adaptation to an HLA profile. We demonstrate that transmission of viruses that are pre-adapted to the HLA molecules expressed in the recipient is associated with impaired immunogenicity, elevated viral load and accelerated CD4(+) T cell decline. Furthermore, the extent of pre-adaptation among circulating viruses explains much of the variation in outcomes attributed to the expression of certain HLA alleles. Thus, viral pre-adaptation exploits 'holes' in the immune response. Accounting for these holes may be key for vaccine strategies seeking to elicit functional responses from viral variants, and to HIV cure strategies that require broad CTL responses to achieve successful eradication of HIV reservoirs.
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20
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Kløverpris HN, Leslie A, Goulder P. Role of HLA Adaptation in HIV Evolution. Front Immunol 2016; 6:665. [PMID: 26834742 PMCID: PMC4716577 DOI: 10.3389/fimmu.2015.00665] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/27/2015] [Indexed: 01/22/2023] Open
Abstract
Killing of HIV-infected cells by CD8+ T-cells imposes strong selection pressure on the virus toward escape. The HLA class I molecules that are successful in mediating some degree of control over the virus are those that tend to present epitopes in conserved regions of the proteome, such as in p24 Gag, in which escape also comes at a significant cost to viral replicative capacity (VRC). In some instances, compensatory mutations can fully correct for the fitness cost of such an escape variant; in others, correction is only partial. The consequences of these events within the HIV-infected host, and at the population level following transmission of escape variants, are discussed. The accumulation of escape mutants in populations over the course of the epidemic already shows instances of protective HLA molecules losing their impact, and in certain cases, a modest decline in HIV virulence in association with population-level increase in mutants that reduce VRC.
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Affiliation(s)
- Henrik N Kløverpris
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban , South Africa
| | - Philip Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Department of Paediatrics, University of Oxford, Oxford, UK
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21
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Kløverpris HN, McGregor R, McLaren JE, Ladell K, Harndahl M, Stryhn A, Carlson JM, Koofhethile C, Gerritsen B, Keşmir C, Chen F, Riddell L, Luzzi G, Leslie A, Walker BD, Ndung'u T, Buus S, Price DA, Goulder PJ. CD8+ TCR Bias and Immunodominance in HIV-1 Infection. THE JOURNAL OF IMMUNOLOGY 2015; 194:5329-45. [PMID: 25911754 DOI: 10.4049/jimmunol.1400854] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 02/25/2015] [Indexed: 12/25/2022]
Abstract
Immunodominance describes a phenomenon whereby the immune system consistently targets only a fraction of the available Ag pool derived from a given pathogen. In the case of CD8(+) T cells, these constrained epitope-targeting patterns are linked to HLA class I expression and determine disease progression. Despite the biological importance of these predetermined response hierarchies, little is known about the factors that control immunodominance in vivo. In this study, we conducted an extensive analysis of CD8(+) T cell responses restricted by a single HLA class I molecule to evaluate the mechanisms that contribute to epitope-targeting frequency and antiviral efficacy in HIV-1 infection. A clear immunodominance hierarchy was observed across 20 epitopes restricted by HLA-B*42:01, which is highly prevalent in populations of African origin. Moreover, in line with previous studies, Gag-specific responses and targeting breadth were associated with lower viral load set-points. However, peptide-HLA-B*42:01 binding affinity and stability were not significantly linked with targeting frequencies. Instead, immunodominance correlated with epitope-specific usage of public TCRs, defined as amino acid residue-identical TRB sequences that occur in multiple individuals. Collectively, these results provide important insights into a potential link between shared TCR recruitment, immunodominance, and antiviral efficacy in a major human infection.
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Affiliation(s)
- Henrik N Kløverpris
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom; Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark; KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Reuben McGregor
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Mikkel Harndahl
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | - Anette Stryhn
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | | | - Catherine Koofhethile
- HIV Pathogenesis Program, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Bram Gerritsen
- Theoretical Biology Group, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Can Keşmir
- Theoretical Biology Group, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading RG1 5AN, United Kingdom
| | - Lynn Riddell
- Department of Genitourinary Medicine, Northamptonshire Healthcare National Health Service Trust, Northampton General Hospital, Cliftonville, Northampton NN1 5BD, United Kingdom
| | - Graz Luzzi
- Department of Sexual Health, Wycombe Hospital, High Wycombe HP11 2TT, United Kingdom
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA 02129; Howard Hughes Medical Institute, Chevy Chase, MD 20815; and
| | - Thumbi Ndung'u
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; HIV Pathogenesis Program, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa; Max Planck Institute for Infection Biology, D-10117 Berlin, Germany
| | - Søren Buus
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Philip J Goulder
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
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22
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Kløverpris HN, Cole DK, Fuller A, Carlson J, Beck K, Schauenburg AJ, Rizkallah PJ, Buus S, Sewell AK, Goulder P. A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape. Retrovirology 2015; 12:20. [PMID: 25808313 PMCID: PMC4347545 DOI: 10.1186/s12977-015-0149-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Presentation of identical HIV-1 peptides by closely related Human Leukocyte Antigen class I (HLAI) molecules can select distinct patterns of escape mutation that have a significant impact on viral fitness and disease progression. The molecular mechanisms by which HLAI micropolymorphisms can induce differential HIV-1 escape patterns within identical peptide epitopes remain unknown. RESULTS Here, we undertook genetic and structural analyses of two immunodominant HIV-1 peptides, Gag180-188 (TPQDLNTML, TL9-p24) and Nef71-79 (RPQVPLRPM, RM9-Nef) that are among the most highly targeted epitopes in the global HIV-1 epidemic. We show that single polymorphisms between different alleles of the HLA-B7 superfamily can induce a conformational switch in peptide conformation that is associated with differential HLAI-specific escape mutation and immune control. A dominant R71K mutation in the Nef71-79 occurred in those with HLA-B*07:02 but not B*42:01/02 or B*81:01. No structural difference in the HLA-epitope complexes was detected to explain this observation. CONCLUSIONS These data suggest that identical peptides presented through very similar HLAI landscapes are recognized as distinct epitopes and provide a novel structural mechanism for previously observed differential HIV-1 escape and disease progression.
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Affiliation(s)
- Henrik N Kløverpris
- />KwaZulu- Natal Research Institute for Tuberculosis and HIV, K-RITH, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- />Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen N, 2200 Denmark
- />Department of Paediatrics, University of Oxford, Peter Medawar Building, Oxford, OX1 3SY UK
| | - David K Cole
- />Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Anna Fuller
- />Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | | | - Konrad Beck
- />Cardiff University School of Dentistry, Heath Park, Cardiff, UK
| | | | | | - Søren Buus
- />Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen N, 2200 Denmark
| | - Andrew K Sewell
- />Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Philip Goulder
- />Department of Paediatrics, University of Oxford, Peter Medawar Building, Oxford, OX1 3SY UK
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23
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Abstract
UNLABELLED The extent to which HIV-1 clade B strains exhibit population-specific adaptations to host HLA alleles remains incompletely known, in part due to incomplete characterization of HLA-associated HIV-1 polymorphisms (HLA-APs) in different global populations. Moreover, it remains unknown to what extent the same HLA alleles may drive significantly different escape pathways across populations. As the Japanese population exhibits distinctive HLA class I allele distributions, comparative analysis of HLA-APs between HIV-1 clade B-infected Japanese and non-Asian cohorts could shed light on these questions. However, HLA-APs remain incompletely mapped in Japan. In a cohort of 430 treatment-naive Japanese with chronic HIV-1 clade B infection, we identified 284 HLA-APs in Gag, Pol, and Nef using phylogenetically corrected methods. The number of HLA-associated substitutions in Pol, notably those restricted by HLA-B*52:01, was weakly inversely correlated with the plasma viral load (pVL), suggesting that the transmission and persistence of B*52:01-driven Pol mutations could modulate the pVL. Differential selection of HLA-APs between HLA subtype members, including those differing only with respect to substitutions outside the peptide-binding groove, was observed, meriting further investigation as to their mechanisms of selection. Notably, two-thirds of HLA-APs identified in Japan had not been reported in previous studies of predominantly Caucasian cohorts and were attributable to HLA alleles unique to, or enriched in, Japan. We also identified 71 cases where the same HLA allele drove significantly different escape pathways in Japan versus predominantly Caucasian cohorts. Our results underscore the distinct global evolution of HIV-1 clade B as a result of host population-specific cellular immune pressures. IMPORTANCE Cytotoxic T lymphocyte (CTL) escape mutations in HIV-1 are broadly predictable based on the HLA class I alleles expressed by the host. Because HLA allele distributions differ among worldwide populations, the pattern and diversity of HLA-associated escape mutations are likely to be somewhat distinct to each race and region. HLA-associated polymorphisms (HLA-APs) in HIV-1 have previously been identified at the population level in European, North American, Australian, and African cohorts; however, large-scale analyses of HIV-1 clade B-specific HLA-APs in Asians are lacking. Differential intraclade HIV-1 adaptation to global populations can be investigated via comparative analyses of HLA-associated polymorphisms across ethnic groups, but such studies are rare. Here, we identify HLA-APs in a large Japanese HIV-1 clade B cohort using phylogenetically informed methods and observe that the majority of them had not been previously characterized in predominantly Caucasian populations. The results highlight HIV's unique adaptation to cellular immune pressures imposed by different global populations.
