1
|
Gillespie GM, Quastel MN, McMichael AJ. HLA-E: Immune Receptor Functional Mechanisms Revealed by Structural Studies. Immunol Rev 2025; 329:e13434. [PMID: 39753525 PMCID: PMC11698700 DOI: 10.1111/imr.13434] [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: 11/15/2024] [Accepted: 12/10/2024] [Indexed: 01/06/2025]
Abstract
HLA-E is a nonclassical, nonpolymorphic, class Ib HLA molecule. Its primary function is to present a conserved nonamer peptide, termed VL9, derived from the signal sequence of classical MHC molecules to the NKG2x-CD94 receptors on NK cells and a subset of T lymphocytes. These receptors regulate the function of NK cells, and the importance of this role, which is conserved across mammalian species, probably accounts for the lack of genetic polymorphism. A second minor function is to present other, weaker binding, pathogen-derived peptides to T lymphocytes. Most of these peptides bind suboptimally to HLA-E, but this binding appears to be enabled by the relative stability of peptide-free, but receptive, HLA-E-β2m complexes. This, in turn, may favor nonclassical antigen processing that may be associated with bacteria infected cells. This review explores how the structure of HLA-E, bound to different peptides and then to NKG2-CD94 or T-cell receptors, relates to HLA-E cell biology and immunology. A detailed understanding of this molecule could open up opportunities for development of universal T-cell and NK-cell-based immunotherapies.
Collapse
MESH Headings
- Humans
- Histocompatibility Antigens Class I/metabolism
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/chemistry
- Animals
- HLA-E Antigens
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Protein Binding
- Antigen Presentation
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/chemistry
- NK Cell Lectin-Like Receptor Subfamily C/metabolism
- Structure-Activity Relationship
- Peptides/chemistry
- Peptides/immunology
- Peptides/metabolism
- NK Cell Lectin-Like Receptor Subfamily D/metabolism
- NK Cell Lectin-Like Receptor Subfamily D/chemistry
- NK Cell Lectin-Like Receptor Subfamily D/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/chemistry
- Protein Conformation
Collapse
Affiliation(s)
| | - Max N. Quastel
- Nuffield Department of Medicine, Center for Immuno‐OncologyUniversity of OxfordOxfordUK
| | - Andrew J. McMichael
- Nuffield Department of Medicine, Center for Immuno‐OncologyUniversity of OxfordOxfordUK
| |
Collapse
|
2
|
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
|
3
|
Amarajeewa AWP, Özcan A, Mukhtiar A, Ren X, Wang Q, Ozbek P, Garstka MA, Serçinoğlu O. Polymorphism in F pocket affects peptide selection and stability of type 1 diabetes-associated HLA-B39 allotypes. Eur J Immunol 2024; 54:e2350683. [PMID: 38549458 DOI: 10.1002/eji.202350683] [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: 07/25/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 10/30/2024]
Abstract
HLA-B*39:06, HLA-B*39:01, and HLA-B*38:01 are closely related HLA allotypes differentially associated with type 1 diabetes (T1D) risk and progression. B*39:06 is highly predisposing, while B*39:01 and B*38:01 are weakly predisposing and protective allotypes, respectively. Here, we aimed to decipher molecular mechanisms underlying the differential association of these allotypes with T1D pathogenesis. We addressed peptide binding and conformational stability of HLA-B allotypes using computational and experimental approaches. Computationally, we found that B*39:06 and B*39:01 allotypes had more rigid peptide-binding grooves and were more promiscuous in binding peptides than B*38:01. Peptidomes of B*39:06 and B*39:01 contained fewer strong binders and were of lower affinity than that of B*38:01. Experimentally, we demonstrated that B*39:06 and B*39:01 had a higher capacity to bind peptides and exit to the cell surface but lower surface levels and were degraded faster than B*38:01. In summary, we propose that promiscuous B*39:06 and B*39:01 may bind suboptimal peptides and transport them the cell surface, where such unstable complexes may contribute to the pathogenesis of T1D.
Collapse
Affiliation(s)
- A W Peshala Amarajeewa
- Department of Urology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Core Research Laboratory, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Aslihan Özcan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
| | - Alveena Mukhtiar
- Core Research Laboratory, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xu Ren
- Department of Urology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Core Research Laboratory, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qianyu Wang
- Core Research Laboratory, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
| | - Malgorzata A Garstka
- Department of Urology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Core Research Laboratory, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Endocrinology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Tumor and Immunology, Precision Medical Institute, Western China Science and Technology Innovation Port, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Türkiye
| |
Collapse
|
4
|
Ren X, Amarajeewa AWP, Jayasinghe MDT, Garstka MA. Differences in F pocket impact on HLA I genetic associations with autoimmune diabetes. Front Immunol 2024; 15:1342335. [PMID: 38596688 PMCID: PMC11003304 DOI: 10.3389/fimmu.2024.1342335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction Human leukocyte antigen (HLA) I molecules present antigenic peptides to activate CD8+ T cells. Type 1 Diabetes (T1D) is an auto-immune disease caused by aberrant activation of the CD8+ T cells that destroy insulin-producing pancreatic β cells. Some HLA I alleles were shown to increase the risk of T1D (T1D-predisposing alleles), while some reduce this risk (T1D-protective alleles). Methods Here, we compared the T1D-predisposing and T1D-protective allotypes concerning peptide binding, maturation, localization and surface expression and correlated it with their sequences and energetic profiles using experimental and computational methods. Results T1D-predisposing allotypes had more peptide-bound forms and higher plasma membrane levels than T1D-protective allotypes. This was related to the fact that position 116 within the F pocket was more conserved and made more optimal contacts with the neighboring residues in T1D-predisposing allotypes than in protective allotypes. Conclusion Our work uncovers that specific polymorphisms in HLA I molecules potentially influence their susceptibility to T1D.
