1
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Lanfermeijer J, van de Ven K, van Dijken H, Hendriks M, Talavera Ormeño CMP, de Heij F, Roholl P, Borghans JAM, van Baarle D, de Jonge J. Modified influenza M1 58-66 peptide vaccination induces non-relevant T-cells and may enhance pathology after challenge. NPJ Vaccines 2023; 8:116. [PMID: 37573454 PMCID: PMC10423225 DOI: 10.1038/s41541-023-00705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/11/2023] [Indexed: 08/14/2023] Open
Abstract
CD8 + T cells are promising targets for vaccination against influenza A virus (IAV) infection. Their induction via peptide vaccination is not trivial, because peptides are weakly immunogenic. One strategy to overcome this is by vaccination with chemically enhanced altered peptide ligands (CPLs), which have improved MHC-binding and immunogenicity. It remains unknown how peptide-modification affects the resulting immune response. We studied the effect of CPLs derived from the influenza M158-66 epitope (GILGFVFTL) on the T-cell response. In HLA-A2*0201 transgenic mice, CPL-vaccination led to higher T-cell frequencies, but only a small percentage of the induced T cells recognized the GILG-wildtype (WT) peptide. CPL-vaccination resulted in a lower richness of the GILG-WT-specific T-cell repertoire and no improved protection against IAV-infection compared to GILG-WT peptide-vaccination. One CPL even appeared to enhance pathology after IAV-challenge. CPL-vaccination thus induces T cells not targeting the original peptide, which may lead to potential unwanted side effects.
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Affiliation(s)
- Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen van de Ven
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Harry van Dijken
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Femke de Heij
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Virology & Immunology Research. Dept Medical Microbiology and Infection prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jørgen de Jonge
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
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2
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Osei-Hwedieh DO, Sedlacek AL, Hernandez LM, Yamoah AA, Iyer SG, Weiss KR, Binder RJ. Immunosurveillance shapes the emergence of neo-epitope landscapes of sarcomas, revealing prime targets for immunotherapy. JCI Insight 2023; 8:e170324. [PMID: 37427594 PMCID: PMC10371341 DOI: 10.1172/jci.insight.170324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
T cells recognize tumor-derived mutated peptides presented on MHC by tumors. The recognition of these neo-epitopes leads to rejection of tumors, an event that is critical for successful cancer immunosurveillance. Determination of tumor-rejecting neo-epitopes in human tumors has proved difficult, though recently developed systems approaches are becoming increasingly useful at evaluating their immunogenicity. We have used the differential aggretope index to determine the neo-epitope burden of sarcomas and observed a conspicuously titrated antigenic landscape, ranging from the highly antigenic osteosarcomas to the low antigenic leiomyosarcomas and liposarcomas. We showed that the antigenic landscape of the tumors inversely reflected the historical T cell responses in the tumor-bearing patients. We predicted that highly antigenic tumors with poor antitumor T cell responses, such as osteosarcomas, would be responsive to T cell-based immunotherapy regimens and demonstrated this in a murine osteosarcoma model. Our study presents a potentially novel pipeline for determining antigenicity of human tumors, provides an accurate predictor of potential neo-epitopes, and will be an important indicator of which cancers to target with T cell-enhancing immunotherapy.
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Affiliation(s)
| | | | | | | | | | - Kurt R. Weiss
- Department of Orthopaedic Surgery, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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3
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Amaya-Ramirez D, Martinez-Enriquez LC, Parra-López C. Usefulness of Docking and Molecular Dynamics in Selecting Tumor Neoantigens to Design Personalized Cancer Vaccines: A Proof of Concept. Vaccines (Basel) 2023; 11:1174. [PMID: 37514989 PMCID: PMC10386133 DOI: 10.3390/vaccines11071174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 07/30/2023] Open
Abstract
Personalized cancer vaccines based on neoantigens are a new and promising treatment for cancer; however, there are still multiple unresolved challenges to using this type of immunotherapy. Among these, the effective identification of immunogenic neoantigens stands out, since the in silico tools used generate a significant portion of false positives. Inclusion of molecular simulation techniques can refine the results these tools produce. In this work, we explored docking and molecular dynamics to study the association between the stability of peptide-HLA complexes and their immunogenicity, using as a proof of concept two HLA-A2-restricted neoantigens that were already evaluated in vitro. The results obtained were in accordance with the in vitro immunogenicity, since the immunogenic neoantigen ASTN1 remained bound at both ends to the HLA-A2 molecule. Additionally, molecular dynamic simulation suggests that position 1 of the peptide has a more relevant role in stabilizing the N-terminus than previously proposed. Likewise, the mutations may have a "delocalized" effect on the peptide-HLA interaction, which means that the mutated amino acid influences the intensity of the interactions of distant amino acids of the peptide with the HLA. These findings allow us to propose the inclusion of molecular simulation techniques to improve the identification of neoantigens for cancer vaccines.
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Affiliation(s)
| | - Laura Camila Martinez-Enriquez
- Grupo de Inmunología y Medicina Traslacional, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Carlos Parra-López
- Grupo de Inmunología y Medicina Traslacional, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
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4
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Chiaro J, Kasanen HH, Whalley T, Capasso C, Grönholm M, Feola S, Peltonen K, Hamdan F, Hernberg M, Mäkelä S, Karhapää H, Brown PE, Martins B, Fusciello M, Ylösmäki EO, Greco D, Kreutzman AS, Mustjoki S, Szomolay B, Cerullo V. Viral Molecular Mimicry Influences the Antitumor Immune Response in Murine and Human Melanoma. Cancer Immunol Res 2021; 9:981-993. [PMID: 34103348 PMCID: PMC8974425 DOI: 10.1158/2326-6066.cir-20-0814] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/29/2021] [Accepted: 06/03/2021] [Indexed: 01/07/2023]
Abstract
Molecular mimicry is one of the leading mechanisms by which infectious agents can induce autoimmunity. Whether a similar mechanism triggers an antitumor immune response is unexplored, and the role of antiviral T cells infiltrating the tumor has remained anecdotal. To address these questions, we first developed a bioinformatic tool to identify tumor peptides with high similarity to viral epitopes. Using peptides identified by this tool, we demonstrated that, in mice, preexisting immunity toward specific viral epitopes enhanced the efficacy of cancer immunotherapy via molecular mimicry in different settings. To understand whether this mechanism could partly explain immunotherapy responsiveness in humans, we analyzed a cohort of patients with melanoma undergoing anti-PD1 treatment who had a high IgG titer for cytomegalovirus (CMV). In this cohort of patients, we showed that high levels of CMV-specific antibodies were associated with prolonged progression-free survival and found that, in some cases, peripheral blood mononuclear cells (PBMC) could cross-react with both melanoma and CMV homologous peptides. Finally, T-cell receptor sequencing revealed expansion of the same CD8+ T-cell clones when PBMCs were expanded with tumor or homologous viral peptides. In conclusion, we have demonstrated that preexisting immunity and molecular mimicry could influence the response to immunotherapies. In addition, we have developed a free online tool that can identify tumor antigens and neoantigens highly similar to pathogen antigens to exploit molecular mimicry and cross-reactive T cells in cancer vaccine development.
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Affiliation(s)
- Jacopo Chiaro
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Henna H.E. Kasanen
- TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Thomas Whalley
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Cristian Capasso
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Mikaela Grönholm
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Sara Feola
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Karita Peltonen
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Firas Hamdan
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Micaela Hernberg
- TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,Department of Oncology, Comprehensive Cancer Center, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Siru Mäkelä
- TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,Department of Oncology, Comprehensive Cancer Center, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Hanna Karhapää
- TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,Department of Oncology, Comprehensive Cancer Center, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Paul E. Brown
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Beatriz Martins
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Manlio Fusciello
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Erkko O. Ylösmäki
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna S. Kreutzman
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland.,Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom.,HiLIFE Helsinki Institute of Life Science, Helsinki, Finland
| | - Barbara Szomolay
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Vincenzo Cerullo
- Laboratory of ImmunoViroTherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.,TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland.,iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.,HiLIFE Helsinki Institute of Life Science, Helsinki, Finland.,Department of Molecular Medicine and Medical Biotechnology and CEINGE, Naples University Federico II, Naples, Italy.,Corresponding Author: Vincenzo Cerullo, Laboratory of ImmunoViroTherapy, Drug Research Program, University of Helsinki, PO Box 56, Helsinki 00790, Finland. Phone: 358 29 4159328; E-mail:
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5
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Abstract
T cells recognize and respond to self antigens in both cancer and autoimmunity. One strategy to influence this response is to incorporate amino acid substitutions into these T cell-specific epitopes. This strategy is being reconsidered now with the goal of increasing time to regression with checkpoint blockade therapies in cancer and antigen-specific immunotherapies in autoimmunity. We discuss how these amino acid substitutions change the interactions with the MHC class I or II molecule and the responding T cell repertoire. Amino acid substitutions in epitopes that are the most effective in therapies bind more strongly to T cell receptor and/or MHC molecules and cross-react with the same repertoire of T cells as the natural antigen.
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Affiliation(s)
- Jill E Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19thAvenue, Aurora, CO 80045, USA.
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19thAvenue, Aurora, CO 80045, USA; Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, 1775 Aurora Court, Aurora, CO 80045, USA
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6
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Yang X, Xie S, Yang X, Cueva JC, Hou X, Tang Z, Yao H, Mo F, Yin S, Liu A, Lu X. Opportunities and Challenges for Antibodies against Intracellular Antigens. Am J Cancer Res 2019; 9:7792-7806. [PMID: 31695801 PMCID: PMC6831482 DOI: 10.7150/thno.35486] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Therapeutic antibodies are one most significant advances in immunotherapy, the development of antibodies against disease-associated MHC-peptide complexes led to the introduction of TCR-like antibodies. TCR-like antibodies combine the recognition of intracellular proteins with the therapeutic potency and versatility of monoclonal antibodies (mAb), offering an unparalleled opportunity to expand the repertoire of therapeutic antibodies available to treat diseases like cancer. This review details the current state of TCR-like antibodies and describes their production, mechanisms as well as their applications. In addition, it presents an insight on the challenges that they must overcome in order to become commercially and clinically validated.