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24
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Hanke T. Conserved immunogens in prime-boost strategies for the next-generation HIV-1 vaccines. Expert Opin Biol Ther 2014; 14:601-16. [PMID: 24490585 DOI: 10.1517/14712598.2014.885946] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Effective vaccines are the best solution for stopping the spread of HIV/AIDS and other infectious diseases. Their development and in-depth understanding of pathogen-host interactions rely on technological advances. AREAS COVERED Rational vaccine development can be effectively approached by conceptual separation of, on one hand, design of immunogens from improving their presentation to the immune system and, on the other, induction of antibodies from induction of killer CD8(+) T cells. The biggest roadblock for many vaccines is the pathogens' variability. This is best tackled by focusing both antibodies and T cells on the functionally most conserved regions of proteins common to many variants, including escape mutants. For vectored vaccines, these 'universal' subunit immunogens are most efficiently delivered using heterologous prime-boost regimens, which can be further optimised by adjuvantation and route of delivery. EXPERT OPINION Development of vaccines against human diseases has many features in common. Acceleration of vaccine discovery depends on basic research and new technologies. Novel strategies should be safely, but rapidly tested in humans. While out-of-the-box thinking is important, vaccine success largely depends on incremental advances best achieved through small, systematic, iterative clinical studies. Failures are inevitable, but the end rewards are huge. The future will be exciting.
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Affiliation(s)
- Tomáš Hanke
- The Jenner Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ , UK
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25
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Longitudinal analysis of an HLA-B*51-restricted epitope in integrase reveals immune escape in early HIV-1 infection. AIDS 2013; 27:313-23. [PMID: 23095315 DOI: 10.1097/qad.0b013e32835b8cf5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To fully define cytotoxic T-lymphocyte (CTL) escape variants of an HLA-B*51-restricted integrase epitope in early HIV-1 infection. DESIGN Ninety-four longitudinally sampled acute/early HIV-1 subtype B-infected participants were assessed to determine HLA-B*51-restricted LPPVVAKEI (LI9) escape variants. METHODS LI9 was sequenced at baseline and subsequent time points. Interferon-γ (IFNγ) ELISpot assays were performed using serial log dilutions of variant LI9 peptides to determine the cellular response and functional avidity. RESULTS There is a significant association between HLA-B*51 expression and an evolving LI9 sequence from baseline to year 1 (P < 0.0001). We detected that the V32I and P30X polymorphisms emerged within HLA-B*51 participants over time. Reversion of the P30S polymorphism was observed by year 1 in one HLA-B*51 participant. LPPIIAKEI and LPSIVAKEI had significantly lower functional avidity compared with LPPVVAKEI and so may be less well recognized by LI9-specific CTLs; a positive IFNγ response to IPSVVAKEI was rarely seen. Functional avidity to wild-type LI9 inversely correlated with viral load (R = 0.448, P = 0.0485). CONCLUSION Our results provide support for the role of HLA-B*51-restricted CTLs and functional avidity in the control of early HIV-1 infection.
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26
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Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CKS, Cotton LA, Knapp DJHF, Riddler SA, Haubrich R, Nelson G, Pfeifer N, DeZiel CE, Heckerman D, Apps R, Carrington M, Mallal S, Harrigan PR, John M, Brumme ZL. Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J Virol 2012; 86:13202-16. [PMID: 23055555 PMCID: PMC3503140 DOI: 10.1128/jvi.01998-12] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/02/2012] [Indexed: 12/11/2022] Open
Abstract
HLA class I-associated polymorphisms identified at the population level mark viral sites under immune pressure by individual HLA alleles. As such, analysis of their distribution, frequency, location, statistical strength, sequence conservation, and other properties offers a unique perspective from which to identify correlates of protective cellular immunity. We analyzed HLA-associated HIV-1 subtype B polymorphisms in 1,888 treatment-naïve, chronically infected individuals using phylogenetically informed methods and identified characteristics of HLA-associated immune pressures that differentiate protective and nonprotective alleles. Over 2,100 HLA-associated HIV-1 polymorphisms were identified, approximately one-third of which occurred inside or within 3 residues of an optimally defined cytotoxic T-lymphocyte (CTL) epitope. Differential CTL escape patterns between closely related HLA alleles were common and increased with greater evolutionary distance between allele group members. Among 9-mer epitopes, mutations at HLA-specific anchor residues represented the most frequently detected escape type: these occurred nearly 2-fold more frequently than expected by chance and were computationally predicted to reduce peptide-HLA binding nearly 10-fold on average. Characteristics associated with protective HLA alleles (defined using hazard ratios for progression to AIDS from natural history cohorts) included the potential to mount broad immune selection pressures across all HIV-1 proteins except Nef, the tendency to drive multisite and/or anchor residue escape mutations within known CTL epitopes, and the ability to strongly select mutations in conserved regions within HIV's structural and functional proteins. Thus, the factors defining protective cellular immune responses may be more complex than simply targeting conserved viral regions. The results provide new information to guide vaccine design and immunogenicity studies.
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Affiliation(s)
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Eric Martin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Mark A. Brockman
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anh Q. Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Celia K. S. Chui
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Laura A. Cotton
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Sharon A. Riddler
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Richard Haubrich
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - George Nelson
- Basic Research Program, Center for Cancer Research Genetics Core, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Nico Pfeifer
- Microsoft Research, Los Angeles, California, USA
| | | | | | - Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA, and Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Charlestown, Massachusetts, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA, and Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Charlestown, Massachusetts, USA
| | - Simon Mallal
- Centre for Clinical Immunology and Biomedical Statistics, Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | | | - Mina John
- Centre for Clinical Immunology and Biomedical Statistics, Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - the International HIV Adaptation Collaborative
- Microsoft Research, Los Angeles, California, USA
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
- Basic Research Program, Center for Cancer Research Genetics Core, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA, and Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Charlestown, Massachusetts, USA
- Centre for Clinical Immunology and Biomedical Statistics, Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
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27
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Sanou MP, De Groot AS, Murphey-Corb M, Levy JA, Yamamoto JK. HIV-1 Vaccine Trials: Evolving Concepts and Designs. Open AIDS J 2012; 6:274-88. [PMID: 23289052 PMCID: PMC3534440 DOI: 10.2174/1874613601206010274] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 12/24/2022] Open
Abstract
An effective prophylactic HIV-1 vaccine is needed to eradicate the HIV/AIDS pandemic but designing such a vaccine is a challenge. Despite many advances in vaccine technology and approaches to generate both humoral and cellular immune responses, major phase-II and -III vaccine trials against HIV/AIDS have resulted in only moderate successes. The modest achievement of the phase-III RV144 prime-boost trial in Thailand re-emphasized the importance of generating robust humoral and cellular responses against HIV. While antibody-directed approaches are being pursued by some groups, others are attempting to develop vaccines targeting cell-mediated immunity, since evidence show CTLs to be important for the control of HIV replication. Phase-I and -IIa multi-epitope vaccine trials have already been conducted with vaccine immunogens consisting of known CTL epitopes conserved across HIV subtypes, but have so far fallen short of inducing robust and consistent anti-HIV CTL responses. The concepts leading to the development of T-cell epitope-based vaccines, the outcomes of related clinical vaccine trials and efforts to enhance the immunogenicity of cell-mediated approaches are summarized in this review. Moreover, we describe a novel approach based on the identification of SIV and FIV antigens which contain conserved HIV-specific T-cell epitopes and represent an alternative method for developing an effective HIV vaccine against global HIV isolates.
