1
|
Rastogi I, Mannone JA, Gibadullin R, Moseman JE, Sidney J, Sette A, McNeel DG, Gellman SH. β-amino acid substitution in the SIINFEKL antigen alters immunological recognition. Cancer Biol Ther 2025; 26:2486141. [PMID: 40200635 PMCID: PMC11988276 DOI: 10.1080/15384047.2025.2486141] [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: 02/18/2025] [Revised: 03/20/2025] [Accepted: 03/24/2025] [Indexed: 04/10/2025] Open
Abstract
BACKGROUND Peptide vaccines offer a direct way to initiate an immunogenic response to a defined antigen epitope. However, peptide vaccines are unstable in vivo, subject to rapid enzymatic proteolysis. Replacement of an α-amino acid residue with a homologous β-amino acid residue (native side chain, but backbone extended by a single CH2 unit) impairs proteolysis at nearby amide bonds. Therefore, antigen analogues containing α-to-β replacements have been examined for functional mimicry of native all-α antigens. Another group previously took this approach in the ovalbumin (OVA) antigen model by evaluating single α-to-β analogues of the murine major histocompatibility complex (MHC) I-restricted peptide SIINFEKL. METHODS We re-examined this set of α/β SIINFEKL antigens. We tested the susceptibility to proteolysis in mouse serum and their ability to activate OVA-antigen-specific CD8 T cells in vitro. Additionally, we tested the α/β antigens in vivo for their ability to induce an antigen-specific immunogenic response in naïve mice and in OVA-expressing tumor-bearing mice. RESULTS The α/β antigens were comparable to the native antigen in their susceptibility to proteolysis in serum. Each α/β antigen was capable of activating antigen-specific CD8 T cells in vitro. However, antigen-specific CD8 T cells induced against α/β antigens in vivo were not cross-reactive to the native antigen. Moreover, immunization with α/β analogues did not elicit anti-tumor effects in tumor-bearing mice. CONCLUSIONS We conclude that even though α/β analogues of the SIINFEKL antigen can elicit a T cell-based response, this class of backbone-modified peptides is not promising from the perspective of antitumor vaccine development.
Collapse
Affiliation(s)
- Ichwaku Rastogi
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - John A. Mannone
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jena E. Moseman
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
| | - Douglas G. McNeel
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
2
|
Wang Y, Chang Y, Yin F, Kang C, Meng Y, Xu F, Liu Y, Zhang Y, Wu C, Fan S, Zhao J. Structural analyses of Cryptosporidium parvum epitopes reveal a novel scheme of decapeptide binding to H-2K b. J Struct Biol 2025; 217:108168. [PMID: 39809366 DOI: 10.1016/j.jsb.2025.108168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 01/07/2025] [Accepted: 01/11/2025] [Indexed: 01/16/2025]
Abstract
Cryptosporidium has gained much attention as a major cause of diarrhea worldwide. Here, we present the first structure of H-2Kb complexed with a decapeptide from Cryptosporidium parvum Gp40/15 protein (Gp40/15-VTF10). In contrast to all published structures, the aromatic residue P3-Phe of Gp40/15-VTF10 is anchored in pocket C rather than the canonical Y/F at P5 or P6 reported for octapeptides and nonapeptides. The results of in vitro refolding assays and circular dichroism experiments showed that the side chains of P3 and P5 play key roles in Gp40/15-VTF10 peptide binding. However, functional analysis of decapeptide epitopes revealed that the Gp40/15-VTF10 peptide did not elicit a strong CD8+T immune response, whereas the decapeptide epitope MEDLE2-INF10 induced a significant CD8+ T-cell response in peptide-immunized C57BL/6 mice. Using a model structure of H-2Kb-INF10 complex, we found that the antigenic decapeptide INF10 exhibits a completely different conformation, with the aromatic anchors P3F and P7F docked into the D and C pockets, respectively, while similar peptide conformation and hydrogen bond interactions between the peptide and major histocompatibility complex were found in the resolved H-2Kb-SVF9 complex. As the H-2Kb molecule predominantly prefers octapeptides with a strong anchor of P5 Y/F (or P6 Y/F for nonapeptides) binding to the C pocket, we propose that P7 Y/F in the C pocket may represent a novel binding mode for decapeptides. The results should increase the accuracy of T-cell epitope prediction and support the development of T-cell epitope vaccines against cryptosporidiosis.
Collapse
Affiliation(s)
- Yongli Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China; College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China
| | - Yankai Chang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Fangyuan Yin
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Chunliu Kang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Yao Meng
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Fukang Xu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Yiran Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Yunxia Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Changjing Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China
| | - Shuhua Fan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, PR China; Institute of Neuroscience and Translational Medicine, Zhoukou Normal University, Zhoukou, PR China.
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China.
| |
Collapse
|
3
|
Kelly JJ, Bloodworth N, Shao Q, Shabanowitz J, Hunt D, Meiler J, Pires MM. A Chemical Approach to Assess the Impact of Post-translational Modification on MHC Peptide Binding and Effector Cell Engagement. ACS Chem Biol 2024; 19:1991-2001. [PMID: 39150956 PMCID: PMC11420952 DOI: 10.1021/acschembio.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/31/2024] [Accepted: 08/08/2024] [Indexed: 08/18/2024]
Abstract
The human major histocompatibility complex (MHC) plays a pivotal role in the presentation of peptidic fragments from proteins, which can originate from self-proteins or from nonhuman antigens, such as those produced by viruses or bacteria. To prevent cytotoxicity against healthy cells, thymocytes expressing T cell receptors (TCRs) that recognize self-peptides are removed from circulation (negative selection), thus leaving T cells that recognize nonself-peptides. Current understanding suggests that post-translationally modified (PTM) proteins and the resulting peptide fragments they generate following proteolysis are largely excluded from negative selection; this feature means that PTMs can generate nonself-peptides that potentially contribute to the development of autoreactive T cells and subsequent autoimmune diseases. Although it is well-established that PTMs are prevalent in peptides present on MHCs, the precise mechanisms by which PTMs influence the antigen presentation machinery remain poorly understood. In the present work, we introduce chemical modifications mimicking PTMs on synthetic peptides. This is the first systematic study isolating the impact of PTMs on MHC binding and also their impact on TCR recognition. Our findings reveal various ways PTMs alter antigen presentation, which could have implications for tumor neoantigen presentation.
Collapse
Affiliation(s)
- Joey J. Kelly
- Department
of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Nathaniel Bloodworth
- Division
of Clinical Pharmacology, Department of MedicineVanderbilt University Medical Center, Nashville, Tennessee 37240, United States
| | - Qianqian Shao
- Department
of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Jeffrey Shabanowitz
- Department
of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Donald Hunt
- Department
of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| | - Jens Meiler
- Division
of Clinical Pharmacology, Department of MedicineVanderbilt University Medical Center, Nashville, Tennessee 37240, United States
- Institute
of Drug Discovery, Faculty of MedicineUniversity
of Leipzig, Leipzig, SAC 04103, Germany
- Center
for Structural Biology Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemistry Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Marcos M. Pires
- Department
of Chemistry University of Virginia Charlottesville, Virginia 22904, United States
| |
Collapse
|
4
|
Drost F, Dorigatti E, Straub A, Hilgendorf P, Wagner KI, Heyer K, López Montes M, Bischl B, Busch DH, Schober K, Schubert B. Predicting T cell receptor functionality against mutant epitopes. CELL GENOMICS 2024; 4:100634. [PMID: 39151427 PMCID: PMC11480844 DOI: 10.1016/j.xgen.2024.100634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 04/22/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Cancer cells and pathogens can evade T cell receptors (TCRs) via mutations in immunogenic epitopes. TCR cross-reactivity (i.e., recognition of multiple epitopes with sequence similarities) can counteract such escape but may cause severe side effects in cell-based immunotherapies through targeting self-antigens. To predict the effect of epitope point mutations on T cell functionality, we here present the random forest-based model Predicting T Cell Epitope-Specific Activation against Mutant Versions (P-TEAM). P-TEAM was trained and tested on three datasets with TCR responses to single-amino-acid mutations of the model epitope SIINFEKL, the tumor neo-epitope VPSVWRSSL, and the human cytomegalovirus antigen NLVPMVATV, totaling 9,690 unique TCR-epitope interactions. P-TEAM was able to accurately classify T cell reactivities and quantitatively predict T cell functionalities for unobserved single-point mutations and unseen TCRs. Overall, P-TEAM provides an effective computational tool to study T cell responses against mutated epitopes.
Collapse
Affiliation(s)
- Felix Drost
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Emilio Dorigatti
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Department of Statistics, Ludwig Maximilian Universität, 80539 Munich, Germany; Munich Center for Machine Learning (MCML), Ludwig Maximilian Universität, 80538 Munich, Germany
| | - Adrian Straub
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany
| | - Philipp Hilgendorf
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany; Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie, und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Karolin I Wagner
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany
| | - Kersten Heyer
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany
| | - Marta López Montes
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany
| | - Bernd Bischl
- Department of Statistics, Ludwig Maximilian Universität, 80539 Munich, Germany; Munich Center for Machine Learning (MCML), Ludwig Maximilian Universität, 80538 Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany; German Center for Infection Research, Deutschen Zentrum für Infektionsforschung (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology, and Hygiene, Technical University of Munich, 81675 Munich, Germany; Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie, und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Benjamin Schubert
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; School of Computation, Information, and Technology, Technical University of Munich, 85748 Garching bei München, Germany.
| |
Collapse
|
5
|
Sharma R, Amdare NP, Ghosh A, Schloss J, Sidney J, Garforth SJ, Lopez Y, Celikgil A, Sette A, Almo SC, DiLorenzo TP. Structural and biochemical analysis of highly similar HLA-B allotypes differentially associated with type 1 diabetes. J Biol Chem 2024; 300:107702. [PMID: 39173948 PMCID: PMC11422593 DOI: 10.1016/j.jbc.2024.107702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/09/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease involving T cell-mediated destruction of the insulin-producing beta cells in the pancreatic islets of Langerhans. CD8+ T cells, responding to beta cell peptides presented by class I major histocompatibility complex (MHC) molecules, are important effectors leading to beta cell elimination. Human leukocyte antigen (HLA) B∗39:06, B∗39:01, and B∗38:01 are closely related class I MHC allotypes that nonetheless show differential association with T1D. HLA-B∗39:06 is the most predisposing of all HLA class I molecules and is associated with early age at disease onset. B∗39:01 is also associated with susceptibility to T1D, but to a lesser extent, though differing from B∗39:06 by only two amino acids. HLA-B∗38:01, in contrast, is associated with protection from the disease. Upon identifying a peptide that binds to both HLA-B∗39:06 and B∗39:01, we determined the respective X-ray structures of the two allotypes presenting this peptide to 1.7 Å resolution. The peptide residues available for T cell receptor contact and those serving as anchors were identified. Analysis of the F pocket of HLA-B∗39:06 and B∗39:01 provided an explanation for the distinct peptide C terminus preferences of the two allotypes. Structure-based modeling of the protective HLA-B∗38:01 suggested a potential reason for its peptide preferences and its reduced propensity to present 8-mer peptides compared to B∗39:06. Notably, the three allotypes showed differential binding to peptides derived from beta cell autoantigens. Taken together, our findings should facilitate identification of disease-relevant candidate T cell epitopes and structure-guided therapeutics to interfere with peptide binding.
