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Le QVC, Youk S, Choi M, Jeon H, Kim WI, Ho CS, Park C. Development of an Immortalized Porcine Fibroblast Cell Panel With Different Swine Leukocyte Antigen Genotypes. Front Genet 2022; 13:815328. [PMID: 35198008 PMCID: PMC8859410 DOI: 10.3389/fgene.2022.815328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Immortalized cell lines are valuable resources to expand the molecular characterization of major histocompatibility complex genes and their presented antigens. We generated a panel of immortalized cell lines by transfecting human telomerase reverse transcriptase (hTERT) into primary fibroblast cells prepared from ear, fetal, and lung tissues of 10 pigs from five breeds and successfully cultured them for 30-45 passages. The cell growth characteristic of the immortalized fibroblasts was similar to that of primary fibroblast, which was unable to form colonies on soft agar. The genotypes of major swine leukocyte antigen (SLA) genes, including three classical class I (SLA-1, -2, and -3) and three class II genes (DQB1, DRB1, and DQA), were determined using high-resolution typing. A total of 58 alleles, including a novel allele for SLA-2, were identified. Each cell line was unique. A cell line derived from a National Institutes of Health miniature pig was homozygous across the six major SLA genes. The expression levels of SLA classical class I genes varied among the cell lines and were slightly upregulated in the immortalized compared to the primary cells based on semiquantitative reverse transcription polymerase chain reaction. The immortalized porcine fibroblast cell lines with diverse SLA haplotypes that were developed in this study have potential to be applied in studies regarding the molecular characteristics and genetic structure of SLA genes and epitope-major histocompatibility complex interactions in pigs.
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Affiliation(s)
- Quy Van Chanh Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - SeungYeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Munjeong Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Chonbuk National University, Iksan, South Korea
| | - Chak-Sum Ho
- Gift of Hope Organ & Tissue Donor Network, Itasca, IL, United States
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
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2
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Bugada LF, Smith MR, Wen F. Rapid Identification of MHCII-Binding Peptides Through Microsphere-Assisted Peptide Screening (MAPS). Methods Mol Biol 2022; 2574:233-250. [PMID: 36087205 DOI: 10.1007/978-1-0716-2712-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CD4+ T cells play a vital role in the immune response, and their function requires T cell receptor (TCR) recognition of peptide epitopes presented in complex with MHC class II (MHCII) molecules. Consequently, rapidly identifying peptides that bind MHCII is critical to understanding and treating infectious disease, cancer, autoimmunity, allergy, and transplant rejection. Computational methods provide a fast, ultrahigh-throughput approach to predict MHCII-binding peptides but lack the accuracy of experimental methods. In contrast, experimental methods offer accurate, quantitative results at the expense of speed. To address the gap between these two approaches, we developed a high-throughput, semiquantitative experimental screening strategy termed microsphere-assisted peptide screening (MAPS). Here, we use the Zika virus envelope protein as an example to demonstrate the rapid identification of MHCII-binding peptides from a single pathogenic protein using MAPS. This process involves several key steps including peptide library design, peptide exchange into MHCII, peptide-MHCII loading onto microspheres, flow cytometry screening, and data analysis to identify peptides that bind to one or more MHCII alleles.
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Affiliation(s)
- Luke F Bugada
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Mason R Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
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3
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Abstract
T cells must recognize pathogen-derived peptides bound to major histocompatibility complexes (MHCs) in order to initiate a cell-mediated immune response against an infection, or to support the development of high-affinity antibody responses. Identifying antigens presented on MHCs by infected cells and professional antigen-presenting cells (APCs) during infection may therefore provide a route toward developing new vaccines. Peptides bound to MHCs can be identified at whole-proteome scale using mass spectrometry-a technique referred to as "immunopeptidomics." This technique has emerged as a powerful tool for identifying potential vaccine targets in the context of many infectious diseases. In this review, we discuss the contributions immunopeptidomic studies have made to understanding antigen presentation and T cell priming in the context of infection and the potential for immunopeptidomics to inform the development of vaccines to address pressing global health problems in infectious disease.
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4
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Ortiz-Mahecha CA, Agudelo WA, Patarroyo MA, Patarroyo ME, Suárez CF. MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models. Brief Bioinform 2021; 22:6274818. [PMID: 33979434 DOI: 10.1093/bib/bbab171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/10/2021] [Accepted: 03/30/2021] [Indexed: 11/12/2022] Open
Abstract
Experimentally estimating peptide-major histocompatibility complex (pMHC) binding affinity has been quite challenging due to the many receptors and the many potential ligands implicated in it. We have thus proposed a straightforward computational methodology considering the different mechanisms involved in pMHC binding to facilitate studying such receptor-ligand interactions. We have developed a pipeline using semi-empirical quantum mechanical methods for calculating pMHC class I and II molecules' binding energy (BE). This pipeline can systematize the methodology for calculating pMHC system BE, enabling the rational design of T-cell epitopes to be used as pharmaceuticals and vaccines.
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Affiliation(s)
| | | | | | | | - Carlos F Suárez
- Fundación Instituto de Inmunología de Colombia, Bogota DC, Colombia
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5
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Mpande CAM, Rozot V, Mosito B, Musvosvi M, Dintwe OB, Bilek N, Hatherill M, Scriba TJ, Nemes E. Immune profiling of Mycobacterium tuberculosis-specific T cells in recent and remote infection. EBioMedicine 2021; 64:103233. [PMID: 33610126 PMCID: PMC7902886 DOI: 10.1016/j.ebiom.2021.103233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Recent Mycobacterium tuberculosis (M.tb) infection is associated with a higher risk of progression to tuberculosis disease, compared to persistent infection after remote exposure. However, current immunodiagnostic tools fail to distinguish between recent and remote infection. We aimed to characterise the immunobiology associated with acquisition of M.tb infection and identify a biomarker that can distinguish recent from remote infection. METHODS Healthy South African adolescents were serially tested with QuantiFERON-TB Gold to define recent (QuantiFERON-TB conversion <6 months) and persistent (QuantiFERON-TB+ for >1.5 year) infection. We characterised M.tb-specific CD4 T cell functional (IFN-γ, TNF, IL-2, CD107, CD154), memory (CD45RA, CCR7, CD27, KLRG-1) and activation (HLA-DR) profiles by flow cytometry after CFP-10/ESAT-6 peptide pool or M.tb lysate stimulation. We then assessed the diagnostic performance of immune profiles that were differentially expressed between individuals with recent or persistent QuantiFERON-TB+. FINDINGS CFP-10/ESAT-6-specific CD4 T cell activation but not functional or memory phenotypes distinguished between individuals with recent and persistent QuantiFERON-TB+. In response to M.tb lysate, recent QuantiFERON-TB+ individuals had lower proportions of highly differentiated IFN-γ+TNF+ CD4 T cells expressing a KLRG-1+ effector phenotype and higher proportions of early differentiated IFN-γ-TNF+IL-2+ and activated CD4 T cells compared to persistent QuantiFERON-TB+ individuals. Among all differentially expressed T cell features CFP-10/ESAT-6-specific CD4 T cell activation was the best performing diagnostic biomarker of recent infection. INTERPRETATION Recent M.tb infection is associated with highly activated and moderately differentiated functional M.tb-specific T cell subsets, that can be used as biomarkers to distinguish between recent and remote infection. FUNDING US National Institutes of Health (NIH), Bill and Melinda Gates Foundation, South African National Research Foundation, South African Medical Research Council, and Aeras.
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Affiliation(s)
- Cheleka A M Mpande
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Boitumelo Mosito
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - One B Dintwe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa.
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- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
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6
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Paul S, Grifoni A, Peters B, Sette A. Major Histocompatibility Complex Binding, Eluted Ligands, and Immunogenicity: Benchmark Testing and Predictions. Front Immunol 2020; 10:3151. [PMID: 32117208 PMCID: PMC7012937 DOI: 10.3389/fimmu.2019.03151] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/30/2019] [Indexed: 01/01/2023] Open
Abstract
Antidrug antibody (ADA) responses impact drug safety, potency, and efficacy. It is generally assumed that ADA responses are associated with human leukocyte antigen (HLA) class II-restricted CD4+ T-cell reactivity. Although this review does not address ADA responses per se, the analysis presented here is relevant to the topic, because measuring or predicting CD4+ T-cell reactivity is a common strategy to address ADA and immunogenicity concerns. Because human CD4+ T-cell reactivity relies on the recognition of peptides bound to HLA class II, prediction, or measurement of the capacity of different peptides to bind or be natural ligands of HLA class II is used as a predictor of CD4+ T-cell reactivity and ADA development. Thus, three different interconnected variables are commonly utilized in predicting T-cell reactivity: major histocompatibility complex (MHC) binding, capacity to be generated as natural HLA ligands, and T-cell immunogenicity. To provide the scientific community with guidance in the relative merit of different approaches, it is necessary to clearly define what outcomes are being considered. Thus, the accuracy of HLA binding predictions varies as a function of what the outcome predicted is, whether it is binding itself, natural processing, or T-cell immunogenicity. Furthermore, it is necessary that the accuracy of prediction is based on rigorous benchmarking, grounded by fair, objective, transparent, and experimental criteria. In this review, we provide our perspective on how different variables and methodologies predict each of the various outcomes and point out knowledge gaps and areas to be addressed by further experimental work.
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Affiliation(s)
- Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
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7
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Footprints of antigen processing boost MHC class II natural ligand predictions. Genome Med 2018; 10:84. [PMID: 30446001 PMCID: PMC6240193 DOI: 10.1186/s13073-018-0594-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Background Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, generated in vitro and therefore lacking information about antigen processing. Methods We generate prediction models of peptide to MHC-II binding trained with naturally eluted ligands derived from mass spectrometry in addition to peptide binding affinity data sets. Results We show that integrated prediction models incorporate identifiable rules of antigen processing. In fact, we observed detectable signals of protease cleavage at defined positions of the ligands. We also hypothesize a role of the length of the terminal ligand protrusions for trimming the peptide to the MHC presented ligand. Conclusions The results of integrating binding affinity and eluted ligand data in a combined model demonstrate improved performance for the prediction of MHC-II ligands and T cell epitopes and foreshadow a new generation of improved peptide to MHC-II prediction tools accounting for the plurality of factors that determine natural presentation of antigens. Electronic supplementary material The online version of this article (10.1186/s13073-018-0594-6) contains supplementary material, which is available to authorized users.
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8
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Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M. NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. THE JOURNAL OF IMMUNOLOGY 2017; 199:3360-3368. [PMID: 28978689 DOI: 10.4049/jimmunol.1700893] [Citation(s) in RCA: 875] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/06/2017] [Indexed: 12/12/2022]
Abstract
Cytotoxic T cells are of central importance in the immune system's response to disease. They recognize defective cells by binding to peptides presented on the cell surface by MHC class I molecules. Peptide binding to MHC molecules is the single most selective step in the Ag-presentation pathway. Therefore, in the quest for T cell epitopes, the prediction of peptide binding to MHC molecules has attracted widespread attention. In the past, predictors of peptide-MHC interactions have primarily been trained on binding affinity data. Recently, an increasing number of MHC-presented peptides identified by mass spectrometry have been reported containing information about peptide-processing steps in the presentation pathway and the length distribution of naturally presented peptides. In this article, we present NetMHCpan-4.0, a method trained on binding affinity and eluted ligand data leveraging the information from both data types. Large-scale benchmarking of the method demonstrates an increase in predictive performance compared with state-of-the-art methods when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes.