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Affiliation(s)
- Missa P Sanou
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL 32611, USA
| | - Anne S De Groot
- EpiVax Inc., University of Rhode Island, Providence, RI 02903, USA
| | - Michael Murphey-Corb
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, E1252 Biomedical Science Tower 200, Lothrop Street, Pittsburgh, PA 15261, USA
| | - Jay A Levy
- Department of Medicine, University of California San Francisco, S-1280, 513 Parnassus Ave, San Francisco, CA 94143, USA
| | - Janet K Yamamoto
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL 32611, USA
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Functional avidity: a measure to predict the efficacy of effector T cells? Clin Dev Immunol 2012; 2012:153863. [PMID: 23227083 PMCID: PMC3511839 DOI: 10.1155/2012/153863] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/22/2012] [Indexed: 01/30/2023]
Abstract
The functional avidity is determined by exposing T-cell populations in vitro to different amounts of cognate antigen. T-cells with high functional avidity respond to low antigen doses. This in vitro measure is thought to correlate well with the in vivo effector capacity of T-cells. We here present the multifaceted factors determining and influencing the functional avidity of T-cells. We outline how changes in the functional avidity can occur over the course of an infection. This process, known as avidity maturation, can occur despite the fact that T-cells express a fixed TCR. Furthermore, examples are provided illustrating the importance of generating T-cell populations that exhibit a high functional avidity when responding to an infection or tumors. Furthermore, we discuss whether criteria based on which we evaluate an effective T-cell response to acute infections can also be applied to chronic infections such as HIV. Finally, we also focus on observations that high-avidity T-cells show higher signs of exhaustion and facilitate the emergence of virus escape variants. The review summarizes our current understanding of how this may occur as well as how T-cells of different functional avidity contribute to antiviral and anti-tumor immunity. Enhancing our knowledge in this field is relevant for tumor immunotherapy and vaccines design.
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Kløverpris HN, Harndahl M, Leslie AJ, Carlson JM, Ismail N, van der Stok M, Huang KHG, Chen F, Riddell L, Steyn D, Goedhals D, van Vuuren C, Frater J, Walker BD, Carrington M, Ndung'u T, Buus S, Goulder P. HIV control through a single nucleotide on the HLA-B locus. J Virol 2012; 86:11493-500. [PMID: 22896606 PMCID: PMC3486337 DOI: 10.1128/jvi.01020-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/23/2012] [Indexed: 12/31/2022] Open
Abstract
Genetic variation within the HLA-B locus has the strongest impact on HIV disease progression of any polymorphisms within the human genome. However, identifying the exact mechanism involved is complicated by several factors. HLA-Bw4 alleles provide ligands for NK cells and for CD8 T cells, and strong linkage disequilibrium between HLA class I alleles complicates the discrimination of individual HLA allelic effects from those of other HLA and non-HLA alleles on the same haplotype. Here, we exploit an experiment of nature involving two recently diverged HLA alleles, HLA-B*42:01 and HLA-B*42:02, which differ by only a single amino acid. Crucially, they occur primarily on identical HLA class I haplotypes and, as Bw6 alleles, do not act as NK cell ligands and are therefore largely unconfounded by other genetic factors. We show that in an outbred cohort (n = 2,093) of HIV C-clade-infected individuals, a single amino acid change at position 9 of the HLA-B molecule critically affects peptide binding and significantly alters the cytotoxic T lymphocyte (CTL) epitopes targeted, measured directly ex vivo by gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay (P = 2 × 10(-10)) and functionally through CTL escape mutation (P = 2 × 10(-8)). HLA-B*42:01, which presents multiple Gag epitopes, is associated with a 0.52 log(10) lower viral-load set point than HLA-B*42:02 (P = 0.02), which presents no p24 Gag epitopes. The magnitude of this effect from a single amino acid difference in the HLA-A*30:01/B*42/Cw*17:01 haplotype is equivalent to 75% of that of HLA-B*57:03, the most protective HLA class I allele in this population. This naturally controlled experiment represents perhaps the clearest demonstration of the direct impact of a particular HIV-specific CTL on disease control.
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The potential role of epitope-specific T-cell receptor diversity in the control of HIV replication. Curr Opin HIV AIDS 2012; 2:177-82. [PMID: 19372884 DOI: 10.1097/coh.0b013e3280ef692f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to assess the influence of T-cell receptor clonotype diversity on the recognition and control of chronic viral infections, and specifically in the case of HIV infection. RECENT FINDINGS The latest publications have examined the role of T-cell receptor repertoires specific for dominant epitopes in the ability to recognize variants and control viremia in chronic viral infections. In the hepatitis C virus and SIV models, diverse T-cell receptor repertoires appear to limit immune escape. In HIV infection, circulating clonotypes may have different functional abilities, showing another potential advantage of diverse clonotypic repertoires. A recent study suggests that at times narrow repertoires against a conserved epitope may be effective, perhaps through the ability to cross-recognize potential epitope variants. SUMMARY The studies discussed in this review have identified T-cell receptor diversity as an important factor for understanding the immune recognition of highly variable viruses. Further studies are needed to determine whether T-cell receptor repertoire analysis of HIV epitope-specific immune responses will provide a more accurate correlate for the control of viremia than conventional immune function assays.
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Abstract
Successful vaccine development for infectious diseases has largely been achieved in settings where natural immunity to the pathogen results in clearance in at least some individuals. HIV presents an additional challenge in that natural clearance of infection does not occur, and the correlates of immune protection are still uncertain. However, partial control of viremia and markedly different outcomes of disease are observed in HIV-infected persons. Here, we examine the antiviral mechanisms implicated by one variable that has been consistently associated with extremes of outcome, namely HLA class I alleles, and in particular HLA-B, and examine the mechanisms by which this modulation is likely to occur and the impact of these interactions on evolution of the virus and the host. Studies to date provide evidence for both HLA-dependent and epitope-dependent influences on viral control and viral evolution and have important implications for the continued quest for an effective HIV vaccine.