Collapse
Affiliation(s)
- Ruby Sharma
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Nitin P Amdare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jennifer Schloss
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Scott J Garforth
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yessenia Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alev Celikgil
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, La Jolla, California, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA; Division of Endocrinology and Diabetes, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA; Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA; Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York, USA.
| |
Collapse
|
6
|
Bloodworth N, Chen W, Hunter K, Patrick D, Palubinsky A, Phillips E, Roeth D, Kalkum M, Mallal S, Davies S, Ao M, Moretti R, Meiler J, Harrison DG. Posttranslationally modified self-peptides promote hypertension in mouse models. J Clin Invest 2024; 134:e174374. [PMID: 39145457 PMCID: PMC11324298 DOI: 10.1172/jci174374] [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: 08/03/2023] [Accepted: 06/13/2024] [Indexed: 08/16/2024] Open
Abstract
Posttranslational modifications can enhance immunogenicity of self-proteins. In several conditions, including hypertension, systemic lupus erythematosus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here, we show that the murine class I major histocompatibility complex (MHC-I) variant H-2Db uniquely presents isoLG-modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins, including sodium glucose transporter 2, cadherin 16, Kelch domain-containing protein 7A, and solute carrier family 23, that are recognized by CD8+ T cells in tissues of hypertensive mice, induce T cell proliferation in vitro, and prime hypertension after adoptive transfer. Finally, we find patterns of isoLG-adducted antigen restriction in class I human leukocyte antigens that are similar to those in murine analogs. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension.
Collapse
Affiliation(s)
| | - Wei Chen
- Division of Clinical Pharmacology, Department of Medicine
| | - Kuniko Hunter
- Division of Clinical Pharmacology, Department of Medicine
| | - David Patrick
- Division of Clinical Pharmacology, Department of Medicine
| | | | - Elizabeth Phillips
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
- Center for Drug Safety and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel Roeth
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Markus Kalkum
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Simon Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Sean Davies
- Division of Clinical Pharmacology, Department of Medicine
| | - Mingfang Ao
- Division of Clinical Pharmacology, Department of Medicine
| | | | - Jens Meiler
- Center for Structural Biology, and
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
- Institute for Drug Discovery, Universität Leipzig Medical School, Leipzig, Germany
| | | |
Collapse
|
7
|
Uslu S, Lee UJ, Tavakolpour S, Abousaway O, Nili A, Bass L, Purwar P, Lacson E, Berland L, Kuhnast A, Clark LM, Picard D, Rakhshandehroo T, Mantri SR, Moravej H, Rashidian M. Development of a Stable Peptide-Major Histocompatibility Complex (MHC) via Sortase and Click Chemistry. ACS Pharmacol Transl Sci 2024; 7:1746-1757. [PMID: 38898944 PMCID: PMC11184609 DOI: 10.1021/acsptsci.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 06/21/2024]
Abstract
T cells play a crucial role in antitumor immune responses and the clearance of infected cells. They identify their targets through the binding of T-cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules present in cancer cells, infected cells, and antigen-presenting cells. This interaction is often weak, requiring multimeric pMHC molecules to enhance the avidity for identifying antigen-specific T cells. Current exchangeable pMHC-I tetramerization methods may overlook TCRs recognizing less stable yet immunogenic peptides. In vivo applications targeting antigen-specific T cells demand the genetic synthesis of a pMHC fusion for each unique peptide antigen, which poses a significant challenge. To address these challenges, we developed a sortase and click chemistry-mediated approach for generating stable pMHC molecules. Leveraging sortase technology, we introduced an azide click-handle near the N-terminus of β2m, proximal to the MHC-peptide-binding groove. Simultaneously, the peptide was engineered with a multi glycine linker and a C-terminal alkyne click-handle. Azide-alkyne click reactions efficiently immobilized the peptide onto the MHC molecule, providing a versatile and efficient method for pMHC generation. The resulting peptide-clicked-MHC specifically binds to its cognate TCR and remains stable for over 3 months at 4 °C in the absence of any additional free peptide. The stability of the pMHC and its affinity to cognate TCRs are influenced by the linker's nature and length. Multi glycine linkers outperform poly(ethylene glycol) (PEG) linkers in this regard. This technology expands the toolkit for identifying and targeting antigen-specific T cells, enhancing our understanding of cancer-specific immune responses, and has the potential to streamline the development of personalized immunotherapies.
Collapse
Affiliation(s)
- Safak
C. Uslu
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Medical
Scientist Training Program, Hacettepe University
Faculty of Medicine, Ankara 06230, Turkey
| | - Uk-Jae Lee
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Soheil Tavakolpour
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Omar Abousaway
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Ali Nili
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Lily Bass
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Pragallabh Purwar
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Edward Lacson
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Lea Berland
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- CNRS,
INSERM, IRCAN, Université Côte d’Azur, 06100 Nice, France
| | - Adrien Kuhnast
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Louise M. Clark
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Delia Picard
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Taha Rakhshandehroo
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Shreya R. Mantri
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Heydar Moravej
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
| | - Mohammad Rashidian
- Department
of Cancer Immunology and Virology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
- Parker
Institute for Cancer Immunotherapy, San Francisco, California 94129, United States
| |
Collapse
|
8
|
Straub A, Grassmann S, Jarosch S, Richter L, Hilgendorf P, Hammel M, Wagner KI, Buchholz VR, Schober K, Busch DH. Recruitment of epitope-specific T cell clones with a low-avidity threshold supports efficacy against mutational escape upon re-infection. Immunity 2023:S1074-7613(23)00179-6. [PMID: 37164014 DOI: 10.1016/j.immuni.2023.04.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/01/2023] [Accepted: 04/13/2023] [Indexed: 05/12/2023]
Abstract
Repetitive pathogen exposure leads to the dominant outgrowth of T cell clones with high T cell receptor (TCR) affinity to the relevant pathogen-associated antigens. However, low-affinity clones are also known to expand and form immunological memory. While these low-affinity clones contribute less immunity to the original pathogen, their role in protection against pathogens harboring immune escape mutations remains unclear. Based on identification of the TCR repertoire and functionality landscape of naive epitope-specific CD8+ T cells, we reconstructed defined repertoires that could be followed as polyclonal populations during immune responses in vivo. We found that selective clonal expansion is governed by clear TCR avidity thresholds. Simultaneously, initial recruitment of broad TCR repertoires provided a polyclonal niche from which flexible secondary responses to mutant epitopes could be recalled. Elucidating how T cell responses develop "from scratch" is informative for the development of enhanced immunotherapies and vaccines.
Collapse
Affiliation(s)
- Adrian Straub
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Simon Grassmann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; The Joseph Sun Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Lena Richter
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Philipp Hilgendorf
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Karolin I Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany.
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Partner site Munich, German Center for Infection Research (DZIF), Munich, Germany.
| |
Collapse
|
9
|
Structural Analyses of a Dominant Cryptosporidium parvum Epitope Presented by H-2K b Offer New Options To Combat Cryptosporidiosis. mBio 2023; 14:e0266622. [PMID: 36602309 PMCID: PMC9973275 DOI: 10.1128/mbio.02666-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cryptosporidium parvum has gained much attention as a major cause of diarrhea in the world, particularly in those with compromised immune systems. The data currently available on how the immune system recognizes C. parvum are growing rapidly, but we lack data on the interactions among host major histocompatibility complex (MHC) diversity and parasitic T-cell epitopes. To identify antigenic epitopes in a murine model, we performed systematic profiling of H-2Kb-restricted peptides by screening the dominant Cryptosporidium antigens. The results revealed that the glycoprotein-derived epitope Gp40/15-SVF9 induced an immunodominant response in C. parvum-recovered C57BL/6 mice, and injection of the cytotoxic-T-lymphocyte (CTL) peptide with the adjuvant activated peptide-specific CD8+ T cells. Notably, the SVF9 epitope was highly conserved across Cryptosporidium hominis, C. parvum, and many other Cryptosporidium species. SVF9 also formed stable peptide-MHC class I (MHC I) complexes with HLA-A*0201, suggesting cross-reactivity between H-2Kb and human MHC I specificities. Crystal structure analyses revealed that the interactions of peptide-MHC surface residues of H-2Kb and HLA-A*0201 are highly conserved. The hydrogen bonds of H-2Kb-SVF9 are similar to those of a dominant epitope presented by HLA-A*0201, which can be recognized by a public human T-cell receptor (TCR). Notably, we found double conformations in position 4 (P4), 5 (P5) of the SVF9 peptide, which showed high flexibility, and multiple peptide conformations generated more molecular surfaces that can potentially be recognized by TCRs. Our findings demonstrate that an immunodominant C. parvum epitope and its homologs from different Cryptosporidium species and subtypes can benefit vaccine development to combat cryptosporidiosis. IMPORTANCE Adaptive immune responses and T lymphocytes have been implicated as important mechanisms of parasite-induced protection. However, the role of CD8+ T lymphocytes in the resolution of C. parvum infection is largely unresolved. Our results revealed that the glycoprotein-derived epitope Gp40/15-SVF9 induced an immunodominant CD8+ T-cell response in C57BL/6 mice. Crystal structure analyses revealed that the interactions of the H-2Kb-SVF9 peptide are similar to those of a dominant epitope presented by HLA-A*0201, which can be recognized by human TCRs. In addition, we found double conformations of the SVF9 peptide, which showed high flexibility and multiple peptide conformations that can potentially be recognized by TCRs.