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Affiliation(s)
- Vanessa Jurtz
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Argentina
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark; .,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Argentina
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9
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Miller A, Asmann Y, Cattaneo L, Braggio E, Keats J, Auclair D, Lonial S, Russell SJ, Stewart AK. High somatic mutation and neoantigen burden are correlated with decreased progression-free survival in multiple myeloma. Blood Cancer J 2017; 7:e612. [PMID: 28937974 PMCID: PMC5709757 DOI: 10.1038/bcj.2017.94] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 06/29/2017] [Indexed: 12/11/2022] Open
Abstract
Tumor-specific mutations can result in immunogenic neoantigens, both of which have been correlated with responsiveness to immune checkpoint inhibitors in highly mutagenic cancers. However, early results of single-agent checkpoint inhibitors in multiple myeloma (MM) have been underwhelming. Therefore, we sought to understand the relationship between mutation and neoantigen landscape of MM patients and responsiveness to therapies. Somatic mutation burden, neoantigen load, and response to therapy were determined using interim data from the MMRF CoMMpass study (NCT01454297) on 664 MM patients. In this population, the mean somatic and missense mutation loads were 405.84(s=608.55) and 63.90(s=95.88) mutations per patient, respectively. There was a positive linear relationship between mutation and neoantigen burdens (R2=0.862). The average predicted neoantigen load was 23.52(s=52.14) neoantigens with an average of 9.40(s=26.97) expressed neoantigens. Survival analysis revealed significantly shorter progression-free survival (PFS) in patients with greater than average somatic missense mutation load (N=163, 0.493 vs 0.726 2-year PFS, P=0.0023) and predicted expressed neoantigen load (N=214, 0.555 vs 0.729 2-year PFS, P=0.0028). This pattern is maintained when stratified by disease stage and cytogenetic abnormalities. Therefore, high mutation and neoantigen load are clinically relevant risk factors that negatively impact survival of MM patients under current standards of care.
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Affiliation(s)
- A Miller
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Y Asmann
- Division of Biomedical Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - L Cattaneo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - E Braggio
- Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - J Keats
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - D Auclair
- Multiple Myeloma Research Foundation, Norwalk CT, USA
| | - S Lonial
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | | | - S J Russell
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Hematology, Mayo Clinic Rochester, MN, USA
| | - A K Stewart
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Hematology and Oncology, Mayo Clinic, Scottsdale, AZ, USA
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10
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Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ. Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity 2017; 46:315-326. [PMID: 28228285 DOI: 10.1016/j.immuni.2017.02.007] [Citation(s) in RCA: 414] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/29/2016] [Accepted: 12/29/2016] [Indexed: 12/11/2022]
Abstract
Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules underlying antigen presentation. However, a key obstacle is the ambiguity that arises from the co-expression of multiple HLA alleles. Here, we have implemented a scalable mono-allelic strategy for profiling the HLA peptidome. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing an application-specific spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of subdominant binding motifs and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural-network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a strategy for systematically learning the rules of endogenous antigen presentation.
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Affiliation(s)
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA; Department of Computer Science, Metropolitan College, Boston University, Boston, MA, 02215, USA
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02142, USA
| | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, 92037, La Jolla, CA
| | - Jonathan Stevens
- Tissue Typing Laboratory, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - William Lane
- Tissue Typing Laboratory, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Guang Lan Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Harvard Medical School, Boston, MA, 02115, USA; Department of Computer Science, Metropolitan College, Boston University, Boston, MA, 02215, USA
| | | | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Center for Cancer Immunology, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Michael S Rooney
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard/MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, 02139 USA; Neon Therapeutics, Cambridge, MA, 02139, USA.
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA.
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11
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Textor A, Schmidt K, Kloetzel PM, Weißbrich B, Perez C, Charo J, Anders K, Sidney J, Sette A, Schumacher TNM, Keller C, Busch DH, Seifert U, Blankenstein T. Preventing tumor escape by targeting a post-proteasomal trimming independent epitope. J Exp Med 2016; 213:2333-2348. [PMID: 27697836 PMCID: PMC5068242 DOI: 10.1084/jem.20160636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/31/2016] [Indexed: 02/05/2023] Open
Abstract
Blankenstein and colleagues describe a novel strategy to avoid tumor escape from adoptive T cell therapy. Adoptive T cell therapy (ATT) can achieve regression of large tumors in mice and humans; however, tumors frequently recur. High target peptide-major histocompatibility complex-I (pMHC) affinity and T cell receptor (TCR)-pMHC affinity are thought to be critical to preventing relapse. Here, we show that targeting two epitopes of the same antigen in the same cancer cells via monospecific T cells, which have similar pMHC and pMHC-TCR affinity, results in eradication of large, established tumors when targeting the apparently subdominant but not the dominant epitope. Only the escape but not the rejection epitope required postproteasomal trimming, which was regulated by IFN-γ, allowing IFN-γ–unresponsive cancer variants to evade. The data describe a novel immune escape mechanism and better define suitable target epitopes for ATT.
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Affiliation(s)
- Ana Textor
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Karin Schmidt
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany.,Institute for Biochemistry, Charité, Campus Mitte, 10117 Berlin, Germany
| | - Peter-M Kloetzel
- Institute for Biochemistry, Charité, Campus Mitte, 10117 Berlin, Germany.,Berlin Institute of Health, 10117 Berlin, Germany
| | - Bianca Weißbrich
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University, 81675 Munich, Germany
| | - Cynthia Perez
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Jehad Charo
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Kathleen Anders
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Ton N M Schumacher
- The Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Christin Keller
- Institute for Biochemistry, Charité, Campus Mitte, 10117 Berlin, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University, 81675 Munich, Germany
| | - Ulrike Seifert
- Institute for Biochemistry, Charité, Campus Mitte, 10117 Berlin, Germany.,Institute for Molecular and Clinical Immunology, Otto-von-Guericke-Universität, 39120 Magdeburg, Germany.,Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Thomas Blankenstein
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany .,Berlin Institute of Health, 10117 Berlin, Germany.,Institute of Immunology, Charité, Campus Buch, 13125 Berlin, Germany
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12
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El Bissati K, Chentoufi AA, Krishack PA, Zhou Y, Woods S, Dubey JP, Vang L, Lykins J, Broderick KE, Mui E, Suzuki Y, Sa Q, Bi S, Cardona N, Verma SK, Fraczek L, Reardon CA, Sidney J, Alexander J, Sette A, Vedvick T, Fox C, Guderian JA, Reed S, Roberts CW, McLeod R. Adjuvanted multi-epitope vaccines protect HLA-A*11:01 transgenic mice against Toxoplasma gondii. JCI Insight 2016; 1:e85955. [PMID: 27699241 DOI: 10.1172/jci.insight.85955] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We created and tested multi-epitope DNA or protein vaccines with TLR4 ligand emulsion adjuvant (gluco glucopyranosyl lipid adjuvant in a stable emulsion [GLA-SE]) for their ability to protect against Toxoplasma gondii in HLA transgenic mice. Our constructs each included 5 of our best down-selected CD8+ T cell-eliciting epitopes, a universal CD4+ helper T lymphocyte epitope (PADRE), and a secretory signal, all arranged for optimal MHC-I presentation. Their capacity to elicit immune and protective responses was studied using immunization of HLA-A*11:01 transgenic mice. These multi-epitope vaccines increased memory CD8+ T cells that produced IFN-γ and protected mice against parasite burden when challenged with T. gondii. Endocytosis of emulsion-trapped protein and cross presentation of the antigens must account for the immunogenicity of our adjuvanted protein. Thus, our work creates an adjuvanted platform assembly of peptides resulting in cross presentation of CD8+ T cell-eliciting epitopes in a vaccine that prevents toxoplasmosis.
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Affiliation(s)
- Kamal El Bissati
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | - Aziz A Chentoufi
- Pathology and Clinical Laboratory Medicine, Department of Immunology, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ying Zhou
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Jitender P Dubey
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, Maryland, USA
| | - Lo Vang
- PaxVax Inc., San Diego, California, USA
| | - Joseph Lykins
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | - Kate E Broderick
- Department of Research and Development, Inovio Pharmaceuticals, Blue Bell, Pennsylvania, USA
| | - Ernest Mui
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | - Yasuhiro Suzuki
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Qila Sa
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Stephanie Bi
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | - Nestor Cardona
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | - Shiv K Verma
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, Maryland, USA
| | - Laura Fraczek
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
| | | | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Tom Vedvick
- Infectious Disease Research Institute, Seattle, Washington, USA
| | - Chris Fox
- Infectious Disease Research Institute, Seattle, Washington, USA
| | | | - Steven Reed
- Infectious Disease Research Institute, Seattle, Washington, USA
| | - Craig W Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Rima McLeod
- Department of Opthalmology and Visual Science; and Department of Pediatrics, Infectious Diseases Division (RM), The University of Chicago, Chicago, Illinois, USA
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13
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Metushi IG, Wriston A, Banerjee P, Gohlke BO, English AM, Lucas A, Moore C, Sidney J, Buus S, Ostrov DA, Mallal S, Phillips E, Shabanowitz J, Hunt DF, Preissner R, Peters B. Acyclovir Has Low but Detectable Influence on HLA-B*57:01 Specificity without Inducing Hypersensitivity. PLoS One 2015; 10:e0124878. [PMID: 26024233 PMCID: PMC4449000 DOI: 10.1371/journal.pone.0124878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/06/2015] [Indexed: 01/11/2023] Open
Abstract
Immune mediated adverse drug reactions (IM-ADRs) remain a significant source of patient morbidity that have more recently been shown to be associated with specific class I and/or II human leukocyte antigen (HLA) alleles. Abacavir-induced hypersensitivity syndrome is a CD8+ T cell dependent IM-ADR that is exclusively mediated by HLA-B*57:01. We and others have previously shown that abacavir can occupy the floor of the peptide binding groove of HLA-B*57:01 molecules, increasing the affinity of certain self peptides resulting in an altered peptide-binding repertoire. Here, we have identified another drug, acyclovir, which appears to act in a similar fashion. As with abacavir, acyclovir showed a dose dependent increase in affinity for peptides with valine and isoleucine at their C-terminus. In agreement with the binding studies, HLA-B*57:01 peptide-elution studies performed in the presence of acyclovir revealed an increased number of endogenously bound peptides with a C-terminal isoleucine. Accordingly, we have hypothesized that acyclovir acts by the same mechanism as abacavir, although our data also suggest the overall effect is much smaller: the largest changes of peptide affinity for acyclovir were 2-5 fold, whereas for abacavir this effect was as much as 1000-fold. Unlike abacavir, acyclovir is not known to cause IM-ADRs. We conclude that the modest effect of acyclovir on HLA binding affinity in contrast to the large effect of abacavir is insufficient to trigger a hypersensitivity syndrome. We further support this by functional in vitro studies where acyclovir, unlike abacavir, was unable to produce an increase in IFN-γ upon expansion of HLA-B*57:01+ PBMCs from healthy donors. Using abacavir and acyclovir as examples we therefore propose an in vitro pre-clinical screening strategy, whereby thresholds can be applied to MHC-peptide binding assays to determine the likelihood that a drug could cause a clinically relevant IM-ADR.