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7
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Brown SD, Holt RA. Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome. Oncoimmunology 2018; 8:1556080. [PMID: 30723589 PMCID: PMC6350689 DOI: 10.1080/2162402x.2018.1556080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023] Open
Abstract
The self-immunopeptidome is the repertoire of all self-peptides that can be presented by the combination of MHC variants carried by an individual, defined by their HLA genotype. Each MHC variant presents a distinct set of self-peptides, and the number of peptides in a set is variable. Subjects carrying MHC variants that present fewer self-peptides should also present fewer mutated peptides, resulting in decreased immune pressure on tumor cells. To explore this, we predicted peptide-MHC binding values using all unique 8-11mer human peptides in the human proteome and all available HLA class I allelic variants, for a total of 134 billion unique peptide--MHC binding predictions. From these predictions, we observe that most peptides are able to be presented by relatively few (< 250) MHC, while some can be presented by upwards of 1,500 different MHC. There is substantial overlap among the repertoires of peptides presented by different MHC and no relationship between the number of peptides presented and HLA population frequency. Nearly 30% of self-peptides are presentable by at least one MHC, leaving 70% of the human peptidome unsurveyed by T cells. We observed similar distributions of predicted self-immunopeptidome sizes in cancer subjects compared to controls, and within the pan-cancer population, predicted self-immunopeptidome size combined with mutational load to predict survival. Self-immunopeptidome analysis revealed evidence for tumor immunoediting and identified specific peptide positions that most influence immunogenicity. Because self-immunopeptidome size is defined by HLA genotypes and approximates neoantigen load, HLA genotyping could offer a rapid predictive biomarker for response to immunotherapy.
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Affiliation(s)
- Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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8
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Ayres CM, Corcelli SA, Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Front Immunol 2017; 8:935. [PMID: 28824655 PMCID: PMC5545744 DOI: 10.3389/fimmu.2017.00935] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 01/28/2023] Open
Abstract
Structural biology of peptides presented by class I and class II MHC proteins has transformed immunology, impacting our understanding of fundamental immune mechanisms and allowing researchers to rationalize immunogenicity and design novel vaccines. However, proteins are not static structures as often inferred from crystallographic structures. Their components move and breathe individually and collectively over a range of timescales. Peptides bound within MHC peptide-binding grooves are no exception and their motions have been shown to impact recognition by T cell and other receptors in ways that influence function. Furthermore, peptides tune the motions of MHC proteins themselves, which impacts recognition of peptide/MHC complexes by other proteins. Here, we review the motional properties of peptides in MHC binding grooves and discuss how peptide properties can influence MHC motions. We briefly review theoretical concepts about protein motion and highlight key data that illustrate immunological consequences. We focus primarily on class I systems due to greater availability of data, but segue into class II systems as the concepts and consequences overlap. We suggest that characterization of the dynamic “energy landscapes” of peptide/MHC complexes and the resulting functional consequences is one of the next frontiers in structural immunology.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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9
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Ayres CM, Riley TP, Corcelli SA, Baker BM. Modeling Sequence-Dependent Peptide Fluctuations in Immunologic Recognition. J Chem Inf Model 2017; 57:1990-1998. [PMID: 28696685 DOI: 10.1021/acs.jcim.7b00118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In cellular immunity, T cells recognize peptide antigens bound and presented by major histocompatibility complex (MHC) proteins. The motions of peptides bound to MHC proteins play a significant role in determining immunogenicity. However, existing approaches for investigating peptide/MHC motional dynamics are challenging or of low throughput, hindering the development of algorithms for predicting immunogenicity from large databases, such as those of tumor or genetically unstable viral genomes. We addressed this by performing extensive molecular dynamics simulations on a large structural database of peptides bound to the most commonly expressed human class-I MHC protein, HLA-A*0201. The simulations reproduced experimental indicators of motion and were used to generate simple models for predicting site-specific, rapid motions of bound peptides through differences in their sequence and chemical composition alone. The models can easily be applied on their own or incorporated into immunogenicity prediction algorithms. Beyond their predictive power, the models provide insight into how amino acid substitutions can influence peptide and protein motions and how dynamic information is communicated across peptides. They also indicate a link between peptide rigidity and hydrophobicity, two features known to be important in influencing cellular immune responses.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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10
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Rosendahl Huber SK, Luimstra JJ, van Beek J, Hoppes R, Jacobi RHJ, Hendriks M, Kapteijn K, Ouwerkerk C, Rodenko B, Ovaa H, de Jonge J. Chemical Modification of Influenza CD8+ T-Cell Epitopes Enhances Their Immunogenicity Regardless of Immunodominance. PLoS One 2016; 11:e0156462. [PMID: 27333291 PMCID: PMC4917206 DOI: 10.1371/journal.pone.0156462] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/13/2016] [Indexed: 11/19/2022] Open
Abstract
T cells are essential players in the defense against infection. By targeting the MHC class I antigen-presenting pathway with peptide-based vaccines, antigen-specific T cells can be induced. However, low immunogenicity of peptides poses a challenge. Here, we set out to increase immunogenicity of influenza-specific CD8+ T cell epitopes. By substituting amino acids in wild type sequences with non-proteogenic amino acids, affinity for MHC can be increased, which may ultimately enhance cytotoxic CD8+ T cell responses. Since preventive vaccines against viruses should induce a broad immune response, we used this method to optimize influenza-specific epitopes of varying dominance. For this purpose, HLA-A*0201 epitopes GILGFVFTL, FMYSDFHFI and NMLSTVLGV were selected in order of decreasing MHC-affinity and dominance. For all epitopes, we designed chemically enhanced altered peptide ligands (CPLs) that exhibited greater binding affinity than their WT counterparts; even binding scores of the high affinity GILGFVFTL epitope could be improved. When HLA-A*0201 transgenic mice were vaccinated with selected CPLs, at least 2 out of 4 CPLs of each epitope showed an increase in IFN-γ responses of splenocytes. Moreover, modification of the low affinity epitope NMLSTVLGV led to an increase in the number of mice that responded. By optimizing three additional influenza epitopes specific for HLA-A*0301, we show that this strategy can be extended to other alleles. Thus, enhancing binding affinity of peptides provides a valuable tool to improve the immunogenicity and range of preventive T cell-targeted peptide vaccines.
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Affiliation(s)
- Sietske K. Rosendahl Huber
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Jolien J. Luimstra
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Institute for Chemical Immunology (ICI), Utrecht, the Netherlands
| | - Josine van Beek
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Rieuwert Hoppes
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ronald H. J. Jacobi
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Hendriks
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kim Kapteijn
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Casper Ouwerkerk
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Boris Rodenko
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Institute for Chemical Immunology (ICI), Utrecht, the Netherlands
| | - Jørgen de Jonge
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- * E-mail:
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11
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Yao S, Liu J, Qi J, Chen R, Zhang N, Liu Y, Wang J, Wu Y, Gao GF, Xia C. Structural Illumination of Equine MHC Class I Molecules Highlights Unconventional Epitope Presentation Manner That Is Evolved in Equine Leukocyte Antigen Alleles. THE JOURNAL OF IMMUNOLOGY 2016; 196:1943-54. [DOI: 10.4049/jimmunol.1501352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 12/03/2015] [Indexed: 01/20/2023]
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12
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Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II, Srivastava PK. Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. J Exp Med 2014; 211:2231-48. [PMID: 25245761 PMCID: PMC4203949 DOI: 10.1084/jem.20141308] [Citation(s) in RCA: 274] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/05/2014] [Indexed: 12/23/2022] Open
Abstract
The mutational repertoire of cancers creates the neoepitopes that make cancers immunogenic. Here, we introduce two novel tools that identify, with relatively high accuracy, the small proportion of neoepitopes (among the hundreds of potential neoepitopes) that protect the host through an antitumor T cell response. The two tools consist of (a) the numerical difference in NetMHC scores between the mutated sequences and their unmutated counterparts, termed the differential agretopic index, and (b) the conformational stability of the MHC I-peptide interaction. Mechanistically, these tools identify neoepitopes that are mutated to create new anchor residues for MHC binding, and render the overall peptide more rigid. Surprisingly, the protective neoepitopes identified here elicit CD8-dependent immunity, even though their affinity for K(d) is orders of magnitude lower than the 500-nM threshold considered reasonable for such interactions. These results greatly expand the universe of target cancer antigens and identify new tools for human cancer immunotherapy.
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Affiliation(s)
- Fei Duan
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT 06030
| | - Jorge Duitama
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269
| | - Sahar Al Seesi
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269
| | - Cory M Ayres
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Arpita P Pawashe
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT 06030
| | - Tatiana Blanchard
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT 06030
| | - David McMahon
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT 06030
| | - John Sidney
- LaJolla Institute of Allergy and Immunology, La Jolla, CA 92037
| | | | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Ion I Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT 06030
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13
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Buhrman JD, Slansky JE. Improving T cell responses to modified peptides in tumor vaccines. Immunol Res 2013; 55:34-47. [PMID: 22936035 DOI: 10.1007/s12026-012-8348-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Immune recognition and elimination of cancerous cells is the primary goal of cancer immunotherapy. However, obstacles including immune tolerance and tumor-induced immunosuppression often limit beneficial immune responses. Vaccination is one proposed intervention that may help to overcome these issues and is an active area of study in cancer immunotherapy. Immunizing with tumor antigenic peptides is a promising, straight-forward vaccine strategy hypothesized to boost preexisting antitumor immunity. However, tumor antigens are often weak T cell agonists, attributable to several mechanisms, including immune self-tolerance and poor immunogenicity of self-derived tumor peptides. One strategy for overcoming these mechanisms is vaccination with mimotopes, or peptide mimics of tumor antigens, which alter the antigen presentation and/or T cell activation to increase the expansion of tumor-specific T cells. Evaluation of mimotope vaccine strategies has revealed that even subtle alterations in peptide sequence can dramatically alter antigen presentation and T cell receptor recognition. Most of this research has been performed using T cell clones, which may not be accurate representations of the naturally occurring antitumor response. The relationship between clones generated after mimotope vaccination and the polyclonal T cell repertoire is unclear. Our work with mimotopes in a mouse model of colon carcinoma has revealed important insights into these issues. We propose that the identification of mimotopes based on stimulation of the naturally responding T cell repertoire will dramatically improve the efficacy of mimotope vaccination.