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Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope. J Virol 2012; 86:12643-54. [PMID: 22973023 DOI: 10.1128/jvi.01381-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The strongest genetic influence on immune control in HIV-1 infection is the HLA class I genotype. Rapid disease progression in B-clade infection has been linked to HLA-B*35 expression, in particular to the less common HLA-B*3502 and HLA-B*3503 subtypes but also to the most prevalent subtype, HLA-B*3501. In these studies we first demonstrated that whereas HLA-B*3501 is associated with a high viral set point in two further B-clade-infected cohorts, in Japan and Mexico, this association does not hold in two large C-clade-infected African cohorts. We tested the hypothesis that clade-specific differences in HLA associations with disease outcomes may be related to distinct targeting of critical CD8(+) T-cell epitopes. We observed that only one epitope was significantly targeted differentially, namely, the Gag-specific epitope NPPIPVGDIY (NY10, Gag positions 253 to 262) (P = 2 × 10(-5)). In common with two other HLA-B*3501-restricted epitopes, in Gag and Nef, that were not targeted differentially, a response toward NY10 was associated with a significantly lower viral set point. Nonimmunogenicity of NY10 in B-clade-infected subjects derives from the Gag-D260E polymorphism present in ∼90% of B-clade sequences, which critically reduces recognition of the Gag NY10 epitope. These data suggest that in spite of any inherent HLA-linked T-cell receptor repertoire differences that may exist, maximizing the breadth of the Gag-specific CD8(+) T-cell response, by the addition of even a single epitope, may be of overriding importance in achieving immune control of HIV infection. This distinction is of direct relevance to development of vaccines designed to optimize the anti-HIV CD8(+) T-cell response in all individuals, irrespective of HLA type.
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Temporal association of HLA-B*81:01- and HLA-B*39:10-mediated HIV-1 p24 sequence evolution with disease progression. J Virol 2012; 86:12013-24. [PMID: 22933291 DOI: 10.1128/jvi.00539-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HLA-B*81:01 and HLA-B*39:10 alleles have been associated with viremic control in HIV-1 subtype C infection. Both alleles restrict the TL9 epitope in p24 Gag, and cytotoxic-T-lymphocyte (CTL)-mediated escape mutations in this epitope have been associated with an in vitro fitness cost to the virus. We investigated the timing and impact of mutations in the TL9 epitope on disease progression in five B*81:01- and two B*39:10-positive subtype C-infected individuals. Whereas both B*39:10 participants sampled at 2 months postinfection had viruses with mutations in the TL9 epitope, in three of the five (3/5) B*81:01 participants, TL9 escape mutations were only detected 10 months after infection, taking an additional 10 to 15 months to reach fixation. In the two remaining B*81:01 individuals, one carried a TL9 escape variant at 2 weeks postinfection, whereas no escape mutations were detected in the virus from the other participant for up to 33 months postinfection, despite CTL targeting of the epitope. In all participants, escape mutations in TL9 were linked to coevolving residues in the region of Gag known to be associated with host tropism. Late escape in TL9, together with coevolution of putative compensatory mutations, coincided with a spontaneous increase in viral loads in two individuals who were otherwise controlling the infection. These results provide in vivo evidence of the detrimental impact of B*81:01-mediated viral evolution, in a single Gag p24 epitope, on the control of viremia.
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McLaren PJ, Ripke S, Pelak K, Weintrob AC, Patsopoulos NA, Jia X, Erlich RL, Lennon NJ, Kadie CM, Heckerman D, Gupta N, Haas DW, Deeks SG, Pereyra F, Walker BD, de Bakker PIW. Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans. Hum Mol Genet 2012; 21:4334-47. [PMID: 22718199 DOI: 10.1093/hmg/dds226] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. Genetic investigations of this phenotype have strongly implicated variation in the class I major histocompatibility complex (MHC) region as key to HIV-1 control. We collected sequence-based classical class I HLA genotypes at 4-digit resolution in HIV-1-infected African American controllers and progressors (n = 1107), and tested them for association with host control using genome-wide single nucleotide polymorphism data to account for population structure. Several classical alleles at HLA-B were associated with host control, including B*57:03 [odds ratio (OR) = 5.1; P= 3.4 × 10(-18)] and B*81:01 (OR = 4.8; P= 1.3 × 10(-9)). Analysis of variable amino acid positions demonstrates that HLA-B position 97 is the most significant association with host control in African Americans (omnibus P = 1.2 × 10(-21)) and explains the signal of several HLA-B alleles, including B*57:03. Within HLA-B, we also identified independent effects at position 116 (omnibus P= 2.8 × 10(-15)) in the canonical F pocket, position 63 in the B pocket (P= 1.5 × 10(-3)) and the non-pocket position 245 (P= 8.8 × 10(-10)), which is thought to influence CD8-binding kinetics. Adjusting for these HLA-B effects, there is evidence for residual association in the MHC region. These results underscore the key role of HLA-B in affecting HIV-1 replication, likely through the molecular interaction between HLA-B and viral peptides presented by infected cells, and suggest that sites outside the peptide-binding pocket also influence HIV-1 control.
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Affiliation(s)
- Paul J McLaren
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJR, Heckerman D. Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J Virol 2012; 86:5230-43. [PMID: 22379086 PMCID: PMC3347390 DOI: 10.1128/jvi.06728-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/20/2012] [Indexed: 11/20/2022] Open
Abstract
The promiscuous presentation of epitopes by similar HLA class I alleles holds promise for a universal T-cell-based HIV-1 vaccine. However, in some instances, cytotoxic T lymphocytes (CTL) restricted by HLA alleles with similar or identical binding motifs are known to target epitopes at different frequencies, with different functional avidities and with different apparent clinical outcomes. Such differences may be illuminated by the association of similar HLA alleles with distinctive escape pathways. Using a novel computational method featuring phylogenetically corrected odds ratios, we systematically analyzed differential patterns of immune escape across all optimally defined epitopes in Gag, Pol, and Nef in 2,126 HIV-1 clade C-infected adults. Overall, we identified 301 polymorphisms in 90 epitopes associated with HLA alleles belonging to shared supertypes. We detected differential escape in 37 of 38 epitopes restricted by more than one allele, which included 278 instances of differential escape at the polymorphism level. The majority (66 to 97%) of these resulted from the selection of unique HLA-specific polymorphisms rather than differential epitope targeting rates, as confirmed by gamma interferon (IFN-γ) enzyme-linked immunosorbent spot assay (ELISPOT) data. Discordant associations between HLA alleles and viral load were frequently observed between allele pairs that selected for differential escape. Furthermore, the total number of associated polymorphisms strongly correlated with average viral load. These studies confirm that differential escape is a widespread phenomenon and may be the norm when two alleles present the same epitope. Given the clinical correlates of immune escape, such heterogeneity suggests that certain epitopes will lead to discordant outcomes if applied universally in a vaccine.
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Keane NM, Roberts SG, Almeida CAM, Krishnan T, Chopra A, Demaine E, Laird R, Tschochner M, Carlson JM, Mallal S, Heckerman D, James I, John M. High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection. Immunol Cell Biol 2012; 90:224-34. [PMID: 21577229 PMCID: PMC3173576 DOI: 10.1038/icb.2011.34] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
HIV-1 mutations, which reduce or abolish CTL responses against virus-infected cells, are frequently selected in acute and chronic HIV infection. Among population HIV-1 sequences, immune selection is evident as human leukocyte antigen (HLA) allele-associated substitutions of amino acids within or near CD8 T-cell epitopes. In these cases, the non-adapted epitope is susceptible to immune recognition until an escape mutation renders the epitope less immunogenic. However, several population-based studies have independently identified HLA-associated viral changes, which lead to the formation of a new T-cell epitope, suggesting that the immune responses that these variants or 'neo-epitopes' elicit provide an evolutionary advantage to the virus rather than the host. Here, we examined the functional characteristics of eight CD8 T-cell responses that result from viral adaptation in 125 HLA-genotyped individuals with chronic HIV-1 infection. Neo-epitopes included well-characterized immunodominant epitopes restricted by common HLA alleles, and in most cases the T-cell responses against the neo-epitope showed significantly greater functional avidity and higher IFNγ production than T cells for non-adapted epitopes, but were not more cytotoxic. Neo-epitope formation and emergence of cognate T-cell response coincident with a rise in viral load was then observed in vivo in an acutely infected individual. These findings show that HIV-1 adaptation not only abrogates the immune recognition of early targeted epitopes, but may also increase immune recognition to other epitopes, which elicit immunodominant but non-protective T-cell responses. These data have implications for immunodominance associated with polyvalent vaccines based on the diversity of chronic HIV-1 sequences.