Collapse
Affiliation(s)
- Xu Ren
- Department of Urology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Endocrinology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - A. W. Peshala Amarajeewa
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | | | - Malgorzata A. Garstka
- Department of Urology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Core Research Laboratory, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Endocrinology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Tumor and Immunology, Precision Medical Institute, Western China Science and Technology Innovation Port, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
| |
Collapse
|
5
|
Meyer M, Parpoulas C, Barthélémy T, Becker JP, Charoentong P, Lyu Y, Börsig S, Bulbuc N, Tessmer C, Weinacht L, Ibberson D, Schmidt P, Pipkorn R, Eichmüller SB, Steinberger P, Lindner K, Poschke I, Platten M, Fröhling S, Riemer AB, Hassel JC, Roberti MP, Jäger D, Zörnig I, Momburg F. MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Front Immunol 2024; 14:1294565. [PMID: 38239352 PMCID: PMC10794645 DOI: 10.3389/fimmu.2023.1294565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
Peptide-loaded MHC class I (pMHC-I) multimers have revolutionized our capabilities to monitor disease-associated T cell responses with high sensitivity and specificity. To improve the discovery of T cell receptors (TCR) targeting neoantigens of individual tumor patients with recombinant MHC molecules, we developed a peptide-loadable MHC class I platform termed MediMer. MediMers are based on soluble disulfide-stabilized β2-microglobulin/heavy chain ectodomain single-chain dimers (dsSCD) that can be easily produced in large quantities in eukaryotic cells and tailored to individual patients' HLA allotypes with only little hands-on time. Upon transient expression in CHO-S cells together with ER-targeted BirA biotin ligase, biotinylated dsSCD are purified from the cell supernatant and are ready to use. We show that CHO-produced dsSCD are free of endogenous peptide ligands. Empty dsSCD from more than 30 different HLA-A,B,C allotypes, that were produced and validated so far, can be loaded with synthetic peptides matching the known binding criteria of the respective allotypes, and stored at low temperature without loss of binding activity. We demonstrate the usability of peptide-loaded dsSCD multimers for the detection of human antigen-specific T cells with comparable sensitivities as multimers generated with peptide-tethered β2m-HLA heavy chain single-chain trimers (SCT) and wild-type peptide-MHC-I complexes prior formed in small-scale refolding reactions. Using allotype-specific, fluorophore-labeled competitor peptides, we present a novel dsSCD-based peptide binding assay capable of interrogating large libraries of in silico predicted neoepitope peptides by flow cytometry in a high-throughput and rapid format. We discovered rare T cell populations with specificity for tumor neoepitopes and epitopes from shared tumor-associated antigens in peripheral blood of a melanoma patient including a so far unreported HLA-C*08:02-restricted NY-ESO-1-specific CD8+ T cell population. Two representative TCR of this T cell population, which could be of potential value for a broader spectrum of patients, were identified by dsSCD-guided single-cell sequencing and were validated by cognate pMHC-I multimer staining and functional responses to autologous peptide-pulsed antigen presenting cells. By deploying the technically accessible dsSCD MHC-I MediMer platform, we hope to significantly improve success rates for the discovery of personalized neoepitope-specific TCR in the future by being able to also cover rare HLA allotypes.
Collapse
Affiliation(s)
- Marten Meyer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Christina Parpoulas
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Titouan Barthélémy
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas P. Becker
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Pornpimol Charoentong
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Yanhong Lyu
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Selina Börsig
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Nadja Bulbuc
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Tessmer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Lisa Weinacht
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Heidelberg University, Heidelberg, Germany
| | - Patrick Schmidt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- GMP and T Cell Therapy, DKFZ, Heidelberg, Germany
| | | | | | - Peter Steinberger
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology, Medical University of Vienna, Vienna, Austria
| | - Katharina Lindner
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center, Mannheim, Germany
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz), Mainz, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika B. Riemer
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Jessica C. Hassel
- Section of DermatoOncology, Department of Dermatology and NCT, Heidelberg University Hospital, Heidelberg, Germany
| | - Maria Paula Roberti
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Dirk Jäger
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Inka Zörnig
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
6
|
Finton KAK, Rupert PB, Friend DJ, Dinca A, Lovelace ES, Buerger M, Rusnac DV, Foote-McNabb U, Chour W, Heath JR, Campbell JS, Pierce RH, Strong RK. Effects of HLA single chain trimer design on peptide presentation and stability. Front Immunol 2023; 14:1170462. [PMID: 37207206 PMCID: PMC10189100 DOI: 10.3389/fimmu.2023.1170462] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
MHC class I "single-chain trimer" molecules, coupling MHC heavy chain, β2-microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.
Collapse
Affiliation(s)
- Kathryn A. K. Finton
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Peter B. Rupert
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Della J. Friend
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Ana Dinca
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Erica S. Lovelace
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Matthew Buerger
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Domnita V. Rusnac
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Ulysses Foote-McNabb
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - William Chour
- Institute for Systems Biology, Seattle, WA, United States
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA, United States
| | - Jean S. Campbell
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Robert H. Pierce
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Roland K. Strong
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| |
Collapse
|
7
|
Kuiper JJ, Prinz JC, Stratikos E, Kuśnierczyk P, Arakawa A, Springer S, Mintoff D, Padjen I, Shumnalieva R, Vural S, Kötter I, van de Sande MG, Boyvat A, de Boer JH, Bertsias G, de Vries N, Krieckaert CL, Leal I, Vidovič Valentinčič N, Tugal-Tutkun I, El Khaldi Ahanach H, Costantino F, Glatigny S, Mrazovac Zimak D, Lötscher F, Kerstens FG, Bakula M, Viera Sousa E, Böhm P, Bosman K, Kenna TJ, Powis SJ, Breban M, Gul A, Bowes J, Lories RJ, Nowatzky J, Wolbink GJ, McGonagle DG, Turkstra F. EULAR study group on ‘MHC-I-opathy’: identifying disease-overarching mechanisms across disciplines and borders. Ann Rheum Dis 2023:ard-2022-222852. [PMID: 36987655 DOI: 10.1136/ard-2022-222852] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/25/2023] [Indexed: 03/29/2023]
Abstract
The ‘MHC-I (major histocompatibility complex class I)-opathy’ concept describes a family of inflammatory conditions with overlapping clinical manifestations and a strong genetic link to the MHC-I antigen presentation pathway. Classical MHC-I-opathies such as spondyloarthritis, Behçet’s disease, psoriasis and birdshot uveitis are widely recognised for their strong association with certain MHC-I alleles and gene variants of the antigen processing aminopeptidases ERAP1 and ERAP2 that implicates altered MHC-I peptide presentation to CD8+T cells in the pathogenesis. Progress in understanding the cause and treatment of these disorders is hampered by patient phenotypic heterogeneity and lack of systematic investigation of the MHC-I pathway.Here, we discuss new insights into the biology of MHC-I-opathies that strongly advocate for disease-overarching and integrated molecular and clinical investigation to decipher underlying disease mechanisms. Because this requires transformative multidisciplinary collaboration, we introduce the EULAR study group on MHC-I-opathies to unite clinical expertise in rheumatology, dermatology and ophthalmology, with fundamental and translational researchers from multiple disciplines such as immunology, genomics and proteomics, alongside patient partners. We prioritise standardisation of disease phenotypes and scientific nomenclature and propose interdisciplinary genetic and translational studies to exploit emerging therapeutic strategies to understand MHC-I-mediated disease mechanisms. These collaborative efforts are required to address outstanding questions in the etiopathogenesis of MHC-I-opathies towards improving patient treatment and prognostication.
