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Sandalova T, Sala BM, Achour A. Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition. Front Chem 2022; 10:861609. [PMID: 36017166 PMCID: PMC9395651 DOI: 10.3389/fchem.2022.861609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Significant advances in mass-spectroscopy (MS) have made it possible to investigate the cellular immunopeptidome, a large collection of MHC-associated epitopes presented on the surface of healthy, stressed and infected cells. These approaches have hitherto allowed the unambiguous identification of large cohorts of epitope sequences that are restricted to specific MHC class I and II molecules, enhancing our understanding of the quantities, qualities and origins of these peptide populations. Most importantly these analyses provide essential information about the immunopeptidome in responses to pathogens, autoimmunity and cancer, and will hopefully allow for future tailored individual therapies. Protein post-translational modifications (PTM) play a key role in cellular functions, and are essential for both maintaining cellular homeostasis and increasing the diversity of the proteome. A significant proportion of proteins is post-translationally modified, and thus a deeper understanding of the importance of PTM epitopes in immunopeptidomes is essential for a thorough and stringent understanding of these peptide populations. The aim of the present review is to provide a structural insight into the impact of PTM peptides on stability of MHC/peptide complexes, and how these may alter/modulate immune responses.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Benedetta Maria Sala
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- *Correspondence: Adnane Achour,
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2
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Ballabio F, Broggini L, Paissoni C, Han X, Peqini K, Sala BM, Sun R, Sandalova T, Barbiroli A, Achour A, Pellegrino S, Ricagno S, Camilloni C. l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics. ACS OMEGA 2022; 7:9622-9635. [PMID: 35350306 PMCID: PMC8945122 DOI: 10.1021/acsomega.1c06964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Presentation of pathogen-derived epitopes by major histocompatibility complex I (MHC-I) can lead to the activation and expansion of specific CD8+ T cell clones, eventually resulting in the destruction of infected target cells. Altered peptide ligands (APLs), designed to elicit immunogenicity toward a wild-type peptide, may affect the overall stability of MHC-I/peptide (pMHC) complexes and modulate the recognition by T cell receptors (TCR). Previous works have demonstrated that proline substitution at position 3 (p3P) of different MHC-restricted epitopes, including the immunodominant LCMV-derived epitope gp33 and escape variants, may be an effective design strategy to increase epitope immunogenicity. These studies hypothesized that the p3P substitution increases peptide rigidity, facilitating TCR binding. Here, molecular dynamics simulations indicate that the p3P modification rigidifies the APLs in solution predisposing them for the MHC-I loading as well as once bound to H-2Db, predisposing them for TCR binding. Our results also indicate that peptide position 6, key for interaction of H-2Db/gp33 with the TCR P14, takes a suboptimal conformation before as well as after binding to the TCR. Analyses of H-2Db in complex with APLs, in which position 6 was subjected to an l- to d-amino acid modification, revealed small conformational changes and comparable pMHC thermal stability. However, the l- to d-modification reduced significantly the binding to P14 even in the presence of the p3P modification. Our combined data highlight the sensitivity of the TCR for the conformational dynamics of pMHC and provide further tools to dissect and modulate TCR binding and immunogenicity via APLs.
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Affiliation(s)
- Federico Ballabio
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| | - Luca Broggini
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
- Institute
of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Cristina Paissoni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| | - Xiao Han
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Kaliroi Peqini
- DISFARM,
Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e
Organica, Università degli Studi
di Milano, Milano 20122, Italy
| | - Benedetta Maria Sala
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Renhua Sun
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Tatyana Sandalova
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Alberto Barbiroli
- Dipartimento
di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milano 20122, Italy
| | - Adnane Achour
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Sara Pellegrino
- DISFARM,
Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e
Organica, Università degli Studi
di Milano, Milano 20122, Italy
| | - Stefano Ricagno
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
- Institute
of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Carlo Camilloni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
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3
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He X, Zhou S, Quinn B, Huang W, Jahagirdar D, Vega M, Ortega J, Long MD, Ito F, Abrams SI, Lovell JF. Position-Scanning Peptide Libraries as Particle Immunogens for Improving CD8 + T-Cell Responses. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2103023. [PMID: 34716694 PMCID: PMC8693074 DOI: 10.1002/advs.202103023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/20/2021] [Indexed: 05/14/2023]
Abstract
Short peptides reflecting major histocompatibility complex (MHC) class I (MHC-I) epitopes frequently lack sufficient immunogenicity to induce robust antigen (Ag)-specific CD8+ T cell responses. In the current work, it is demonstrated that position-scanning peptide libraries themselves can serve as improved immunogens, inducing Ag-specific CD8+ T cells with greater frequency and function than the wild-type epitope. The approach involves displaying the entire position-scanning library onto immunogenic nanoliposomes. Each library contains the MHC-I epitope with a single randomized position. When a recently identified MHC-I epitope in the glycoprotein gp70 envelope protein of murine leukemia virus (MuLV) is assessed, only one of the eight positional libraries tested, randomized at amino acid position 5 (Pos5), shows enhanced induction of Ag-specific CD8+ T cells. A second MHC-I epitope from gp70 is assessed in the same manner and shows, in contrast, multiple positional libraries (Pos1, Pos3, Pos5, and Pos8) as well as the library mixture give rise to enhanced CD8+ T cell responses. The library mixture Pos1-3-5-8 induces a more diverse epitope-specific T-cell repertoire with superior antitumor efficacy compared to an established single mutation mimotope (AH1-A5). These data show that positional peptide libraries can serve as immunogens for improving CD8+ T-cell responses against endogenously expressed MHC-I epitopes.