Collapse
|
10
|
Irie H, Morita K, Matsuda M, Koizumi M, Mochizuki S. Tyrosinase-Related Protein2 Peptide with Replacement of N-Terminus Residue by Cysteine Binds to H-2K b and Induces Antigen-Specific Cytotoxic T Lymphocytes after Conjugation with CpG-DNA. Bioconjug Chem 2023; 34:433-442. [PMID: 36708315 DOI: 10.1021/acs.bioconjchem.2c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recent studies have shown the potent efficacy of peptide-based vaccines for cancer immunotherapy. Immunological performance is optimized through the co-delivery of adjuvant and antigenic peptide molecules to antigen-presenting cells simultaneously. In our previous study, we showed that a conjugate consisting of 40-mer CpG-DNA and an antigenic ovalbumin peptide through disulfide bonding could efficiently induce ovalbumin-specific cytotoxic T lymphocyte (CTL) responses in vivo. In this study, based on the conjugation design, we prepared a conjugate consisting of 30-mer CpG-DNA (CpG30) and a cancer antigenic peptide of Tyrosinase-related protein 2 (TRP2180-188) using a cysteine residue attached at the N-terminus of TRP2180-188. However, the immunization of mice with this conjugate did not induce efficient TRP2180-188-specific immune responses. It was thought that the resultant peptide (10-mer) cleaved from the conjugate might be too long to fit into the H-2Kb molecule because the optimal length for binding to it is 8-9 amino acids. We newly designed a conjugate consisting of CpG30 and the C-TRP2181-188 peptide (9-mer), in which the N-terminal serine residue of TRP2180-188 is replaced by a cysteine. By adjusting the peptide length, we succeeded in inducing strong TRP2180-188 peptide-specific CTL activity upon immunization with the CpG30-C-TRP2181-188 conjugate. Furthermore, various CpG30-C-TRP2181-188 conjugates having other CpG-DNA sequences or cysteine analogues also induced the same level of CTL activity. Therefore, CpG-C-peptide conjugates prepared by replacement of the amino acid residue at the N-terminus with a cysteine residue could be a new and effective platform for peptide vaccines for targeting specific antigens of cancers and infectious diseases.
Collapse
Affiliation(s)
- Hitomi Irie
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Koji Morita
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Miyu Matsuda
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| |
Collapse
|
11
|
Grace BE, Backlund CM, Morgan DM, Kang BH, Singh NK, Huisman BD, Rappazzo CG, Moynihan KD, Maiorino L, Dobson CS, Kyung T, Gordon KS, Holec PV, Mbah OCT, Garafola D, Wu S, Love JC, Wittrup KD, Irvine DJ, Birnbaum ME. Identification of Highly Cross-Reactive Mimotopes for a Public T Cell Response in Murine Melanoma. Front Immunol 2022; 13:886683. [PMID: 35812387 PMCID: PMC9260506 DOI: 10.3389/fimmu.2022.886683] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
While immune checkpoint blockade results in durable responses for some patients, many others have not experienced such benefits. These treatments rely upon reinvigorating specific T cell-antigen interactions. However, it is often unknown what antigens are being recognized by T cells or how to potently induce antigen-specific responses in a broadly applicable manner. Here, we characterized the CD8+ T cell response to a murine model of melanoma following combination immunotherapy to determine the basis of tumor recognition. Sequencing of tumor-infiltrating T cells revealed a repertoire of highly homologous TCR sequences that were particularly expanded in treated mice and which recognized an antigen from an endogenous retrovirus. While vaccination against this peptide failed to raise a protective T cell response in vivo, engineered antigen mimotopes induced a significant expansion of CD8+ T cells cross-reactive to the original antigen. Vaccination with mimotopes resulted in killing of antigen-loaded cells in vivo yet showed modest survival benefit in a prophylactic vaccine paradigm. Together, this work demonstrates the identification of a dominant tumor-associated antigen and generation of mimotopes which can induce robust functional T cell responses that are cross-reactive to the endogenous antigen across multiple individuals.
Collapse
Affiliation(s)
- Beth E. Grace
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Coralie M. Backlund
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Duncan M. Morgan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Byong H. Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Nishant K. Singh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Brooke D. Huisman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - C. Garrett Rappazzo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kelly D. Moynihan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Laura Maiorino
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Connor S. Dobson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Taeyoon Kyung
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Khloe S. Gordon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Patrick V. Holec
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Daniel Garafola
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Shengwei Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - K. Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Michael E. Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
- *Correspondence: Michael E. Birnbaum,
| |
Collapse
|
12
|
Lantz O, Teyton L. Identification of T cell antigens in the 21st century, as difficult as ever. Semin Immunol 2022; 60:101659. [PMID: 36183497 PMCID: PMC10332289 DOI: 10.1016/j.smim.2022.101659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Identifying antigens recognized by T cells is still challenging, particularly for innate like T cells that do not recognize peptides but small metabolites or lipids in the context of MHC-like molecules or see non-MHC restricted antigens. The fundamental reason for this situation is the low affinity of T cell receptors for their ligands coupled with a level of degeneracy that makes them bind to similar surfaces on antigen presenting cells. Herein we will describe non-exhaustively some of the methods that were used to identify peptide antigens and briefly mention the high throughput methods more recently proposed for that purpose. We will then present how the molecules recognized by innate like T cells (NKT, MAIT and γδ T cells) were discovered. We will show that serendipity was instrumental in many cases.
Collapse
Affiliation(s)
- Olivier Lantz
- INSERM U932, PSL University, Institut Curie, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, Paris 75005, France; Centre d'investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428) Institut Curie, Paris 75005, France
| | - Luc Teyton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
13
|
He X, Zhou S, Quinn B, Jahagirdar D, Ortega J, Long MD, Abrams SI, Lovell JF. An In Vivo Screen to Identify Short Peptide Mimotopes with Enhanced Antitumor Immunogenicity. Cancer Immunol Res 2022; 10:314-326. [PMID: 34992135 DOI: 10.1158/2326-6066.cir-21-0332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 11/16/2022]
Abstract
Tumor-associated self-antigens are potential cancer vaccine targets but suffer from limited immunogenicity. There are examples of mutated, short self-peptides inducing epitope-specific CD8⁺ T cells more efficiently than the wild-type epitope, but current approaches cannot yet reliably identify such epitopes, which are referred to as enhanced mimotopes ("e-mimotopes"). Here, we present a generalized strategy to develop e-mimotopes, using the tyrosinase-related protein 2 (Trp2) peptide Trp2180-188, which is a murine major histocompatibility complex class I (MHC-I) epitope, as a test case. Using a vaccine adjuvant that induces peptide particle formation and strong cellular responses with nanogram antigen doses, a two-step method systematically identified e-mimotope candidates with murine immunization. First, position-scanning peptide micro libraries were generated in which each position of the wild-type epitope sequence was randomized. Randomization of only one specific residue of the Trp2 epitope increased antitumor immunogenicity. Second, all 20 amino acids were individually substituted and tested at that position, enabling the identification of two e-mimotopes with single amino-acid mutations. Despite similar MHC-I affinity compared to the wild-type epitope, e-mimotope immunization elicited improved Trp2-specific cytotoxic T-cell phenotypes and improved T-cell receptor affinity for both the e-mimotopes and the native epitope, resulting in better outcomes in multiple prophylactic and therapeutic tumor models. The screening method was also applied to other targets with other murine MHC-I restriction elements, including epitopes within glycoprotein 70 and Wilms' Tumor Gene 1, to identify additional e-mimotopes with enhanced potency.
Collapse
Affiliation(s)
- Xuedan He
- Biomedical Engineering, University at Buffalo, State University of New York
| | - Shiqi Zhou
- Biomedical Engineering, University at Buffalo, State University of New York
| | - Breandan Quinn
- Biomedical Engineering, University at Buffalo, State University of New York
| | | | | | - Mark D Long
- Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center
| | | | - Jonathan F Lovell
- Biomedical Engineering, University at Buffalo, State University of New York
| |
Collapse
|
14
|
Jin S, Zhuo SH, Takemoto Y, Li YM, Uesugi M. Self-assembling small-molecule adjuvants as antigen nano-carriers. Chem Commun (Camb) 2022; 58:12228-12231. [DOI: 10.1039/d2cc05016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nano-carrier adjuvant for antigens: the co-delivery of antigens and adjuvants and the high degree of antigen presentation are achieved by conjugating peptide antigens with cholicamide, a self-assembling small molecule adjuvant.
Collapse
Affiliation(s)
- Shuyu Jin
- Graduate School of Medicine, Kyoto University, Uji, Kyoto 611-0011, Japan
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shao-hua Zhuo
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yasushi Takemoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yan-mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
- Beijing Institute for Brain Disorders, Beijing 100069, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, China
| |
Collapse
|
15
|
Ma J, Ayres CM, Hellman LM, Devlin JR, Baker BM. Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor. J Biol Chem 2021; 296:100686. [PMID: 33891944 PMCID: PMC8138769 DOI: 10.1016/j.jbc.2021.100686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Using a variety of activating and inhibitory receptors, natural killer (NK) cells protect against disease by eliminating cells that have downregulated class I major histocompatibility complex (MHC) proteins, such as in response to cell transformation or viral infection. The inhibitory murine NK receptor Ly49C specifically recognizes the class I MHC protein H-2Kb. Unusual among NK receptors, Ly49C exhibits a peptide-dependent sensitivity to H-2Kb recognition, which has not been explained despite detailed structural studies. To gain further insight into Ly49C peptide sensitivity, we examined Ly49C recognition biochemically and through the lens of dynamic allostery. We found that the peptide sensitivity of Ly49C arises through small differences in H-2Kb-binding affinity. Although molecular dynamics simulations supported a role for peptide-dependent protein dynamics in producing these differences in binding affinity, calorimetric measurements indicated an enthalpically as opposed to entropically driven process. A quantitative linkage analysis showed that this emerges from peptide-dependent dynamic tuning of electrostatic interactions across the Ly49C–H-2Kb interface. We propose a model whereby different peptides alter the flexibility of H-2Kb, which in turn changes the strength of electrostatic interactions across the protein–protein interface. Our results provide a quantitative assessment of how peptides alter Ly49C-binding affinity, suggest the underlying mechanism, and demonstrate peptide-driven allostery at work in class I MHC proteins. Lastly, our model provides a solution for how dynamic allostery could impact binding of some, but not all, class I MHC partners depending on the structural and chemical composition of the interfaces.
Collapse
Affiliation(s)
- Jiaqi Ma
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA
| | - Jason R Devlin
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.
| |
Collapse
|
16
|
Sun X, Tokunaga R, Nagai Y, Miyahara R, Kishimura A, Kawakami S, Katayama Y, Mori T. Ligand Design for Specific MHC Class I Molecules on the Cell Surface. Biochemistry 2020; 59:4646-4653. [PMID: 33252220 DOI: 10.1021/acs.biochem.0c00735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have validated that ligand peptides designed from antigen peptides could be used for targeting specific major histocompatibility complex class I (MHC-I) molecules on the cell surface. To design the ligand peptides, we used reported antigen peptides for each MHC-I molecule with high binding affinity. From the crystal structure of the peptide/MHC-I complexes, we determined a modifiable residue in the antigen peptides and replaced this residue with a lysine with an ε-amine group modified with functional molecules. The designed ligand peptides successfully bound to cells expressing the corresponding MHC-I molecules via exchange of peptides bound to MHC-I. We demonstrated that the peptide ligands could be used to transport a protein or a liposome to cells expressing the corresponding MHC-I. This strategy may be useful for targeted delivery to cells overexpressing MHC-I, which have been observed in autoimmune diseases.