Collapse
Affiliation(s)
- Jonas Jw Kuiper
- Department of Ophthalmology, Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Jörg C Prinz
- University Hospital, department of Dermatology and Allergy, Ludwig Maximilians University Munich, Munchen, Germany
| | - Efstratios Stratikos
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Institute of Immunology and Experimental Therapy Ludwik Hirszfeld Polish Academy of Sciences, Wroclaw, Poland
| | - Akiko Arakawa
- University Hospital, department of Dermatology and Allergy, Ludwig Maximilians University Munich, Munchen, Germany
| | | | - Dillon Mintoff
- Department of Dermatology, Mater Dei Hospital, Msida, Malta
- Department of Pathology, University of Malta Faculty of Medicine and Surgery, Msida, Malta
| | - Ivan Padjen
- Division of Clinical Immunology and Rheumatology, University Hospital Centre Zagreb Department of Internal Medicine, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Russka Shumnalieva
- Clinic of Rheumatology, Department of Rheumatology, Medical University of Sofia, Sofia, Bulgaria
| | - Seçil Vural
- School of Medicine, Department of Dermatology, Koç University, Istanbul, Turkey
| | - Ina Kötter
- Clinic for Rheumatology and Immunology, Bad Bramdsted Hospital, Bad Bramstedt, Germany
- Division of Rheumatology and Systemic Inflammatory Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marleen G van de Sande
- University of Amsterdam, Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Institute for Infection & Immunity, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC) | Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ayşe Boyvat
- Department of Dermatology, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Joke H de Boer
- Department of Ophthalmology, Center for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - George Bertsias
- Department of Rheumatology and Clinical Immunology, University of Crete School of Medicine, Iraklio, Greece
- Laboratory of Autoimmunity-Inflammation, Institute of Molecular Biology and Biotechnology, Heraklion, Greece
| | - Niek de Vries
- University of Amsterdam, Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam Institute for Infection & Immunity, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC) | Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Charlotte Lm Krieckaert
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department of Rheumatology, Reade Hoofdlocatie Dr Jan van Breemenstraat, Amsterdam, The Netherlands
| | - Inês Leal
- Department of Ophthalmology, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte EPE, Lisboa, Portugal
- Centro de Estudeos das Ciencias da Visão, Universidade de Lisboa Faculdade de Medicina, Lisboa, Portugal
| | - Nataša Vidovič Valentinčič
- University Eye Clinic, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ilknur Tugal-Tutkun
- Department of Ophthalmology, Istanbul University Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Hanane El Khaldi Ahanach
- Departement of Ophthalmology, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Department of Ophthalmology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Félicie Costantino
- Service de Rheumatology, Hospital Ambroise-Pare, Boulogne-Billancourt, France
- Infection & Inflammation, UMR 1173, Inserm, UVSQ, University Paris-Saclay, Montigny-le-Bretonneux, France
| | - Simon Glatigny
- Infection & Inflammation, UMR 1173, Inserm, UVSQ/Université Paris Saclay, Montigny-le-Bretonneux, France
- Laboratoire d'Excellence Inflamex, Paris, France
| | | | - Fabian Lötscher
- Department of Rheumatology and Immunology, Inselspital University Hospital Bern, University of Bern, Bern, Switzerland
| | - Floor G Kerstens
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department of Rheumatology, Reade Hoofdlocatie Dr Jan van Breemenstraat, Amsterdam, The Netherlands
| | - Marija Bakula
- Division of Clinical Immunology and Rheumatology, University Hospital Centre Zagreb Department of Internal Medicine, Zagreb, Croatia
| | - Elsa Viera Sousa
- Rheumatology Research Unit Molecular João Lobo Antunes, University of Lisbon Medical Faculty, Lisboa, Portugal
- Rheumatology DepartmentSanta Maria Centro Hospital, Academic Medical Centre of Lisbon, Lisboa, Portugal
| | - Peter Böhm
- Patientpartner, German League against Rheumatism, Bonn, Germany
| | - Kees Bosman
- Patientpartner, Nationale Vereniging ReumaZorg, Nijmegen, The Netherlands
| | - Tony J Kenna
- Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Simon J Powis
- School of Medicine, University of St Andrews School of Medicine, St Andrews, UK
| | - Maxime Breban
- Service de Rheumatology, Hospital Ambroise-Pare, Boulogne-Billancourt, France
- Infection & Inflammation, UMR 1173, Inserm, UVSQ, University Paris-Saclay, Montigny-le-Bretonneux, France
| | - Ahmet Gul
- Division of Rheumatology, Istanbul University Istanbul Faculty of Medicine, Istanbul, Turkey
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Center, The University of Manchester, Manchester, UK
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rik Ju Lories
- Department of Rheumatology, KU Leuven University Hospitals Leuven, Leuven, Belgium
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Johannes Nowatzky
- Department of Medicine, Division of Rheumatology, NYU Langone Behçet's Disease Program, NYU Langone Ocular Rheumatology Program, New York University Grossman School of Medicine, New York University, New York, New York, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Gerrit Jan Wolbink
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Dennis G McGonagle
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Franktien Turkstra
- Amsterdam Rheumatology and immunology Center (ARC)| Reade, Amsterdam, The Netherlands
- Department of Rheumatology, Reade Hoofdlocatie Dr Jan van Breemenstraat, Amsterdam, The Netherlands
| |
Collapse
|
8
|
Sun Y, Young MC, Woodward CH, Danon JN, Truong H, Gupta S, Winters TJ, Burslem G, Sgourakis NG. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533266. [PMID: 36993702 PMCID: PMC10055308 DOI: 10.1101/2023.03.18.533266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The polymorphic nature and intrinsic instability of class I major histocompatibility complex (MHC-I) and MHC-like molecules loaded with suboptimal peptides, metabolites, or glycolipids presents a fundamental challenge for identifying disease-relevant antigens and antigen-specific T cell receptors (TCRs), hindering the development of autologous therapeutics. Here, we leverage the positive allosteric coupling between the peptide and light chain (β 2 microglobulin, β 2 m) subunits for binding to the MHC-I heavy chain (HC) through an engineered disulfide bond bridging conserved epitopes across the HC/β 2 m interface, to generate conformationally stable, open MHC-I molecules. Biophysical characterization shows that open MHC-I molecules are properly folded protein complexes of enhanced thermal stability compared to the wild type, when loaded with low- to intermediate-affinity peptides. Using solution NMR, we characterize the effects of the disulfide bond on the conformation and dynamics of the MHC-I structure, ranging from local changes in β 2 m interacting sites of the peptide binding groove to long-range effects on the α 2-1 helix and α 3 domain. The interchain disulfide bond stabilizes empty MHC-I molecules in a peptide-receptive, open conformation to promote peptide exchange across multiple human leucocyte antigen (HLA) allotypes, covering representatives from five HLA-A, six HLA-B supertypes, and oligomorphic HLA-Ib molecules. Our structural design, combined with conditional β-peptide ligands, provides a universal platform for generating ready-to-load MHC-I systems of enhanced stability, enabling a range of approaches to screen antigenic epitope libraries and probe polyclonal TCR repertoires in the context of highly polymorphic HLA-I allotypes, as well as oligomorphic nonclassical molecules. Significance Statement We outline a structure-guided approach for generating conformationally stable, open MHC-I molecules with enhanced ligand exchange kinetics spanning five HLA-A, all HLA-B supertypes, and oligomorphic HLA-Ib allotypes. We present direct evidence of positive allosteric cooperativity between peptide binding and β 2 m association with the heavy chain by solution NMR and HDX-MS spectroscopy. We demonstrate that covalently linked β 2 m serves as a conformational chaperone to stabilize empty MHC-I molecules in a peptide-receptive state, by inducing an open conformation and preventing intrinsically unstable heterodimers from irreversible aggregation. Our study provides structural and biophysical insights into the conformational properties of MHC-I ternary complexes, which can be further applied to improve the design of ultra-stable, universal ligand exchange systems in a pan-HLA allelic setting.