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Affiliation(s)
- Xuedan He
- University at BuffaloState University of New YorkBuffaloNY14260USA
| | - Shiqi Zhou
- University at BuffaloState University of New YorkBuffaloNY14260USA
| | - Breandan Quinn
- University at BuffaloState University of New YorkBuffaloNY14260USA
| | - Wei‐Chiao Huang
- University at BuffaloState University of New YorkBuffaloNY14260USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell BiologyMcGill University MontrealQuebecH3A1Y2Canada
| | - Michael Vega
- Division of Research and Innovation PartnershipsNorthern Illinois UniversityDeKalbIL60115USA
| | - Joaquin Ortega
- Department of Anatomy and Cell BiologyMcGill University MontrealQuebecH3A1Y2Canada
| | - Mark D. Long
- Department of Cancer Genetics and GenomicsRoswell Park Comprehensive Cancer Center (RPCCC)BuffaloNY14263USA
| | - Fumito Ito
- Department of ImmunologyRoswell Park Comprehensive Cancer CenterBuffaloNY14263USA
- Center for ImmunotherapyRoswell Park Comprehensive Cancer CenterBuffaloNY14263USA
- Department of Surgical OncologyRoswell Park Comprehensive Cancer CenterBuffaloNY14263USA
| | - Scott I. Abrams
- Department of ImmunologyRoswell Park Comprehensive Cancer CenterBuffaloNY14263USA
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4
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Huang C, Chen J, Ding F, Yang L, Zhang S, Wang X, Shi Y, Zhu Y. Related parameters of affinity and stability prediction of HLA-A*2402 restricted antigen peptides based on molecular docking. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:673. [PMID: 33987371 PMCID: PMC8106073 DOI: 10.21037/atm-21-630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Major histocompatibility complex class I (MHC-I) plays an important role in cell immune response, and stable interaction between polypeptides and MHC-I ensures efficient presentation of polypeptide-MHC-I (pMHC-I) molecular complexes to T cells. The aim of this study was to explore ways to improve the affinity and stability of the p-Human Leukocyte Antigen (HLA)-A*2402 complex. Methods The peptide sequences of the restricted antigen peptides for HLA-A*2402 and the results of the in vitro competitive binding test were retrieved from the literature. The affinity values were predicted using NetMHCpan v4.1 server, and the stability values were predicted using the NetMHCstab v1.0 server. Auto Vina was used to dock peptides to HLA-A*2402 protein in a flexible docking manner, while Flexpepdock was employed to optimize the docking morphology. Maestro was used to analyze the intermolecular forces and the binding affinity of the complex, while MM-GBSA was used to calculate the binding free energy values. Results The intermolecular interactions that maintained the affinity and stability of peptide-HLA-A*2402 complex relied mainly on HB, followed by pi stack. The binding affinity values of molecular docking were associated with the predicted values of affinity and stability, the binding affinity and the binding free energy, as well as the intermolecular force pi-stack. The pi stack had a significant negative correlation with binding affinity and binding free energy. The replacement of the residues of the polypeptides that did not form pi-stack interactions with HLA-A*2402 improved the affinity and/or stability compared to before replacement. Conclusions The generation and increase in the number of pi-stacks between peptides and HLA-A*2402 molecules may help improve the affinity and stability of p-HLA-A*2402 complexes. The prediction of intermolecular forces and binding affinity of peptide-HLA by means of molecular docking is a supplement to the current commonly used prediction databases.