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Affiliation(s)
- Jonathan D Buhrman
- Integrated Department of Immunology, University of Colorado School of Medicine, National Jewish Health, Denver, CO 80206, USA
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14
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Park MS, Park SY, Miller KR, Collins EJ, Lee HY. Accurate structure prediction of peptide-MHC complexes for identifying highly immunogenic antigens. Mol Immunol 2013; 56:81-90. [PMID: 23688437 DOI: 10.1016/j.molimm.2013.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 12/26/2022]
Abstract
Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide-MHC complex. Here, we present an in silico protocol for predicting peptide-MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide-MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.
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Affiliation(s)
- Min-Sun Park
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, NY 14642, USA
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15
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Jordan KR, Buhrman JD, Sprague J, Moore BL, Gao D, Kappler JW, Slansky JE. TCR hypervariable regions expressed by T cells that respond to effective tumor vaccines. Cancer Immunol Immunother 2012; 61:1627-38. [PMID: 22350070 PMCID: PMC3410973 DOI: 10.1007/s00262-012-1217-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/30/2012] [Indexed: 12/31/2022]
Abstract
A major goal of immunotherapy for cancer is the activation of T cell responses against tumor-associated antigens (TAAs). One important strategy for improving antitumor immunity is vaccination with peptide variants of TAAs. Understanding the mechanisms underlying the expansion of T cells that respond to the native tumor antigen is an important step in developing effective peptide-variant vaccines. Using an immunogenic mouse colon cancer model, we compare the binding properties and the TCR genes expressed by T cells elicited by peptide variants that elicit variable antitumor immunity directly ex vivo. The steady-state affinity of the natural tumor antigen for the T cells responding to effective peptide vaccines was higher relative to ineffective peptides, consistent with their improved function. Ex vivo analysis showed that T cells responding to the effective peptides expressed a CDR3β motif, which was also shared by T cells responding to the natural antigen and not those responding to the less effective peptide vaccines. Importantly, these data demonstrate that peptide vaccines can expand T cells that naturally respond to tumor antigens, resulting in more effective antitumor immunity. Future immunotherapies may require similar stringent analysis of the responding T cells to select optimal peptides as vaccine candidates.
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Affiliation(s)
- Kimberly R Jordan
- Integrated Department of Immunology, School of Medicine, University of Colorado Denver, 1400 Jackson Street, Room K511, Denver, CO 80206, USA
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16
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Liblau RS, Wekerle H, Tisch RM. Cumulative autoimmunity: T cell clones recognizing several self-epitopes exhibit enhanced pathogenicity. Front Immunol 2011; 2:47. [PMID: 22566837 PMCID: PMC3342376 DOI: 10.3389/fimmu.2011.00047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 09/10/2011] [Indexed: 11/24/2022] Open
Abstract
T cell receptor (TCR) recognition is intrinsically polyspecific. In the field of autoimmunity, recognition of both self- and microbial peptides by a single TCR has led to the concept of molecular mimicry. However, findings made by our group and others clearly demonstrate that a given TCR can also recognize multiple distinct self-peptides. Based on experimental data we argue that recognition of several self-peptides increases the pathogenicity of an autoreactive T cell; a property we refer to as “cumulative autoimmunity.” The mechanisms of such increased pathogenicity, and the implications of cumulative autoimmunity regarding the pathophysiology of T cell-mediated autoimmune diseases will be discussed.
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17
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Borbulevych OY, Piepenbrink KH, Baker BM. Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics. THE JOURNAL OF IMMUNOLOGY 2011; 186:2950-8. [PMID: 21282516 DOI: 10.4049/jimmunol.1003150] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The αβ TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1-associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD-HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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18
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Peptide vaccines prevent tumor growth by activating T cells that respond to native tumor antigens. Proc Natl Acad Sci U S A 2010; 107:4652-7. [PMID: 20133772 DOI: 10.1073/pnas.0914879107] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptide vaccines enhance the response of T cells toward tumor antigens and represent a strategy to augment antigen-independent immunotherapies of cancer. However, peptide vaccines that include native tumor antigens rarely prevent tumor growth. We have assembled a set of peptide variants for a mouse-colon tumor model to determine how to improve T-cell responses. These peptides have similar affinity for MHC molecules, but differ in the affinity of the peptide-MHC/T-cell receptor interaction with a tumor-specific T-cell clone. We systematically demonstrated that effective antitumor responses are generated after vaccination with variant peptides that stimulate the largest proportion of endogenous T cells specific for the native tumor antigen. Importantly, we found some variant peptides that strongly stimulated a specific T-cell clone in vitro, but elicited fewer tumor-specific T cells in vivo, and were not protective. The T cells expanded by the effective vaccines responded to the wild-type antigen by making cytokines and killing target cells, whereas most of the T cells expanded by the ineffective vaccines only responded to the peptide variants. We conclude that peptide-variant vaccines are most effective when the peptides react with a large responsive part of the tumor-specific T-cell repertoire.
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19
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Armstrong K, Piepenbrink K, Baker B. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochem J 2008; 415:183-96. [PMID: 18800968 PMCID: PMC2782316 DOI: 10.1042/bj20080850] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/23/2008] [Accepted: 07/09/2008] [Indexed: 01/07/2023]
Abstract
A necessary feature of the immune system, TCR (T-cell receptor) cross-reactivity has been implicated in numerous autoimmune pathologies and is an underlying cause of transplant rejection. Early studies of the interactions of alphabeta TCRs (T-cell receptors) with their peptide-MHC ligands suggested that conformational plasticity in the TCR CDR (complementarity determining region) loops is a dominant contributor to T-cell cross-reactivity. Since these initial studies, the database of TCRs whose structures have been solved both bound and free is now large enough to permit general conclusions to be drawn about the extent of TCR plasticity and the types and locations of motion that occur. In the present paper, we review the conformational differences between free and bound TCRs, quantifying the structural changes that occur and discussing their possible roles in specificity and cross-reactivity. We show that, rather than undergoing major structural alterations or 'folding' upon binding, the majority of TCR CDR loops shift by relatively small amounts. The structural changes that do occur are dominated by hinge-bending motions, with loop remodelling usually occurring near loop apexes. As predicted from previous studies, the largest changes are in the hypervariable CDR3alpha and CDR3beta loops, although in some cases the germline-encoded CDR1alpha and CDR2alpha loops shift in magnitudes that approximate those of the CDR3 loops. Intriguingly, the smallest shifts are in the germline-encoded loops of the beta-chain, consistent with recent suggestions that the TCR beta domain may drive ligand recognition.
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Affiliation(s)
- Kathryn M. Armstrong
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Kurt H. Piepenbrink
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Brian M. Baker
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
- †Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
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20
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Armstrong KM, Insaidoo FK, Baker BM. Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities. J Mol Recognit 2008; 21:275-87. [PMID: 18496839 DOI: 10.1002/jmr.896] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
alphabeta T-cell receptors (TCRs) recognize peptide antigens presented by class I or class II major histocompatibility complex molecules (pMHC). Here we review the use of thermodynamic measurements in the study of TCR-pMHC interactions, with attention to the diversity in binding thermodynamics and how this is related to the variation in TCR-pMHC interfaces. We show that there is no enthalpic or entropic signature for TCR binding; rather, enthalpy and entropy changes vary in a compensatory manner that reflects a narrow free energy window for the interactions that have been characterized. Binding enthalpy and entropy changes do not correlate with structural features such as buried surface area or the number of hydrogen bonds within TCR-pMHC interfaces, possibly reflecting the myriad of contributors to binding thermodynamics, but likely also reflecting a reliance on van't Hoff over calorimetric measurements and the unaccounted influence of equilibria linked to binding. TCR-pMHC binding heat capacity changes likewise vary considerably. In some cases, the heat capacity changes are consistent with conformational differences between bound and free receptors, but there is little data indicating these conformational differences represent the need to organize disordered CDR loops. In this regard, we discuss how thermodynamics may provide additional insight into conformational changes occurring upon TCR binding. Finally, we highlight opportunities for the further use of thermodynamic measurements in the study of TCR-pMHC interactions, not only for understanding TCR binding in general, but also for understanding specifics of individual interactions and the engineering of TCRs with desired molecular recognition properties.
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Affiliation(s)
- Kathryn M Armstrong
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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21
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Beltrami A, Rossmann M, Fiorillo MT, Paladini F, Sorrentino R, Saenger W, Kumar P, Ziegler A, Uchanska-Ziegler B. Citrullination-dependent differential presentation of a self-peptide by HLA-B27 subtypes. J Biol Chem 2008; 283:27189-99. [PMID: 18650441 DOI: 10.1074/jbc.m802818200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Inflammatory processes are accompanied by the posttranslational modification of certain arginine residues within proteins to yield citrulline, although it is largely unknown how this modification influences antigen presentation. We employed crystallographic and functional studies to investigate whether the exchange of arginine to citrulline affects the display of a peptide by two human major histocompatibility antigen class I subtypes, HLA-B(*)2705 and HLA-B(*)2709. Both differ only in residue 116 within the peptide binding groove despite their differential association with ankylosing spondylitis, an inflammatory rheumatic disorder. The crystal structures described here show that a modified self-peptide, pVIPR-U5 (RRKWURWHL; U = citrulline), is presented by the two HLA-B27 molecules in distinct conformations. These binding modes differ not only drastically from each other but also from the conformations exhibited by the non-citrullinated peptide in a given subtype. The differential reactivity of HLA-B27-restricted cytotoxic T cells with modified or unmodified pVIPR supports the structural findings and shows that the presentation of citrullinated peptides has the potential to influence immune responses.