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Affiliation(s)
- Imir G. Metushi
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Amanda Wriston
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Priyanka Banerjee
- Charite—University Medicine Berlin, Institute of Physiology & Experimental Clinical Research Center, Berlin, Germany
- Graduate School of Computational Systems Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bjoern Oliver Gohlke
- Charite—University Medicine Berlin, Institute of Physiology & Experimental Clinical Research Center, Berlin, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - A. Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Andrew Lucas
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Carrie Moore
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Soren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Pathology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Robert Preissner
- Charite—University Medicine Berlin, Institute of Physiology & Experimental Clinical Research Center, Berlin, Germany
- Graduate School of Computational Systems Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
- * E-mail:
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14
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Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M. Automated benchmarking of peptide-MHC class I binding predictions. ACTA ACUST UNITED AC 2015; 31:2174-81. [PMID: 25717196 DOI: 10.1093/bioinformatics/btv123] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/21/2015] [Indexed: 01/31/2023]
Abstract
MOTIVATION Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study. RESULTS The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB. AVAILABILITY AND IMPLEMENTATION Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join. CONTACT mniel@cbs.dtu.dk or bpeters@liai.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas Trolle
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Imir G Metushi
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Jason A Greenbaum
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Yohan Kim
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - John Sidney
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Alessandro Sette
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Bjoern Peters
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
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15
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Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T. Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial. J Virol 2014; 88:8242-55. [PMID: 24829343 PMCID: PMC4135964 DOI: 10.1128/jvi.01164-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The RV144 HIV-1 vaccine trial demonstrated partial efficacy of 31% against HIV-1 infection. Studies into possible correlates of protection found that antibodies specific to the V1 and V2 (V1/V2) region of envelope correlated inversely with infection risk and that viruses isolated from trial participants contained genetic signatures of vaccine-induced pressure in the V1/V2 region. We explored the hypothesis that the genetic signatures in V1 and V2 could be partly attributed to selection by vaccine-primed T cells. We performed a T-cell-based sieve analysis of breakthrough viruses in the RV144 trial and found evidence of predicted HLA binding escape that was greater in vaccine versus placebo recipients. The predicted escape depended on class I HLA A*02- and A*11-restricted epitopes in the MN strain rgp120 vaccine immunogen. Though we hypothesized that this was indicative of postacquisition selection pressure, we also found that vaccine efficacy (VE) was greater in A*02-positive (A*02(+)) participants than in A*02(-) participants (VE = 54% versus 3%, P = 0.05). Vaccine efficacy against viruses with a lysine residue at site 169, important to antibody binding and implicated in vaccine-induced immune pressure, was also greater in A*02(+) participants (VE = 74% versus 15%, P = 0.02). Additionally, a reanalysis of vaccine-induced immune responses that focused on those that were shown to correlate with infection risk suggested that the humoral responses may have differed in A*02(+) participants. These exploratory and hypothesis-generating analyses indicate there may be an association between a class I HLA allele and vaccine efficacy, highlighting the importance of considering HLA alleles and host immune genetics in HIV vaccine trials. IMPORTANCE The RV144 trial was the first to show efficacy against HIV-1 infection. Subsequently, much effort has been directed toward understanding the mechanisms of protection. Here, we conducted a T-cell-based sieve analysis, which compared the genetic sequences of viruses isolated from infected vaccine and placebo recipients. Though we hypothesized that the observed sieve effect indicated postacquisition T-cell selection, we also found that vaccine efficacy was greater for participants who expressed HLA A*02, an allele implicated in the sieve analysis. Though HLA alleles have been associated with disease progression and viral load in HIV-1 infection, these data are the first to suggest the association of a class I HLA allele and vaccine efficacy. While these statistical analyses do not provide mechanistic evidence of protection in RV144, they generate testable hypotheses for the HIV vaccine community and they highlight the importance of assessing the impact of host immune genetics in vaccine-induced immunity and protection. (This study has been registered at ClinicalTrials.gov under registration no. NCT00223080.).
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Affiliation(s)
- Andrew J Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sue Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John McNevin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Youyi Fong
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daryl Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Paul T Edlefsen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Brendan B Larsen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | | | | | - Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hasan Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Philip Konopa
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Snehal Nariya
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Julia N Stoddard
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Kim Wong
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Hong Zhao
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Wenjie Deng
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Brandon S Maust
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Shana Howell
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Adam Bates
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Michelle Lazzaro
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | | | - Esther Lei
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Andrea Bradfield
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Grace Ibitamuno
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | | | | | | | | | | | - Merlin L Robb
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | | | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Silver Spring, Maryland, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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16
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Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia. Blood 2014; 124:453-62. [PMID: 24891321 DOI: 10.1182/blood-2014-04-567933] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genome sequencing has revealed a large number of shared and personal somatic mutations across human cancers. In principle, any genetic alteration affecting a protein-coding region has the potential to generate mutated peptides that are presented by surface HLA class I proteins that might be recognized by cytotoxic T cells. To test this possibility, we implemented a streamlined approach for the prediction and validation of such neoantigens derived from individual tumors and presented by patient-specific HLA alleles. We applied our computational pipeline to 91 chronic lymphocytic leukemias (CLLs) that underwent whole-exome sequencing (WES). We predicted ∼22 mutated HLA-binding peptides per leukemia (derived from ∼16 missense mutations) and experimentally confirmed HLA binding for ∼55% of such peptides. Two CLL patients that achieved long-term remission following allogeneic hematopoietic stem cell transplantation were monitored for CD8(+) T-cell responses against predicted or confirmed HLA-binding peptides. Long-lived cytotoxic T-cell responses were detected against peptides generated from personal tumor mutations in ALMS1, C6ORF89, and FNDC3B presented on tumor cells. Finally, we applied our computational pipeline to WES data (N = 2488 samples) across 13 different cancer types and estimated dozens to thousands of predicted neoantigens per individual tumor, suggesting that neoantigens are frequent in most tumors.
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17
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Nascimento EJM, Mailliard RB, Khan AM, Sidney J, Sette A, Guzman N, Paulaitis M, de Melo AB, Cordeiro MT, Gil LVG, Lemonnier F, Rinaldo C, August JT, Marques ETA. Identification of conserved and HLA promiscuous DENV3 T-cell epitopes. PLoS Negl Trop Dis 2013; 7:e2497. [PMID: 24130917 PMCID: PMC3794980 DOI: 10.1371/journal.pntd.0002497] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 09/09/2013] [Indexed: 12/31/2022] Open
Abstract
Anti-dengue T-cell responses have been implicated in both protection and immunopathology. However, most of the T-cell studies for dengue include few epitopes, with limited knowledge of their inter-serotype variation and the breadth of their human leukocyte antigen (HLA) affinity. In order to expand our knowledge of HLA-restricted dengue epitopes, we screened T-cell responses against 477 overlapping peptides derived from structural and non-structural proteins of the dengue virus serotype 3 (DENV3) by use of HLA class I and II transgenic mice (TgM): A2, A24, B7, DR2, DR3 and DR4. TgM were inoculated with peptides pools and the T-cell immunogenic peptides were identified by ELISPOT. Nine HLA class I and 97 HLA class II novel DENV3 epitopes were identified based on immunogenicity in TgM and their HLA affinity was further confirmed by binding assays analysis. A subset of these epitopes activated memory T-cells from DENV3 immune volunteers and was also capable of priming naïve T-cells, ex vivo, from dengue IgG negative individuals. Analysis of inter- and intra-serotype variation of such an epitope (A02-restricted) allowed us to identify altered peptide ligands not only in DENV3 but also in other DENV serotypes. These studies also characterized the HLA promiscuity of 23 HLA class II epitopes bearing highly conserved sequences, six of which could bind to more than 10 different HLA molecules representing a large percentage of the global population. These epitope data are invaluable to investigate the role of T-cells in dengue immunity/pathogenesis and vaccine design. Although there is an increased recognition of the role of T-cells in both dengue pathogenesis and protection, comprehensive analysis of T-cell activation during dengue infection is hampered by the small repertoire of known human dengue T-cell epitopes. Although dengue serotype 3 (DENV3) is responsible for numerous outbreaks worldwide, most of the known epitopes are from studies of dengue 2 serotype (DENV2). In this study, we identified novel DENV3 T-cell epitopes in HLA transgenic mice that were confirmed by HLA binding assays. A subset of these epitopes activated memory T-cells from subjects who were dengue IgG positive and primed naïve T-cells from dengue IgG negative individuals. Notably, some of HLA class II epitopes bearing highly conserved regions common to all four dengue serotypes could bind to multiple HLAs. We postulate that these highly conserved and HLA promiscuous T-helper epitopes can be important components of a dengue tetravalent vaccine.
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Affiliation(s)
- Eduardo J. M. Nascimento
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (EJMN); , (ETAM)
| | - Robbie B. Mailliard
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Asif M. Khan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Perdana University Graduate School of Medicine, Serdang, Selangor Darul Ehsan, Malaysia
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Nicole Guzman
- Department of Chemical & Biomolecular Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Michael Paulaitis
- Department of Chemical & Biomolecular Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Andréa Barbosa de Melo
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
| | - Marli T. Cordeiro
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
| | - Laura V. G. Gil
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
| | | | - Charles Rinaldo
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ernesto T. A. Marques
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
- * E-mail: (EJMN); , (ETAM)
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18
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Chen S, Li Y, Depontieu FR, McMiller TL, English AM, Shabanowitz J, Kos F, Sidney J, Sette A, Rosenberg SA, Hunt DF, Mariuzza RA, Topalian SL. Structure-based design of altered MHC class II-restricted peptide ligands with heterogeneous immunogenicity. THE JOURNAL OF IMMUNOLOGY 2013; 191:5097-106. [PMID: 24108701 DOI: 10.4049/jimmunol.1300467] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Insights gained from characterizing MHC-peptide-TCR interactions have held the promise that directed structural modifications can have predictable functional consequences. The ability to manipulate T cell reactivity synthetically or through genetic engineering might thus be translated into new therapies for common diseases such as cancer and autoimmune disorders. In the current study, we determined the crystal structure of HLA-DR4 in complex with the nonmutated dominant gp100 epitope gp10044-59, associated with many melanomas. Altered peptide ligands (APLs) were designed to enhance MHC binding and hence T cell recognition of gp100 in HLA-DR4(+) melanoma patients. Increased MHC binding of several APLs was observed, validating this approach biochemically. Nevertheless, heterogeneous preferences of CD4(+) T cells from several HLA-DR4(+) melanoma patients for different gp100 APLs suggested highly variable TCR usage, even among six patients who had been vaccinated against the wild-type gp100 peptide. This heterogeneity prevented the selection of an APL candidate for developing an improved generic gp100 vaccine in melanoma. Our results are consistent with the idea that even conservative changes in MHC anchor residues may result in subtle, yet crucial, effects on peptide contacts with the TCR or on peptide dynamics, such that alterations intended to enhance immunogenicity may be unpredictable or counterproductive. They also underscore a critical knowledge gap that needs to be filled before structural and in vitro observations can be used reliably to devise new immunotherapies for cancer and other disorders.
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Affiliation(s)
- Shuming Chen
- Department of Surgery, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
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19
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Abstract
The paramyxovirus pneumonia virus of mice (PVM) is a rodent model of human respiratory syncytial virus (hRSV) pathogenesis. Here we characterized the PVM-specific CD8(+) T-cell repertoire in susceptible C57BL/6 mice. In total, 15 PVM-specific CD8(+) T-cell epitopes restricted by H-2D(b) and/or H-2K(b) were identified. These data open the door for using widely profiled, genetically manipulated C57BL/6 mice to study the contribution of epitope-specific CD8(+) T cells to PVM pathogenesis.