Collapse
|
9
|
Opening opportunities for K d determination and screening of MHC peptide complexes. Commun Biol 2022; 5:488. [PMID: 35606511 PMCID: PMC9127112 DOI: 10.1038/s42003-022-03366-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/13/2022] [Indexed: 01/15/2023] Open
Abstract
An essential element of adaptive immunity is selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes. Using native mass spectrometry, we analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule and, due to its unique stability, we determine binding affinities of complexes loaded with truncated or charge-reduced peptides. We find that the two anchor positions can be stabilized independently, and we further analyze the contribution of additional amino acid positions to the binding strength. As a complement to computational prediction tools, our method estimates binding strength of even low-affinity peptides to MHC class I complexes quickly and efficiently. It has huge potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases, autoimmunity, vaccine design, and cancer immunotherapy. The authors present a sensitive and rapid method to determine the binding strength of MHC class 1 peptide complexes using native mass spectrometry.
Collapse
|
10
|
Dirscherl C, Löchte S, Hein Z, Kopicki JD, Harders AR, Linden N, Karner A, Preiner J, Weghuber J, Garcia-Alai M, Uetrecht C, Zacharias M, Piehler J, Lanzerstorfer P, Springer S. Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers. J Cell Sci 2022; 135:jcs259489. [PMID: 35393611 DOI: 10.1242/jcs.259498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/30/2022] [Indexed: 11/20/2022] Open
Abstract
At the plasma membrane of mammalian cells, major histocompatibility complex class I molecules (MHC-I) present antigenic peptides to cytotoxic T cells. Following the loss of the peptide and the light chain beta-2 microglobulin (β2m, encoded by B2M), the resulting free heavy chains (FHCs) can associate into homotypic complexes in the plasma membrane. Here, we investigate the stoichiometry and dynamics of MHC-I FHCs assemblies by combining a micropattern assay with fluorescence recovery after photobleaching (FRAP) and with single-molecule co-tracking. We identify non-covalent MHC-I FHC dimers, with dimerization mediated by the α3 domain, as the prevalent species at the plasma membrane, leading a moderate decrease in the diffusion coefficient. MHC-I FHC dimers show increased tendency to cluster into higher order oligomers as concluded from an increased immobile fraction with higher single-molecule colocalization. In vitro studies with isolated proteins in conjunction with molecular docking and dynamics simulations suggest that in the complexes, the α3 domain of one FHC binds to another FHC in a manner similar to that seen for β2m.
Collapse
Affiliation(s)
- Cindy Dirscherl
- School of Science, Jacobs University Bremen, 28759 Bremen, Germany
| | - Sara Löchte
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Zeynep Hein
- School of Science, Jacobs University Bremen, 28759 Bremen, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | | | - Noemi Linden
- School of Science, Jacobs University Bremen, 28759 Bremen, Germany
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
- European XFEL, 22869 Schenefeld, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, 85748 Garching, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | | | | |
Collapse
|
11
|
Barber C, De Souza VA, Paterson RL, Martin‐Urdiroz M, Mulakkal NC, Srikannathasan V, Connolly M, Phillips G, Foong‐Leong T, Pengelly R, Karuppiah V, Grant T, Dembek M, Verma A, Gibbs‐Howe D, Blicher TH, Knox A, Robinson RA, Cole DK, Leonard S. Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. Eur J Immunol 2022; 52:618-632. [PMID: 35108401 PMCID: PMC9306587 DOI: 10.1002/eji.202149745] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 11/26/2021] [Accepted: 01/12/2022] [Indexed: 12/02/2022]
Abstract
The nonpolymorphic class Ib molecule, HLA-E, primarily presents peptides from HLA class Ia leader peptides, providing an inhibitory signal to NK cells via CD94/NKG2 interactions. Although peptides of pathogenic origin can also be presented by HLA-E to T cells, the molecular basis underpinning their role in antigen surveillance is largely unknown. Here, we solved a co-complex crystal structure of a TCR with an HLA-E presented peptide (pHLA-E) from bacterial (Mycobacterium tuberculosis) origin, and the first TCR-pHLA-E complex with a noncanonically presented peptide from viral (HIV) origin. The structures provided a molecular foundation to develop a novel method to introduce cysteine traps using non-natural amino acid chemistry that stabilized pHLA-E complexes while maintaining native interface contacts between the TCRs and different pHLA-E complexes. These pHLA-E monomers could be used to isolate pHLA-E-specific T cells, with obvious utility for studying pHLA-E restricted T cells, and for the identification of putative therapeutic TCRs.
Collapse
|
12
|
Son ET, Faridi P, Paul-Heng M, Leong ML, English K, Ramarathinam SH, Braun A, Dudek NL, Alexander IE, Lisowski L, Bertolino P, Bowen DG, Purcell AW, Mifsud NA, Sharland AF. The self-peptide repertoire plays a critical role in transplant tolerance induction. J Clin Invest 2021; 131:e146771. [PMID: 34428180 PMCID: PMC8553557 DOI: 10.1172/jci146771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 08/18/2021] [Indexed: 11/17/2022] Open
Abstract
While direct allorecognition underpins both solid organ allograft rejection and tolerance induction, the specific molecular targets of most directly alloreactive CD8+ T cells have not been defined. In this study, we used a combination of genetically engineered major histocompatibility complex class I (MHC I) constructs, mice with a hepatocyte-specific mutation in the class I antigen-presentation pathway, and immunopeptidomic analysis to provide definitive evidence for the contribution of the peptide cargo of allogeneic MHC I molecules to transplant tolerance induction. We established a systematic approach for the discovery of directly recognized pMHC epitopes and identified 17 strongly immunogenic H-2Kb-associated peptides recognized by CD8+ T cells from B10.BR (H-2k) mice, 13 of which were also recognized by BALB/c (H-2d) mice. As few as 5 different tetramers used together were able to identify a high proportion of alloreactive T cells within a polyclonal population, suggesting that there are immunodominant allogeneic MHC-peptide complexes that can account for a large component of the alloresponse.