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Affiliation(s)
- Niamh M Keane
- Centre for Clinical Immunology and Biomedical Statistics, Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
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Currier JR, Robb ML, Michael NL, Marovich MA. Defining epitope coverage requirements for T cell-based HIV vaccines: theoretical considerations and practical applications. J Transl Med 2011; 9:212. [PMID: 22152192 PMCID: PMC3284408 DOI: 10.1186/1479-5876-9-212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 12/08/2011] [Indexed: 11/16/2022] Open
Abstract
Background HIV vaccine development must address the genetic diversity and plasticity of the virus that permits the presentation of diverse genetic forms to the immune system and subsequent escape from immune pressure. Assessment of potential HIV strain coverage by candidate T cell-based vaccines (whether natural sequence or computationally optimized products) is now a critical component in interpreting candidate vaccine suitability. Methods We have utilized an N-mer identity algorithm to represent T cell epitopes and explore potential coverage of the global HIV pandemic using natural sequences derived from candidate HIV vaccines. Breadth (the number of T cell epitopes generated) and depth (the variant coverage within a T cell epitope) analyses have been incorporated into the model to explore vaccine coverage requirements in terms of the number of discrete T cell epitopes generated. Results We show that when multiple epitope generation by a vaccine product is considered a far more nuanced appraisal of the potential HIV strain coverage of the vaccine product emerges. By considering epitope breadth and depth several important observations were made: (1) epitope breadth requirements to reach particular levels of vaccine coverage, even for natural sequence-based vaccine products is not necessarily an intractable problem for the immune system; (2) increasing the valency (number of T cell epitope variants present) of vaccine products dramatically decreases the epitope requirements to reach particular coverage levels for any epidemic; (3) considering multiple-hit models (more than one exact epitope match with an incoming HIV strain) places a significantly higher requirement upon epitope breadth in order to reach a given level of coverage, to the point where low valency natural sequence based products would not practically be able to generate sufficient epitopes. Conclusions When HIV vaccine sequences are compared against datasets of potential incoming viruses important metrics such as the minimum epitope count required to reach a desired level of coverage can be easily calculated. We propose that such analyses can be applied early in the planning stages and during the execution phase of a vaccine trial to explore theoretical and empirical suitability of a vaccine product to a particular epidemic setting.
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Mothe B, Llano A, Ibarrondo J, Daniels M, Miranda C, Zamarreño J, Bach V, Zuniga R, Pérez-Álvarez S, Berger CT, Puertas MC, Martinez-Picado J, Rolland M, Farfan M, Szinger JJ, Hildebrand WH, Yang OO, Sanchez-Merino V, Brumme CJ, Brumme ZL, Heckerman D, Allen TM, Mullins JI, Gómez G, Goulder PJ, Walker BD, Gatell JM, Clotet B, Korber BT, Sanchez J, Brander C. Definition of the viral targets of protective HIV-1-specific T cell responses. J Transl Med 2011; 9:208. [PMID: 22152067 PMCID: PMC3292987 DOI: 10.1186/1479-5876-9-208] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/07/2011] [Indexed: 02/08/2023] Open
Abstract
Background The efficacy of the CTL component of a future HIV-1 vaccine will depend on the induction of responses with the most potent antiviral activity and broad HLA class I restriction. However, current HIV vaccine designs are largely based on viral sequence alignments only, not incorporating experimental data on T cell function and specificity. Methods Here, 950 untreated HIV-1 clade B or -C infected individuals were tested for responses to sets of 410 overlapping peptides (OLP) spanning the entire HIV-1 proteome. For each OLP, a "protective ratio" (PR) was calculated as the ratio of median viral loads (VL) between OLP non-responders and responders. Results For both clades, there was a negative relationship between the PR and the entropy of the OLP sequence. There was also a significant additive effect of multiple responses to beneficial OLP. Responses to beneficial OLP were of significantly higher functional avidity than responses to non-beneficial OLP. They also had superior in-vitro antiviral activities and, importantly, were at least as predictive of individuals' viral loads than their HLA class I genotypes. Conclusions The data thus identify immunogen sequence candidates for HIV and provide an approach for T cell immunogen design applicable to other viral infections.
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Affiliation(s)
- Beatriz Mothe
- Irsicaixa AIDS Research Institute-HIVACAT, Badalona, Spain
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Peretz Y, Marra O, Thomas R, Legault D, Côté P, Boulassel MR, Rouleau D, Routy JP, Sékaly RP, Tsoukas CM, Tremblay C, Bernard NF. Relative contribution of HIV-specific functional lymphocyte subsets restricted by protective and non-protective HLA alleles. Viral Immunol 2011; 24:189-98. [PMID: 21668360 DOI: 10.1089/vim.2010.0117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of major histocompatibility complex (MHC) class I alleles such as B*57 and B*27 are associated with slow HIV disease progression. HIV-specific immune responses in slow progressors (SP) are characterized by a poly-functional profile. We previously observed within infected subjects that HIV peptide-specific responses could differ from each other in their functional composition. We investigate here whether responses restricted by MHC class I alleles associated with slow disease progression have a more poly-functional profile than responses restricted by other alleles. We stimulated peripheral blood mononuclear cells (PBMCs) isolated from 36 chronically HIV-infected individuals with a panel of optimal peptides restricted by the HLA alleles expressed by each subject, and assessed the contribution of single IL-2-, single IFN-γ-, and IFN-γ/IL-2-secreting lymphocytes to the total response measured using a dual color ELISPOT assay. The contribution of functional subsets to responses restricted by HLA B*57/B*27 was similar in SP and progressors. For responses restricted by other MHC class I alleles, dual IFN-γ/IL-2-secreting lymphocytes contributed significantly more to the total response in SP than progressors. Within SP subjects, peptides restricted by both B*57/B*27 and other alleles stimulated responses with similar functional profiles. In progressors, peptides restricted by B*57/B*27 stimulated responses composed of a significantly greater proportion of IFN-γ/IL-2-secreting cells than peptides restricted by other alleles. Within progressors, the contribution of IFN-γ/IL-2-secreting lymphocytes was greater to epitopes restricted by protective HLA alleles compared with responses restricted by other alleles. HLA haplotypes influence the relative functional composition of HIV-specific responses.
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Affiliation(s)
- Yoav Peretz
- National Immune Monitoring Laboratory (NIML), Genome Québec, Montreal, Québec, Canada
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Gag cytotoxic T lymphocyte escape mutations can increase sensitivity of HIV-1 to human TRIM5alpha, linking intrinsic and acquired immunity. J Virol 2011; 85:11846-54. [PMID: 21917976 DOI: 10.1128/jvi.05201-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although laboratory-adapted HIV-1 strains are largely resistant to the human restriction factor TRIM5α (hTRIM5α), we have recently shown that some viruses carrying capsid (CA) sequences from clinical isolates can be more sensitive to this restriction factor. In this study we evaluated the contribution to this phenotype of CA mutations known to be associated with escape from cytotoxic T lymphocyte (CTL) responses. Recombinant viruses carrying HIV-1 CA sequences from NL4-3 and three different clinical isolates were prepared, along with variants in which mutations associated with CTL resistance were modified by site-directed mutagenesis, and the infectivities of these viruses in target cells expressing hTRIM5α and cells in which TRIM5α activity had been inhibited by overexpression of TRIM5γ were compared. For both hTRIM5α-sensitive viruses studied, CTL-associated mutations were found to be responsible for this phenotype. Both CTL resistance mutations occurring within HLA-restricted CA epitopes and compensatory mutations occurring outside CTL epitopes influenced hTRIM5α sensitivity, and mutations associated with CTL resistance selected in prior hosts can contribute to this effect. The impact of CTL resistance mutations on hTRIM5α sensitivity was context dependent, because mutations shown to be responsible for the TRIM5α-sensitive phenotype in viruses from one patient could have little or no impact on this parameter when introduced into another virus. No fixed relationship between changes in hTRIM5α sensitivity and infectivity was discernible in our studies. Taken together, these findings suggest that CTL mutations may influence HIV-1 replication by modifying both viral infectivity and sensitivity to TRIM5α.