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Priyadarshini V, Pradhan D, Munikumar M, Swargam S, Umamaheswari A, Rajasekhar D. Genome-based approaches to develop epitope-driven subunit vaccines against pathogens of infective endocarditis. J Biomol Struct Dyn 2013; 32:876-89. [PMID: 24404767 DOI: 10.1080/07391102.2013.795871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Infective endocarditis (IE) has emerged as a public health problem due to changes in the etiologic spectrum and due to involvement of resistant bacterial strains with increased virulence. Developing potent vaccine is an important strategy to tackle IE. Complete genome sequences of eight selected pathogens of IE paved the way to design common T-cell driven subunit vaccines. Comparative genomics and subtractive genomic analysis were applied to identify adinosine tri phosphate (ATP)-binding cassette (ABC) transporter ATP-binding protein from Streptococcus mitis (reference organism) as common vaccine target. Reverse vaccinology technique was implemented using computational tools such as ProPred, SYFPEITHI, and Immune epitope database. Twenty-one T-cell epitopes were predicted from ABC transporter ATP-binding protein. Multiple sequence alignment of ABC transporter ATP-binding protein from eight selected IE pathogens was performed to identify six conserved T-cell epitopes. The six selected T-cell epitopes were further evaluated at structure level for HLA-DRB binding through homology modeling and molecular docking analysis using Maestro v9.2. The proposed six T-cell epitopes showed better binding affinity with the selected HLA-DRB alleles. Subsequently, the docking complexes of T-cell epitope and HLA-DRBs were ranked based on XP Gscore. The T-cell epitope (208-LNYITPDVV-216)-HLA-DRB1(∗)0101 (1T5 W) complex having the best XP Gscore (-13.25 kcal/mol) was assessed for conformational stability and interaction stability through molecular dynamic simulation for 10 ns using Desmond v3.2. The simulation results revealed that the HLA-DRB-epitope complex was stable throughout the simulation time. Thus, the epitope would be ideal candidate for T-cell driven subunit vaccine design against infective endocarditis.
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Affiliation(s)
- Vani Priyadarshini
- a SVIMS Bioinformatics Centre, SVIMS University , Tirupati , Andhra Pradesh , 517507 , India
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21
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Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A. Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles. Immunogenetics 2013; 65:371-86. [PMID: 23417323 PMCID: PMC3633659 DOI: 10.1007/s00251-013-0686-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 01/23/2013] [Indexed: 02/07/2023]
Abstract
Chinese rhesus macaques are of particular interest in simian immunodeficiency virus/human immunodeficiency virus (SIV/HIV) research as these animals have prolonged kinetics of disease progression to acquired immunodeficiency syndrome (AIDS), compared to their Indian counterparts, suggesting that they may be a better model for HIV. Nevertheless, the specific mechanism(s) accounting for these kinetics remains unclear. The study of major histocompatibility complex (MHC) molecules, including their MHC/peptide-binding motifs, provides valuable information for measuring cellular immune responses and deciphering outcomes of infection and vaccine efficacy. In this study, we have provided detailed characterization of six prevalent Chinese rhesus macaque MHC class I alleles, yielding a combined phenotypic frequency of 29 %. The peptide-binding specificity of two of these alleles, Mamu-A2*01:02 and Mamu-B*010:01, as well as the previously characterized allele Mamu-B*003:01 (and Indian rhesus Mamu-B*003:01), was found to be analogous to that of alleles in the HLA-B27 supertype family. Specific alleles in the HLA-B27 supertype family, including HLA-B*27:05, have been associated with long-term nonprogression to AIDS in humans. All six alleles characterized in the present study were found to have specificities analogous to HLA supertype alleles. These data contribute to the concept that Chinese rhesus macaque MHC immunogenetics is more similar to HLA than their Indian rhesus macaque counterparts and thereby warrants further studies to decipher the role of these alleles in the context of SIV infection.
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Affiliation(s)
- Bianca R Mothé
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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22
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Engels B, Engelhard VH, Sidney J, Sette A, Binder DC, Liu RB, Kranz DM, Meredith SC, Rowley DA, Schreiber H. Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity. Cancer Cell 2013; 23:516-26. [PMID: 23597565 PMCID: PMC3658176 DOI: 10.1016/j.ccr.2013.03.018] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 02/21/2013] [Accepted: 03/19/2013] [Indexed: 01/24/2023]
Abstract
Cancers often relapse after adoptive therapy, even though specific T cells kill cells from the same cancer efficiently in vitro. We found that tumor eradication by T cells required high affinities of the targeted peptides for major histocompatibility complex (MHC) class I. Affinities of at least 10 nM were required for relapse-free regression. Only high-affinity peptide-MHC interactions led to efficient cross-presentation of antigen, thereby stimulating cognate T cells to secrete cytokines. These findings highlight the importance of targeting peptides with high affinity for MHC class I when designing T cell-based immunotherapy.
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Affiliation(s)
- Boris Engels
- Department of Pathology, Committee on Immunology and Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA.
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A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population. Immunogenetics 2013; 65:357-70. [PMID: 23392739 DOI: 10.1007/s00251-013-0684-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/19/2013] [Indexed: 01/04/2023]
Abstract
Classic ways to determine MHC restriction involve inhibition with locus-specific antibodies and antigen presentation assays with panels of cell lines matched or mismatched at the various loci of interest. However, these determinations are often complicated by T cell epitope degeneracy and promiscuity. We describe a selection of 46 HLA DR, DQ, and DP specificities that provide worldwide population (phenotypic) coverage of almost 90 % at each locus, and account for over 66 % of all genes at each locus. This panel afforded coverage of at least four HLA class II alleles in over 95 % of the individuals in four study populations of diverse ethnicity from the USA and South Africa. Next, a panel of single HLA class II-transfected cell lines, corresponding to these 46 allelic variants was assembled, consisting of lines previously developed and 15 novel lines generated for the present study. The novel lines were validated by assessing their HLA class II expression by FACS analysis, the in vitro peptide binding activity of HLA molecules purified from the cell lines, and their antigen presenting capacity to T cell lines of known restriction. We also show that these HLA class II-transfected cell lines can be used to rapidly and unambiguously determine HLA restriction of epitopes recognized by an individual donor in a single experiment. This panel of lines will enable high throughput determination of HLA restriction, enabling better characterization of HLA class II-restricted T cell responses and facilitating the development of HLA tetrameric staining reagents.
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24
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de Melo AB, Nascimento EJM, Braga-Neto U, Dhalia R, Silva AM, Oelke M, Schneck JP, Sidney J, Sette A, Montenegro SML, Marques ETA. T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs. PLoS Negl Trop Dis 2013; 7:e1938. [PMID: 23383350 PMCID: PMC3561163 DOI: 10.1371/journal.pntd.0001938] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
The yellow fever vaccines (YF-17D-204 and 17DD) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env) and nonstructural (NS) proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4(+) and CD8(+) T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines.
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Affiliation(s)
- Andréa Barbosa de Melo
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Eduardo J. M. Nascimento
- Center for Vaccine Research, Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ulisses Braga-Neto
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Rafael Dhalia
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Ana Maria Silva
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Mathias Oelke
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jonathan P. Schneck
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, United States of America
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, United States of America
| | - Silvia M. L. Montenegro
- Department of Immunology, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Ernesto T. A. Marques
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
- Center for Vaccine Research, Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Schulten V, Oseroff C, Alam R, Broide D, Vijayanand P, Peters B, Sette A. The identification of potentially pathogenic and therapeutic epitopes from common human allergens. Ann Allergy Asthma Immunol 2012; 110:7-10. [PMID: 23244651 DOI: 10.1016/j.anai.2012.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/01/2012] [Accepted: 10/23/2012] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To outline the processes involved in large-scale T-cell epitope identification from common allergens and illustrate their relevance to development of allergy specific immunotherapy. DATA SOURCES A set of studies recently published by our laboratory illustrating high-throughput identification of allergen specific T-cell epitopes. STUDY SELECTION T-cell responses contribute both directly and indirectly to allergy-related disease. However, the molecular targets (epitopes) recognized by allergen-specific T cells are largely undefined. We review several different studies in the last 2 years that identified novel T-cell epitopes from a panel of 32 different allergen sources. RESULTS Allergen-specific T-cell responses are highly heterogeneous. Epitopes prevalently recognized in allergic patients are often capable of binding to multiple HLA class II molecules. This feature can be used to predict these promiscuous epitopes by bioinformatic predictions. This approach was validated in the Timothy grass system and then applied to a panel of 31 other allergen sources. CONCLUSION T-cell epitopes for common allergens have been identified, and a general method to identify epitopes from additional allergens has been validated. Characterization of epitopes for common allergens might enable new diagnostics and immunotherapy regimens. These data will also allow the study of T-cell responses in different patient populations and throughout disease progression.
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Almeida RR, Rosa DS, Ribeiro SP, Santana VC, Kallás EG, Sidney J, Sette A, Kalil J, Cunha-Neto E. Broad and cross-clade CD4+ T-cell responses elicited by a DNA vaccine encoding highly conserved and promiscuous HIV-1 M-group consensus peptides. PLoS One 2012; 7:e45267. [PMID: 23028895 PMCID: PMC3445454 DOI: 10.1371/journal.pone.0045267] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/15/2012] [Indexed: 11/19/2022] Open
Abstract
T-cell based vaccine approaches have emerged to counteract HIV-1/AIDS. Broad, polyfunctional and cytotoxic CD4+ T-cell responses have been associated with control of HIV-1 replication, which supports the inclusion of CD4+ T-cell epitopes in vaccines. A successful HIV-1 vaccine should also be designed to overcome viral genetic diversity and be able to confer immunity in a high proportion of immunized individuals from a diverse HLA-bearing population. In this study, we rationally designed a multiepitopic DNA vaccine in order to elicit broad and cross-clade CD4+ T-cell responses against highly conserved and promiscuous peptides from the HIV-1 M-group consensus sequence. We identified 27 conserved, multiple HLA-DR-binding peptides in the HIV-1 M-group consensus sequences of Gag, Pol, Nef, Vif, Vpr, Rev and Vpu using the TEPITOPE algorithm. The peptides bound in vitro to an average of 12 out of the 17 tested HLA-DR molecules and also to several molecules such as HLA-DP, -DQ and murine IAb and IAd. Sixteen out of the 27 peptides were recognized by PBMC from patients infected with different HIV-1 variants and 72% of such patients recognized at least 1 peptide. Immunization with a DNA vaccine (HIVBr27) encoding the identified peptides elicited IFN-γ secretion against 11 out of the 27 peptides in BALB/c mice; CD4+ and CD8+ T-cell proliferation was observed against 8 and 6 peptides, respectively. HIVBr27 immunization elicited cross-clade T-cell responses against several HIV-1 peptide variants. Polyfunctional CD4+ and CD8+ T cells, able to simultaneously proliferate and produce IFN-γ and TNF-α, were also observed. This vaccine concept may cope with HIV-1 genetic diversity as well as provide increased population coverage, which are desirable features for an efficacious strategy against HIV-1/AIDS.
