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Pfafferott K, Deshpande P, McKinnon E, Merani S, Lucas A, Heckerman D, Mallal S, John M, Gaudieri S, Lucas M. Anti-hepatitis C virus T-cell immunity in the context of multiple exposures to the virus. PLoS One 2015; 10:e0130420. [PMID: 26107956 PMCID: PMC4480353 DOI: 10.1371/journal.pone.0130420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/20/2015] [Indexed: 01/08/2023] Open
Abstract
Characterisation of Hepatitis C virus (HCV)-specific CD8+ T-cell responses in the context of multiple HCV exposures is critical to identify broadly protective immune responses necessary for an effective HCV vaccine against the different HCV genotypes. However, host and viral genetic diversity complicates vaccine development. To compensate for the observed variation in circulating autologous viruses and host molecules that restrict antigen presentation (human leucocyte antigens; HLA), this study used a reverse genomics approach that identified sites of viral adaptation to HLA-restricted T-cell immune pressure to predict genotype-specific HCV CD8+ T-cell targets. Peptides representing these putative HCV CD8+ T-cell targets, and their adapted form, were used in individualised IFN-γ ELISpot assays to screen for HCV-specific T-cell responses in 133 HCV-seropositive subjects with high-risk of multiple HCV exposures. The data obtained from this study i) confirmed that genetic studies of viral evolution is an effective approach to detect novel in vivo HCV T-cell targets, ii) showed that HCV-specific T-cell epitopes can be recognised in their adapted form and would not have been detected using wild-type peptides and iii) showed that HCV-specific T-cell (but not antibody) responses against alternate genotypes in chronic HCV-infected subjects are readily found, implying clearance of previous alternate genotype infection. In summary, HCV adaptation to HLA Class I-restricted T-cell responses plays a central role in anti-HCV immunity and multiple HCV genotype exposure is highly prevalent in at-risk exposure populations, which are important considerations for future vaccine design.
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Affiliation(s)
- Katja Pfafferott
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Pooja Deshpande
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Crawley, Western Australia, Australia
| | - Elizabeth McKinnon
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Shahzma Merani
- Centre for Forensic Science, University of Western Australia, Crawley, Western Australia, Australia
| | - Andrew Lucas
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - David Heckerman
- Microsoft Research, Microsoft, Redmond, Washington, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine and Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Crawley, Western Australia, Australia
- * E-mail:
| | - Michaela Lucas
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- School of Medicine and Pharmacology, Harry Perkins Institute, University of Western Australia, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
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Paul S, Dillon MBC, Arlehamn CSL, Huang H, Davis MM, McKinney DM, Scriba TJ, Sidney J, Peters B, Sette A. A population response analysis approach to assign class II HLA-epitope restrictions. THE JOURNAL OF IMMUNOLOGY 2015; 194:6164-6176. [PMID: 25948811 DOI: 10.4049/jimmunol.1403074] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/04/2015] [Indexed: 11/19/2022]
Abstract
Identification of the specific HLA locus and allele presenting an epitope for recognition by specific TCRs (HLA restriction) is necessary to fully characterize the immune response to Ags. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, using response data in an HLA-typed population. However, simple odds ratio (OR) calculations can be problematic when dealing with large numbers of subjects and Ags, and because the same epitope can be presented by multiple alleles (epitope promiscuity). In this study, we develop a tool, denominated Restrictor Analysis Tool for Epitopes, to extract inferred restriction from HLA class II-typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II-typed subjects by calculating ORs and relative frequencies from simple data tables. The program is validated by: 1) analyzing data of previously determined HLA restrictions; 2) experimentally determining in selected individuals new HLA restrictions using HLA-transfected cell lines; and 3) predicting HLA restriction of particular peptides and showing that corresponding HLA class II tetramers efficiently bind to epitope-specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of OR values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The Restrictor Analysis Tool for Epitopes program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types.