Collapse
Affiliation(s)
- Xizheng Sun
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Reika Tokunaga
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoko Nagai
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ryo Miyahara
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Akihiro Kishimura
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,International Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shigeru Kawakami
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Yoshiki Katayama
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,International Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Advanced Medical Innovation, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan.,Department of Biomedical Engineering, Chung Yuan Christian University, 200 Chung Pei Road, Chung Li, 32023 ROC, Taiwan
| | - Takeshi Mori
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
17
|
Irie H, Morita K, Koizumi M, Mochizuki S. Immune Responses and Antitumor Effect through Delivering to Antigen Presenting Cells by Optimized Conjugates Consisting of CpG-DNA and Antigenic Peptide. Bioconjug Chem 2020; 31:2585-2595. [PMID: 33151667 DOI: 10.1021/acs.bioconjchem.0c00523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Immunotherapy using antigen-specific cytotoxic T lymphocytes (CTLs) has become one of the most attractive strategies for cancer treatment. For the induction of antigen-specific CTLs in vivo, the co-delivery of CpG-DNAs and antigens to the same antigen-presenting cells (APCs) is a promising strategy. In this study, we prepared conjugates consisting of 40mer of CpG-DNA (CpG40) and antigenic peptide (OVA257-264), which have the following distinctive features: (1) multiple CpG motifs in a molecule; (2) cleavage in the cytosol because of the disulfide bonding via cysteine residue between peptide and CpG-DNA; (3) conjugation designed to induce antigen presentation on MHC class I molecules. Immunization with the conjugate CpG40-C-OVA257-264 at the mouse tail base induced strong CTL activity at a very low peptide dose of 20 ng/head. It was found that the conjugates were internalized into C-type mannose receptor 1 (MRC1)-expressing cells in inguinal lymph nodes, indicating that the CpG portion in the conjugate acts as not only an adjuvant for the activation of TLR9 but also a carrier to APCs expressing MRC1. In a tumor-bearing mice model, mice immunized with CpG40-C-OVA257-264 conjugates exhibited long delays in tumor growth compared with those treated with PBS, OVA257-264 alone, or a mixture of CpG40 and OVA257-264. Therefore, CpG-C-peptide conjugates could be a new and effective platform for peptide vaccine for the treatment of cancers and infectious diseases.
Collapse
Affiliation(s)
- Hitomi Irie
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Koji Morita
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| |
Collapse
|
18
|
Sutiwisesak R, Hicks ND, Boyce S, Murphy KC, Papavinasasundaram K, Carpenter SM, Boucau J, Joshi N, Le Gall S, Fortune SM, Sassetti CM, Behar SM. A natural polymorphism of Mycobacterium tuberculosis in the esxH gene disrupts immunodomination by the TB10.4-specific CD8 T cell response. PLoS Pathog 2020; 16:e1009000. [PMID: 33075106 PMCID: PMC7597557 DOI: 10.1371/journal.ppat.1009000] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/29/2020] [Accepted: 09/23/2020] [Indexed: 12/20/2022] Open
Abstract
CD8 T cells provide limited protection against Mycobacterium
tuberculosis (Mtb) infection in the mouse model. As Mtb causes
chronic infection in mice and humans, we hypothesize that Mtb impairs T cell
responses as an immune evasion strategy. TB10.4 is an immunodominant antigen in
people, nonhuman primates, and mice, which is encoded by the
esxH gene. In C57BL/6 mice, 30–50% of pulmonary CD8 T cells
recognize the TB10.44−11 epitope. However, TB10.4-specific CD8 T
cells fail to recognize Mtb-infected macrophages. We speculate that Mtb elicits
immunodominant CD8 T cell responses to antigens that are inefficiently presented
by infected cells, thereby focusing CD8 T cells on nonprotective antigens. Here,
we leverage naturally occurring polymorphisms in esxH, which
frequently occur in lineage 1 strains, to test this “decoy hypothesis”. Using
the clinical isolate 667, which contains an EsxHA10T polymorphism, we
observe a drastic change in the hierarchy of CD8 T cells. Using isogenic
Erd.EsxHA10T and Erd.EsxHWT strains, we prove that
this polymorphism alters the hierarchy of immunodominant CD8 T cell responses.
Our data are best explained by immunodomination, a mechanism by which
competition for APC leads to dominant responses suppressing subdominant
responses. These results were surprising as the variant epitope can bind to
H2-Kb and is recognized by TB10.4-specific CD8 T cells. The
dramatic change in TB10.4-specific CD8 responses resulted from increased
proteolytic degradation of A10T variant, which destroyed the
TB10.44-11epitope. Importantly, this polymorphism affected T cell
priming and recognition of infected cells. These data support a model in which
nonprotective CD8 T cells become immunodominant and suppress subdominant
responses. Thus, polymorphisms between clinical Mtb strains, and BCG or H37Rv
sequence-based vaccines could lead to a mismatch between T cells that are primed
by vaccines and the epitopes presented by infected cells. Reprograming host
immune responses should be considered in the future design of vaccines. An important question for vaccine developers is the relative potency of CD4 vs.
CD8 T cells against Mtb, as strategies differ for eliciting these different T
cell subsets. Despite robust antigen-specific pulmonary CD8 T cell responses,
CD4 T cells mediate more protection than CD8 T cells in the murine model. Most
CD8 T cells recognize a single antigen, TB10.4, which is encoded by the
esxH gene. Based on finding that
TB10.44−11-specific CD8 T cells poorly recognize Mtb-infected
macrophages, we hypothesized that Mtb evades detection by CD8 T cells and
focuses the CD8 T cell response on non-protective antigen. We termed these
antigens “decoy antigens.” To test this hypothesis, we took advantage of a
natural variant of the esxH gene, which contains an A10T
polymorphism within the TB10.44−11 epitope. This polymorphism
drastically alters the hierarchy of CD8 T cell responses elicited by Mtb. These
data suggest that immunodomination by the TB10.4 epitope acts to suppress
subdominant CD8 T cell responses to other Mtb antigens, impairing the CD8 T cell
response to other Mtb antigens, some of which might be presented by Mtb-infected
macrophages and be targets of protective immunity. Importantly, this single
amino acid polymorphism, which does not significantly alter MHC-binding or T
cell recognition, alters the half-life of the epitope and consequently, has a
profound effect on CD8 T cell priming and recognition of infected cells. These
data also provide a mechanism that could be exploited to manipulate the
hierarchy of immunodominant responses.
Collapse
Affiliation(s)
- Rujapak Sutiwisesak
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Nathan D. Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan
School of Public Health, Boston, Massachusetts, United States of
America
| | - Shayla Boyce
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Kenan C. Murphy
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Stephen M. Carpenter
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, Massachusetts
Institute of Technology and Harvard University, Cambridge, MA, United States of
America
| | - Neelambari Joshi
- Ragon Institute of Massachusetts General Hospital, Massachusetts
Institute of Technology and Harvard University, Cambridge, MA, United States of
America
| | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts
Institute of Technology and Harvard University, Cambridge, MA, United States of
America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan
School of Public Health, Boston, Massachusetts, United States of
America
| | - Christopher M. Sassetti
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Samuel M. Behar
- Immunology and Microbiology Program, Graduate School of Biomedical
Science, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- Department of Microbiology and Physiological Systems, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
- * E-mail:
| |
Collapse
|
19
|
Li Y, Frei AW, Yang EY, Labrada-Miravet I, Sun C, Rong Y, Samojlik MM, Bayer AL, Stabler CL. In vitro platform establishes antigen-specific CD8 + T cell cytotoxicity to encapsulated cells via indirect antigen recognition. Biomaterials 2020; 256:120182. [PMID: 32599358 PMCID: PMC7480933 DOI: 10.1016/j.biomaterials.2020.120182] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 02/07/2023]
Abstract
The curative potential of non-autologous cellular therapy is hindered by the requirement of anti-rejection therapy. Cellular encapsulation within nondegradable biomaterials has the potential to inhibit immune rejection, but the efficacy of this approach in robust preclinical and clinical models remains poor. While the responses of innate immune cells to the encapsulating material have been characterized, little attention has been paid to the contributions of adaptive immunity in encapsulated graft destabilization. Avoiding the limitations of animal models, we established an efficient, antigen-specific in vitro platform capable of delineating direct and indirect host T cell recognition to microencapsulated cellular grafts and evaluated their consequential impacts. Using ovalbumin (OVA) as a model antigen, we determined that alginate microencapsulation abrogates direct CD8+ T cell activation by interrupting donor-host interaction; however, indirect T cell activation, mediated by host antigen presenting cells (APCs) primed with shed donor antigens, still occurs. These activated T cells imparted cytotoxicity on the encapsulated cells, likely via diffusion of cytotoxic solutes. Overall, this platform delivers unique mechanistic insight into the impacts of hydrogel encapsulation on host adaptive immune responses, comprehensively addressing a long-standing hypothesis of the field. Furthermore, it provides an efficient benchtop screening tool for the investigation of new encapsulation methods and/or synergistic immunomodulatory agents.
Collapse
Affiliation(s)
- Ying Li
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA; Graduate Program in Biomedical Sciences, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Anthony W Frei
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Ethan Y Yang
- Diabetes Research Institute, College of Medicine, University of Miami, Miami, FL, USA
| | - Irayme Labrada-Miravet
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Chuqiao Sun
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Yanan Rong
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Magdalena M Samojlik
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Allison L Bayer
- Diabetes Research Institute, College of Medicine, University of Miami, Miami, FL, USA; Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Cherie L Stabler
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA; Graduate Program in Biomedical Sciences, College of Medicine, University of Florida, Gainesville, FL, USA; University of Florida Diabetes Institute, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
20
|
Kinetically distinct processing pathways diversify the CD8 + T cell response to a single viral epitope. Proc Natl Acad Sci U S A 2020; 117:19399-19407. [PMID: 32719124 DOI: 10.1073/pnas.2004372117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The source proteins from which CD8+ T cell-activating peptides are derived remain enigmatic. Glycoproteins are particularly challenging in this regard owing to several potential trafficking routes within the cell. By engineering a glycoprotein-derived epitope to contain an N-linked glycosylation site, we determined that optimal CD8+ T cell expansion and function were induced by the peptides that are rapidly produced from the exceedingly minor fraction of protein mislocalized to the cytosol. In contrast, peptides derived from the much larger fraction that undergoes translocation and quality control are produced with delayed kinetics and induce suboptimal CD8+ T cell responses. This dual system of peptide generation enhances CD8+ T cell participation in diversifying both antigenicity and the kinetics of peptide display.