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Affiliation(s)
- Rafael Ribeiro Almeida
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Daniela Santoro Rosa
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
- Division of Immunology-Federal University of São Paulo-UNIFESP, São Paulo, Brazil
| | - Susan Pereira Ribeiro
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
| | - Vinicius Canato Santana
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Esper Georges Kallás
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
| | - John Sidney
- Center for Infectious Disease, Allergy and Asthma Research, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Alessandro Sette
- Center for Infectious Disease, Allergy and Asthma Research, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Jorge Kalil
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Heart Institute (InCor), University of São Paulo School of Medicine, São Paulo, Brazil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Laboratory of Clinical Immunology and Allergy-LIM60, Division of Clinical Immunology and Allergy, Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Heart Institute (InCor), University of São Paulo School of Medicine, São Paulo, Brazil
- Institute for Investigation in Immunology-INCT, São Paulo, Brazil
- * E-mail:
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Cai A, Keskin DB, DeLuca DS, Alonso A, Zhang W, Zhang GL, Hammond NN, Nardi V, Stone RM, Neuberg D, Sidney J, Brusic V, Wu CJ. Mutated BCR-ABL generates immunogenic T-cell epitopes in CML patients. Clin Cancer Res 2012; 18:5761-72. [PMID: 22912393 DOI: 10.1158/1078-0432.ccr-12-1182] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Characterization of an approach to identify leukemia neoantigens arising in the context of drug resistance. EXPERIMENTAL DESIGN We assessed whether leukemia neoantigens could be generated from drug-resistant mutations in BCR-ABL after imatinib relapse in patients with chronic myelogenous leukemia (CML). RESULTS We computationally predicted that approximately 70 peptides derived from 26 BCR-ABL mutations would bind eight common alleles of MHC class I (IC(50) < 1,000 nmol/L). Seven of nine imatinib-resistant CML patients were predicted to generate at least 1 peptide that binds autologous HLA alleles. We predicted and confirmed that an E255K mutation-derived peptide would bind HLA-A3 with high affinity (IC(50) = 28 nmol/L), and showed that this peptide is endogenously processed and presented. Polyfunctional E255K-specific CD8+ T cells were detected in two imatinib-resistant HLA-A3+ CML patients concurrent with an effective anti-CML response to further therapy. CONCLUSIONS Our in vitro studies support the hypothesis that leukemia-driven genetic alterations are targeted by the immune system in association with a clinical response, and suggest the possibility of immunizing relapsed patients with CML against newly acquired tumor neoantigens.
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Affiliation(s)
- Ann Cai
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
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Oseroff C, Sidney J, Vita R, Tripple V, McKinney DM, Southwood S, Brodie TM, Sallusto F, Grey H, Alam R, Broide D, Greenbaum JA, Kolla R, Peters B, Sette A. T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 189:1800-11. [PMID: 22786768 PMCID: PMC3411923 DOI: 10.4049/jimmunol.1200850] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A panel of 133 allergens derived from 28 different sources, including fungi, trees, grasses, weeds, and indoor allergens, was surveyed utilizing prediction of HLA class II-binding peptides and ELISPOT assays with PBMC from allergic donors, resulting in the identification of 257 T cell epitopes. More than 90% of the epitopes were novel, and for 14 allergen sources were the first ever identified to our knowledge. The epitopes identified in the different allergen sources summed up to a variable fraction of the total extract response. In cases of allergens in which the identified T cell epitopes accounted for a minor fraction of the extract response, fewer known protein sequences were available, suggesting that for low epitope coverage allergen sources, additional allergen proteins remain to be identified. IL-5 and IFN-γ responses were measured as prototype Th2 and Th1 responses, respectively. Whereas in some cases (e.g., orchard grass, Alternaria, cypress, and Russian thistle) IL-5 production greatly exceeded IFN-γ, in others (e.g., Aspergillus, Penicillum, and alder) the production of IFN-γ exceeded IL-5. Thus, different allergen sources are associated with variable polarization of the responding T cells. The present study represents the most comprehensive survey to date of human allergen-derived T cell epitopes. These epitopes might be used to characterize T cell phenotype/T cell plasticity as a function of seasonality, or as a result of specific immunotherapy treatment or varying disease severity (asthma or rhinitis).
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Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Randi Vita
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Victoria Tripple
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - Scott Southwood
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Tess M. Brodie
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | | | - Howard Grey
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - David Broide
- University of California, San Diego, La Jolla, CA, 92037
| | | | - Ravi Kolla
- 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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29
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Oseroff C, Sidney J, Tripple V, Grey H, Wood R, Broide DH, Greenbaum J, Kolla R, Peters B, Pomés A, Sette A. Analysis of T cell responses to the major allergens from German cockroach: epitope specificity and relationship to IgE production. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 189:679-88. [PMID: 22706084 PMCID: PMC3392449 DOI: 10.4049/jimmunol.1200694] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Bla g allergens are major targets of IgE responses associated with cockroach allergies. However, little is known about corresponding T cell responses, despite their potential involvement in immunopathology and the clinical efficacy of specific immunotherapy. Bioinformatic predictions of the capacity of Bla g 1, 2, 4, 5, 6, and 7 peptides to bind HLA-DR, -DP, and -DQ molecules, and PBMC responses from 30 allergic donors, identified 25 T cell epitopes. Five immunodominant epitopes accounted for more than half of the response. Bla g 5, the most dominant allergen, accounted for 65% of the response, and Bla g 6 accounted for 20%. Bla g 5 induced both IL-5 and IFN-γ responses, whereas Bla g 6 induced mostly IL-5, and, conversely, Bla g 2 induced only IFN-γ. Thus, responses to allergens within a source are independently regulated, suggesting a critical role for the allergen itself, and not extraneous stimulation from other allergens or copresented immunomodulators. In comparing Ab with T cell responses for several donor/allergen combinations, we detected IgE titers in the absence of detectable T cell responses, suggesting that unlinked T cell-B cell help might support development of IgE responses. Finally, specific immunotherapy resulted in IL-5 down modulation, which was not associated with development of IFN-γ or IL-10 responses to any of the Bla g-derived peptides. In summary, the characteristics of T cell responses to Bla g allergens appear uncorrelated with IgE responses. Monitoring these responses may therefore yield important information relevant to understanding cockroach allergies and their treatment.
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Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Victoria Tripple
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Howard Grey
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Robert Wood
- The Johns Hopkins University, Baltimore, MD, 21201
| | | | - Jason Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Ravi Kolla
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, 22903
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
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30
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Antal Z, Baker JC, Smith C, Jarchum I, Babad J, Mukherjee G, Yang Y, Sidney J, Sette A, Santamaria P, DiLorenzo TP. Beyond HLA-A*0201: new HLA-transgenic nonobese diabetic mouse models of type 1 diabetes identify the insulin C-peptide as a rich source of CD8+ T cell epitopes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 188:5766-75. [PMID: 22539795 PMCID: PMC3358524 DOI: 10.4049/jimmunol.1102930] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Type 1 diabetes is an autoimmune disease characterized by T cell responses to β cell Ags, including insulin. Investigations employing the NOD mouse model of the disease have revealed an essential role for β cell-specific CD8(+) T cells in the pathogenic process. As CD8(+) T cells specific for β cell Ags are also present in patients, these reactivities have the potential to serve as therapeutic targets or markers for autoimmune activity. NOD mice transgenic for human class I MHC molecules have previously been employed to identify T cell epitopes having important relevance to the human disease. However, most studies have focused exclusively on HLA-A*0201. To broaden the reach of epitope-based monitoring and therapeutic strategies, we have looked beyond this allele and developed NOD mice expressing human β(2)-microglobulin and HLA-A*1101 or HLA-B*0702, which are representative members of the A3 and B7 HLA supertypes, respectively. We have used islet-infiltrating T cells spontaneously arising in these strains to identify β cell peptides recognized in the context of the transgenic HLA molecules. This work has identified the insulin C-peptide as an abundant source of CD8(+) T cell epitopes. Responses to these epitopes should be of considerable utility for immune monitoring, as they cannot reflect an immune reaction to exogenously administered insulin, which lacks the C-peptide. Because the peptides bound by one supertype member were found to bind certain other members also, the epitopes identified in this study have the potential to result in therapeutic and monitoring tools applicable to large numbers of patients and at-risk individuals.
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Affiliation(s)
- Zoltan Antal
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Pediatric Endocrinology, Children's Hospital at Montefiore, Bronx, NY 10467
| | - Jason C. Baker
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Medicine (Division of Endocrinology), Albert Einstein College of Medicine, Bronx, NY 10461
| | - Carla Smith
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Irene Jarchum
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Jeffrey Babad
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Gayatri Mukherjee
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Yang Yang
- Julia McFarlane Diabetes Research Centre, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Pere Santamaria
- Julia McFarlane Diabetes Research Centre, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Teresa P. DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Medicine (Division of Endocrinology), Albert Einstein College of Medicine, Bronx, NY 10461
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Moore C, Sidney J, English AM, Wriston A, Hunt DF, Shabanowitz J, Southwood S, Bradley K, Lafont BAP, Mothé BR, Sette A. Identification of the peptide-binding motif recognized by the pigtail macaque class I MHC molecule Mane-A1*082:01 (Mane A*0301). Immunogenetics 2012; 64:461-8. [PMID: 22278177 PMCID: PMC3626442 DOI: 10.1007/s00251-012-0600-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/13/2012] [Indexed: 11/29/2022]
Abstract
Rhesus and pigtail macaques have proven to be valuable animal models for several important human diseases, including HIV, where they exhibit similar pathology and disease progression. Because rhesus macaques have been extensively characterized in terms of their major histocompatibility complex (MHC) class I alleles, their demand has soared, making them increasingly difficult to obtain for research purposes. This problem has been exacerbated by a continued export ban in place since 1978. Pigtail macaques represent a potential alternative animal model. However, because their MHC class I alleles have not been characterized in detail, their use has been hindered. To address this, in the present study, we have characterized the peptide binding specificity of the pigtail macaque class I allele Mane-A1*082:01 (formerly known as Mane A*0301), representative of the second most common MHC class I antigen detected across several cohorts. The motif was defined on the basis of binding studies utilizing purified MHC protein and panels of single amino acid substitution analog peptides, as well as sequences of peptide ligands eluted from Mane-A1*082:01. Based on these analyses, Mane-A1*082:01 was found to recognize a motif with H in position 2 and the aromatic residues F and Y, or the hydrophobic/aliphatic residue M, at the C-terminus. Finally, analysis of the binding of a combinatorial peptide library allowed the generation of a detailed quantitative motif that proved effective in the prediction of a set of high-affinity binders derived from chimeric SIV/HIV, an important model virus for studying HIV infection in humans.
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Affiliation(s)
- Carrie Moore
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - A. Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Amanda Wriston
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Donald F. Hunt
- Department of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Scott Southwood
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Kate Bradley
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bernard A. P. Lafont
- Non-Human Primate Immunogenetics and Cellular Immunology Unit, Laboratory of Molecular Microbiology, NIAID/NIH, Bethesda, MD 20892, USA
| | - Bianca R. Mothé
- Department of Biological Sciences, California State University–San Marcos, San Marcos, CA 92069, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proc Natl Acad Sci U S A 2012; 109:9959-64. [PMID: 22645359 DOI: 10.1073/pnas.1207934109] [Citation(s) in RCA: 297] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Idiosyncratic adverse drug reactions are unpredictable, dose-independent and potentially life threatening; this makes them a major factor contributing to the cost and uncertainty of drug development. Clinical data suggest that many such reactions involve immune mechanisms, and genetic association studies have identified strong linkages between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8(+) T cells that required HLA-B*57:01 molecules for their function; however, the mechanism by which abacavir induces this pathologic T-cell response remains unclear. Here we show that abacavir can bind within the F pocket of the peptide-binding groove of HLA-B*57:01, thereby altering its specificity. This provides an explanation for HLA-linked idiosyncratic adverse drug reactions, namely that drugs can alter the repertoire of self-peptides presented to T cells, thus causing the equivalent of an alloreactive T-cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir and that were recognized by T cells of hypersensitive patients. The assays that we have established can be applied to test additional compounds with suspected HLA-linked hypersensitivities in vitro. Where successful, these assays could speed up the discovery and mechanistic understanding of HLA-linked hypersensitivities, and guide the development of safer drugs.