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Berger CT, Frahm N, Price DA, Mothe B, Ghebremichael M, Hartman KL, Henry LM, Brenchley JM, Ruff LE, Venturi V, Pereyra F, Sidney J, Sette A, Douek DC, Walker BD, Kaufmann DE, Brander C. High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control. J Virol 2011; 85:9334-45. [PMID: 21752903 PMCID: PMC3165743 DOI: 10.1128/jvi.00460-11] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/30/2011] [Indexed: 12/20/2022] Open
Abstract
Virus-specific cytotoxic T lymphocytes (CTL) with high levels of functional avidity have been associated with viral clearance in hepatitis C virus infection and with enhanced antiviral protective immunity in animal models. However, the role of functional avidity as a determinant of HIV-specific CTL efficacy remains to be assessed. Here we measured the functional avidities of HIV-specific CTL responses targeting 20 different, optimally defined CTL epitopes restricted by 13 different HLA class I alleles in a cohort comprising 44 HIV controllers and 68 HIV noncontrollers. Responses restricted by HLA-B alleles and responses targeting epitopes located in HIV Gag exhibited significantly higher functional avidities than responses restricted by HLA-A or HLA-C molecules (P = 0.0003) or responses targeting epitopes outside Gag (P < 0.0001). The functional avidities of Gag-specific and HLA-B-restricted responses were higher in HIV controllers than in noncontrollers (P = 0.014 and P = 0.018) and were not restored in HIV noncontrollers initiating antiretroviral therapy. T-cell receptor (TCR) analyses revealed narrower TCR repertoires in higher-avidity CTL populations, which were dominated by public TCR sequences in HIV controllers. Together, these data link the presence of high-avidity Gag-specific and HLA-B-restricted CTL responses with viral suppression in vivo and provide new insights into the immune parameters that mediate spontaneous control of HIV infection.
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Affiliation(s)
- Christoph T. Berger
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Nicole Frahm
- Fred Hutchinson Cancer Research Center/NIAID HIV Vaccine Trials Network (HVTN), Seattle, Washington
| | - David A. Price
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
- Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
| | - Beatriz Mothe
- Lluita contra la Sida Foundation, Hospital Germans Trias i Pujol, Universitat Autònoma de Badalona, Barcelona, Spain
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Musie Ghebremichael
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kari L. Hartman
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Leah M. Henry
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Laura E. Ruff
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Daniel E. Kaufmann
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Christian Brander
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
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Rao X, Hoof I, Fontaine Costa AICA, van Baarle D, Keşmir C. HLA class I allele promiscuity revisited. Immunogenetics 2011; 63:691-701. [PMID: 21695550 PMCID: PMC3190086 DOI: 10.1007/s00251-011-0552-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 06/10/2011] [Indexed: 12/02/2022]
Abstract
The peptide repertoire presented on human leukocyte antigen (HLA) class I molecules is largely determined by the structure of the peptide binding groove. It is expected that the molecules having similar grooves (i.e., belonging to the same supertype) might present similar/overlapping peptides. However, the extent of promiscuity among HLA class I ligands remains controversial: while in many studies T cell responses are detected against epitopes presented by alternative molecules across HLA class I supertypes and loci, peptide elution studies report minute overlaps between the peptide repertoires of even related HLA molecules. To get more insight into the promiscuous peptide binding by HLA molecules, we analyzed the HLA peptide binding data from the large epitope repository, Immune Epitope Database (IEDB), and further performed in silico analysis to estimate the promiscuity at the population level. Both analyses suggest that an unexpectedly large fraction of HLA ligands (>50%) bind two or more HLA molecules, often across supertype or even loci. These results suggest that different HLA class I molecules can nevertheless present largely overlapping peptide sets, and that “functional” HLA polymorphism on individual and population level is probably much lower than previously anticipated.
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Affiliation(s)
- Xiangyu Rao
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Ilka Hoof
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | | | - Debbie van Baarle
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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Maness NJ, Walsh AD, Rudersdorf RA, Erickson PA, Piaskowski SM, Wilson NA, Watkins DI. Chinese origin rhesus macaque major histocompatibility complex class I molecules promiscuously present epitopes from SIV associated with molecules of Indian origin; implications for immunodominance and viral escape. Immunogenetics 2011; 63:587-97. [PMID: 21626440 DOI: 10.1007/s00251-011-0538-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 05/19/2011] [Indexed: 01/21/2023]
Abstract
The presentation of identical peptides by different major histocompatibility complex class I (MHC-I) molecules, termed promiscuity, is a controversial feature of T cell-mediated immunity to pathogens. The astounding diversity of MHC-I molecules in human populations, presumably to enable binding of equally diverse peptides, implies promiscuity would be a rare phenomenon. However, if it occurs, it would have important implications for immunity. We screened 77 animals for responses to peptides known to bind MHC-I molecules that were not expressed by these animals. Some cases of supposed promiscuity were determined to be the result of either non-identical optimal peptides or were simply not mapped to the correct MHC-I molecule in previous studies. Cases of promiscuity, however, were associated with alterations of immunodominance hierarchies, either in terms of the repertoire of peptides presented by the different MHC-I molecules or in the magnitude of the responses directed against the epitopes themselves. Specifically, we found that the Mamu-B*017:01-restricted peptides Vif HW8 and cRW9 were also presented by Mamu-A2*05:26 and targeted by an animal expressing that allele. We also found that the normally subdominant Mamu-A1*001:01 presented peptide Gag QI9 was also presented by Mamu-B*056:01. Both A2*05:26 and B*056:01 are molecules typically or exclusively expressed by animals of Chinese origin. These data clearly demonstrate that MHC-I epitope promiscuity, though rare, might have important implications for immunodominance and for the transmission of escape mutations, depending on the relative frequencies of the given alleles in a population.
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Affiliation(s)
- Nicholas James Maness
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, WI 53711, USA.
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44
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Matthews PC, Adland E, Listgarten J, Leslie A, Mkhwanazi N, Carlson JM, Harndahl M, Stryhn A, Payne RP, Ogwu A, Huang KHG, Frater J, Paioni P, Kloverpris H, Jooste P, Goedhals D, van Vuuren C, Steyn D, Riddell L, Chen F, Luzzi G, Balachandran T, Ndung'u T, Buus S, Carrington M, Shapiro R, Heckerman D, Goulder PJR. HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:5675-86. [PMID: 21498667 PMCID: PMC3738002 DOI: 10.4049/jimmunol.1003711] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The potential contribution of HLA-A alleles to viremic control in chronic HIV type 1 (HIV-1) infection has been relatively understudied compared with HLA-B. In these studies, we show that HLA-A*7401 is associated with favorable viremic control in extended southern African cohorts of >2100 C-clade-infected subjects. We present evidence that HLA-A*7401 operates an effect that is independent of HLA-B*5703, with which it is in linkage disequilibrium in some populations, to mediate lowered viremia. We describe a novel statistical approach to detecting additive effects between class I alleles in control of HIV-1 disease, highlighting improved viremic control in subjects with HLA-A*7401 combined with HLA-B*57. In common with HLA-B alleles that are associated with effective control of viremia, HLA-A*7401 presents highly targeted epitopes in several proteins, including Gag, Pol, Rev, and Nef, of which the Gag epitopes appear immunodominant. We identify eight novel putative HLA-A*7401-restricted epitopes, of which three have been defined to the optimal epitope. In common with HLA-B alleles linked with slow progression, viremic control through an HLA-A*7401-restricted response appears to be associated with the selection of escape mutants within Gag epitopes that reduce viral replicative capacity. These studies highlight the potentially important contribution of an HLA-A allele to immune control of HIV infection, which may have been concealed by a stronger effect mediated by an HLA-B allele with which it is in linkage disequilibrium. In addition, these studies identify a factor contributing to different HIV disease outcomes in individuals expressing HLA-B*5703.