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Affiliation(s)
- Alessandra Beltrami
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
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22
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Borbulevych OY, Insaidoo FK, Baxter TK, Powell DJ, Johnson LA, Restifo NP, Baker BM. Structures of MART-126/27-35 Peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. J Mol Biol 2007; 372:1123-36. [PMID: 17719062 PMCID: PMC2134917 DOI: 10.1016/j.jmb.2007.07.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/07/2007] [Accepted: 07/10/2007] [Indexed: 11/24/2022]
Abstract
Small structural changes in peptides presented by major histocompatibility complex (MHC) molecules often result in large changes in immunogenicity, supporting the notion that T cell receptors are exquisitely sensitive to antigen structure. Yet there are striking examples of TCR recognition of structurally dissimilar ligands. The resulting unpredictability of how T cells will respond to different or modified antigens impacts both our understanding of the physical bases for TCR specificity as well as efforts to engineer peptides for immunomodulation. In cancer immunotherapy, epitopes and variants derived from the MART-1/Melan-A protein are widely used as clinical vaccines. Two overlapping epitopes spanning amino acid residues 26 through 35 are of particular interest: numerous clinical studies have been performed using variants of the MART-1 26-35 decamer, although only the 27-35 nonamer has been found on the surface of targeted melanoma cells. Here, we show that the 26-35 and 27-35 peptides adopt strikingly different conformations when bound to HLA-A2. Nevertheless, clonally distinct MART-1(26/27-35)-reactive T cells show broad cross-reactivity towards these ligands. Simultaneously, however, many of the cross-reactive T cells remain unable to recognize anchor-modified variants with very subtle structural differences. These dichotomous observations challenge our thinking about how structural information on unligated peptide/MHC complexes should be best used when addressing questions of TCR specificity. Our findings also indicate that caution is warranted in the design of immunotherapeutics based on the MART-1 26/27-35 epitopes, as neither cross-reactivity nor selectivity is predictable based on the analysis of the structures alone.
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Affiliation(s)
- Oleg Y. Borbulevych
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
- Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame Notre Dame, IN 46530, USA
| | - Francis K. Insaidoo
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
| | - Tiffany K. Baxter
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
| | - Daniel J. Powell
- National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA
| | - Laura A. Johnson
- National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA
| | - Nicholas P. Restifo
- National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
- Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame Notre Dame, IN 46530, USA
- *E-mail address of the corresponding author:
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23
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Michielin O, Blanchet JS, Fagerberg T, Valmori D, Rubio-Godoy V, Speiser D, Ayyoub M, Alves P, Luescher I, Gairin JE, Cerottini JC, Romero P. Tinkering with nature: the tale of optimizing peptide based cancer vaccines. Cancer Treat Res 2007; 123:267-91. [PMID: 16211875 DOI: 10.1007/0-387-27545-2_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Olivier Michielin
- Office of Information Technology, Ludwig Institute for Cancer Research, Epalinges, Switzerland
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24
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McCarthy C, Shepherd D, Fleire S, Stronge VS, Koch M, Illarionov PA, Bossi G, Salio M, Denkberg G, Reddington F, Tarlton A, Reddy BG, Schmidt RR, Reiter Y, Griffiths GM, van der Merwe PA, Besra GS, Jones EY, Batista FD, Cerundolo V. The length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation. ACTA ACUST UNITED AC 2007; 204:1131-44. [PMID: 17485514 PMCID: PMC2118584 DOI: 10.1084/jem.20062342] [Citation(s) in RCA: 192] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CD1d-restricted lymphocytes recognize a broad lipid range. However, how CD1d-restricted lymphocytes translate T cell receptor (TCR) recognition of lipids with similar group heads into distinct biological responses remains unclear. Using a soluble invariant NKT (iNKT) TCR and a newly engineered antibody specific for alpha-galactosylceramide (alpha-GalCer)-human CD1d (hCD1d) complexes, we measured the affinity of binding of iNKT TCR to hCD1d molecules loaded with a panel of alpha-GalCer analogues and assessed the rate of dissociation of alpha-GalCer and alpha-GalCer analogues from hCD1d molecules. We extended this analysis by studying iNKT cell synapse formation and iNKT cell activation by the same panel of alpha-GalCer analogues. Our results indicate the unique role of the lipid chain occupying the hCD1d F' channel in modulating TCR binding affinity to hCD1d-lipid complexes, the formation of stable immunological synapse, and cell activation. These data are consistent with previously described conformational changes between empty and loaded hCD1d molecules (Koch, M., V.S. Stronge, D. Shepherd, S.D. Gadola, B. Mathew, G. Ritter, A.R. Fersht, G.S. Besra, R.R. Schmidt, E.Y. Jones, and V. Cerundolo. 2005. Nat. Immunol 6:819-826), suggesting that incomplete occupation of the hCD1d F' channel results in conformational differences at the TCR recognition surface. This indirect effect provides a general mechanism by which lipid-specific lymphocytes are capable of recognizing both the group head and the length of lipid antigens, ensuring greater specificity of antigen recognition.
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Affiliation(s)
- Corinna McCarthy
- Tumour Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
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25
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McMahan RH, McWilliams JA, Jordan KR, Dow SW, Wilson DB, Slansky JE. Relating TCR-peptide-MHC affinity to immunogenicity for the design of tumor vaccines. J Clin Invest 2006; 116:2543-51. [PMID: 16932807 PMCID: PMC1551931 DOI: 10.1172/jci26936] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 06/20/2006] [Indexed: 12/22/2022] Open
Abstract
One approach to enhancing the T cell response to tumors is vaccination with mimotopes, mimics of tumor epitopes. While mimotopes can stimulate proliferation of T cells that recognize tumor-associated antigens (TAAs), this expansion does not always correlate with control of tumor growth. We hypothesized that vaccination with mimotopes of optimal affinity in this interaction will improve antitumor immunity. Using a combinatorial peptide library and a cytotoxic T lymphocyte clone that recognizes a TAA, we identified a panel of mimotopes that, when complexed with MHC, bound the TAA-specific TCR with a range of affinities. As expected, in vitro assays showed that the affinity of the TCR-peptide-MHC (TCR-pMHC) interaction correlated with activity of the T cell clone. However, only vaccination with mimotopes in the intermediate-affinity range elicited functional T cells and provided protection against tumor growth in vivo. Vaccination with mimotopes with the highest-affinity TCR-pMHC interactions elicited TAA-specific T cells to the tumor, but did not control tumor growth at any of the peptide concentrations tested. Further analysis of these T cells showed functional defects in response to the TAA. Thus, stimulation of an antitumor response by mimotopes may be optimal with peptides that increase but do not maximize the affinity of the TCR-pMHC interaction.
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Affiliation(s)
- Rachel H. McMahan
- Integrated Department of Immunology, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, USA.
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Torrey Pines Institute for Molecular Studies, San Diego, California, USA
| | - Jennifer A. McWilliams
- Integrated Department of Immunology, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, USA.
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Torrey Pines Institute for Molecular Studies, San Diego, California, USA
| | - Kimberly R. Jordan
- Integrated Department of Immunology, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, USA.
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Torrey Pines Institute for Molecular Studies, San Diego, California, USA
| | - Steven W. Dow
- Integrated Department of Immunology, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, USA.
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Torrey Pines Institute for Molecular Studies, San Diego, California, USA
| | - Darcy B. Wilson
- Integrated Department of Immunology, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, USA.
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Torrey Pines Institute for Molecular Studies, San Diego, California, USA
| | - Jill E. Slansky
- Integrated Department of Immunology, University of Colorado at Denver and Health Sciences Center, Denver, Colorado, USA.
Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.
Torrey Pines Institute for Molecular Studies, San Diego, California, USA
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26
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Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Turner RV, Damirjian M, Wojnarowicz A, Biddison WE, Baker BM. T cell receptor recognition via cooperative conformational plasticity. J Mol Biol 2006; 363:228-43. [PMID: 16962135 DOI: 10.1016/j.jmb.2006.08.045] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 08/15/2006] [Accepted: 08/16/2006] [Indexed: 11/25/2022]
Abstract
Although T cell receptor cross-reactivity is a fundamental property of the immune system and is implicated in numerous autoimmune pathologies, the molecular mechanisms by which T cell receptors can recognize and respond to diverse ligands are incompletely understood. In the current study we examined the response of the human T cell lymphotropic virus-1 (HTLV-1) Tax-specific T cell receptor (TCR) A6 to a panel of structurally distinct haptens coupled to the Tax 11-19 peptide with a lysine substitution at position 5 (Tax5K, LLFG[K-hapten]PVYV). The A6 TCR could cross-reactively recognize one of these haptenated peptides, Tax-5K-4-(3-Indolyl)-butyric acid (IBA), presented by HLA-A*0201. The crystal structures of Tax5K-IBA/HLA-A2 free and in complex with A6 reveal that binding is mediated by a mechanism of cooperative conformational plasticity involving conformational changes on both sides of the protein-protein interface, including the TCR complementarity determining region (CDR) loops, Valpha/Vbeta domain orientation, and the hapten-modified peptide. Our findings illustrate the complex role that protein dynamics can play in TCR cross-reactivity and highlight that T cell receptor recognition of ligand can be achieved through diverse and complex molecular mechanisms that can occur simultaneously in the interface, not limited to molecular mimicry and CDR loop shifts.
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Affiliation(s)
- Susan J Gagnon
- Molecular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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27
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Bordner AJ, Abagyan R. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 2006; 63:512-26. [PMID: 16470819 DOI: 10.1002/prot.20831] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased-Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all-atom MHC model. Our method was tested by a comparison of the results of cross-docking 14 peptides into HLA-A*0201 and 9 peptides into H-2K(b) as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 A backbone RMSD) for cross-docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 A illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA-A*0201 binders or nonbinders. In contrast with sequence-based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H-2K(b)), not used for training, with comparable prediction accuracy.
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Affiliation(s)
- Andrew J Bordner
- Department of Molecular Biology, The Scripps Research Institute, San Diego, California, USA.
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28
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Mittendorf EA, Storrer CE, Foley RJ, Harris K, Jama Y, Shriver CD, Ponniah S, Peoples GE. Evaluation of the HER2/neu-derived peptide GP2 for use in a peptide-based breast cancer vaccine trial. Cancer 2006; 106:2309-17. [PMID: 16596621 DOI: 10.1002/cncr.21849] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND E75 and GP2 are human leukocyte antigen (HLA)-A2-restricted immunogenic peptides derived from the HER2/neu protein. In a E75 peptide-based vaccine trial, preexisting immunity and epitope spreading to GP2 was detected. The purpose of this study was to further investigate GP2 for potential use in vaccination strategies. Importantly, a naturally occurring polymorphism (I-->V at position 2, 2VGP2) associated with increased breast cancer risk was addressed. METHODS Prevaccination peripheral blood samples (PBMC) from HLA-A2 breast cancer patients and CD8+ T cells from HLA-A2 healthy donors were stimulated with autologous dendritic cells (DC) pulsed with GP2 and tested in standard cytotoxicity assays with HER2/neu+ tumor cells or GP2- or 2VGP2-loaded T2 targets. Additional cytotoxicity experiments used effectors stimulated with DC pulsed with E75, GP2, or the combination of E75+GP2. RESULTS GP2-stimulated prevaccination PBMC from 28 patients demonstrated killing of MCF-7, SKOV3-A2, and the HLA-A2- control target SKOV3 of 28.8+/-3.7% (P<.01), 29.5+/-4.0% (P<.01), and 16.9+/-2.7%, respectively. When compared with E75, GP2-stimulated CD8+ T cells lysed HER2/neu+ targets at 43.8+/-5.2% versus 44.2+/-5.7% for E75 (P=.87). When combined, an additive effect was noted with 58.6+/-5.4% lysis (P=.05). GP2-stimulated CD8+ T cells specifically recognized both GP2-loaded (19.6+/-5.7%) and 2VGP2-loaded T2 targets (17.7+/-5.2%). CONCLUSIONS GP2 is a clinically relevant HER2/neu-derived peptide with immunogenicity comparable to that of E75. Importantly, GP2-specific effectors recognize 2VGP2-expressing targets; therefore, a GP2 vaccine should be effective in patients carrying this polymorphism. GP2 may be most beneficial used in a multiepitope vaccine.