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Burke KP, Munshaw S, Osburn WO, Levine J, Liu L, Sidney J, Sette A, Ray SC, Cox AL. Immunogenicity and cross-reactivity of a representative ancestral sequence in hepatitis C virus infection. THE JOURNAL OF IMMUNOLOGY 2012; 188:5177-88. [PMID: 22508927 DOI: 10.4049/jimmunol.1103008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vaccines designed to prevent or to treat hepatitis C viral infection must achieve maximum cross-reactivity against widely divergent circulating strains. Rational approaches for sequence selection to maximize immunogenicity and minimize genetic distance across circulating strains may enhance vaccine induction of optimal cytotoxic T cell responses. We assessed T cell recognition of potential hepatitis C virus (HCV) vaccine sequences generated using three rational approaches: combining epitopes with predicted tight binding to the MHC, consensus sequence (most common amino acid at each position), and representative ancestral sequence that had been derived using bayesian phylogenetic tools. No correlation was seen between peptide-MHC binding affinity and frequency of recognition, as measured by an IFN-γ T cell response in HLA-matched HCV-infected individuals. Peptides encoding representative, consensus, and natural variant sequences were then tested for the capacity to expand CD8 T cell populations and to elicit cross-reactive CD8 T cell responses. CD8(+) T cells expanded with representative sequence HCV generally more broadly and robustly recognized highly diverse circulating HCV strains than did T cells expanded with either consensus sequence or naturally occurring sequence variants. These data support the use of representative sequence in HCV vaccine design.
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Affiliation(s)
- Kelly P Burke
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Schreiber K, Arina A, Engels B, Spiotto MT, Sidney J, Sette A, Karrison TG, Weichselbaum RR, Rowley DA, Schreiber H. Spleen cells from young but not old immunized mice eradicate large established cancers. Clin Cancer Res 2012; 18:2526-33. [PMID: 22415314 PMCID: PMC5354938 DOI: 10.1158/1078-0432.ccr-12-0127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE Solid tumors that have grown two weeks or longer in mice and have diameters larger than 1 cm are histologically indistinguishable from autochthonous human cancers. When experimental tumors reach this clinically relevant size, they are usually refractory to most immunotherapies but may be destroyed by adoptive T-cell transfer. However, TCR-transgenic T cells and/or tumor cells overexpressing antigens are frequently used in these experiments. Here we studied the requirements for destroying clinical size, unmanipulated 8101 tumors by adoptive cell therapy. EXPERIMENTAL DESIGN 8101 arose in an old mouse after chronic exposure to UV light. A cancer line was established, which was never serially transplanted. The immunodominant CD8(+) T cell-recognized antigen of this tumor is caused by a somatic tumor-specific mutation in the RNA helicase p68. 8101 tumors were treated with spleen cells from young naive, or young and old immunized mice to ascertain the characteristics of immune cells that lead to rejection. RESULTS Here we show that the mutant p68 peptide has an exceptionally high affinity to the presenting MHC class I molecule K(b) and that spleen cells from immunized young syngeneic mice adoptively transferred to Rag(-/-) or cancer-suppressed euthymic mice eradicate 8101 tumors larger than 1 cm in average diameter and established for several weeks. Spleen cells from naive young mice or from old and boosted (reimmunized) mice were ineffective. CONCLUSIONS Relapse-free destruction of large and long-established tumors expressing a genuine very high-affinity tumor-specific antigen can be achieved by using adoptive transfer of lymphocytes from immunized young individuals.
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Affiliation(s)
- Karin Schreiber
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA.
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Reed JS, Sidney J, Piaskowski SM, Glidden CE, León EJ, Burwitz BJ, Kolar HL, Eernisse CM, Furlott JR, Maness NJ, Walsh AD, Rudersdorf RA, Bardet W, McMurtrey CP, O’Connor DH, Hildebrand WH, Sette A, Watkins DI, Wilson NA. The role of MHC class I allele Mamu-A*07 during SIV(mac)239 infection. Immunogenetics 2011; 63:789-807. [PMID: 21732180 PMCID: PMC3706270 DOI: 10.1007/s00251-011-0541-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 05/19/2011] [Indexed: 01/23/2023]
Abstract
Virus-specific CD8(+) T cells play an important role in controlling HIV/SIV replication. These T cells recognize intracellular pathogen-derived peptides displayed on the cell surface by individual MHC class I molecules. In the SIV-infected rhesus macaque model, five Mamu class I alleles have been thoroughly characterized with regard to peptide binding, and a sixth was shown to be uninvolved. In this study, we describe the peptide binding of Mamu-A1*007:01 (formerly Mamu-A*07), an allele present in roughly 5.08% of Indian-origin rhesus macaques (n = 63 of 1,240). We determined a preliminary binding motif by eluting and sequencing endogenously bound ligands. Subsequently, we used a positional scanning combinatorial library and panels of single amino acid substitution analogs to further characterize peptide binding of this allele and derive a quantitative motif. Using this motif, we selected and tested 200 peptides derived from SIV(mac)239 for their capacity to bind Mamu-A1*007:01; 33 were found to bind with an affinity of 500 nM or better. We then used PBMC from SIV-infected or vaccinated but uninfected, A1*007:01-positive rhesus macaques in IFN-γ Elispot assays to screen the peptides for T-cell reactivity. In all, 11 of the peptides elicited IFN-γ(+) T-cell responses. Six represent novel A1*007:01-restricted epitopes. Furthermore, both Sanger and ultradeep pyrosequencing demonstrated the accumulation of amino acid substitutions within four of these six regions, suggestive of selective pressure on the virus by antigen-specific CD8(+) T cells. Thus, it appears that Mamu-A1*007:01 presents SIV-derived peptides to antigen-specific CD8(+) T cells and is part of the immune response to SIV(mac)239.
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Affiliation(s)
- Jason S. Reed
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, San Diego, CA 92109
| | - Shari M. Piaskowski
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Chrystal E. Glidden
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Enrique J. León
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Benjamin J. Burwitz
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Holly L. Kolar
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | | | - Jessica R. Furlott
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Nicholas J. Maness
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Andrew D. Walsh
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Richard A. Rudersdorf
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Wilfried Bardet
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Curtis P. McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - William H. Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, San Diego, CA 92109
| | - David I. Watkins
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
| | - Nancy A. Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53711
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Lundegaard C, Lund O, Nielsen M. Prediction of epitopes using neural network based methods. J Immunol Methods 2011; 374:26-34. [PMID: 21047511 PMCID: PMC3134633 DOI: 10.1016/j.jim.2010.10.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/23/2010] [Accepted: 10/27/2010] [Indexed: 10/18/2022]
Abstract
In this paper, we describe the methodologies behind three different aspects of the NetMHC family for prediction of MHC class I binding, mainly to HLAs. We have updated the prediction servers, NetMHC-3.2, NetMHCpan-2.2, and a new consensus method, NetMHCcons, which, in their previous versions, have been evaluated to be among the very best performing MHC:peptide binding predictors available. Here we describe the background for these methods, and the rationale behind the different optimization steps implemented in the methods. We go through the practical use of the methods, which are publicly available in the form of relatively fast and simple web interfaces. Furthermore, we will review results obtained in actual epitope discovery projects where previous implementations of the described methods have been used in the initial selection of potential epitopes. Selected potential epitopes were all evaluated experimentally using ex vivo assays.
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Affiliation(s)
- Claus Lundegaard
- Center for Biological Sequence Analysis, DTU Systems Biology, Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, DTU Systems Biology, Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, DTU Systems Biology, Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark
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Toxoplasma gondii HLA-B*0702-restricted GRA7(20-28) peptide with adjuvants and a universal helper T cell epitope elicits CD8(+) T cells producing interferon-γ and reduces parasite burden in HLA-B*0702 mice. Hum Immunol 2011; 73:1-10. [PMID: 22027386 DOI: 10.1016/j.humimm.2011.10.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 09/10/2011] [Accepted: 10/03/2011] [Indexed: 11/21/2022]
Abstract
The ability of CD8(+) T cells to act as cytolytic effectors and produce interferon-γ (IFN-γ) was demonstrated to mediate resistance to Toxoplasma gondii in murine models because of the recognition of peptides restricted by murine major histocompatibility complex (MHC) class I molecules. However, no T gondii-specific HLA-B07-restricted peptides were proven protective against T gondii. Recently, 2 T gondii-specific HLA-B*0702-restricted T cell epitopes, GRA7(20-28) (LPQFATAAT) and GRA3(27-35) (VPFVVFLVA), displayed high-affinity binding to HLA-B*0702 and elicited IFN-γ from peripheral blood mononuclear cells of seropositive HLA-B*07 persons. Herein, these peptides were evaluated to determine whether they could elicit IFN-γ in splenocytes of HLA-B*0702 transgenic mice when administered with adjuvants and protect against subsequent challenge. Peptide-specific IFN-γ-producing T cells were identified by enzyme-linked immunosorbent spot and proliferation assays utilizing splenic T lymphocytes from human lymphocyte antigen (HLA) transgenic mice. When HLA-B*0702 mice were immunized with one of the identified epitopes, GRA7(20-28) in conjunction with a universal CD4(+) T cell epitope (PADRE) and adjuvants (CD4(+) T cell adjuvant, GLA-SE, and TLR2 stimulatory Pam(2)Cys for CD8(+) T cells), this immunization induced CD8(+) T cells to produce IFN-γ and protected mice against high parasite burden when challenged with T gondii. This work demonstrates the feasibility of bioinformatics followed by an empiric approach based on HLA binding to test this biologic activity for identifying protective HLA-B*0702-restricted T gondii peptides and adjuvants that elicit protective immune responses in HLA-B*0702 mice.