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Affiliation(s)
- Philippa C Matthews
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
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45
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VINNER LASSE, HOLMGREN BIRGITTA, JENSEN KRISTOFFERJ, ESBJORNSSON JOAKIM, BORGGREN M, HENTZE JULIEL, KARLSSON INGRID, ANDRESEN BETINAS, GRAM GREGERSJ, KLOVERPRIS HENRIK, AABY PETER, DA SILVA ZACARIASJOSÉ, FENYÖ EVAMARIA, FOMSGAARD ANDERS. Sequence analysis of HIV-1 isolates from Guinea-Bissau: selection of vaccine epitopes relevant in both West African and European countries. APMIS 2011; 119:487-97. [DOI: 10.1111/j.1600-0463.2011.02763.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Jia X, McLaren PJ, Ripke S, Brumme CJ, Pulit SL, Telenti A, Carrington M, Kadie CM, Carlson JM, Heckerman D, de Bakker PI, Pereyra F, de Bakker PI, Graham RR, Plenge RM, Deeks SG, Walker BD, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Carrington M, Gao X, Qi Y, Yuki Y, Pereyra F, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O’Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DML, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Walker BD, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, Deeks SG, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O’Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC, Olender SA, Ostrowski M, Owen WF, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Robbins GK, Rodes B, Rodriguez M, Rose RC, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, Wout AV, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010; 330:1551-7. [PMID: 21051598 PMCID: PMC3235490 DOI: 10.1126/science.1195271] [Citation(s) in RCA: 913] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA-viral peptide interaction as the major factor modulating durable control of HIV infection.
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Affiliation(s)
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoming Jia
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
| | - Paul J. McLaren
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Xiaoming Jia
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
| | - Paul J. McLaren
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephan Ripke
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Center for Human Genetic Research, MGH, Harvard Medical School, Boston, MA, USA
| | - Chanson J. Brumme
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Sara L. Pulit
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | | | | | | | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | | | - Robert M. Plenge
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven G. Deeks
- University of California San Francisco, San Francisco, CA, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | | | | | | | - Leela Davies
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amy Camargo
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Supriya Gupta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Noël P. Burtt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Namrata Gupta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Emily Cutrell
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Rachel Rosenberg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Kristin L. Moss
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Paul Lemay
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jessica O’Leary
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Todd Schaefer
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Pranshu Verma
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Ildiko Toth
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Brian Block
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Brett Baker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Alissa Rothchild
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jeffrey Lian
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jacqueline Proudfoot
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Donna Marie L. Alvino
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Seanna Vine
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Marylyn M. Addo
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Todd M. Allen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Marcus Altfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Hendrik Streeck
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - David W. Haas
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel R. Kuritzkes
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Roy M. Gulick
- Weill Medical College of Cornell University, New York, NY, USA
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | | | | | - Paul E. Sax
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S. Daar
- University of California Los Angeles, Los Angeles, CA, USA
| | - Heather J. Ribaudo
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | - Brian Agan
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | | | | | | | - Kathryn Anastos
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ben Anderson
- St. Leonards Medical Centre, St. Leonards, Australia
| | | | | | | | - David Bangsberg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- MGH, Harvard Medical School, Boston, MA, USA
| | - Daniel Barbaro
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | | | | | - Simon Barton
- Chelsea and Westminster Hospital, St. Stephen’s Centre, London, UK
| | | | | | - Suzane Bazner
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | | | - Nicole F. Bernard
- Research Institute, McGill University Health Centre, Montreal General Hospital, Montreal, Canada
| | | | - Christopher Birch
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | - Emilie T. Boudreaux
- Louisiana State University Health Sciences Center, University Medical Center East Clinic, Lafayatte, LA, USA
| | - Meg Bradley
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - James F. Braun
- Physicians’ Research Network, Callen-Lorde Community Health Center, New York, NY, USA
| | | | | | | | | | | | - Larry M. Bush
- University of Miami-Miller School of Medicine, Lake Worth, FL, USA
| | | | | | | | | | | | | | | | | | | | - Nancy Chez
- H.E.L.P./Project Samaritan, Bronx, NY, USA
| | - Lisa M. Chirch
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | - Lillian E. Cohn
- 9th Street Internal Medicine Associates, Philadelphia, PA, USA
| | - Brian Conway
- University of British Columbia, Vancouver, Canada
| | - David A. Cooper
- National Centre in HIV Epidemiology and Clinical Research, Sydney, Australia
| | | | - David T. Cox
- Metro Infectious Disease Consultants, Indianapolis, IN, USA
| | | | | | | | | | - Jennifer S. Daly
- University of Massachusetts Memorial Medical Center, Worcester, MA, USA
| | | | - Kristine Davis
- University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - Steven G. Deeks
- University of California San Francisco, San Francisco, CA, USA
| | | | - Craig A. Dietz
- The Kansas City Free Health Clinic, Kansas City, MO, USA
| | - Eleanor Dunham
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | - Joseph J. Eron
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Claire E. Farel
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Helen Ferlazzo
- Visiting Nurse Association of Central New Jersey, Community Health Center, Asbury Park, NJ, USA
| | | | | | | | | | - Neel K. French
- Private Practice of Neel K. French, M.D., Chicago, IL, USA
| | | | | | | | - Joel E. Gallant
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Efrain Garcia
- Private Practice of Efrain Garcia, M.D., Miami, FL, USA
| | | | - Joseph C. Gathe
- Private Practice of Joseph C. Gathe Jr., M.D., Houston, TX, USA
| | | | | | | | - Ian Gilson
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | | | | | | | | | | | - W. David Hardy
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Sonya Heath
- University of Alabama, Birmingham, Birmingham, AL, USA
| | | | | | - Melissa Hladek
- The Catholic University of America, School of Nursing, Washington, DC, USA
| | | | | | - Ricky K. Hsu
- New York University Medical Center, New York, NY, USA
| | | | - Peter Hunt
- University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Hupert
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | | | - Hans Jaeger
- HIV Research and Clinical Care Centre, Munich, Germany
| | | | - Mina John
- Murdoch University, Murdoch, Australia
| | - Jennifer A. Johnson
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Heather Johnson
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | - Kay Johnson
- University of Cincinnati, Cincinnati, OH, USA
| | - Jennifer Joly
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Wayne Kurisu
- Sharp Rees Stealy Medical Center, San Diego, CA, USA
| | - Douglas S. Kwon
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Harry Lampiris
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Jean M.L. Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Janice Lemoine
- Greater Lawrence Family Health Center, Lawrence, MA, USA
| | - Jay A. Levy
- University of California San Francisco, San Francisco, CA, USA
| | - Josep M. Llibre
- Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | | | - Anne Y. Liu
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Dawn Loy
- Infectious Disease Associates, Sarasota, FL, USA
| | | | - Alan Man
- Kaiser Permanente, Portland, OR, USA
| | | | | | - Martin Markowitz
- Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY, USA
| | - Rui Marques
- Deruico Doencas Infecciosas, Porto, Portugal
| | | | | | | | | | | | | | - Katherine McGowan
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dawn McIntyre
- Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Gavin X. Mcleod
- College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Prema Menezes
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Greg Mesa
- Highland Medical Associates, Hendersonville, NC, USA