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Affiliation(s)
- Elizabeth A Mittendorf
- Clinical Breast Care Project, Department of Surgery, Walter Reed Army Medical Center, Washington, DC, USA
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29
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Joseph MA, Mitchell ML, Evanseck JD, Kovacs JR, Jia L, Shen H, Meng WS. Secondary anchor substitutions in an HLA-A*0201-restricted T-cell epitope derived from Her-2/neu. Mol Immunol 2006; 44:322-31. [PMID: 16597462 PMCID: PMC2430429 DOI: 10.1016/j.molimm.2006.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
We investigated analogues of GP2 (IISAVVGIL), an HLA-A*0201-restricted T-cell epitope derived from residues 654-662 in the tumor-associated antigen (TAA) Her-2/neu. One limiting factor of GP2 is its poor affinity for HLA-A*0201. Conformational analysis revealed the P5-P7 region in GP2 appears to be linked to the stability of P9 side chain interaction with the MHC molecule. To identify variants of GP2 with enhanced presentation to HLA-A*0201, we tested V6S, V6T, V6Q, G7P, G7F, T6F7, and Q6F7 for their capacity to stabilize cell surface HLA-A*0201 molecules. Of the mono-substituted variants, V6Q and G7F exhibited superior stabilization as compared to GP2. Molecular dynamics simulations suggest the improved binding can be attributed to concerted motions in the central and C-terminal regions of the peptide. These data support the notion that amino acids in HLA-A*0201 epitopes may be inter-dependent. Priming HLA-A*0201 transgenic mice with G7F-loaded syngeneic dendritic cells stimulated mouse T cells to produce a higher level of INFgamma than mice immunized with GP2.
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Affiliation(s)
- Matthew A. Joseph
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Megan L. Mitchell
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Jeffrey D. Evanseck
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, United States
| | - Jeffrey R. Kovacs
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Liang Jia
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Hongmei Shen
- Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Wilson S. Meng
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
- Corresponding author at: Duquesne University, Mellon Hall 413, 600 Forbes Avenue, Pittsburgh, PA 15282, United States. Tel.: +1 412 396 6366; fax: +1 412 396 4660. E-mail address: (W.S. Meng)
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30
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Doytchinova IA, Flower DR. Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding. Mol Immunol 2006; 43:2037-44. [PMID: 16524630 DOI: 10.1016/j.molimm.2005.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 11/03/2005] [Accepted: 12/23/2005] [Indexed: 01/03/2023]
Abstract
Cleavage by the proteasome is responsible for generating the C terminus of T-cell epitopes. Modeling the process of proteasome cleavage as part of a multi-step algorithm for T-cell epitope prediction will reduce the number of non-binders and increase the overall accuracy of the predictive algorithm. Quantitative matrix-based models for prediction of the proteasome cleavage sites in a protein were developed using a training set of 489 naturally processed T-cell epitopes (nonamer peptides) associated with HLA-A and HLA-B molecules. The models were validated using an external test set of 227 T-cell epitopes. The performance of the models was good, identifying 76% of the C-termini correctly. The best model of proteasome cleavage was incorporated as the first step in a three-step algorithm for T-cell epitope prediction, where subsequent steps predicted TAP affinity and MHC binding using previously derived models.
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31
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Noy R, Eppel M, Haus-Cohen M, Klechevsky E, Mekler O, Michaeli Y, Denkberg G, Reiter Y. T-cell receptor-like antibodies: novel reagents for clinical cancer immunology and immunotherapy. Expert Rev Anticancer Ther 2006; 5:523-36. [PMID: 16250828 DOI: 10.1586/14737140.5.3.523] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Major histocompatibility complex class I molecules play a central role in the immune response against a variety of cells that have undergone malignant transformation by shaping the T-cell repertoire and presenting peptide antigens from endogeneous antigens to CD8+ cytotoxic T-cells. Diseased tumor or virus-infected cells are present on class I major histocompatibility complex molecule peptides that are derived from tumor-associated antigens or viral-derived proteins. Due to their unique specificity, such major histocompatibility complex-peptide complexes are a desirable target for novel approaches in immunotherapy. Targeted delivery of toxins or other cytotoxic drugs to cells which express specific major histocompatibility complex-peptide complexes that are involved in the immune response against cancer or viral infections would allow for a specific immunotherapeutic treatment of these diseases. It has recently been demonstrated that antibodies with the antigen-specific, major histocompatibility complex-restricted specificity of T-cells can be generated by taking advantage of the selection power of phage display technology. In addition to their tumor targeting capabilities, antibodies that mimic the fine specificity of T-cell receptors can serve as valuable research reagents that enable study of human class I peptide-major histocompatibility complex ligand presentation, as well as T-cell receptor peptide-major histocompatibility complex interactions. T-cell receptor-like antibody molecules may prove to be useful tools for studying major histocompatibility complex class I antigen presentation in health and disease as well as for therapeutic purposes in cancer, infectious diseases and autoimmune disorders.
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Affiliation(s)
- Roy Noy
- Technion-Israel Institute of Technology, Faculty of Biology, Haifa 32000, Israel
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32
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Thilo C, Berglund P, Applequist SE, Yewdell JW, Ljunggren HG, Achour A. Dissection of the interaction of the human cytomegalovirus-derived US2 protein with major histocompatibility complex class I molecules: prominent role of a single arginine residue in human leukocyte antigen-A2. J Biol Chem 2006; 281:8950-7. [PMID: 16452487 DOI: 10.1074/jbc.m507121200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human cytomegalovirus encodes several proteins that interfere with expression of major histocompatibility complex (MHC) class I molecules on the surface of infected cells. The unique short protein 2 (US2) binds to many MHC class I allomorphs in the endoplasmic reticulum, preventing cell surface expression of the class I molecule in question. The molecular interactions underlying US2 binding to MHC class I molecules and its allele specificity have not been fully clarified. In the present study, we first compared the sequences and the structures of US2 retained versus non-retained human leukocyte antigen (HLA) class I allomorphs to identify MHC residues of potential importance for US2 binding. On the basis of this analysis, 18 individual HLA-A2 mutants were generated and the ability of full-length US2 to bind wild-type and mutated HLA-A2 complexes was assessed. We demonstrate that Arg181 plays a critical role in US2-mediated inhibition of HLA-A2 cell surface expression. The structural comparison of all known crystal structures of HLA-A2 either alone, or in complex with T cell receptor or the CD8 co-receptor, indicates that binding of US2 to HLA-A2 results in a unique, large conformational change of the side chain of Arg181. However, although the presence of Arg181 seems to be a prerequisite for US2 binding to HLA-A2, it is not sufficient for binding to all MHC class I alleles.
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Affiliation(s)
- Claudia Thilo
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
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33
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Fagerberg T, Cerottini JC, Michielin O. Structural prediction of peptides bound to MHC class I. J Mol Biol 2005; 356:521-46. [PMID: 16368108 DOI: 10.1016/j.jmb.2005.11.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 11/16/2005] [Accepted: 11/17/2005] [Indexed: 11/29/2022]
Abstract
An ab initio structure prediction approach adapted to the peptide-major histocompatibility complex (MHC) class I system is presented. Based on structure comparisons of a large set of peptide-MHC class I complexes, a molecular dynamics protocol is proposed using simulated annealing (SA) cycles to sample the conformational space of the peptide in its fixed MHC environment. A set of 14 peptide-human leukocyte antigen (HLA) A0201 and 27 peptide-non-HLA A0201 complexes for which X-ray structures are available is used to test the accuracy of the prediction method. For each complex, 1000 peptide conformers are obtained from the SA sampling. A graph theory clustering algorithm based on heavy atom root-mean-square deviation (RMSD) values is applied to the sampled conformers. The clusters are ranked using cluster size, mean effective or conformational free energies, with solvation free energies computed using Generalized Born MV 2 (GB-MV2) and Poisson-Boltzmann (PB) continuum models. The final conformation is chosen as the center of the best-ranked cluster. With conformational free energies, the overall prediction success is 83% using a 1.00 Angstroms crystal RMSD criterion for main-chain atoms, and 76% using a 1.50 Angstroms RMSD criterion for heavy atoms. The prediction success is even higher for the set of 14 peptide-HLA A0201 complexes: 100% of the peptides have main-chain RMSD values < or =1.00 Angstroms and 93% of the peptides have heavy atom RMSD values < or =1.50 Angstroms. This structure prediction method can be applied to complexes of natural or modified antigenic peptides in their MHC environment with the aim to perform rational structure-based optimizations of tumor vaccines.