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Weiskopf D, Yauch LE, Angelo MA, John DV, Greenbaum JA, Sidney J, Kolla RV, De Silva AD, de Silva AM, Grey H, Peters B, Shresta S, Sette A. Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design. THE JOURNAL OF IMMUNOLOGY 2011; 187:4268-79. [PMID: 21918184 DOI: 10.4049/jimmunol.1101970] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The frequency of dengue virus (DENV) infection has increased dramatically in the last few decades, and the lack of a vaccine has led to significant morbidity and mortality worldwide. To date, a convenient murine system to study human T cell responses to DENV has not been available. Mice transgenic for HLA are widely used to model human immune responses, and it has been shown that mouse-passaged DENV is able to replicate to significant levels in IFN-α/βR(-/-) mice. To cover a wide range of HLA phenotypes, we backcrossed IFN-α/βR(-/-) mice with HLA A*0201, A*0101, A*1101, B*0702, and DRB1*0101-transgenic mice. A DENV proteome-wide screen identified a total of 42 epitopes across all HLA-transgenic IFN-α/βR(-/-) strains tested. In contrast, only eight of these elicited responses in the corresponding IFN-α/βR(+/+) mice. We were able to identify T cell epitopes from 9 out of the 10 DENV proteins. However, the majority of responses were derived from the highly conserved nonstructural proteins NS3 and NS5. The relevance of this model is further demonstrated by the fact that most of the epitopes identified in our murine system are also recognized by PBMC from DENV-exposed human donors, and a dominance of HLA B*0702-restricted responses has been detected in both systems. Our results provide new insights into HLA-restricted T cell responses against DENV, and we describe in this study a novel murine model that allows the investigation of T cell-mediated immune mechanisms relevant to vaccine design.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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Zhang GL, Lin HH, Keskin DB, Reinherz EL, Brusic V. Dana-Farber repository for machine learning in immunology. J Immunol Methods 2011; 374:18-25. [PMID: 21782820 DOI: 10.1016/j.jim.2011.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/06/2011] [Indexed: 11/27/2022]
Abstract
The immune system is characterized by high combinatorial complexity that necessitates the use of specialized computational tools for analysis of immunological data. Machine learning (ML) algorithms are used in combination with classical experimentation for the selection of vaccine targets and in computational simulations that reduce the number of necessary experiments. The development of ML algorithms requires standardized data sets, consistent measurement methods, and uniform scales. To bridge the gap between the immunology community and the ML community, we designed a repository for machine learning in immunology named Dana-Farber Repository for Machine Learning in Immunology (DFRMLI). This repository provides standardized data sets of HLA-binding peptides with all binding affinities mapped onto a common scale. It also provides a list of experimentally validated naturally processed T cell epitopes derived from tumor or virus antigens. The DFRMLI data were preprocessed and ensure consistency, comparability, detailed descriptions, and statistically meaningful sample sizes for peptides that bind to various HLA molecules. The repository is accessible at http://bio.dfci.harvard.edu/DFRMLI/.
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Affiliation(s)
- Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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Chen C, Dow C, Wang P, Sidney J, Read A, Harmsen A, Samuel JE, Peters B. Identification of CD4+ T cell epitopes in C. burnetii antigens targeted by antibody responses. PLoS One 2011; 6:e17712. [PMID: 21423609 PMCID: PMC3057979 DOI: 10.1371/journal.pone.0017712] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 02/11/2011] [Indexed: 02/02/2023] Open
Abstract
Coxiella burnetii is an obligate intracellular Gram-negative bacterium that causes acute Q fever and chronic infections in humans. A killed, whole cell vaccine is efficacious, but vaccination can result in severe local or systemic adverse reactions. Although T cell responses are considered pivotal for vaccine derived protective immunity, the epitope targets of CD4+ T cell responses in C. burnetii vaccination have not been elucidated. Since mapping CD4+ epitopes in a genome with over 2,000 ORFs is resource intensive, we focused on 7 antigens that were known to be targeted by antibody responses. 117 candidate peptides were selected from these antigens based on bioinformatics predictions of binding to the murine MHC class II molecule H-2 IAb. We screened these peptides for recognition by IFN-γ producing CD4+ T cell in phase I C. burnetii whole cell vaccine (PI-WCV) vaccinated C57BL/6 mice and identified 8 distinct epitopes from four different proteins. The identified epitope targets account for 8% of the total vaccination induced IFN-γ producing CD4+ T cells. Given that less than 0.4% of the antigens contained in C. burnetii were screened, this suggests that prioritizing antigens targeted by antibody responses is an efficient strategy to identify at least a subset of CD4+ targets in large pathogens. Finally, we examined the nature of linkage between CD4+ T cell and antibody responses in PI-WCV vaccinated mice. We found a surprisingly non-uniform pattern in the help provided by epitope specific CD4+ T cells for antibody production, which can be specific for the epitope source antigen as well as non-specific. This suggests that a complete map of CD4+ response targets in PI-WCV vaccinated mice will likely include antigens against which no antibody responses are made.
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Affiliation(s)
- Chen Chen
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Courtney Dow
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology (LIAI), La Jolla, California, United States of America
| | - Peng Wang
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology (LIAI), La Jolla, California, United States of America
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology (LIAI), La Jolla, California, United States of America
| | - Amanda Read
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - Allen Harmsen
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - James E. Samuel
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology (LIAI), La Jolla, California, United States of America
- * E-mail:
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St Leger AJ, Peters B, Sidney J, Sette A, Hendricks RL. Defining the herpes simplex virus-specific CD8+ T cell repertoire in C57BL/6 mice. THE JOURNAL OF IMMUNOLOGY 2011; 186:3927-33. [PMID: 21357536 DOI: 10.4049/jimmunol.1003735] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HSV type 1 (HSV-1) expresses its genes sequentially as immediate early (α), early (β), leaky late (γ1), and true late (γ2), where viral DNA synthesis is an absolute prerequisite only for γ2 gene expression. The γ1 protein glycoprotein B (gB) contains a strongly immunodominant CD8(+) T cell epitope (gB(498-505)) that is recognized by 50% of both the CD8(+) effector T cells in acutely infected trigeminal ganglia (TG) and the CD8(+) memory T cells in latently infected TG. Of 376 predicted HSV-1 CD8(+) T cell epitopes in C57BL/6 mice, 19 (gB(498-505) and 18 subdominant epitopes) stimulated CD8(+) T cells in the spleens and TG of HSV-1 acutely infected mice. These 19 epitopes identified virtually all CD8(+) T cells in the infected TG that represent all or the vast majority of the HSV-specific CD8(+) TCR repertoire. Only 11 of ∼84 HSV-1 proteins are recognized by CD8(+) T cells, and most (∼80%) are expressed before viral DNA synthesis. Neither the immunodominance of gB(498-505) nor the dominance hierarchy of the subdominant epitopes is due solely to MHC or TCR affinity. We conclude that the vast majority of CD8(+) T cells in HSV-1 acutely infected TG are HSV specific, that HSV-1 β and γ1 proteins that are expressed before viral DNA synthesis are favored targets of CD8(+) T cells, and that dominance within the TCR repertoire is likely due to the frequency or expansion and survival characteristics of CD8(+) T cell precursors.
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Affiliation(s)
- Anthony J St Leger
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities. Immunogenetics 2011; 63:275-90. [PMID: 21274527 PMCID: PMC3068250 DOI: 10.1007/s00251-010-0502-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/07/2010] [Indexed: 01/15/2023]
Abstract
The Simian immunodeficiency virus (SIV)-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection and AIDS-related research, despite the potential that macaques of Chinese origin is a more relevant model. Ongoing efforts to further characterize the Chinese rhesus macaques' major histocompatibility complex (MHC) for composition and function should facilitate greater utilization of the species. Previous studies have demonstrated that Chinese-origin M. mulatta (Mamu) class I alleles are more polymorphic than their Indian counterparts, perhaps inferring a model more representative of human MHC, human leukocyte antigen (HLA). Furthermore, the Chinese rhesus macaque class I allele Mamu-A1*02201, the most frequent allele thus far identified, has recently been characterized and shown to be an HLA-B7 supertype analog, the most frequent supertype in human populations. In this study, we have characterized two additional alleles expressed with high frequency in Chinese rhesus macaques, Mamu-A1*02601 and Mamu-B*08301. Upon the development of MHC-peptide-binding assays and definition of their associated motifs, we reveal that these Mamu alleles share peptide-binding characteristics with the HLA-A2 and HLA-A3 supertypes, respectively, the next most frequent human supertypes after HLA-B7. These data suggest that Chinese rhesus macaques may indeed be a more representative model of HLA gene diversity and function as compared to the species of Indian origin and therefore a better model for investigating human immune responses.
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Cong H, Mui EJ, Witola WH, Sidney J, Alexander J, Sette A, Maewal A, McLeod R. Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted CD8+T cell epitope based, adjuvanted vaccine protective against Toxoplasma gondii. Immunome Res 2010; 6:12. [PMID: 21129215 PMCID: PMC3009956 DOI: 10.1186/1745-7580-6-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/03/2010] [Indexed: 11/17/2022] Open
Abstract
Background Toxoplasmosis causes loss of life, cognitive and motor function, and sight. A vaccine is greatly needed to prevent this disease. The purpose of this study was to use an immmunosense approach to develop a foundation for development of vaccines to protect humans with the HLA-A03 supertype. Three peptides had been identified with high binding scores for HLA-A03 supertypes using bioinformatic algorhythms, high measured binding affinity for HLA-A03 supertype molecules, and ability to elicit IFN-γ production by human HLA-A03 supertype peripheral blood CD8+ T cells from seropositive but not seronegative persons. Results Herein, when these peptides were administered with the universal CD4+T cell epitope PADRE (AKFVAAWTLKAAA) and formulated as lipopeptides, or administered with GLA-SE either alone, or with Pam2Cys added, we found we successfully created preparations that induced IFN-γ and reduced parasite burden in HLA-A*1101(an HLA-A03 supertype allele) transgenic mice. GLA-SE is a novel emulsified synthetic TLR4 ligand that is known to facilitate development of T Helper 1 cell (TH1) responses. Then, so our peptides would include those expressed in tachyzoites, bradyzoites and sporozoites from both Type I and II parasites, we used our approaches which had identified the initial peptides. We identified additional peptides using bioinformatics, binding affinity assays, and study of responses of HLA-A03 human cells. Lastly, we found that immunization of HLA-A*1101 transgenic mice with all the pooled peptides administered with PADRE, GLA-SE, and Pam2Cys is an effective way to elicit IFN-γ producing CD8+ splenic T cells and protection. Immunizations included the following peptides together: KSFKDILPK (SAG1224-232); AMLTAFFLR (GRA6164-172); RSFKDLLKK (GRA7134-142); STFWPCLLR (SAG2C13-21); SSAYVFSVK(SPA250-258); and AVVSLLRLLK(SPA89-98). This immunization elicited robust protection, measured as reduced parasite burden using a luciferase transfected parasite, luciferin, this novel, HLA transgenic mouse model, and imaging with a Xenogen camera. Conclusions Toxoplasma gondii peptides elicit HLA-A03 restricted, IFN-γ producing, CD8+ T cells in humans and mice. These peptides administered with adjuvants reduce parasite burden in HLA-A*1101 transgenic mice. This work provides a foundation for immunosense based vaccines. It also defines novel adjuvants for newly identified peptides for vaccines to prevent toxoplasmosis in those with HLA-A03 supertype alleles.
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Affiliation(s)
- Hua Cong
- Departments of Surgery (Ophthalmology and Visual Sciences) and Pediatrics (Infectious Disease), Committees on Immunology, Molecular Medicine, and Genetics, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, Illinois 60637, USA.
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44
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Lundegaard C, Hoof I, Lund O, Nielsen M. State of the art and challenges in sequence based T-cell epitope prediction. Immunome Res 2010; 6 Suppl 2:S3. [PMID: 21067545 PMCID: PMC2981877 DOI: 10.1186/1745-7580-6-s2-s3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Sequence based T-cell epitope predictions have improved immensely in the last decade. From predictions of peptide binding to major histocompatibility complex molecules with moderate accuracy, limited allele coverage, and no good estimates of the other events in the antigen-processing pathway, the field has evolved significantly. Methods have now been developed that produce highly accurate binding predictions for many alleles and integrate both proteasomal cleavage and transport events. Moreover have so-called pan-specific methods been developed, which allow for prediction of peptide binding to MHC alleles characterized by limited or no peptide binding data. Most of the developed methods are publicly available, and have proven to be very useful as a shortcut in epitope discovery. Here, we will go through some of the history of sequence-based predictions of helper as well as cytotoxic T cell epitopes. We will focus on some of the most accurate methods and their basic background.