Collapse
Affiliation(s)
- Eric T. Son
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Pouya Faridi
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Moumita Paul-Heng
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Mario L. Leong
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Kieran English
- Liver Immunology Group and AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sri H. Ramarathinam
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Asolina Braun
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nadine L. Dudek
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Ian E. Alexander
- Gene Therapy Research Unit, Children’s Medical Research Institute, The University of Sydney, Faculty of Medicine and Health and Sydney Children’s Hospitals Network, Westmead, New South Wales, Australia
- The University of Sydney, Sydney Medical School, Discipline of Child and Adolescent Health, Westmead, New South Wales, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
- Vector and Genome Engineering Facility, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
- Military Institute of Medicine, Laboratory of Molecular Oncology and Innovative Therapies, Warsaw, Poland
| | - Patrick Bertolino
- Liver Immunology Group and AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - David G. Bowen
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
- Liver Immunology Group and AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Nicole A. Mifsud
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Alexandra F. Sharland
- Transplantation Immunobiology Group, University of Sydney Central Clinical School, Charles Perkins Centre, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| |
Collapse
|
13
|
Robinson RA, McMurran C, McCully ML, Cole DK. Engineering soluble T-cell receptors for therapy. FEBS J 2021; 288:6159-6173. [PMID: 33624424 PMCID: PMC8596704 DOI: 10.1111/febs.15780] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
Immunotherapy approaches that target peptide-human leukocyte antigen (pHLA) complexes are becoming highly attractive because of their potential to access virtually all foreign and cellular proteins. For this reason, there has been considerable interest in the development of the natural ligand for pHLA, the T-cell receptor (TCR), as a soluble drug to target disease-associated pHLA presented at the cell surface. However, native TCR stability is suboptimal for soluble drug development, and natural TCRs generally have weak affinities for pHLAs, limiting their potential to reach efficacious receptor occupancy levels as soluble drugs. To overcome these limitations and make full use of the TCR as a soluble drug platform, several protein engineering solutions have been applied to TCRs to enhance both their stability and affinity, with a focus on retaining target specificity and selectivity. Here, we review these advances and look to the future for the next generation of soluble TCR-based therapies that can target monomorphic HLA-like proteins presenting both peptide and nonpeptide antigens.
Collapse
|
14
|
Peptide-HLA-based immunotherapeutics platforms for direct modulation of antigen-specific T cells. Sci Rep 2021; 11:19220. [PMID: 34584159 PMCID: PMC8479091 DOI: 10.1038/s41598-021-98716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
Targeted pharmacologic activation of antigen-specific (AgS) T cells may bypass limitations inherent in current T cell-based cancer therapies. We describe two immunotherapeutics platforms for selective delivery of costimulatory ligands and peptide-HLA (pHLA) to AgS T cells. We engineered and deployed on these platforms an affinity-attenuated variant of interleukin-2, which selectively expands oligoclonal and polyfunctional AgS T cells in vitro and synergizes with CD80 signals for superior proliferation versus peptide stimulation.
Collapse
|
15
|
Qatato M, Venugopalan V, Al-Hashimi A, Rehders M, Valentine AD, Hein Z, Dallto U, Springer S, Brix K. Trace Amine-Associated Receptor 1 Trafficking to Cilia of Thyroid Epithelial Cells. Cells 2021; 10:cells10061518. [PMID: 34208608 PMCID: PMC8234161 DOI: 10.3390/cells10061518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 12/14/2022] Open
Abstract
Trace amine-associated receptor 1 (rodent Taar1/human TAAR1) is a G protein-coupled receptor that is mainly recognized for its functions in neuromodulation. Previous in vitro studies suggested that Taar1 may signal from intracellular compartments. However, we have shown Taar1 to localize apically and on ciliary extensions in rodent thyrocytes, suggesting that at least in the thyroid, Taar1 may signal from the cilia at the apical plasma membrane domain of thyrocytes in situ, where it is exposed to the content of the follicle lumen containing putative Taar1 ligands. This study was designed to explore mouse Taar1 (mTaar1) trafficking, heterologously expressed in human and rat thyroid cell lines in order to establish an in vitro system in which Taar1 signaling from the cell surface can be studied in future. The results showed that chimeric mTaar1-EGFP traffics to the apical cell surface and localizes particularly to spherical structures of polarized thyroid cells, procilia, and primary cilia upon serum-starvation. Moreover, mTaar1-EGFP appears to form high molecular mass forms, possibly homodimers and tetramers, in stably expressing human thyroid cell lines. However, only monomeric mTaar1-EGFP was cell surface biotinylated in polarized human thyrocytes. In polarized rat thyrocytes, mTaar1-EGFP is retained in the endoplasmic reticulum, while cilia were reached by mTaar1-EGFP transiently co-expressed in combination with an HA-tagged construct of the related mTaar5. We conclude that Taar1 trafficking to cilia depends on their integrity. The results further suggest that an in vitro cell model was established that recapitulates Taar1 trafficking in thyrocytes in situ, in principle, and will enable studying Taar1 signaling in future, thus extending our general understanding of its potential significance for thyroid autoregulation.
Collapse
|
16
|
Lis N, Hein Z, Ghanwat SS, Ramnarayan VR, Chambers BJ, Springer S. The murine cytomegalovirus immunoevasin gp40/m152 inhibits NKG2D receptor RAE-1γ by intracellular retention and cell surface masking. J Cell Sci 2021; 134:269012. [PMID: 34085696 DOI: 10.1242/jcs.257428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
NKG2D (also known as KLRK1) is a crucial natural killer (NK) cell-activating receptor, and the murine cytomegalovirus (MCMV) employs multiple immunoevasins to avoid NKG2D-mediated activation. One of the MCMV immunoevasins, gp40 (m152), downregulates the cell surface NKG2D ligand RAE-1γ (also known as Raet1c) thus limiting NK cell activation. This study establishes the molecular mechanism by which gp40 retains RAE-1γ in the secretory pathway. Using flow cytometry and pulse-chase analysis, we demonstrate that gp40 retains RAE-1γ in the early secretory pathway, and that this effect depends on the binding of gp40 to a host protein, TMED10, a member of the p24 protein family. We also show that the TMED10-based retention mechanism can be saturated, and that gp40 has a backup mechanism as it masks RAE-1γ on the cell surface, blocking the interaction with the NKG2D receptor and thus NK cell activation.