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Affiliation(s)
- Theres Fagerberg
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
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34
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Bernardeau K, Gouard S, David G, Ruellan AL, Devys A, Barbet J, Bonneville M, Chérel M, Davodeau F. Assessment of CD8 involvement in T cell clone avidity by direct measurement of HLA-A2/Mage3 complex density using a high-affinity TCR like monoclonal antibody. Eur J Immunol 2005; 35:2864-75. [PMID: 16163672 DOI: 10.1002/eji.200526307] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide affinity for MHC molecules determines the number of MHC/peptide complexes stabilized at the cell surface in in vitro tests or in vaccination protocols. We isolated a high affinity monoclonal antibody specific for the HLA-A2/Mage3 complex that enables an equilibrium binding assay to be performed on T2 cell line loaded with a range of Mage3 peptides. Binding of Mage3 to the HLA-A2 molecule can be modeled by a standard receptor-ligand interaction characterized by an affinity constant. This model enables the measurement of the affinity of other immunogenic peptides for HLA-A2 by a competition test and the calculation of the density of complexes stabilized at the T2 cell surface for all peptide concentrations. Quantification of the HLA-A2/Mage3 complexes at target cell surfaces was used to estimate the number of complexes required to reach cytotoxicity ED50 of human T cell clones sorted from an unprimed repertoire. We confirm with this antibody the direct relationship between clone avidity and TCR affinity, and the moderate contribution of the CD8 co-receptor in the reinforcement of TCR-MHC/peptide contact. Nevertheless, CD8 plays a critical role in the amplification of the specific signal to establish an efficient T cell response at low specific complex densities found in physiological situations.
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Affiliation(s)
- Karine Bernardeau
- INSERM U601, Institut de Biologie, and Université Nantes, Nantes, France
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35
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Chen JL, Stewart-Jones G, Bossi G, Lissin NM, Wooldridge L, Choi EML, Held G, Dunbar PR, Esnouf RM, Sami M, Boulter JM, Rizkallah P, Renner C, Sewell A, van der Merwe PA, Jakobsen BK, Griffiths G, Jones EY, Cerundolo V. Structural and kinetic basis for heightened immunogenicity of T cell vaccines. ACTA ACUST UNITED AC 2005; 201:1243-55. [PMID: 15837811 PMCID: PMC2213140 DOI: 10.1084/jem.20042323] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Analogue peptides with enhanced binding affinity to major histocompatibility class (MHC) I molecules are currently being used in cancer patients to elicit stronger T cell responses. However, it remains unclear as to how alterations of anchor residues may affect T cell receptor (TCR) recognition. We correlate functional, thermodynamic, and structural parameters of TCR–peptide–MHC binding and demonstrate the effect of anchor residue modifications of the human histocompatibility leukocyte antigens (HLA)–A2 tumor epitope NY–ESO-1157–165–SLLMWITQC on TCR recognition. The crystal structure of the wild-type peptide complexed with a specific TCR shows that TCR binding centers on two prominent, sequential, peptide sidechains, methionine–tryptophan. Cysteine-to-valine substitution at peptide position 9, while optimizing peptide binding to the MHC, repositions the peptide main chain and generates subtly enhanced interactions between the analogue peptide and the TCR. Binding analyses confirm tighter binding of the analogue peptide to HLA–A2 and improved soluble TCR binding. Recognition of analogue peptide stimulates faster polarization of lytic granules to the immunological synapse, reduces dependence on CD8 binding, and induces greater numbers of cross-reactive cytotoxic T lymphocyte to SLLMWITQC. These results provide important insights into heightened immunogenicity of analogue peptides and highlight the importance of incorporating structural data into the process of rational optimization of superagonist peptides for clinical trials.
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MESH Headings
- Animals
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/immunology
- Cancer Vaccines/chemistry
- Cancer Vaccines/pharmacology
- Cell Line, Tumor
- Chemokine CCL4
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/immunology
- Immunization
- Interferon-gamma/analysis
- Macrophage Inflammatory Proteins/analysis
- Major Histocompatibility Complex/immunology
- Membrane Proteins/chemistry
- Membrane Proteins/immunology
- Mice
- Mice, Transgenic
- Peptides/chemistry
- Peptides/immunology
- Protein Binding/immunology
- Protein Conformation
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Spleen/cytology
- Spleen/drug effects
- Spleen/immunology
- T-Lymphocytes, Cytotoxic/immunology
- Transfection
- Vaccines, Synthetic/chemistry
- Vaccines, Synthetic/pharmacology
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Affiliation(s)
- Ji-Li Chen
- Tumour Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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36
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Borbulevych OY, Baxter TK, Yu Z, Restifo NP, Baker BM. Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design. THE JOURNAL OF IMMUNOLOGY 2005; 174:4812-20. [PMID: 15814707 PMCID: PMC2241749 DOI: 10.4049/jimmunol.174.8.4812] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The use of "anchor-fixed" altered peptide ligands is of considerable interest in the development of therapeutic vaccines for cancer and infectious diseases, but the mechanism by which successful altered peptide ligands elicit enhanced immunity is unclear. In this study, we have determined the crystallographic structure of a major tumor rejection Ag, gp100(209-217), in complex with the HLA-A*0201 (HLA-A2) molecule, as well as the structure of a modified version of the peptide which substitutes methionine for threonine at position 2 (T2M; gp100(209-2M)). The T2M-modified peptide, which is more immunogenic in vitro and in vivo, binds HLA-A2 with a approximately 9-fold greater affinity and has a approximately 7-fold slower dissociation rate at physiological temperature. Within the limit of the crystallographic data, the T2M substitution does not alter the structure of the peptide/HLA-A2 complex. Consistent with this finding, in peripheral blood from 95 human subjects, we were unable to identify higher frequencies of T cells specific for either the native or modified peptide. These data strongly support the conclusion that the greater immunogenicity of the gp100(209-2M) peptide is due to the enhanced stability of the peptide/MHC complex, validating the anchor-fixing approach for generating therapeutic vaccine candidates. Thermodynamic data suggest that the enhanced stability of the T2M-modified peptide/HLA-A2 complex is attributable to the increased hydrophobicity of the modified peptide, but the gain due to hydrophobicity is offset considerably by the loss of a hydrogen bond made by the native peptide to the HLA-A2 molecule. Our findings have broad implications for the optimization of current vaccine-design strategies.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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37
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Miley MJ, Messaoudi I, Metzner BM, Wu Y, Nikolich-Zugich J, Fremont DH. Structural basis for the restoration of TCR recognition of an MHC allelic variant by peptide secondary anchor substitution. ACTA ACUST UNITED AC 2004; 200:1445-54. [PMID: 15557346 PMCID: PMC2211956 DOI: 10.1084/jem.20040217] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Major histocompatibility complex (MHC) class I variants H-2Kb and H-2Kbm8 differ primarily in the B pocket of the peptide-binding groove, which serves to sequester the P2 secondary anchor residue. This polymorphism determines resistance to lethal herpes simplex virus (HSV-1) infection by modulating T cell responses to the immunodominant glycoprotein B498-505 epitope, HSV8. We studied the molecular basis of these effects and confirmed that T cell receptors raised against Kb–HSV8 cannot recognize H-2Kbm8–HSV8. However, substitution of SerP2 to GluP2 (peptide H2E) reversed T cell receptor (TCR) recognition; H-2Kbm8–H2E was recognized whereas H-2Kb–H2E was not. Insight into the structural basis of this discrimination was obtained by determining the crystal structures of all four MHC class I molecules in complex with bound peptide (pMHCs). Surprisingly, we find no concerted pMHC surface differences that can explain the differential TCR recognition. However, a correlation is apparent between the recognition data and the underlying peptide-binding groove chemistry of the B pocket, revealing that secondary anchor residues can profoundly affect TCR engagement through mechanisms distinct from the alteration of the resting state conformation of the pMHC surface.
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Affiliation(s)
- Michael J Miley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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38
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Ida K, Kawaguchi S, Sato Y, Tsukahara T, Nabeta Y, Sahara H, Ikeda H, Torigoe T, Ichimiya S, Kamiguchi K, Wada T, Nagoya S, Hiraga H, Kawai A, Ishii T, Araki N, Myoui A, Matsumoto S, Ozaki T, Yoshikawa H, Yamashita T, Sato N. Crisscross CTL induction by SYT-SSX junction peptide and its HLA-A*2402 anchor substitute. THE JOURNAL OF IMMUNOLOGY 2004; 173:1436-43. [PMID: 15240740 DOI: 10.4049/jimmunol.173.2.1436] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To investigate the effects of anchor substitutions in SYT-SSX junction peptide, an HLA-A24 anchor residue (position 9) of the SYT-SSX B peptide (GYDQIMPKK) was substituted to more favorable residues according to the HLA-A24-binding motif. Among four substitutes constructed, a substitute with isoleucine (termed K9I peptide) most apparently enhanced the affinity for HLA-A24 molecule. Subsequent in vitro CTL induction analysis using PBMCs of 15 HLA-A24(+) synovial sarcoma patients revealed that the original B peptide allowed to induce synovial sarcoma-specific CTLs from 7 patients (47%), whereas such CTLs were inducible from 12 patients (80%) with K9I peptide. Moreover, the extent of cytotoxicity against HLA-A24(+) synovial sarcoma cell lines was higher in K9I peptide-induced CTLs than B peptide-induced CTLs. Influence of anchor substitution on peptide/TCR interaction was evaluated by cytotoxicity assays against autologous cells and tetramer analysis. CTLs induced from a synovial sarcoma patient using K9I peptide did not lyse autologous PHA blasts or EBV-infected B cells. In vitro stimulations of PBMCs from 5 HLA-A24(+) synovial sarcoma patients with K9I peptide increased the frequency of T cells reacting with both HLA-A24/K9I peptide tetramer and HLA-A24/B peptide tetramer. In contrast, the frequency of T cells reacting with HLA/HIV-derived peptide tetramer remained low. These findings support the validity in design of anchor residue substitution in SYT-SSX fusion gene-derived peptide, and provide a potential clue to the current stagnation in vaccination trials of fusion gene-derived natural junction peptides.
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Affiliation(s)
- Kazunori Ida
- Department of Orthopaedic Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
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39
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Leggatt GR, Narayan S, Fernando GJP, Frazer IH. Changes to peptide structure, not concentration, contribute to expansion of the lowest avidity cytotoxic T lymphocytes. J Leukoc Biol 2004; 76:787-95. [PMID: 15240746 DOI: 10.1189/jlb.0104026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The efficient in vitro expansion of antigen-specific CD8+ cytotoxic T lymphocytes (CTL) for use in adoptive immunotherapy represents an important clinical goal. Furthermore, the avidity of expanded CTL populations often correlates closely with clinical outcome. In our study, high-avidity CTL lines could be expanded ex vivo from an antigen-primed animal using low peptide concentration, and intermediate peptide concentrations favored the generation of lower avidity CTL. Further increases in peptide concentration during culture inhibited the expansion of all peptide-specific CD8+ cells. In contrast, a single amino acid variant peptide efficiently generated functional CTL populations at high or low peptide concentration, which responded to wild-type epitope with the lowest average avidity seen in this study. We propose that for some peptides, the efficient generation of low-avidity CTL responses will be favored by stimulation with altered peptide rather than high concentrations of wild-type epitope. In addition, some variant peptides designed to have improved binding to major histocompatibility complex class I may reduce rather than enhance the functional avidity for the wild-type peptide of ex vivo-expanded CTL. These observations are relevant to in vitro expansion of CTL for immunotherapy and strategies to elicit regulatory or therapeutic immunity to neo-self-antigen when central tolerance has eliminated high-avidity, cognate T cells.