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Affiliation(s)
- Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Myles B C Dillon
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - Huang Huang
- The Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Mark M Davis
- The Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | | | - Thomas Jens Scriba
- Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
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Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D. Statistical resolution of ambiguous HLA typing data. PLoS Comput Biol 2008; 4:e1000016. [PMID: 18392148 PMCID: PMC2289775 DOI: 10.1371/journal.pcbi.1000016] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 01/30/2008] [Indexed: 11/18/2022] Open
Abstract
High-resolution HLA typing plays a central role in many areas of immunology, such as in identifying immunogenetic risk factors for disease, in studying how the genomes of pathogens evolve in response to immune selection pressures, and also in vaccine design, where identification of HLA-restricted epitopes may be used to guide the selection of vaccine immunogens. Perhaps one of the most immediate applications is in direct medical decisions concerning the matching of stem cell transplant donors to unrelated recipients. However, high-resolution HLA typing is frequently unavailable due to its high cost or the inability to re-type historical data. In this paper, we introduce and evaluate a method for statistical, in silico refinement of ambiguous and/or low-resolution HLA data. Our method, which requires an independent, high-resolution training data set drawn from the same population as the data to be refined, uses linkage disequilibrium in HLA haplotypes as well as four-digit allele frequency data to probabilistically refine HLA typings. Central to our approach is the use of haplotype inference. We introduce new methodology to this area, improving upon the Expectation-Maximization (EM)-based approaches currently used within the HLA community. Our improvements are achieved by using a parsimonious parameterization for haplotype distributions and by smoothing the maximum likelihood (ML) solution. These improvements make it possible to scale the refinement to a larger number of alleles and loci in a more computationally efficient and stable manner. We also show how to augment our method in order to incorporate ethnicity information (as HLA allele distributions vary widely according to race/ethnicity as well as geographic area), and demonstrate the potential utility of this experimentally. A tool based on our approach is freely available for research purposes at http://microsoft.com/science.
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Affiliation(s)
| | - Zabrina Brumme
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Carl Kadie
- Microsoft Research, Redmond, Washington, United States of America
| | - Gao Xiaojiang
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
| | - Bruce Walker
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Frederick, Maryland, United States of America
| | - Mary Carrington
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
| | - Philip Goulder
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - David Heckerman
- Microsoft Research, Redmond, Washington, United States of America
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Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, Hraber P, Hewitt HS, Linde CH, Kavanagh DG, Woodberry T, Henry LM, Faircloth K, Listgarten J, Kadie C, Jojic N, Sango K, Brown NV, Pae E, Zaman MT, Bihl F, Khatri A, John M, Mallal S, Marincola FM, Walker BD, Sette A, Heckerman D, Korber BT, Brander C. Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol 2007; 37:2419-33. [PMID: 17705138 PMCID: PMC2628559 DOI: 10.1002/eji.200737365] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Promiscuous binding of T helper epitopes to MHC class II molecules has been well established, but few examples of promiscuous class I-restricted epitopes exist. To address the extent of promiscuity of HLA class I peptides, responses to 242 well-defined viral epitopes were tested in 100 subjects regardless of the individuals' HLA type. Surprisingly, half of all detected responses were seen in the absence of the originally reported restricting HLA class I allele, and only 3% of epitopes were recognized exclusively in the presence of their original allele. Functional assays confirmed the frequent recognition of HLA class I-restricted T cell epitopes on several alternative alleles across HLA class I supertypes and encoded on different class I loci. These data have significant implications for the understanding of MHC class I-restricted antigen presentation and vaccine development.
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Affiliation(s)
- Nicole Frahm
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Karina Yusim
- Theoretical Biophysics, Los Alamos National Laboratory, Los Alamos, NM
| | - Todd J. Suscovich
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | | | - John Sidney
- La Jolla Institute of Allergy and Immunology, Redmond, WA
| | - Peter Hraber
- Theoretical Biophysics, Los Alamos National Laboratory, Los Alamos, NM
| | - Hannah S. Hewitt
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Caitlyn H. Linde
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Daniel G. Kavanagh
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Tonia Woodberry
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Leah M. Henry
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Kellie Faircloth
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | | | | | | | - Kaori Sango
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Nancy V. Brown
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Eunice Pae
- Fenway Community Health Center, Boston, MA
| | | | - Florian Bihl
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Ashok Khatri
- Endocrine Unit, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | - Mina John
- Centre for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital and Murdoch University, Perth, Australia
| | - Simon Mallal
- Centre for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital and Murdoch University, Perth, Australia
| | | | - Bruce D. Walker
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
| | | | | | - Bette T. Korber
- Theoretical Biophysics, Los Alamos National Laboratory, Los Alamos, NM
- Santa Fe Institute, Santa Fe, NM, USA
| | - Christian Brander
- Partners AIDS Research Center, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, MA
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