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Affiliation(s)
- Claus Lundegaard
- The Technical University of Denmark - DTU, Dept. of Systems Biology, Center for Biological Sequence Analysis - CBS, Kemitorvet 208, DK-2800 Kgs. Lyngby, Denmark
| | - Ilka Hoof
- Utrecht University, Theoretical Biology/Bioinformatics, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ole Lund
- The Technical University of Denmark - DTU, Dept. of Systems Biology, Center for Biological Sequence Analysis - CBS, Kemitorvet 208, DK-2800 Kgs. Lyngby, Denmark
| | - Morten Nielsen
- The Technical University of Denmark - DTU, Dept. of Systems Biology, Center for Biological Sequence Analysis - CBS, Kemitorvet 208, DK-2800 Kgs. Lyngby, Denmark
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45
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Sidney J, Steen A, Moore C, Ngo S, Chung J, Peters B, Sette A. Divergent motifs but overlapping binding repertoires of six HLA-DQ molecules frequently expressed in the worldwide human population. THE JOURNAL OF IMMUNOLOGY 2010; 185:4189-98. [PMID: 20810981 DOI: 10.4049/jimmunol.1001006] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge of the binding repertoires and specificities of HLA-DQ molecules is somewhat limited and contradictory, partly because of the scarcity of reports addressing some of the most common molecules and possibly because of the diversity of the techniques used. In this paper, we report the development of high-throughput binding assays for the six most common DQ molecules in the general worldwide population. Using comprehensive panels of single substitution analogs of specific ligands, we derived detailed binding motifs for DQA1*0501/DQB1*0301, DQA1*0401/DQB1*0402, and DQA1*0101/DQB1*0501 and more detailed motifs for DQA1*0501/DQB1*0201, DQA1*0301/DQB1*0302, and DQA1*0102/DQB1*0602, previously characterized on the basis of sets of eluted ligands and/or limited sets of substituted peptides. In contrast to what has previously been observed for DR and DP molecules, DQ motifs were generally less clearly defined in terms of chemical specificity and, strikingly, had little overlap with each other. However, testing a panel of peptides spanning a set of Phleum pratense Ags, and panels of known DQ epitopes, revealed a surprisingly significant and substantial overlap in the repertoire of peptides bound by these DQ molecules. Although the mechanism underlying these apparently contradictory findings is not clear, it likely reflects the peculiar mode of interaction between DQ (and not DR or DP) molecules and their peptide ligands. Because the DQ molecules studied are found in >85% of the general human population, these findings have important implications for epitope identification studies and monitoring of DQ-restricted immune responses.
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Affiliation(s)
- John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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46
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Cecconi V, Moro M, Del Mare S, Sidney J, Bachi A, Longhi R, Sette A, Protti MP, Dellabona P, Casorati G. The CD4+ T-cell epitope-binding register is a critical parameter when generating functional HLA-DR tetramers with promiscuous peptides. Eur J Immunol 2010; 40:1603-16. [PMID: 20306469 DOI: 10.1002/eji.200940123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Detection of CD4(+) T cells specific for tumor-associated antigens is critical to investigate the spontaneous tumor immunosurveillance and to monitor immunotherapy protocols in patients. We investigated the ability of HLA-DR 1101 multimers to detect CD4(+) T cells specific for three highly promiscuous MAGE-A3 derived peptides: MAGE-A3(191-205) (p39), MAGE-A3(281-295) (p57) and MAGE-A3(286-300) (p58). Tetramers stained specific CD4(+) T cells only when loaded with p39, although all peptides activated the specific T cells when presented by plastic-bound HLA-DR 1101 monomers. This suggested that tetramer staining ability was determined by the mode rather than the affinity of peptide binding to HLA-DR 1101. We hypothesized that peptides should bear a single P1 anchor residue to bind all arms of the multimer in a homogeneous register to generate peptide-HLA-DR conformers with maximal avidity. Bioinformatics analysis indicated that p39 contained one putative P1 anchor residue, whereas the other two peptides contained multiple ones. Designing p57 and p58 analogues containing a single anchor residue generated HLA-DR 1101 tetramers that stained specific CD4(+) T cells. Producing HLA-DR 1101 monomers linked with the optimized MAGE-A3 analogues, but not with the original epitopes, further improved tetramer efficiency. Optimization of CD4(+) T-cell epitope-binding registers is thus critical to generate functional HLA-DR tetramers.
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Affiliation(s)
- Virginia Cecconi
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
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47
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The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype. Immunogenetics 2010; 62:451-64. [PMID: 20480161 PMCID: PMC2890073 DOI: 10.1007/s00251-010-0450-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Accepted: 04/19/2010] [Indexed: 01/30/2023]
Abstract
Of the two rhesus macaque subspecies used for AIDS studies, the Simian immunodeficiency virus-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection, providing both insight into pathogenesis and a system for testing novel vaccines. Despite the Chinese rhesus macaque potentially being a more relevant model for AIDS outcomes than the Indian rhesus macaque, the Chinese-origin rhesus macaques have not been well-characterized for their major histocompatibility complex (MHC) composition and function, reducing their greater utilization. In this study, we characterized a total of 50 unique Chinese rhesus macaques from several varying origins for their entire MHC class I allele composition and identified a total of 58 unique complete MHC class I sequences. Only nine of the sequences had been associated with Indian rhesus macaques, and 28/58 (48.3%) of the sequences identified were novel. From all MHC alleles detected, we prioritized Mamu-A1*02201 for functional characterization based on its higher frequency of expression. Upon the development of MHC/peptide binding assays and definition of its associated motif, we revealed that this allele shares peptide binding characteristics with the HLA-B7 supertype, the most frequent supertype in human populations. These studies provide the first functional characterization of an MHC class I molecule in the context of Chinese rhesus macaques and the first instance of HLA-B7 analogy for rhesus macaques.
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48
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IMMUNOCAT-a data management system for epitope mapping studies. J Biomed Biotechnol 2010; 2010:856842. [PMID: 20490281 PMCID: PMC2871663 DOI: 10.1155/2010/856842] [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: 11/30/2009] [Accepted: 03/07/2010] [Indexed: 12/16/2022] Open
Abstract
To enable rationale vaccine design, studies of molecular and cellular mechanisms of immune recognition need to be linked with clinical studies in humans. A major challenge in conducting such translational research studies lies in the management and integration of large amounts and various types of data collected from multiple sources. For this purpose, we have established “IMMUNOCAT”, an interactive data management system for the epitope discovery research projects conducted by our group. The system provides functions to store, query, and analyze clinical and experimental data, enabling efficient, systematic, and integrative data management. We demonstrate how IMMUNOCAT is utilized in a large-scale research contract that aims to identify epitopes in common allergens recognized by T cells from human donors, in order to facilitate the rational design of allergy vaccines. At clinical sites, demographic information and disease history of each enrolled donor are captured, followed by results of an allergen skin test and blood draw. At the laboratory site, T cells derived from blood samples are tested for reactivity against a panel of peptides derived from common human allergens. IMMUNOCAT stores results from these T cell assays along with MHC:peptide binding data, results from RAST tests for antibody titers in donor serum, and the respective donor HLA typing results. Through this system, we are able to perform queries and integrated analyses of the various types of data. This provides a case study for the use of bioinformatics and information management techniques to track and analyze data produced in a translational research study aimed at epitope identification.
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49
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Tan TG, Mui E, Cong H, Witola WH, Montpetit A, Muench SP, Sidney J, Alexander J, Sette A, Grigg ME, Maewal A, McLeod R. Identification of T. gondii epitopes, adjuvants, and host genetic factors that influence protection of mice and humans. Vaccine 2010; 28:3977-89. [PMID: 20347630 DOI: 10.1016/j.vaccine.2010.03.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/09/2010] [Accepted: 03/15/2010] [Indexed: 11/19/2022]
Abstract
Toxoplasma gondii is an intracellular parasite that causes severe neurologic and ocular disease in immune-compromised and congenitally infected individuals. There is no vaccine protective against human toxoplasmosis. Herein, immunization of L(d) mice with HF10 (HPGSVNEFDF) with palmitic acid moieties or a monophosphoryl lipid A derivative elicited potent IFN-gamma production from L(d)-restricted CD8(+) T cells in vitro and protected mice. CD8(+) T cell peptide epitopes from T. gondii dense granule proteins GRA 3, 6, 7, and Sag 1, immunogenic in humans for HLA-A02(+), HLA-A03(+), and HLA-B07(+) cells were identified. Since peptide repertoire presented by MHC class I molecules to CD8(+) T cells is shaped by endoplasmic reticulum-associated aminopeptidase (ERAAP), polymorphisms in the human ERAAP gene ERAP1 were studied and associate with susceptibility to human congenital toxoplasmosis (p<0.05). These results have important implications for vaccine development.
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MESH Headings
- Adjuvants, Immunologic/pharmacology
- Aminopeptidases/genetics
- Animals
- Antigens, Protozoan/immunology
- CD8-Positive T-Lymphocytes/immunology
- Epitopes, T-Lymphocyte/immunology
- Female
- Genetic Predisposition to Disease
- HLA-A Antigens/immunology
- HLA-B Antigens/immunology
- Humans
- Interferon-gamma/immunology
- Leukocytes, Mononuclear/immunology
- Lipopeptides/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Minor Histocompatibility Antigens
- Models, Molecular
- Polymorphism, Genetic
- Protozoan Proteins/immunology
- Protozoan Vaccines/immunology
- Toxoplasma/immunology
- Toxoplasmosis/genetics
- Toxoplasmosis/immunology
- Toxoplasmosis, Congenital/genetics
- Toxoplasmosis, Congenital/immunology
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Affiliation(s)
- Tze Guan Tan
- Department of Surgery, Committees on Immunology, Molecular Medicine, and Genetics, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, IL 60637, USA
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50
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Two kinetic patterns of epitope-specific CD8 T-cell responses following murine gammaherpesvirus 68 infection. J Virol 2010; 84:2881-92. [PMID: 20053740 DOI: 10.1128/jvi.02229-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Murine gammaherpesvirus 68 (gammaHV68) provides an important experimental model for understanding mechanisms of immune control of the latent human gammaherpesviruses. Antiviral CD8 T cells play a key role throughout three separate phases of the infection: clearance of lytic virus, control of the latency amplification stage, and prevention of reactivation of latently infected cells. Previous analyses have shown that T-cell responses to two well-characterized epitopes derived from ORF6 and ORF61 progress with distinct kinetics. ORF6(487)-specific cells predominate early in infection and then decline rapidly, whereas ORF61(524)-specific cells continue to expand through early latency, due to sustained epitope expression. However, the paucity of identified epitopes to this virus has limited our understanding of the overall complexities of CD8 T-cell immune control throughout infection. Here we screened 1,383 predicted H-2(b)-restricted peptides and identified 33 responses, of which 21 have not previously been reported. Kinetic analysis revealed a spectrum of T-cell responses based on the rapidity of their decline after the peak acute response that generally corresponded to the expression patterns of the two previously characterized epitopes. The slowly declining responses that were maintained during latency amplification proliferated more rapidly and underwent maturation of functional avidity over time. Furthermore, the kinetics of decline was accelerated following infection with a latency-null mutant virus. Overall, the data show that gammaHV68 infection elicits a highly heterogeneous CD8 T-cell response that segregates into two distinctive kinetic patterns controlled by differential epitope expression during the lytic and latency amplification stages of infection.
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