Collapse
|
21
|
Yuzuriha K, Yoshida A, Li S, Kishimura A, Mori T, Katayama Y. Synthesis of peptide conjugates with vitamins for induction of antigen-specific immunotolerance. J Pept Sci 2020; 26:e3275. [PMID: 32671962 DOI: 10.1002/psc.3275] [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: 03/23/2020] [Revised: 06/06/2020] [Accepted: 06/20/2020] [Indexed: 11/07/2022]
Abstract
In this report, we designed conjugates of an antigen peptide with the immunosuppressive vitamins all-trans retinoic acid (ATRA) and vitamin D3 for efficient induction of antigen-specific immunotolerance. We established a synthetic scheme for the preparation of the peptide-vitamin conjugates, which the chemically unstable vitamins tolerated. Among the obtained conjugates, the ATRA conjugate successfully suppressed inflammatory effects in macrophages and dendritic cells and induced antigen presentation in dendritic cells. This synthetic method of conjugate is conceivably applicable to other antigen peptides for induction of antigen-specific immunotolerance.
Collapse
Affiliation(s)
- Kazuki Yuzuriha
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Ayaka Yoshida
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Shunyi Li
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Akihiro Kishimura
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka, 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 819-0395, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, 819-0395, Japan.,International Research Center for Molecular Systems, Kyushu University, Fukuoka, 819-0395, Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka, 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 819-0395, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Fukuoka, 819-0395, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, 819-0395, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, 819-0395, Japan.,International Research Center for Molecular Systems, Kyushu University, Fukuoka, 819-0395, Japan.,Centre for Advanced Medicine Innovation, Kyushu University, Fukuoka, 812-8582, Japan.,Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan City, ROC, 32023, Taiwan
| |
Collapse
|
22
|
Xiao J, Xiang W, Zhang Y, Peng W, Zhao M, Niu L, Chai Y, Qi J, Wang F, Qi P, Pan C, Han L, Wang M, Kaufman J, Gao GF, Liu WJ. An Invariant Arginine in Common with MHC Class II Allows Extension at the C-Terminal End of Peptides Bound to Chicken MHC Class I. THE JOURNAL OF IMMUNOLOGY 2018; 201:3084-3095. [PMID: 30341185 DOI: 10.4049/jimmunol.1800611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022]
Abstract
MHC molecules are found in all jawed vertebrates and are known to present peptides to T lymphocytes. In mammals, peptides can hang out either end of the peptide-binding groove of classical class II molecules, whereas the N and C termini of peptides are typically tightly bound to specific pockets in classical class I molecules. The chicken MHC, like many nonmammalian vertebrates, has a single dominantly expressed classical class I molecule encoded by the BF2 locus. We determined the structures of BF2*1201 bound to two peptides and found that the C terminus of one peptide hangs outside of the groove with a conformation much like the peptides bound to class II molecules. We found that BF2*1201 binds many peptides that hang out of the groove at the C terminus, and the sequences and structures of this MHC class I allele were determined to investigate the basis for this phenomenon. The classical class I molecules of mammals have a nearly invariant Tyr (Tyr84 in humans) that coordinates the peptide C terminus, but all classical class I molecules outside of mammals have an Arg in that position in common with mammalian class II molecules. We find that this invariant Arg residue switches conformation to allow peptides to hang out of the groove of BF2*1201, suggesting that this phenomenon is common in chickens and other nonmammalian vertebrates, perhaps allowing the single dominantly expressed class I molecule to bind a larger repertoire of peptides.
Collapse
Affiliation(s)
- Jin Xiao
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wangzhen Xiang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yongli Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Weiyu Peng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Niu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Wang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China
| | - Peng Qi
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China
| | - Chungang Pan
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Ming Wang
- Key Laboratory of Veterinary Bioproduction and Chemical Medicine of the Ministry of Agriculture, Engineering and Technology Research Center for Beijing Veterinary Peptide Vaccine Design and Preparation, Zhongmu Institutes of China Animal Husbandry Industry Co. Ltd., Beijing 100095, China.,College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; .,Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 1QP, United Kingdom; and
| | - George F Gao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; .,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,China Research Network of Immunity and Health, Beijing Institutes of Life Science Chinese Academy of Sciences, Beijing 100101, China
| | - William J Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China; .,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| |
Collapse
|
23
|
Lifelong CMV infection improves immune defense in old mice by broadening the mobilized TCR repertoire against third-party infection. Proc Natl Acad Sci U S A 2018; 115:E6817-E6825. [PMID: 29967140 DOI: 10.1073/pnas.1719451115] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lifelong interactions between host and the ubiquitous and persistent cytomegalovirus (CMV) have been proposed to contribute to the age-related decline in immunity. Prior work from us and others found some support for that idea, yet evidence that this led to increased vulnerability to other infections was not obtained. Moreover, evidence has accumulated that CMV infection can be beneficial to immune defense in young/adult mice and humans, dominantly via enhanced innate immunity. Here, we describe an unexpected impact of murine CMV (MCMV) upon the T cell response of old mice to Listeria monocytogenes expressing the model antigen, OVA (Lm-OVA). Single-cell sequencing of the OVA-specific CD8 T cell receptor β (TCRβ) repertoire of old mice demonstrated that old MCMV-infected mice recruited many diverse clonotypes that afforded broad and often more efficient recognition of antigenic peptide variants. This stood in contrast to old control mice, which exhibited strong narrowing and homogenization of the elicited repertoire. High-throughput sequencing of the total naïve CD8 TCRβ repertoire showed that many of these diverse OVA-specific clonotypes were present in the naïve CD8 repertoire of mice in all groups (adult, old control, and old MCMV+) yet were only recruited into the Lm-OVA response in MCMV+ old mice. These results have profound implications for our understanding of T cell immunity over a life span and suggest that our coevolution with CMV may include surprising, potentially positive impacts on adaptive heterologous immunity in late life.
Collapse
|
24
|
van der Gracht AMF, de Geus MAR, Camps MGM, Ruckwardt TJ, Sarris AJC, Bremmers J, Maurits E, Pawlak JB, Posthoorn MM, Bonger KM, Filippov DV, Overkleeft HS, Robillard MS, Ossendorp F, van Kasteren SI. Chemical Control over T-Cell Activation in Vivo Using Deprotection of trans-Cyclooctene-Modified Epitopes. ACS Chem Biol 2018; 13:1569-1576. [PMID: 29733186 PMCID: PMC6006443 DOI: 10.1021/acschembio.8b00155] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Activation
of a cytotoxic T-cell is a complex multistep process,
and tools to study the molecular events and their dynamics that result
in T-cell activation in situ and in vivo are scarce. Here, we report the design and use of conditional epitopes
for time-controlled T-cell activation in vivo. We
show that trans-cyclooctene-protected SIINFEKL (with
the lysine amine masked) is unable to elicit the T-cell response characteristic
for the free SIINFEKL epitope. Epitope uncaging by means of an inverse-electron
demand Diels–Alder (IEDDA) event restored T-cell activation
and provided temporal control of T-cell proliferation in vivo.
Collapse
Affiliation(s)
- Anouk M. F. van der Gracht
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mark A. R. de Geus
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcel G. M. Camps
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institute of Health, 40 Convent Drive, Building 40, Bethesda, Maryland 20814, United States
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Jessica Bremmers
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elmer Maurits
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Joanna B. Pawlak
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Michelle M. Posthoorn
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kimberly M. Bonger
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marc S. Robillard
- Tagworks Pharmaceuticals, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ferry Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
25
|
Papakyriakou A, Reeves E, Beton M, Mikolajek H, Douglas L, Cooper G, Elliott T, Werner JM, James E. The partial dissociation of MHC class I-bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1. J Biol Chem 2018; 293:7538-7548. [PMID: 29599287 PMCID: PMC5961055 DOI: 10.1074/jbc.ra117.000313] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/22/2018] [Indexed: 01/19/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 process N-terminally extended antigenic precursors for optimal loading onto major histocompatibility complex class I (MHC I) molecules. We and others have demonstrated that ERAP1 processes peptides bound to MHC I, but the underlying mechanism is unknown. To this end, we utilized single-chain trimers (SCT) of the ovalbumin-derived epitope SIINFEKL (SL8) tethered to the H2-Kb MHC I determinant from mouse and introduced three substitutions, E63A, K66A, and W167A, at the A-pocket of the peptide-binding groove in the MHC I heavy chain, which interact with the N termini of peptides. These variants significantly decreased SL8-presenting SCT at the cell surface in the presence of ERAP1, but did not affect overall SCT expression, indicating that ERAP1 trims the SL8 N terminus. Comparison of the X-ray crystal structures of WT and three variant SCTs revealed only minor perturbations of the peptide-binding domain in the variants. However, molecular dynamics simulations suggested that SL8 can dissociate partially within a sub-microsecond timescale, exposing its N terminus to the solvent. We also found that the C terminus of MHC I-bound SL8 remains deeply buried in the F-pocket of MHC I. Furthermore, free-energy calculations revealed that the three SCT variants exhibit lower free-energy barriers of N terminus dissociation than the WT Kb Taken together, our results are consistent with a previously observed model in which the partial dissociation of bound peptides from MHC I exposes their N terminus to trimming by ERAP1, whereas their C terminus is anchored at the F-pocket.