| | | | - Dirk Meyer-Olson
- Medizinische Hochschule, Abteilung Klinische Immunologie, Hannover, Germany
| | | | | | | | - Ellen H. Nagami
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Iris Nagin
- Lower East Side Service Center, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Eunice Pae
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | - Moti Ramgopal
- Midway Immunology and Research Center, Fort Pierce, FL, USA
| | - Almas Rathod
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - J. Ravishankar
- State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | | | | | | | | | - Berta Rodes
- Fundacion para la Investigacion Biomedica del Hospital Carlos III, Madrid, Spain
| | | | | | | | | | - Polly E. Ross
- Western North Carolina Community Health Services, Asheville, NC, USA
| | - David S. Rubin
- New York Hospital Medical Center of Queens, Flushing, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Paul Stabile
- William F. Ryan Community Health Center, New York, NY, USA
| | | | | | - Francine Stein
- Visiting Nurse Association of Central New Jersey, Community Health Center, Asbury Park, NJ, USA
| | | | | | | | | | | | | | | | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - William Theisen
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Phuong D. Trinh
- Montgomery Infectious Disease Associates, Silver Spring, MD, USA
| | - Alice Tsao
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Peggy Ueda
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Emilia Valadas
- Hospital de Santa Maria, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | | | - Isabel Vecino
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | | | - Barbara H. Wade
- Infectious Diseases Associates of Northwest Florida, Pensacola, FL, USA
| | | | | | | | | | | | | | - Steve Weis
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | - David A. Wheeler
- Clinical Alliance for Research and Education-Infectious Diseases, Annandale, VA, USA
| | - David J. White
- Hawthorn House, Birmingham Heartlands Hospital, Birmingham, UK
| | - Ed Wilkins
- North Manchester General Hospital, Manchester, UK
| | | | | | | | | | - Otto O. Yang
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Beth Zeeman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Meng Zhao
- United Health Services Hospitals, Binghamton, NY, USA
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47
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Ndongala ML, Kamya P, Boulet S, Peretz Y, Rouleau D, Tremblay C, Leblanc R, Côté P, Baril JG, Thomas R, Vézina S, Boulassel MR, Routy JP, Sékaly RP, Bernard NF. Changes in function of HIV-specific T-cell responses with increasing time from infection. Viral Immunol 2010; 23:159-68. [PMID: 20373996 DOI: 10.1089/vim.2009.0084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recently HIV-infected individuals have virus-specific responses characterized by IFN-gamma/IL-2 secretion and proliferation rarely seen in chronic infection. To investigate the timing of loss of HIV-specific T-cell function, we screened cells from 59 treatment-naïve HIV-infected individuals with known dates of infection for proteome-wide responses secreting IFN-gamma/IL-2 and IFN-gamma alone by ELISPOT. HIV peptide-specific proliferation was assessed by carboxyfluorescein diacetate succinimidyl ester (CFSE) dilution. The contribution of IFN-gamma/IL-2 and IFN-gamma-only secretion to the total HIV-specific response was compared in subjects infected <6, 6-12, and 12-36 mo earlier. The frequency of IFN-gamma/IL-2-secreting cells fell, while that of IFN-gamma-only secretion rose with time from infection. HIV peptide-specific proliferative responses were almost exclusively mediated by CD8(+) T cells, and were significantly lower in cells obtained from the 12-36 mo versus < 6 mo post-infection groups. By the second year of infection there was a significant difference in these functions compared to those assessed within 6 mo.
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Affiliation(s)
- Michel L Ndongala
- Research Institute of the McGill University Health Center, Montréal, Québec, Canada
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48
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Koehler RN, Walsh AM, Sanders-Buell EE, Eller LA, Eller M, Currier JR, Bautista CT, Wabwire-Mangen F, Hoelscher M, Maboko L, Kim J, Michael NL, Robb ML, McCutchan FE, Kijak GH. High-throughput high-resolution class I HLA genotyping in East Africa. PLoS One 2010; 5:e10751. [PMID: 20505773 PMCID: PMC2873994 DOI: 10.1371/journal.pone.0010751] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/14/2010] [Indexed: 11/18/2022] Open
Abstract
HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy.
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Affiliation(s)
- Rebecca N. Koehler
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Anne M. Walsh
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Eric E. Sanders-Buell
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Leigh Anne Eller
- Makerere University Walter Reed Research Project, Henry M. Jackson Foundation, Kampala, Uganda
| | - Michael Eller
- Makerere University Walter Reed Research Project, Henry M. Jackson Foundation, Kampala, Uganda
| | - Jeffrey R. Currier
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Christian T. Bautista
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | | | - Michael Hoelscher
- Department of Infectious Diseases and Tropical Medicine, University of Munich, Munich, Germany
- Mbeya Medical Research Program, Mbeya, Tanzania
| | | | - Jerome Kim
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Merlin L. Robb
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Francine E. McCutchan
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Gustavo H. Kijak
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
- * E-mail:
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49
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John M, Heckerman D, James I, Park LP, Carlson JM, Chopra A, Gaudieri S, Nolan D, Haas DW, Riddler SA, Haubrich R, Mallal S. Adaptive interactions between HLA and HIV-1: highly divergent selection imposed by HLA class I molecules with common supertype motifs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 184:4368-77. [PMID: 20231689 PMCID: PMC3011274 DOI: 10.4049/jimmunol.0903745] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Currently, 1.1 million individuals in the United States are living with HIV-1 infection. Although this is a relatively small proportion of the global pandemic, the remarkable mix of ancestries in the United States, drawn together over the past two centuries of continuous population migrations, provides an important and unique perspective on adaptive interactions between HIV-1 and human genetic diversity. HIV-1 is a rapidly adaptable organism and mutates within or near immune epitopes that are determined by the HLA class I genotype of the infected host. We characterized HLA-associated polymorphisms across the full HIV-1 proteome in a large, ethnically diverse national United States cohort of HIV-1-infected individuals. We found a striking divergence in the immunoselection patterns associated with HLA variants that have very similar or identical peptide-binding specificities but are differentially distributed among racial/ethnic groups. Although their similarity in peptide binding functionally clusters these HLA variants into supertypes, their differences at sites within the peptide-binding groove contribute to race-specific selection effects on circulating HIV-1 viruses. This suggests that the interactions between the HLA/HIV peptide complex and the TCR vary significantly within HLA supertype groups, which, in turn, influences HIV-1 evolution.
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Affiliation(s)
- Mina John
- Centre for Clinical Immunology and Biomedical Statistics, Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia.
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50
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Abstract
The role of human leukocyte antigen (HLA) class I supertypes in controlling human immunodeficiency virus type 1 (HIV-1) infection in African Americans has not been established. We examined the effects of the HLA-A and HLA-B alleles and supertypes on the outcomes of HIV-1 clade B infection among 338 African American women and adolescents. HLA-B58 and -B62 supertypes (B58s and B62s) were associated with favorable HIV-1 disease control (proportional odds ratio [POR] of 0.33 and 95% confidence interval [95% CI] of 0.21 to 0.52 for the former and POR of 0.26 and 95% CI of 0.09 to 0.73 for the latter); B7s and B44s were associated with unfavorable disease control (POR of 2.39 and 95% CI of 1.54 to 3.73 for the former and POR of 1.63 and 95% CI of 1.08 to 2.47 for the latter). In general, individual alleles within specific B supertypes exerted relatively homogeneous effects. A notable exception was B27s, whose protective influence (POR, 0.58; 95% CI, 0.35 to 0.94) was masked by the opposing effect of its member allele B*1510. The associations of most B supertypes (e.g., B58s and B7s) were largely explained either by well-known effects of constituent B alleles or by effects of previously unimplicated B alleles aggregated into a particular supertype (e.g., B44s and B62s). A higher frequency of HLA-B genotypic supertypes correlated with a higher mean viral load (VL) and lower mean CD4 count (Pearson's r = 0.63 and 0.62, respectively; P = 0.03). Among the genotypic supertypes, B58s and its member allele B*57 contributed disproportionately to the explainable VL variation. The study demonstrated the dominant role of HLA-B supertypes in HIV-1 clade B-infected African Americans and further dissected the contributions of individual class I alleles and their population frequencies to the supertype effects.
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