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Affiliation(s)
- Graham R Leggatt
- Centre for Immunology and Cancer Research, University of Queensland, Princess Alexandra Hospital, Brisbane, Australia.
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40
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Baxter TK, Gagnon SJ, Davis-Harrison RL, Beck JC, Binz AK, Turner RV, Biddison WE, Baker BM. Strategic Mutations in the Class I Major Histocompatibility Complex HLA-A2 Independently Affect Both Peptide Binding and T Cell Receptor Recognition. J Biol Chem 2004; 279:29175-84. [PMID: 15131131 DOI: 10.1074/jbc.m403372200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutational studies of T cell receptor (TCR) contact residues on the surface of the human class I major histocompatibility complex (MHC) molecule HLA-A2 have identified a "functional hot spot" that comprises Arg(65) and Lys(66) and is involved in recognition by most peptide-specific HLA-A2-restricted TCRs. Although there is a significant amount of functional data on the effects of mutations at these positions, there is comparatively little biochemical information that could illuminate their mode of action. Here, we have used a combination of fluorescence anisotropy, functional assays, and Biacore binding experiments to examine the effects of mutations at these positions on the peptide-MHC interaction and TCR recognition. The results indicate that mutations at both position 65 and position 66 influence peptide binding by HLA-A2 to various extents. In particular, mutations at position 66 result in significantly increased peptide dissociation rates. However, these effects are independent of their effects on TCR recognition, and the Arg(65)-Lys(66) region thus represents a true "hot spot" for TCR recognition. We also made the observation that in vitro T cell reactivity does not scale with the half-life of the peptide-MHC complex, as is often assumed. Finally, position 66 is implicated in the "dual recognition" of both peptide and TCR, emphasizing the multiple roles of the class I MHC peptide-binding domain.
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Affiliation(s)
- Tiffany K Baxter
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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41
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Velloso LM, Michaëlsson J, Ljunggren HG, Schneider G, Achour A. Determination of Structural Principles Underlying Three Different Modes of Lymphocytic Choriomeningitis Virus Escape from CTL Recognition. THE JOURNAL OF IMMUNOLOGY 2004; 172:5504-11. [PMID: 15100292 DOI: 10.4049/jimmunol.172.9.5504] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lymphocytic choriomeningitis virus infection of H-2(b) mice generates a strong CD8(+) CTL response mainly directed toward three immunodominant epitopes, one of which, gp33, is presented by both H-2D(b) and H-2K(b) MHC class I molecules. This CTL response acts as a selective agent for the emergence of viral escape variants. These variants generate altered peptide ligands (APLs) that, when presented by class I MHC molecules, antagonize CTL recognition and ultimately allow the virus to evade the cellular immune response. The emergence of APLs of the gp33 epitope is particularly advantageous for LCMV, as it allows viral escape in the context of both H-2D(b) and H-2K(b) MHC class I molecules. We have determined crystal structures of three different APLs of gp33 in complex with both H-2D(b) and H-2K(b). Comparison between these APL/MHC structures and those of the index gp33 peptide/MHC reveals the structural basis for three different strategies used by LCMV viral escape mutations: 1) conformational changes in peptide and MHC residues that are potential TCR contacts, 2) impairment of APL binding to the MHC peptide binding cleft, and 3) introduction of subtle changes at the TCR/pMHC interface, such as the removal of a single hydroxyl group.
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MESH Headings
- Amino Acid Substitution/genetics
- Animals
- Antigen Presentation/genetics
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Glycoproteins/chemistry
- Glycoproteins/genetics
- Glycoproteins/immunology
- H-2 Antigens/chemistry
- H-2 Antigens/genetics
- H-2 Antigens/immunology
- Leucine/genetics
- Lymphocytic choriomeningitis virus/genetics
- Lymphocytic choriomeningitis virus/immunology
- Mice
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Phenylalanine/genetics
- Protein Binding/genetics
- Protein Binding/immunology
- Protein Conformation
- Protein Structure, Tertiary/genetics
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Structure-Activity Relationship
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- T-Lymphocytes, Cytotoxic/virology
- Tyrosine/genetics
- Valine/genetics
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Lucas Malard Velloso
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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42
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Müller MR, Grünebach F, Nencioni A, Brossart P. Transfection of dendritic cells with RNA induces CD4- and CD8-mediated T cell immunity against breast carcinomas and reveals the immunodominance of presented T cell epitopes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:5892-6. [PMID: 12794115 DOI: 10.4049/jimmunol.170.12.5892] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Transfection of dendritic cells (DC) with tumor-derived RNA has recently been shown to elicit tumor-specific CTL capable of recognizing and lysing a variety of tumor cells. In our study we analyzed the induction of HLA class I- and II-restricted T cell responses against MCF-7 breast cancer cells. Using this approach we were able to elicit CD4- and CD8-mediated antitumor responses. The CTL specifically lysed MCF-7 cells and DC electroporated with MCF-7 RNA, but spared control cell lines. The specificity of the cytotoxic activity was confirmed in cold target inhibition assays and using mAbs blocking HLA class I molecules. Interestingly, these polyclonal cytotoxic T cells recognized selectively two epitopes derived from the MUC1 and Her-2/neu tumor Ags. The induced Th cells were found to be entirely HLA class II restricted and showed a significant cross-reactivity to a renal cell carcinoma cell line, similar to the results obtained with cytotoxic T cells.
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MESH Headings
- Antigen Presentation/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Line, Transformed
- Cytotoxicity, Immunologic/genetics
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Humans
- Immunity, Cellular/genetics
- Immunodominant Epitopes/genetics
- Immunodominant Epitopes/immunology
- Immunodominant Epitopes/metabolism
- Lymphocyte Activation/genetics
- Mucin-1/genetics
- Mucin-1/immunology
- Mucin-1/metabolism
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- RNA, Neoplasm/genetics
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/immunology
- Receptor, ErbB-2/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- Transfection/methods
- Tumor Cells, Cultured
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Affiliation(s)
- Martin R Müller
- Department of Hematology, Oncology, and Immunology, University of Tübingen, Tübingen, Germany
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43
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Murata M, Warren EH, Riddell SR. A human minor histocompatibility antigen resulting from differential expression due to a gene deletion. J Exp Med 2003; 197:1279-89. [PMID: 12743171 PMCID: PMC2193779 DOI: 10.1084/jem.20030044] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Minor histocompatibility antigens (minor H antigens) are targets of graft-versus-host disease and graft-versus-leukemia responses after allogeneic human leukocyte antigen identical hematopoietic stem cell transplantation. Only a few human minor H antigens have been molecularly characterized and in all cases, amino acid differences between homologous donor and recipient proteins due to nucleotide polymorphisms in the respective genes were responsible for immunogenicity. Here, we have used cDNA expression cloning to identify a novel human minor H antigen encoded by UGT2B17, an autosomal gene in the multigene UDP-glycosyltransferase 2 family that is selectively expressed in liver, intestine, and antigen-presenting cells. In contrast to previously defined human minor H antigens, UGT2B17 is immunogenic because of differential expression of the protein in donor and recipient cells as a consequence of a homozygous gene deletion in the donor. Deletion of individual members of large gene families is a common form of genetic variation in the population and our results provide the first evidence that differential protein expression as a consequence of gene deletion is a mechanism for generating minor H antigens in humans.
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Affiliation(s)
- Makoto Murata
- D3-100, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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44
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Riley JP, Rosenberg SA, Parkhurst MR. Stimulation of tumor-reactive T lymphocytes using mixtures of synthetic peptides derived from tumor-associated antigens with diverse MHC binding affinities. J Immunol Methods 2003; 276:103-19. [PMID: 12738363 DOI: 10.1016/s0022-1759(03)00078-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of reverse immunology may be necessary to identify new tumor-associated antigens, particularly for cancers, against which tumor-reactive T cell populations have been difficult to establish. One approach has been to screen peptides derived from a candidate antigen with high major histocompatibility complex (MHC) binding affinities for the induction of tumor-reactive T lymphocytes in vitro. However, many candidate antigens that are overexpressed in tumors are nonmutated self-proteins, and unlike foreign or mutated proteins, immunodominant epitopes may not be expressed at high density on the surface of tumor cells. Therefore, to identify tumor-associated epitopes, it may be necessary to screen large panels of peptides with wide ranges of MHC binding affinities. The current methodology of stimulating peripheral blood lymphocytes (PBL) from donors expressing the MHC molecule of interest with individual peptides is impractical for screening such large panels. Therefore, we evaluated the use of mixtures of peptides with variable MHC binding affinities for the induction of tumor-reactive T lymphocytes with the melanoma antigens gp100 and an alternate isoform of tyrosinase-related protein 2 (TRP2-6b) as models. A mixture of 10 known human leukocyte antigen (HLA)-A*0201-restricted peptides from gp100 induced melanoma-reactive cytotoxic T lymphoycte (CTL) from multiple patients with metastatic melanoma. The majority of these T cell populations recognized the known immunodominant epitopes gp100:209-217 and gp100:280-288, even though the HLA-A*0201 binding affinities of these peptides were much lower than other peptides in the mixture. Similarly, melanoma-reactive CTL were generated with a mixture of HLA-A*0201-restricted peptides from TRP2-6b, and these responses were directed against the previously identified tumor-associated epitopes TRP2-6b:180-188, TRP2-6b:288-296 and TRP2-6b:403-411. These results suggest that the use of peptide mixtures may facilitate the identification of new tumor-associated antigens through the application of reverse immunology.