Collapse
Affiliation(s)
- Athanasios Papakyriakou
- From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
| | - Emma Reeves
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom
| | - Mary Beton
- From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
| | - Halina Mikolajek
- From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
| | - Leon Douglas
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
| | - Grace Cooper
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom
| | - Jörn M Werner
- From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
| | - Edward James
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom
| |
Collapse
|
26
|
Cakir-Koc R, Budama-Kilinc Y, Kokcu Y, Kecel-Gunduz S. Molecular docking of immunogenic peptide of Toxoplasma gondii and encapsulation with polymer as vaccine candidate. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:744-754. [DOI: 10.1080/21691401.2018.1469024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Rabia Cakir-Koc
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | | | - Yagmur Kokcu
- Graduate School of Engineering and Sciences, Istanbul University, Istanbul, Turkey
| | - Serda Kecel-Gunduz
- Physics Department, Faculty of Science, Istanbul University, Istanbul, Turkey
| |
Collapse
|
27
|
Hilton HG, McMurtrey CP, Han AS, Djaoud Z, Guethlein LA, Blokhuis JH, Pugh JL, Goyos A, Horowitz A, Buchli R, Jackson KW, Bardet W, Bushnell DA, Robinson PJ, Mendoza JL, Birnbaum ME, Nielsen M, Garcia KC, Hildebrand WH, Parham P. The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep 2018; 19:1394-1405. [PMID: 28514659 PMCID: PMC5510751 DOI: 10.1016/j.celrep.2017.04.059] [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: 10/10/2016] [Revised: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023] Open
Abstract
HLA-B∗46:01 was formed by an intergenic mini-conversion, between HLA-B∗15:01 and HLA-C∗01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B∗46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B∗46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B∗46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B∗46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B∗46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia. The interlocus recombinant HLA-B∗46:01 is found at high frequency in Southeast Asia HLA-B∗46:01 has a low-diversity peptidome that is distinct from both its parents A subset of HLA-B∗46:01 peptides provides ligands for the NK cell receptor KIR2DL3 The unique features of HLA-B∗46:01 correlate with protection against leprosy
Collapse
Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Curtis P McMurtrey
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alex S Han
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zakia Djaoud
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jeroen H Blokhuis
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jason L Pugh
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ana Goyos
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amir Horowitz
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, OK 73104, USA
| | - Ken W Jackson
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wilfred Bardet
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David A Bushnell
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip J Robinson
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Juan L Mendoza
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael E Birnbaum
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - K Christopher Garcia
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William H Hildebrand
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
28
|
Pawlak JB, Hos BJ, van de Graaff MJ, Megantari OA, Meeuwenoord N, Overkleeft HS, Filippov DV, Ossendorp F, van Kasteren SI. The Optimization of Bioorthogonal Epitope Ligation within MHC-I Complexes. ACS Chem Biol 2016; 11:3172-3178. [PMID: 27704768 DOI: 10.1021/acschembio.6b00498] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antigen recognition followed by the activation of cytotoxic T-cells (CTLs) is a key step in adaptive immunity, resulting in clearance of viruses and cancers. The repertoire of peptides that have the ability to bind to the major histocompatibility type-I (MHC-I) is enormous, but the approaches available for studying the diversity of the peptide repertoire on a cell are limited. Here, we explore the use of bioorthogonal chemistry to quantify specific peptide-MHC-I complexes (pMHC-I) on cells. We show that modifying epitope peptides with bioorthogonal groups in surface accessible positions allows wild-type-like MHC-I binding and bioorthogonal ligation using fluorogenic chromophores in combination with a Cu(I)-catalyzed Huisgen cycloaddition reaction. We expect that this approach will make a powerful addition to the antigen presentation toolkit as for the first time it allows quantification of antigenic peptides for which no detection tools exist.
Collapse
Affiliation(s)
- Joanna B. Pawlak
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Brett J. Hos
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center and The Institute for Chemical Immunology, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Michel J. van de Graaff
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Otty A. Megantari
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Nico Meeuwenoord
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ferry Ossendorp
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center and The Institute for Chemical Immunology, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
29
|
ATZIN-MÉNDEZ J, LÓPEZ-GONZÁLEZ J, BÁEZ R, ARENAS-DEL ANGEL M, MONTAÑO L, SILVA-ADAYA D, LASCURAIN R, GOROCICA P. Expansion of quiescent lung adenocarcinoma CD8+ T cells by MUC1-8-mer peptide-T2 cell-β2 microglobulin complexes. Oncol Rep 2016; 35:33-42. [PMID: 26498650 PMCID: PMC4699617 DOI: 10.3892/or.2015.4328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022] Open
Abstract
Adoptive immunotherapy requires the isolation of CD8+ T cells specific for tumor-associated antigens, their expansion in vitro and their transfusion to the patient to mediate a therapeutic effect. MUC1 is an important adenocarcinoma antigen immunogenic for T cells. The MUC1-derived SAPDTRPA (MUC1-8-mer) peptide is a potent epitope recognized by CD8+ T cells in murine models. Likewise, the T2 cell line has been used as an antigen-presenting cell to activate CD8+ T cells, but so far MUC1 has not been assessed in this context. We evaluated whether the MUC1-8-mer peptide can be presented by T2 cells to expand CD25+CD8+ T cells isolated from HLA-A2+ lung adenocarcinoma patients with stage III or IV tumors. The results showed that MUC1-8-mer peptide-loaded T2 cells activated CD8+ T cells from cancer HLA-A2+ patients when anti-CD2, anti-CD28 antibodies and IL-2 were added. The percentage of CD25+CD8+ T cells was 3-fold higher than those in the non-stimulated cells (P=0.018). HLA-A2+ patient cells showed a significant difference (2.3-fold higher) in activation status than HLA-A2+ healthy control cells (P=0.04). Moreover, 77.6% of MUC1-8-mer peptide-specific CD8+ T cells proliferated following a second stimulation with MUC1-8-mer peptide-loaded T2 cells after 10 days of cell culture. There were significant differences in the percentage of basal CD25+CD8+ T cells in relation to the cancer stage; this difference disappeared after MUC1-8-mer peptide stimulation. In conclusion, expansion of CD25+CD8+ T cells by MUC1-8 peptide-loaded T2 cells plus costimulatory signals via CD2, CD28 and IL-2 can be useful in adoptive immunotherapy.
Collapse
Affiliation(s)
- J.A. ATZIN-MÉNDEZ
- Department of Research in Biochemistry, National Institute of Respiratory Diseases 'Ismael Cosio Villegas', Mexico, DF 14080, Mexico
| | - J.S. LÓPEZ-GONZÁLEZ
- Lung Cancer Laboratory, National Institute of Respiratory Diseases 'Ismael Cosio Villegas', Mexico, DF 14080, Mexico
| | - R. BÁEZ
- Clinical Oncology and Pneumology, National Institute of Respiratory Diseases 'Ismael Cosio Villegas', Mexico, DF 14080, Mexico
| | - M.C. ARENAS-DEL ANGEL
- Department of Biochemistry, National Autonomous University of Mexico, Mexico, DF 04510, Mexico
| | - L.F. MONTAÑO
- Immunobiology Laboratory, Department of Cell and Tissue Biology, Faculty of Medicine, National Autonomous University of Mexico, Mexico, DF 04510, Mexico
| | - D. SILVA-ADAYA
- Experimental Laboratory for Neurodegenerative Diseases, National Institute of Neurology and Neurosurgery, Mexico, DF 14269, Mexico
| | - R. LASCURAIN
- Department of Research in Biochemistry, National Institute of Respiratory Diseases 'Ismael Cosio Villegas', Mexico, DF 14080, Mexico
- Department of Biochemistry, National Autonomous University of Mexico, Mexico, DF 04510, Mexico
| | - P. GOROCICA
- Department of Research in Biochemistry, National Institute of Respiratory Diseases 'Ismael Cosio Villegas', Mexico, DF 14080, Mexico
| |
Collapse
|
30
|
Abualrous ET, Saini SK, Ramnarayan VR, Ilca FT, Zacharias M, Springer S. The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study. PLoS One 2015; 10:e0135421. [PMID: 26270965 PMCID: PMC4535769 DOI: 10.1371/journal.pone.0135421] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 07/21/2015] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex (MHC) class I molecules (proteins) bind peptides of eight to ten amino acids to present them at the cell surface to cytotoxic T cells. The class I binding groove binds the peptide via hydrogen bonds with the peptide termini and via diverse interactions with the anchor residue side chains of the peptide. To elucidate which of these interactions is most important for the thermodynamic and kinetic stability of the peptide-bound state, we have combined molecular dynamics simulations and experimental approaches in an investigation of the conformational dynamics and binding parameters of a murine class I molecule (H-2Kb) with optimal and truncated natural peptide epitopes. We show that the F pocket region dominates the conformational and thermodynamic properties of the binding groove, and that therefore the binding of the C terminus of the peptide to the F pocket region plays a crucial role in bringing about the peptide-bound state of MHC class I.
Collapse
Affiliation(s)
- Esam Tolba Abualrous
- Department of Chemistry and Life Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
- Department of Physics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sunil Kumar Saini
- Department of Chemistry and Life Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Venkat Raman Ramnarayan
- Department of Chemistry and Life Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Florin Tudor Ilca
- Department of Chemistry and Life Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Sebastian Springer
- Department of Chemistry and Life Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
- * E-mail:
| |
Collapse
|
31
|
Marquez EA, Kane KP. Identities of P2 and P3 Residues of H-2Kb-Bound Peptides Determine Mouse Ly49C Recognition. PLoS One 2015; 10:e0131308. [PMID: 26147851 PMCID: PMC4493100 DOI: 10.1371/journal.pone.0131308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/31/2015] [Indexed: 11/18/2022] Open
Abstract
Ly49 receptors can be peptide selective in their recognition of MHC-I-peptide complexes, affording them a level of discrimination beyond detecting the presence or absence of specific MHC-I allele products. Despite this ability, little is understood regarding the properties that enable some peptides, when bound to MHC-I molecules, to support Ly49 recognition, but not others. Using RMA-S target cells expressing MHC-I molecules loaded with individual peptides and effector cells expressing the ectodomain of the inhibitory Ly49C receptor, we found that two adjacent amino acid residues, P2 and P3, both buried in the peptide binding groove of H-2Kb, determine mouse Ly49C specificity. If both are aliphatic residues, this is supportive. Whereas, small amino acids at P2 and aromatic amino acids at the P3 auxiliary anchor residue are detrimental to Ly49C recognition. These results resemble those with a rat Ly49 where the identity of a peptide anchor residue determines recognition, suggesting that dependence on specific peptide residues buried in the MHC-I peptide-binding groove may be fundamental to Ly49 peptide selectivity and recognition.
Collapse
Affiliation(s)
- Elsa A. Marquez
- Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin P. Kane
- Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
| |
Collapse
|
32
|
Pawlak JB, Gential GPP, Ruckwardt TJ, Bremmers JS, Meeuwenoord NJ, Ossendorp FA, Overkleeft HS, Filippov DV, van Kasteren SI. Bioorthogonal deprotection on the dendritic cell surface for chemical control of antigen cross-presentation. Angew Chem Int Ed Engl 2015; 54:5628-31. [PMID: 25784151 DOI: 10.1002/anie.201500301] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Indexed: 11/10/2022]
Abstract
The activation of CD8(+) T-cells requires the uptake of exogenous polypeptide antigens and proteolytic processing of these antigens to octamer or nonamer peptides, which are loaded on MHC-I complexes and presented to the T-cell. By using an azide as a bioorthogonal protecting group rather than as a ligation handle, masked antigens were generated-antigens that are not recognized by their cognate T-cell unless they are deprotected on the cell using a Staudinger reduction.