Collapse
Affiliation(s)
- Natalia Lis
- Department of Life Sciences and Chemistry, Jacobs University, Bremen 28759, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University, Bremen 28759, Germany
| | - Swapnil S Ghanwat
- Department of Life Sciences and Chemistry, Jacobs University, Bremen 28759, Germany
| | - Venkat R Ramnarayan
- Department of Life Sciences and Chemistry, Jacobs University, Bremen 28759, Germany
| | - Benedict J Chambers
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm 14152, Sweden
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen 28759, Germany
| |
Collapse
|
17
|
McShan AC, Devlin CA, Morozov GI, Overall SA, Moschidi D, Akella N, Procko E, Sgourakis NG. TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap. Nat Commun 2021; 12:3174. [PMID: 34039964 PMCID: PMC8154891 DOI: 10.1038/s41467-021-23225-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/16/2021] [Indexed: 11/08/2022] Open
Abstract
Chaperones Tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting high-affinity peptides in the MHC-I groove (editing). While X-ray and cryo-EM snapshots of MHC-I in complex with TAPBPR and Tapasin, respectively, have provided important insights into the peptide-deficient MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Based on structural and functional data, a loop sequence of variable lengths has been proposed to stabilize empty MHC-I molecules through direct interactions with the floor of the groove. Using deep mutagenesis on two complementary expression systems, we find that important residues for the Tapasin/TAPBPR chaperoning activity are located on a large scaffolding surface, excluding the loop. Conversely, loop mutations influence TAPBPR interactions with properly conformed MHC-I molecules, relevant for peptide editing. Detailed biophysical characterization by solution NMR, ITC and FP-based assays shows that the loop hovers above the MHC-I groove to promote the capture of incoming peptides. Our results suggest that the longer loop of TAPBPR lowers the affinity requirements for peptide selection to facilitate peptide loading under conditions and subcellular compartments of reduced ligand concentration, and to prevent disassembly of high-affinity peptide-MHC-I complexes that are transiently interrogated by TAPBPR during editing.
Collapse
Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christine A Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Giora I Morozov
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah A Overall
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Danai Moschidi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Neha Akella
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA.
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
18
|
Geng J, Raghavan M. Conformational sensing of major histocompatibility complex (MHC) class I molecules by immune receptors and intracellular assembly factors. Curr Opin Immunol 2021; 70:67-74. [PMID: 33857912 DOI: 10.1016/j.coi.2021.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Major histocompatibility complex class I (MHC-I) molecules play a critical role in both innate and adaptive immune responses. The heterodimeric complex of a polymorphic MHC-I heavy chain and a conserved light chain binds to a diverse set of peptides which are presented at the cell surface. Peptide-free (empty) versions of MHC-I molecules are typically retained intracellularly due to their low stability and bound by endoplasmic reticulum chaperones and assembly factors. However, emerging evidence suggests that at least some MHC-I allotypes are relatively stable and detectable at the cell-surface as peptide-deficient conformers, under some conditions. Such MHC-I conformers interact with multiple immune receptors to mediate various immunological functions. Furthermore, conformational sensing of MHC-I molecules by intracellular assembly factors and endoplasmic reticulum chaperones influences the peptide repertoire, with profound consequences for immunity. In this review, we discuss recent advances relating to MHC-I conformational variations and their pathophysiological implications.
Collapse
Affiliation(s)
- Jie Geng
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
19
|
Ablack JN, Ortiz J, Bajaj J, Trinh K, Lagarrigue F, Cantor JM, Reya T, Ginsberg MH. MARCH Proteins Mediate Responses to Antitumor Antibodies. THE JOURNAL OF IMMUNOLOGY 2020; 205:2883-2892. [PMID: 33077644 DOI: 10.4049/jimmunol.1901245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 08/26/2020] [Indexed: 12/26/2022]
Abstract
CD98, which is required for the rapid proliferation of both normal and cancer cells, and MET, the hepatocyte growth factor receptor, are potential targets for therapeutic antitumor Abs. In this study, we report that the antiproliferative activity of a prototype anti-CD98 Ab, UM7F8, is due to Ab-induced membrane-associated ring CH (MARCH) E3 ubiquitin ligase-mediated ubiquitination and downregulation of cell surface CD98. MARCH1-mediated ubiquitination of CD98 is required for UM7F8's capacity to reduce CD98 surface expression and its capacity to inhibit the proliferation of murine T cells. Similarly, CD98 ubiquitination is required for UM7F8's capacity to block the colony-forming ability of murine leukemia-initiating cells. To test the potential generality of the paradigm that MARCH E3 ligases can mediate the antiproliferative response to antitumor Abs, we examined the potential effects of MARCH proteins on responses to emibetuzumab, an anti-MET Ab currently in clinical trials for various cancers. We report that MET surface expression is reduced by MARCH1, 4, or 8-mediated ubiquitination and that emibetuzumab-induced MET ubiquitination contributes to its capacity to downregulate MET and inhibit human tumor cell proliferation. Thus, MARCH E3 ligases can act as cofactors for antitumor Abs that target cell surface proteins, suggesting that the MARCH protein repertoire of cells is a determinant of their response to such Abs.
Collapse
Affiliation(s)
- Jailal N Ablack
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093; and
| | - Jesus Ortiz
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093; and
| | - Jeevisha Bajaj
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093
| | - Kathleen Trinh
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093; and
| | - Frederic Lagarrigue
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093; and
| | - Joseph M Cantor
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093; and
| | - Tannishtha Reya
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093
| | - Mark H Ginsberg
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093; and
| |
Collapse
|
20
|
Destabilizing single chain major histocompatibility complex class I protein for repurposed enterokinase proteolysis. Sci Rep 2020; 10:14897. [PMID: 32913247 PMCID: PMC7483518 DOI: 10.1038/s41598-020-71785-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/18/2020] [Indexed: 11/08/2022] Open
Abstract
The lack of a high throughput assay for screening stabilizing peptides prior to building a library of peptide-major histocompatibility complex class I (pMHC-I) molecules has motivated the continual use of in silico tools without biophysical characterization. Here, based on de novo protein fragmentation, the EASY MHC-I (EZ MHC-I) assay favors peptide antigen screening to an unheralded hands-on time of seconds per peptide due to the empty single chain MHC-I protein instability. Unlike tedious traditional labeling- and antibody-based MHC-I assays, repurposed enterokinase directly fragments the unstable single MHC-I chain protein unless rescued by a stabilizing peptide under luminal condition. Herein, the principle behind EZ MHC-I assay not only characterizes the overlooked stability as a known better indicator of immunogenicity than classical affinity but also the novel use of enterokinase from the duodenum to target destabilized MHC-I protein not bearing the standard Asp-Asp-Asp-Asp-Lys motif, which may protend to other protein instability-based assays.