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Affiliation(s)
- John P Riley
- Surgery Branch, National Cancer Institute, National Institutes of Health, Room 2B42, Building 10, 9000 Rockville Pike, Bethesda, MD 20892-1502, USA
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45
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Kiessling R, Wei WZ, Herrmann F, Lindencrona JA, Choudhury A, Kono K, Seliger B. Cellular immunity to the Her-2/neu protooncogene. Adv Cancer Res 2003; 85:101-44. [PMID: 12374283 DOI: 10.1016/s0065-230x(02)85004-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Her-2/neu (HER-2) is a 185-kDa receptor-like glycoprotein that is overexpressed by a variety of tumors such as breast, ovarian, gastric, and colorectal carcinomas. Overexpression of this oncogene is directly associated with malignant transformation of epithelial cells. The frequency of HER-2 overexpression varies among the different types of cancers, but universally represents a marker of poor prognosis. The critical role of HER-2 in epithelial oncogenesis as well as its selective overexpression on malignant tissues makes it an ideal target for immunotherapy. Antibodies and T cells reactive to HER-2 are known to naturally occur in patients with HER-2 positive tumors, confirming the immunogenicity of the molecule. Both antibodies as well as T cells reactive to HER-2 have been utilized for immunotherapy of HER-2 positive tumors. The "humanized" monoclonal antibody Herceptin has been tested in several clinical trials and found to be an effective adjuvant therapy for HER-2 positive breast and ovarian cancer patients. However, the frequency of patients responding to Herceptin is limited and a majority of patients initially responding to Herceptin develop resistance within a year of treatment. The use of vaccination strategies that generate T cell responses with or without accompanying antibody responses may serve to mitigate the problem. Various strategies for generating T cell-mediated responses against HER-2 are currently being examined in animal models or in clinical trials. The potential advantages of the various approaches to immunotherapy, their pitfalls, and the mechanisms by which HER-2 positive tumors can evade immune responses are discussed in this review.
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Affiliation(s)
- Rolf Kiessling
- Department of Oncology, Karolinska Institutet, Stockholm, Sweden
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46
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Cohen CJ, Denkberg G, Lev A, Epel M, Reiter Y. Recombinant antibodies with MHC-restricted, peptide-specific, T-cell receptor-like specificity: new tools to study antigen presentation and TCR-peptide-MHC interactions. J Mol Recognit 2003; 16:324-32. [PMID: 14523945 DOI: 10.1002/jmr.640] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The advent in recent years of the application of tetrameric arrays of class I peptide-MHC complexes now enables us to detect and study rare populations of antigen-specific CD8+ T cells. However, available methods cannot visualize or determine the number and distribution of these TCR ligands on individual cells or detect antigen-presenting cells (APCs) in tissues. Here we describe a new approach that enables study of human class I peptide-MHC ligand-presentation as well as TCR-peptide-MHC interactions. Such studies are facilitated by applying novel tools in the form of peptide-specific, HLA-A2-restricted human recombinant antibodies directed toward a large variety of tumor-associated as well as viral T-cell epitope peptides. Using a large human antibody phage display library, a large panel of recombinant antibodies that are specific for a particular peptide-MHC class I complex in a peptide-dependent, MHC-restricted manner was isolated. These antibodies were used to directly visualize the specific MHC-peptide complex on tumor cells, antigen-presenting cells or virus-infected cells by flow cytometry. They enabled direct quantitation of the number of MHC-peptide complexes as well as in situ detection of the complex on the surface of APCs after naturally occurring active intracellular processing of the cognate antigen. These studies will enable also the development of a new class of targeting molecules to deliver drugs or toxins to tumor or virus-infected cells. Thus, we demonstrate our ability to transform the unique fine specificity but low intrinsic affinity of TCRs into high-affinity soluble antibody molecules endowed with a TCR-like specificity toward human tumor or viral epitopes. These molecules may prove to be crucial useful tools for studying MHC class I antigen presentation in health and disease as well as for therapeutic purposes in cancer, infectious diseases and autoimmune disorders.
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Affiliation(s)
- Cyril J Cohen
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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47
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Denkberg G, Klechevsky E, Reiter Y. Modification of a tumor-derived peptide at an HLA-A2 anchor residue can alter the conformation of the MHC-peptide complex: probing with TCR-like recombinant antibodies. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 169:4399-407. [PMID: 12370373 DOI: 10.4049/jimmunol.169.8.4399] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A common assumption about peptide binding to the class I MHC complex is that each residue in the peptide binds independently. Based on this assumption, modifications in class I MHC anchor positions were used to improve the binding properties of low-affinity peptides (termed altered peptide ligands), especially in the case when tumor-associated peptides are used for immunotherapy. Using a new molecular tool in the form of recombinant Abs endowed with Ag-specific MHC-restricted specificity of T cells, we show that changes in the identity of anchor residues may have significant effects, such as altering the conformation of the peptide-MHC complex, and as a consequence, may affect the TCR-contacting residues. We herein demonstrate that the binding of TCR-like recombinant Abs, specific for the melanoma differentiation Ag gp100 T cell epitope G9-209, is entirely dependent on the identity of a single peptide anchor residue at position 2. An example is shown in which TCR-like Abs can recognize the specific complex only when a modified peptide, G9-209-2 M, with improved affinity to HLA-A2 was used, but not with the unmodified natural peptide. Importantly, these results demonstrate, using a novel molecular tool, that modifications at anchor residues can dramatically influence the conformation of the MHC peptide groove and thus may have a profound effect on TCR interactions. Moreover, these results may have important implications in designing modifications in peptides for cancer immunotherapy, because most such peptides studied are of low affinity.
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MESH Headings
- Amino Acid Substitution
- Binding Sites, Antibody
- Cell Line, Transformed
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- Humans
- Immunoglobulin Fab Fragments/isolation & purification
- Immunoglobulin Fab Fragments/metabolism
- Membrane Glycoproteins/immunology
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/immunology
- Neoplasm Proteins/metabolism
- Oligopeptides/chemistry
- Oligopeptides/immunology
- Oligopeptides/metabolism
- Peptide Library
- Protein Conformation
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Structure-Activity Relationship
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Tumor Cells, Cultured
- gp100 Melanoma Antigen
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Affiliation(s)
- Galit Denkberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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48
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Rivoltini L, Carrabba M, Huber V, Castelli C, Novellino L, Dalerba P, Mortarini R, Arancia G, Anichini A, Fais S, Parmiani G. Immunity to cancer: attack and escape in T lymphocyte-tumor cell interaction. Immunol Rev 2002; 188:97-113. [PMID: 12445284 DOI: 10.1034/j.1600-065x.2002.18809.x] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tumor cells may express antigens which are recognized in a form of HLA/peptide complexes by T cells. The frequency at which different antigens are seen by T cells of melanoma patients and healthy donors was evaluated by human leukocyte antigen (HLA)/peptide tetramer technology which stains T cells bearing the specific receptor for a given epitope. By this technique, it was found that the majority of metastatic melanoma patients can recognize differentiation antigens (particularly Melan-A/MART-1), whereas such a recognition is scanty in the early phase of the disease and in healthy subjects. Despite the presence of melanoma-specific T cells infiltrating tumor lesions, tumor rejection rarely occurs. Among the different mechanisms of such inefficient antitumor response, this review discusses the possible anti-T-cell counterattack mediated by FasL-positive tumor cells, and shows that FasL is located in the cytoplasm of melanoma cells and is transported in the tumor microenvironment through the release of melanosomes. Additionally, mechanisms of suboptimal T cell activation through tumor cell expression of peptide analogs with antagonist activity are described, together with the possibility of overcoming such anergy induction by the usage of optimized tumor epitopes. Down-modulation of HLA expression by target tumor cells and its multiple mechanisms is also considered. Finally, we discuss the role of inducible nitric oxide synthases in determining the inhibition of apoptosis in melanoma cells, which can make such tumor cells resistant to the T-cell attack.
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Affiliation(s)
- Licia Rivoltini
- Units of Human Tumor Immunotherapy and Immunobiology, Istituto Nazionale Tumori, Milan, Italy
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49
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Abstract
Administration of synthetic peptides derived from proteins uniquely or overexpressed in tumor cells (tumor-associated antigens) can elicit tumor-specific immune responses in vivo. This is because cytotoxic T lymphocytes can recognize and lyse tumor cells that display peptides derived from tumor-associated antigens (TAAs) in the context of class I major histocompatibility complex (MHC) molecules. TAA peptides, in contrast to peptides of viral origin, generally bind weakly to the MHC molecule. In many cases, this explains the poor magnitude of T cell response directed at the tumor in vivo. Improving MHC binding as a strategy to upregulate antigen recognition can convert low affinity TAA peptides into useful tools in clinical trial settings. High-resolution structures of class I MHC molecules reported over the past two decades provided the framework for designing peptides that can induce optimal T cell response. This review will discuss the basic and clinical aspects of modifying native TAA peptides as tumor vaccines.
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Affiliation(s)
- Wilson S Meng
- Division of Pharmaceutical Sciences, Duquesne University, Mylan School of Pharmacy, Pittsburgh, Pennsylvania 15282, USA.
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50
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Buslepp J, Zhao R, Donnini D, Loftus D, Saad M, Appella E, Collins EJ. T cell activity correlates with oligomeric peptide-major histocompatibility complex binding on T cell surface. J Biol Chem 2001; 276:47320-8. [PMID: 11584024 DOI: 10.1074/jbc.m109231200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recognition of virally infected cells by CD8+ T cells requires differentiation between self and nonself peptide-class I major histocompatibility complexes (pMHC). Recognition of foreign pMHC by host T cells is a major factor in the rejection of transplanted organs from the same species (allotransplant) or different species (xenotransplant). AHIII12.2 is a murine T cell clone that recognizes the xenogeneic (human) class I MHC HLA-A2.1 molecule (A2) and the syngeneic murine class I MHC H-2 D(b) molecule (D(b)). Recognition of both A2 and D(b) are peptide-dependent, and the sequences of the peptides recognized have been determined. Alterations in the antigenic peptides bound to A2 cause large changes in AHIII12.2 T cell responsiveness. Crystal structures of three representative peptides (agonist, null, and antagonist) bound to A2 partially explain the changes in AHIII12.2 responsiveness. Using class I pMHC octamers, a strong correlation is seen between T cell activity and the affinity of pMHC complexes for the T cell receptor. However, contrary to previous studies, we see similar half-lives for the pMHC multimers bound to the AHIII12.2 cell surface.
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Affiliation(s)
- J Buslepp
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
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