Collapse
Affiliation(s)
- Joanna B Pawlak
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden (The Netherlands)
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Pawlak JB, Gential GPP, Ruckwardt TJ, Bremmers JS, Meeuwenoord NJ, Ossendorp FA, Overkleeft HS, Filippov DV, van Kasteren SI. Bioorthogonal Deprotection on the Dendritic Cell Surface for Chemical Control of Antigen Cross-Presentation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
34
|
Holm BE, Bergmann AC, Hansen PR, Koch C, Houen G, Trier NH. Antibodies with specificity for native and denatured forms of ovalbumin differ in reactivity between enzyme-linked immunosorbent assays. APMIS 2014; 123:136-45. [DOI: 10.1111/apm.12329] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/24/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Bettina Eide Holm
- Department of Clinical Biochemistry, Immunology and Genetics; Statens Serum Institute; Copenhagen Denmark
| | - Ann Christina Bergmann
- Department of Clinical Biochemistry, Immunology and Genetics; Statens Serum Institute; Copenhagen Denmark
- Department of Biochemistry and Molecular Biology; Southern University of Denmark; Odense Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Claus Koch
- Department of Cancer and Inflammation; Institute for Molecular Medicine; Southern University of Denmark; Odense Denmark
| | - Gunnar Houen
- Department of Clinical Biochemistry, Immunology and Genetics; Statens Serum Institute; Copenhagen Denmark
| | - Nicole Hartwig Trier
- Department of Clinical Biochemistry, Immunology and Genetics; Statens Serum Institute; Copenhagen Denmark
| |
Collapse
|
35
|
Godinho-Silva C, Marques S, Fontinha D, Veiga-Fernandes H, Stevenson PG, Simas JP. Defining immune engagement thresholds for in vivo control of virus-driven lymphoproliferation. PLoS Pathog 2014; 10:e1004220. [PMID: 24967892 PMCID: PMC4072806 DOI: 10.1371/journal.ppat.1004220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/13/2014] [Indexed: 12/26/2022] Open
Abstract
Persistent infections are subject to constant surveillance by CD8+ cytotoxic T cells (CTL). Their control should therefore depend on MHC class I-restricted epitope presentation. Many epitopes are described for γ-herpesviruses and form a basis for prospective immunotherapies and vaccines. However the quantitative requirements of in vivo immune control for epitope presentation and recognition remain poorly defined. We used Murid Herpesvirus-4 (MuHV-4) to determine for a latently expressed viral epitope how MHC class-I binding and CTL functional avidity impact on host colonization. Tracking MuHV-4 recombinants that differed only in epitope presentation, we found little latitude for sub-optimal MHC class I binding before immune control failed. By contrast, control remained effective across a wide range of T cell functional avidities. Thus, we could define critical engagement thresholds for the in vivo immune control of virus-driven B cell proliferation. Chronic viral infections cause huge morbidity and mortality worldwide. γ-herpesviruses provide an example relevant to all human demographics, causing, inter alia, Hodgkin's disease, Burkitt's lymphoma, Kaposi's Sarcoma, and nasopharyngeal carcinoma. The proliferation of latently infected B cells and their control by CD8+ T cells are central to pathogenesis. Although many viral T cell targets have been identified in vitro, the functional impact of their engagement in vivo remains ill-defined. With the well-established Murid Herpesvirus-4 infection model, we used a range of recombinant viruses to define functional thresholds for the engagement of a latently expressed viral epitope. These data advance significantly our understanding of how the immune system must function to control γ-herpesvirus infection, with implications for vaccination and anti-cancer immunotherapy.
Collapse
Affiliation(s)
- Cristina Godinho-Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Sofia Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Henrique Veiga-Fernandes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Philip G. Stevenson
- Sir Albert Sakzewski Virus Research Center and Queensland and Children's Medical Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - J. Pedro Simas
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| |
Collapse
|
36
|
Croft NP, Purcell AW. Peptidomimetics: modifying peptides in the pursuit of better vaccines. Expert Rev Vaccines 2014; 10:211-26. [DOI: 10.1586/erv.10.161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
37
|
Zoete V, Irving M, Ferber M, Cuendet MA, Michielin O. Structure-Based, Rational Design of T Cell Receptors. Front Immunol 2013; 4:268. [PMID: 24062738 PMCID: PMC3770923 DOI: 10.3389/fimmu.2013.00268] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157–165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, KD = ∼1 − 5 μM. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function, in line with the “half-life” model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.
Collapse
Affiliation(s)
- V Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics , Lausanne , Switzerland
| | | | | | | | | |
Collapse
|
38
|
Koch CP, Perna AM, Pillong M, Todoroff NK, Wrede P, Folkers G, Hiss JA, Schneider G. Scrutinizing MHC-I binding peptides and their limits of variation. PLoS Comput Biol 2013; 9:e1003088. [PMID: 23754940 PMCID: PMC3674988 DOI: 10.1371/journal.pcbi.1003088] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/23/2013] [Indexed: 12/20/2022] Open
Abstract
Designed peptides that bind to major histocompatibility protein I (MHC-I) allomorphs bear the promise of representing epitopes that stimulate a desired immune response. A rigorous bioinformatical exploration of sequence patterns hidden in peptides that bind to the mouse MHC-I allomorph H-2Kb is presented. We exemplify and validate these motif findings by systematically dissecting the epitope SIINFEKL and analyzing the resulting fragments for their binding potential to H-2Kb in a thermal denaturation assay. The results demonstrate that only fragments exclusively retaining the carboxy- or amino-terminus of the reference peptide exhibit significant binding potential, with the N-terminal pentapeptide SIINF as shortest ligand. This study demonstrates that sophisticated machine-learning algorithms excel at extracting fine-grained patterns from peptide sequence data and predicting MHC-I binding peptides, thereby considerably extending existing linear prediction models and providing a fresh view on the computer-based molecular design of future synthetic vaccines. The server for prediction is available at http://modlab-cadd.ethz.ch (SLiDER tool, MHC-I version 2012). Future success in vaccine development will critically depend on identifying potent epitopes with reduced side effects. Among such candidate molecules, immunogenic peptides binding to major histocompatibility protein I (MHC-I) represent a preferred class of biomolecules for vaccine design. Computational models assist in the selection of the best candidate peptides by providing a mathematical rationale for antigen recognition by MHC-I. Here we present a machine-learning model that was trained on recognizing features of known MHC-I binding and non-binding peptide sequences with sustained accuracy. We were able to biochemically validate the computational predictions in a direct binding assay measuring complex formation between synthesized candidate peptides and MHC-I. Strong correspondence between the predictions and the experimentally determined binding potential corroborate the machine-learning model as viable for future antigen design. Thus, our study provides a concept for rapidly finding innovative MHC-I binding peptides with limited experimental effort.
Collapse
Affiliation(s)
- Christian P. Koch
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Anna M. Perna
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Max Pillong
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Nickolay K. Todoroff
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Paul Wrede
- Charite-Universitätsmedizin Berlin, Molekularbiologie und Bioinformatik, Berlin, Germany
| | - Gerd Folkers
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Jan A. Hiss
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
| | - Gisbert Schneider
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Zürich, Switzerland
- * E-mail:
| |
Collapse
|
39
|
Koch CP, Pillong M, Hiss JA, Schneider G. Computational Resources for MHC Ligand Identification. Mol Inform 2013; 32:326-36. [PMID: 27481589 DOI: 10.1002/minf.201300042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 04/04/2013] [Indexed: 01/16/2023]
Abstract
Advances in the high-throughput determination of functional modulators of major histocompatibility complex (MHC) and improved computational predictions of MHC ligands have rendered the rational design of immunomodulatory peptides feasible. Proteome-derived peptides and 'reverse vaccinology' by computational means will play a driving role in future vaccine design. Here we review the molecular mechanisms of the MHC mediated immune response, present the computational approaches that have emerged in this area of biotechnology, and provide an overview of publicly available computational resources for predicting and designing new peptidic MHC ligands.
Collapse
Affiliation(s)
- Christian P Koch
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
| | - Max Pillong
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
| | - Jan A Hiss
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
| | - Gisbert Schneider
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland.
| |
Collapse
|
40
|
Xie J, Huppa JB, Newell EW, Huang J, Ebert PJR, Li QJ, Davis MM. Photocrosslinkable pMHC monomers stain T cells specifically and cause ligand-bound TCRs to be 'preferentially' transported to the cSMAC. Nat Immunol 2012; 13:674-80. [PMID: 22660579 PMCID: PMC3645478 DOI: 10.1038/ni.2344] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 05/15/2012] [Indexed: 12/15/2022]
Abstract
The binding of T cell antigen receptors (TCRs) to specific complexes of peptide and major histocompatibility complex (pMHC) is typically of very low affinity, which necessitates the use of multimeric pMHC complexes to label T lymphocytes stably. We report here the development of pMHC complexes able to be crosslinked by ultraviolet irradiation; even as monomers, these efficiently and specifically stained cognate T cells. We also used this reagent to probe T cell activation and found that a covalently bound pMHC was more stimulatory than an agonist pMHC on lipid bilayers. This finding suggested that serial engagement of TCRs is dispensable for activation when a substantial fraction of TCRs are stably engaged. Finally, pMHC-bound TCRs were 'preferentially' transported into the central supramolecular activation cluster after activation, which suggested that ligand engagement enabled linkage of the TCR and its associated CD3 signaling molecules to the cytoskeleton.
Collapse
Affiliation(s)
- Jianming Xie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | | | | | | | | | | | | |
Collapse
|
41
|
Immunodominance: a pivotal principle in host response to viral infections. Clin Immunol 2012; 143:99-115. [PMID: 22391152 DOI: 10.1016/j.clim.2012.01.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/25/2012] [Accepted: 01/28/2012] [Indexed: 11/24/2022]
Abstract
We encounter pathogens on a daily basis and our immune system has evolved to mount an immune response following an infection. An interesting phenomenon that has evolved in response to clearing bacterial and viral infections is called immunodominance. Immunodominance refers to the phenomenon that, despite co-expression of multiple major histocompatibility complex class I alleles by host cells and the potential generation of hundreds of distinct antigenic peptides for recognition following an infection, a large portion of the anti-viral cytotoxic T lymphocyte population targets only some peptide/MHC class I complexes. Here we review the main factors contributing to immunodominance in relation to influenza A and HIV infection. Of special interest are the factors contributing to immunodominance in humans and rodents following influenza A infection. By critically reviewing these findings, we hope to improve understanding of the challenges facing the discovery of new factors enabling better anti-viral vaccine strategies in the future.
Collapse
|
42
|
Zeng L, Sullivan LC, Vivian JP, Walpole NG, Harpur CM, Rossjohn J, Clements CS, Brooks AG. A structural basis for antigen presentation by the MHC class Ib molecule, Qa-1b. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 188:302-10. [PMID: 22131332 DOI: 10.4049/jimmunol.1102379] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The primary function of the monomorphic MHC class Ib molecule Qa-1(b) is to present peptides derived from the leader sequences of other MHC class I molecules for recognition by the CD94-NKG2 receptors expressed by NK and T cells. Whereas the mode of peptide presentation by its ortholog HLA-E, and subsequent recognition by CD94-NKG2A, is known, the molecular basis of Qa-1(b) function is unclear. We have assessed the interaction between Qa-1(b) and CD94-NKG2A and shown that they interact with an affinity of 17 μM. Furthermore, we have determined the structure of Qa-1(b) bound to the leader sequence peptide, Qdm (AMAPRTLLL), to a resolution of 1.9 Å and compared it with that of HLA-E. The crystal structure provided a basis for understanding the restricted peptide repertoire of Qa-1(b). Whereas the Qa-1(b-AMAPRTLLL) complex was similar to that of HLA-E, significant sequence and structural differences were observed between the respective Ag-binding clefts. However, the conformation of the Qdm peptide bound by Qa-1(b) was very similar to that of peptide bound to HLA-E. Although a number of conserved innate receptors can recognize heterologous ligands from other species, the structural differences between Qa-1(b) and HLA-E manifested in CD94-NKG2A ligand recognition being species specific despite similarities in peptide sequence and conformation. Collectively, our data illustrate the structural homology between Qa-1(b) and HLA-E and provide a structural basis for understanding peptide repertoire selection and the specificity of the interaction of Qa-1(b) with CD94-NKG2 receptors.