Collapse
|
21
|
Al-Hashimi A, Venugopalan V, Sereesongsaeng N, Tedelind S, Pinzaru AM, Hein Z, Springer S, Weber E, Führer D, Scott CJ, Burden RE, Brix K. Significance of nuclear cathepsin V in normal thyroid epithelial and carcinoma cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118846. [PMID: 32910988 DOI: 10.1016/j.bbamcr.2020.118846] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/29/2020] [Indexed: 12/11/2022]
Abstract
Altered expression and/or localization of cysteine cathepsins is believed to involve in thyroid diseases including cancer. Here, we examined the localization of cathepsins B and V in human thyroid tissue sections of different pathological conditions by immunolabeling and morphometry. Cathepsin B was mostly found within endo-lysosomes as expected. In contrast, cathepsin V was detected within nuclei, predominantly in cells of cold nodules, follicular and papillary thyroid carcinoma tissue, while it was less often detected in this unusual localization in hot nodules and goiter tissue. To understand the significance of nuclear cathepsin V in thyroid cells, this study aimed to establish a cellular model of stable nuclear cathepsin V expression. As representative of a specific form lacking the signal peptide and part of the propeptide, N-terminally truncated cathepsin V fused to eGFP recapitulated the nuclear localization of endogenous cathepsin V throughout the cell cycle in Nthy-ori 3-1 cells. Interestingly, the N-terminally truncated cathepsin V-eGFP was more abundant in the nuclei during S phase. These findings suggested a possible contribution of nuclear cathepsin V forms to cell cycle progression. Indeed, we found that N-terminally truncated cathepsin V-eGFP expressing cells were more proliferative than those expressing full-length cathepsin V-eGFP or wild type controls. We conclude that a specific molecular form of cathepsin V localizes to the nucleus of thyroid epithelial and carcinoma cells, where it might involve in deregulated pathways leading to hyperproliferation. These findings highlight the necessity to better understand cathepsin trafficking in health and disease. In particular, cell type specificity of mislocalization of cysteine cathepsins, which otherwise act in a functionally redundant manner, seems to be important to understand their non-canonical roles in cell cycle progression.
Collapse
Affiliation(s)
- Alaa Al-Hashimi
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Vaishnavi Venugopalan
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | | | - Sofia Tedelind
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Alexandra M Pinzaru
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Ekkehard Weber
- Institute of Physiological Chemistry, Martin Luther University Halle-Wittenberg, Hollystrasse 1, D-06114 Halle-Saale, Germany
| | - Dagmar Führer
- Universität Duisburg-Essen, Universitätsklinikum Essen (AöR), Klinik für Endokrinologie, Diabetologie und Stoffwechsel, Hufeland Strasse 55, D-45177 Essen, Germany
| | - Christopher J Scott
- Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Roberta E Burden
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Klaudia Brix
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
| |
Collapse
|
22
|
Kulicke C, Karamooz E, Lewinsohn D, Harriff M. Covering All the Bases: Complementary MR1 Antigen Presentation Pathways Sample Diverse Antigens and Intracellular Compartments. Front Immunol 2020; 11:2034. [PMID: 32983150 PMCID: PMC7492589 DOI: 10.3389/fimmu.2020.02034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
The ubiquitously expressed, monomorphic MHC class Ib molecule MHC class I-related protein 1 (MR1) presents microbial metabolites to mucosal-associated invariant T (MAIT) cells. However, recent work demonstrates that both the ligands bound by MR1 and the T cells restricted by it are more diverse than originally thought. It is becoming increasingly clear that MR1 is capable of presenting a remarkable variety of both microbial and non-microbial small molecule antigens to a diverse group of MR1-restricted T cells (MR1Ts) and that the antigen presentation pathway differs between exogenously delivered antigen and intracellular microbial infection. These distinct antigen presentation pathways suggest that MR1 shares features of both MHC class I and MHC class II antigen presentation, enabling it to sample diverse intracellular compartments and capture antigen of both intracellular and extracellular origin. Here, we review recent developments and new insights into the cellular mechanisms of MR1-dependent antigen presentation with a focus on microbial MR1T cell antigens.
Collapse
Affiliation(s)
- Corinna Kulicke
- Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States.,VA Portland Health Care System, Research and Development, Portland, OR, United States
| | - Elham Karamooz
- Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States.,VA Portland Health Care System, Research and Development, Portland, OR, United States
| | - David Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States.,VA Portland Health Care System, Research and Development, Portland, OR, United States.,Department of Pediatrics, Oregon Health and Science University, Portland, OR, United States.,Department of Molecular and Microbial Immunology, Oregon Health and Science University, Portland, OR, United States
| | - Melanie Harriff
- Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States.,VA Portland Health Care System, Research and Development, Portland, OR, United States.,Department of Molecular and Microbial Immunology, Oregon Health and Science University, Portland, OR, United States
| |
Collapse
|
23
|
Balam S, Kesselring R, Eggenhofer E, Blaimer S, Evert K, Evert M, Schlitt HJ, Geissler EK, van Blijswijk J, Lee S, Reis e Sousa C, Brunner SM, Fichtner-Feigl S. Cross-presentation of dead-cell-associated antigens by DNGR-1 + dendritic cells contributes to chronic allograft rejection in mice. Eur J Immunol 2020; 50:2041-2054. [PMID: 32640051 DOI: 10.1002/eji.201948501] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 01/06/2023]
Abstract
The purpose of this study was to elucidate whether DC NK lectin group receptor-1 (DNGR-1)-dependent cross-presentation of dead-cell-associated antigens occurs after transplantation and contributes to CD8+ T cell responses, chronic allograft rejection (CAR), and fibrosis. BALB/c or C57BL/6 hearts were heterotopically transplanted into WT, Clec9a-/- , or Batf3-/- recipient C57BL/6 mice. Allografts were analyzed for cell infiltration, CD8+ T cell activation, fibrogenesis, and CAR using immunohistochemistry, Western blot, qRT2 -PCR, and flow cytometry. Allografts displayed infiltration by recipient DNGR-1+ DCs, signs of CAR, and fibrosis. Allografts in Clec9a-/- recipients showed reduced CAR (p < 0.0001), fibrosis (P = 0.0137), CD8+ cell infiltration (P < 0.0001), and effector cytokine levels compared to WT recipients. Batf3-deficiency greatly reduced DNGR-1+ DC-infiltration, CAR (P < 0.0001), and fibrosis (P = 0.0382). CD8 cells infiltrating allografts of cytochrome C treated recipients, showed reduced production of CD8 effector cytokines (P < 0.05). Further, alloreactive CD8+ T cell response in indirect pathway IFN-γ ELISPOT was reduced in Clec9a-/- recipient mice (P = 0.0283). Blockade of DNGR-1 by antibody, similar to genetic elimination of the receptor, reduced CAR (P = 0.0003), fibrosis (P = 0.0273), infiltration of CD8+ cells (p = 0.0006), and effector cytokine levels. DNGR-1-dependent alloantigen cross-presentation by DNGR-1+ DCs induces alloreactive CD8+ cells that induce CAR and fibrosis. Antibody against DNGR-1 can block this process and prevent CAR and fibrosis.