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Affiliation(s)
- Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Fei Ding
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Lili Yang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Siyu Zhang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xuechun Wang
- Zhejiang Chinese Medical University 4th School of Clinical Medicine, Hangzhou, China
| | - Yanfei Shi
- Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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5
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Duru AD, Sun R, Allerbring EB, Chadderton J, Kadri N, Han X, Peqini K, Uchtenhagen H, Madhurantakam C, Pellegrino S, Sandalova T, Nygren PÅ, Turner SJ, Achour A. Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination. PLoS Pathog 2020; 16:e1008244. [PMID: 32365082 PMCID: PMC7224568 DOI: 10.1371/journal.ppat.1008244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/14/2020] [Accepted: 04/11/2020] [Indexed: 12/16/2022] Open
Abstract
Viral escape from CD8+ cytotoxic T lymphocyte responses correlates with disease progression and represents a significant challenge for vaccination. Here, we demonstrate that CD8+ T cell recognition of the naturally occurring MHC-I-restricted LCMV-associated immune escape variant Y4F is restored following vaccination with a proline-altered peptide ligand (APL). The APL increases MHC/peptide (pMHC) complex stability, rigidifies the peptide and facilitates T cell receptor (TCR) recognition through reduced entropy costs. Structural analyses of pMHC complexes before and after TCR binding, combined with biophysical analyses, revealed that although the TCR binds similarly to all complexes, the p3P modification alters the conformations of a very limited amount of specific MHC and peptide residues, facilitating efficient TCR recognition. This approach can be easily introduced in peptides restricted to other MHC alleles, and can be combined with currently available and future vaccination protocols in order to prevent viral immune escape.
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Affiliation(s)
- Adil Doganay Duru
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- NSU Cell Therapy Institute & Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Eva B. Allerbring
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Jesseka Chadderton
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Nadir Kadri
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Kaliroi Peqini
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Hannes Uchtenhagen
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Chaithanya Madhurantakam
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI, School of Advanced Studies, New Delhi, India
| | - Sara Pellegrino
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Stephen J. Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- * E-mail:
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6
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Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin. Proc Natl Acad Sci U S A 2019; 116:5055-5060. [PMID: 30808808 DOI: 10.1073/pnas.1807656116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
MHC-I epitope presentation to CD8+ T cells is directly dependent on peptide loading and selection during antigen processing. However, the exact molecular bases underlying peptide selection and binding by MHC-I remain largely unknown. Within the peptide-loading complex, the peptide editor tapasin is key to the selection of MHC-I-bound peptides. Here, we have determined an ensemble of crystal structures of MHC-I in complex with the peptide exchange-associated dipeptide GL, as well as the tapasin-associated scoop loop, alone or in combination with candidate epitopes. These results combined with mutation analyses allow us to propose a molecular model underlying MHC-I peptide selection by tapasin. The N termini of bound peptides most probably bind first in the N-terminal and middle region of the MHC-I peptide binding cleft, upon which the peptide C termini are tested for their capacity to dislodge the tapasin scoop loop from the F pocket of the MHC-I cleft. Our results also indicate important differences in peptide selection between different MHC-I alleles.
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7
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Clancy-Thompson E, Devlin CA, Tyler PM, Servos MM, Ali LR, Ventre KS, Bhuiyan MA, Bruck PT, Birnbaum ME, Dougan SK. Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8 + T Cell-Effector Responses. Cancer Immunol Res 2018; 6:1524-1536. [PMID: 30352798 DOI: 10.1158/2326-6066.cir-18-0348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/03/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
T-cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen-presenting cell. The circumstances of this initial priming have ramifications on the fate of the newly primed T cell. Newly primed CD8+ T cells can embark onto different trajectories, with some becoming short-lived effector cells and others adopting a tissue resident or memory cell fate. To determine whether T-cell priming influences the quality of the effector T-cell response to tumors, we used transnuclear CD8+ T cells that recognize the melanoma antigen TRP1 using TRP1high or TRP1low TCRs that differ in both affinity and fine specificity. From a series of altered peptide ligands, we identified a point mutation (K8) in a nonanchor residue that, when analyzed crystallographically and biophysically, destabilized the peptide interaction with the MHC binding groove. In vitro, the K8 peptide induced robust proliferation of both TRP1high and TRP1low CD8+ T cells but did not induce expression of PD-1. Cytokine production from K8-stimulated TRP1 cells was minimal, whereas cytotoxicity was increased. Upon transfer into B16 tumor-bearing mice, the reference peptide (TRP1-M9)- and K8-stimulated TRP1 cells were equally effective at controlling tumor growth but accomplished this through different mechanisms. TRP1-M9-stimulated cells produced more IFNγ, whereas K8-stimulated cells accumulated to higher numbers and were more cytotoxic. We, therefore, conclude that TCR recognition of weakly binding peptides during priming can skew the effector function of tumor-specific CD8+ T cells.
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Affiliation(s)
- Eleanor Clancy-Thompson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Christine A Devlin
- Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts
| | - Paul M Tyler
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mariah M Servos
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lestat R Ali
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Katherine S Ventre
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - M Aladdin Bhuiyan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick T Bruck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts.
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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