Collapse
Affiliation(s)
- Li Zeng
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Denton AE, Wesselingh R, Gras S, Guillonneau C, Olson MR, Mintern JD, Zeng W, Jackson DC, Rossjohn J, Hodgkin PD, Doherty PC, Turner SJ. Affinity thresholds for naive CD8+ CTL activation by peptides and engineered influenza A viruses. THE JOURNAL OF IMMUNOLOGY 2011; 187:5733-44. [PMID: 22039305 DOI: 10.4049/jimmunol.1003937] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
High-avidity interactions between TCRs and peptide + class I MHC (pMHCI) epitopes drive CTL activation and expansion. Intriguing questions remain concerning the constraints determining optimal TCR/pMHCI binding. The present analysis uses the TCR transgenic OT-I model to assess how varying profiles of TCR/pMHCI avidity influence naive CTL proliferation and the acquisition of effector function following exposure to the cognate H-2K(b)/OVA(257-264) (SIINFEKL) epitope and to mutants provided as peptide or in engineered influenza A viruses. Stimulating naive OT-I CD8(+) T cells in vitro with SIINFEKL induced full CTL proliferation and differentiation that was largely independent of any need for costimulation. By contrast, in vitro activation with the low-affinity EIINFEKL or SIIGFEKL ligands depended on the provision of IL-2 and other costimulatory signals. Importantly, although they did generate potent endogenous responses, infection of mice with influenza A viruses expressing these same OVA(257) variants failed to induce the activation of adoptively transferred naive OT-I CTLps, an effect that was only partially overcome by priming with a lipopeptide vaccine. Subsequent structural and biophysical analysis of H2-K(b)OVA(257), H2-K(b)E1, and H2-K(b)G4 established that these variations introduce small changes at the pMHCI interface and decrease epitope stability in ways that would likely impact cell surface presentation and recognition. Overall, it seems that there is an activation threshold for naive CTLps, that minimal alterations in peptide sequence can have profound effects, and that the antigenic requirements for the in vitro and in vivo induction of CTL proliferation and effector function differ substantially.
Collapse
Affiliation(s)
- Alice E Denton
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Lim TS, Mortellaro A, Lim CT, Hämmerling GJ, Ricciardi-Castagnoli P. Mechanical interactions between dendritic cells and T cells correlate with T cell responsiveness. THE JOURNAL OF IMMUNOLOGY 2011; 187:258-65. [PMID: 21622857 DOI: 10.4049/jimmunol.1100267] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ag recognition is achieved through the communication across intercellular contacts between T cells and APCs such as dendritic cells (DC). Despite remarkable progress in delineating detailed molecular components at the intercellular contacts, little is known about the functional roles of physical cross-junctional adhesion between T and DC in shaping T cell responses. In addition, the mechanisms underlying sensitivity and specificity of Ag discrimination by T cells at intercellular contacts remain to be elucidated. In this study, we use single-cell force spectroscopy to probe the mechanical interactions between DC and T cells in response to stimulation with a panel of altered peptide ligands. The results show that intercellular interactions of DC-T cell conjugates exhibited different ranges of interaction forces in peptide-dependent manners that match the ability of the peptides to activate T cells. Elevated calcium mobilization and IL-2 secretion by T cells were only promoted in response to antigenic peptides that induce strong interaction forces, suggesting that mechanically stable DC-T cell contacts are crucial for driving T cell activation. Strong interactions were not solely dependent on cell-surface molecules such as TCRs and the adhesion molecule LFA-1, but were also controlled by cytoskeletal dynamics and the integrity of membrane lipid rafts. These data provide novel mechanical insights into the effect of Ag affinity on intercellular contacts that align with T cell responsiveness.
Collapse
Affiliation(s)
- Tong Seng Lim
- Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore.
| | | | | | | | | |
Collapse
|
45
|
Expression and Purification of Isotopically Enriched MHC Binding Immunogenic Peptides for NMR Studies. Int J Pept Res Ther 2011. [DOI: 10.1007/s10989-011-9251-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
46
|
Homology modeling and molecular dynamics simulations of MUC1-9/H-2Kb complex suggest novel binding interactions. J Mol Model 2010; 17:1817-29. [DOI: 10.1007/s00894-010-0884-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 10/19/2010] [Indexed: 11/26/2022]
|
47
|
Bui MR, Hodson V, King T, Leopold D, Dai S, Fiolkoski V, Oakes S, Duke R, Apelian D, Franzusoff A, DeGregori J. Mutation-specific control of BCR-ABL T315I positive leukemia with a recombinant yeast-based therapeutic vaccine in a murine model. Vaccine 2010; 28:6028-35. [PMID: 20619375 PMCID: PMC3066561 DOI: 10.1016/j.vaccine.2010.06.085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 06/28/2010] [Indexed: 01/19/2023]
Abstract
Chromosomal translocations generating the BCR-ABL oncogene cause chronic myeloid leukemia (CML) and a subset of acute lymphoblastic leukemia. The BCR-ABL(T315I) mutation confers drug resistance to FDA-approved targeted therapeutics imatinib mesylate, dasatinib, and nilotinib. We tested the ability of a recombinant yeast-based vaccine expressing the T315I-mutated BCR-ABL antigen to stimulate an anti-BCR-ABL(T315I) immune response. The yeast-based immunotherapy significantly reduced or eliminated BCR-ABL(T315I) leukemia cells from the peripheral blood of immunized animals and extended leukemia-free survival in a murine model of BCR-ABL(+) leukemia compared to animals receiving sham injection or yeast expressing ovalbumin. With immunization, leukemic cells harboring BCR-ABL(T315I) were selectively eliminated after challenge with a mixed population of BCR-ABL and BCR-ABL(T315I) leukemias. In summary, yeast-based immunotherapy represents a novel approach against the emergence of cancer drug resistance by the pre-emptive targeted ablation of tumor escape mutants.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Cancer Vaccines/immunology
- Disease-Free Survival
- Fusion Proteins, bcr-abl/immunology
- Genes, MHC Class I
- Immunotherapy
- Leukemia, Experimental/immunology
- Leukemia, Experimental/therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Protein Structure, Tertiary
- Saccharomyces cerevisiae
- Vaccines, Synthetic/immunology
Collapse
Affiliation(s)
- Melanie R Bui
- University of Colorado Denver School of Medicine, Aurora, CO, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Chen W, Jia Z, Zhang T, Zhang N, Lin C, Gao F, Wang L, Li X, Jiang Y, Li X, Gao GF, Xia C. MHC Class I Presentation and Regulation by IFN in Bony Fish Determined by Molecular Analysis of the Class I Locus in Grass Carp. THE JOURNAL OF IMMUNOLOGY 2010; 185:2209-21. [DOI: 10.4049/jimmunol.1000347] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
49
|
Juang J, Ebert PJ, Feng D, Garcia KC, Krogsgaard M, Davis MM. Peptide-MHC heterodimers show that thymic positive selection requires a more restricted set of self-peptides than negative selection. J Exp Med 2010; 207:1223-34. [PMID: 20457759 PMCID: PMC2882826 DOI: 10.1084/jem.20092170] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 04/08/2010] [Indexed: 11/04/2022] Open
Abstract
T cell selection and maturation in the thymus depends on the interactions between T cell receptors (TCRs) and different self-peptide-major histocompatibility complex (pMHC) molecules. We show that the affinity of the OT-I TCR for its endogenous positively selecting ligands, Catnb-H-2Kb and Cappa1-H-2Kb, is significantly lower than for previously reported positively selecting altered peptide ligands. To understand how these extremely weak endogenous ligands produce signals in maturing thymocytes, we generated soluble monomeric and dimeric peptide-H-2Kb ligands. Soluble monomeric ovalbumin (OVA)-Kb molecules elicited no detectable signaling in OT-I thymocytes, whereas heterodimers of OVA-Kb paired with positively selecting or nonselecting endogenous peptides, but not an engineered null peptide, induced deletion. In contrast, dimer-induced positive selection was much more sensitive to the identity of the partner peptide. Catnb-Kb-Catnb-Kb homodimers, but not heterodimers of Catnb-Kb paired with a nonselecting peptide-Kb, induced positive selection, even though both ligands bind the OT-I TCR with detectable affinity. Thus, both positive and negative selection can be driven by dimeric but not monomeric ligands. In addition, positive selection has much more stringent requirements for the partner self-pMHC.
Collapse
Affiliation(s)
- Jeremy Juang
- The Department of Microbiology and Immunology, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Peter J.R. Ebert
- The Department of Microbiology and Immunology, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Dan Feng
- The Department of Microbiology and Immunology, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - K. Christopher Garcia
- The Department of Microbiology and Immunology, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Michelle Krogsgaard
- Department of Pathology and New York University Cancer Institute, New York University School of Medicine, New York, NY 10016
| | - Mark M. Davis
- The Department of Microbiology and Immunology, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| |
Collapse
|
50
|
Praveen PVK, Yaneva R, Kalbacher H, Springer S. Tapasin edits peptides on MHC class I molecules by accelerating peptide exchange. Eur J Immunol 2010; 40:214-24. [PMID: 20017190 DOI: 10.1002/eji.200939342] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The endoplasmic reticulum (ER) protein tapasin is essential for the loading of high-affinity peptides onto MHC class I molecules. It mediates peptide editing, i.e. the binding of peptides of successively higher affinity until class I molecules pass ER quality control and exit to the cell surface. The molecular mechanism of action of tapasin is unknown. We describe here the reconstitution of tapasin-mediated peptide editing on class I molecules in the lumen of microsomal membranes. We find that in a competitive situation between high- and low-affinity peptides, tapasin mediates the binding of the high-affinity peptide to class I by accelerating the dissociation of the peptide from an unstable intermediate of the binding reaction.
Collapse
Affiliation(s)
- P V K Praveen
- Biochemistry and Cell Biology, Jacobs University Bremen, Bremen, Germany
| | | | | | | |
Collapse
|