Collapse
Affiliation(s)
- Saidou Balam
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | - Rebecca Kesselring
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | - Elke Eggenhofer
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | - Stephanie Blaimer
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | - Katja Evert
- Department of Pathology, University Medical Center Regensburg, Regensburg, Germany
| | - Matthias Evert
- Department of Pathology, University Medical Center Regensburg, Regensburg, Germany
| | - Hans J Schlitt
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | - Edward K Geissler
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | | | - Sonia Lee
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | | | - Stefan M Brunner
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany
| | - Stefan Fichtner-Feigl
- Department of Surgery, University Medical Center Regensburg, Regensburg, Germany.,Department of General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany
| |
Collapse
|
24
|
Moritz A, Anjanappa R, Wagner C, Bunk S, Hofmann M, Pszolla G, Saikia A, Garcia-Alai M, Meijers R, Rammensee HG, Springer S, Maurer D. High-throughput peptide-MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules. Sci Immunol 2020; 4:4/37/eaav0860. [PMID: 31324691 DOI: 10.1126/sciimmunol.aav0860] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/21/2019] [Indexed: 12/26/2022]
Abstract
Major histocompatibility complex (MHC) class I molecules present short peptide ligands on the cell surface for interrogation by cytotoxic CD8+ T cells. MHC class I complexes presenting tumor-associated peptides such as neoantigens represent key targets of cancer immunotherapy approaches currently in development, making them important for efficacy and safety screenings. Without peptide ligand, MHC class I complexes are unstable and decay quickly, making the production of soluble monomers for analytical purposes labor intensive. We have developed a disulfide-stabilized HLA-A*02:01 molecule that is stable without peptide but can form peptide-MHC complexes (pMHCs) with ligands of choice in a one-step loading procedure. We illustrate the similarity between the engineered mutant and the wild-type molecule with respect to affinity of wild-type or affinity-matured T cell receptors (TCRs) and present a crystal structure corroborating the binding kinetics measurements. In addition, we demonstrate a high-throughput binding kinetics measurement platform to analyze the binding characteristics of bispecific TCR (bsTCR) molecules against diverse pMHC libraries produced with the disulfide-stabilized HLA-A*02:01 molecule. We show that bsTCR affinities for pMHCs are indicative of in vitro function and generate a bsTCR binding motif to identify potential off-target interactions in the human proteome. These findings showcase the potential of the platform and the engineered HLA-A*02:01 molecule in the emerging field of pMHC-targeting biologics.
Collapse
Affiliation(s)
- Andreas Moritz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany. .,Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | | | | | - Ankur Saikia
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | | |
Collapse
|
25
|
Serçinoğlu O, Ozbek P. Sequence-structure-function relationships in class I MHC: A local frustration perspective. PLoS One 2020; 15:e0232849. [PMID: 32421728 PMCID: PMC7233585 DOI: 10.1371/journal.pone.0232849] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with HLA in a common diagonal binding mode, and KIR-HLA interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the human MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.
Collapse
Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Faculty of Engineering, Fener, Rize, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Faculty of Engineering, Goztepe, Istanbul, Turkey
- * E-mail:
| |
Collapse
|
26
|
Hopkins JR, Crean RM, Catici DAM, Sewell AK, Arcus VL, Van der Kamp MW, Cole DK, Pudney CR. Peptide cargo tunes a network of correlated motions in human leucocyte antigens. FEBS J 2020; 287:3777-3793. [PMID: 32134551 PMCID: PMC8651013 DOI: 10.1111/febs.15278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
Most biomolecular interactions are typically thought to increase the (local) rigidity of a complex, for example, in drug‐target binding. However, detailed analysis of specific biomolecular complexes can reveal a more subtle interplay between binding and rigidity. Here, we focussed on the human leucocyte antigen (HLA), which plays a crucial role in the adaptive immune system by presenting peptides for recognition by the αβ T‐cell receptor (TCR). The role that the peptide plays in tuning HLA flexibility during TCR recognition is potentially crucial in determining the functional outcome of an immune response, with obvious relevance to the growing list of immunotherapies that target the T‐cell compartment. We have applied high‐pressure/temperature perturbation experiments, combined with molecular dynamics simulations, to explore the drivers that affect molecular flexibility for a series of different peptide–HLA complexes. We find that different peptide sequences affect peptide–HLA flexibility in different ways, with the peptide cargo tuning a network of correlated motions throughout the pHLA complex, including in areas remote from the peptide‐binding interface, in a manner that could influence T‐cell antigen discrimination.
Collapse
Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Rory M Crean
- Department of Biology and Biochemistry, University of Bath, UK.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | | | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Christopher R Pudney
- Department of Biology and Biochemistry, University of Bath, UK.,Centre for Therapeutic Innovation, University of Bath, UK
| |
Collapse
|
27
|
Sagert L, Hennig F, Thomas C, Tampé R. A loop structure allows TAPBPR to exert its dual function as MHC I chaperone and peptide editor. eLife 2020; 9:55326. [PMID: 32167472 PMCID: PMC7117912 DOI: 10.7554/elife.55326] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/12/2020] [Indexed: 01/18/2023] Open
Abstract
Adaptive immunity vitally depends on major histocompatibility complex class I (MHC I) molecules loaded with peptides. Selective loading of peptides onto MHC I, referred to as peptide editing, is catalyzed by tapasin and the tapasin-related TAPBPR. An important catalytic role has been ascribed to a structural feature in TAPBPR called the scoop loop, but the exact function of the scoop loop remains elusive. Here, using a reconstituted system of defined peptide-exchange components including human TAPBPR variants, we uncover a substantial contribution of the scoop loop to the stability of the MHC I-chaperone complex and to peptide editing. We reveal that the scoop loop of TAPBPR functions as an internal peptide surrogate in peptide-depleted environments stabilizing empty MHC I and impeding peptide rebinding. The scoop loop thereby acts as an additional selectivity filter in shaping the repertoire of presented peptide epitopes and the formation of a hierarchical immune response.
Collapse
Affiliation(s)
- Lina Sagert
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Hennig
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| |
Collapse
|
28
|
Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection. Nat Commun 2020; 11:1314. [PMID: 32161266 PMCID: PMC7066147 DOI: 10.1038/s41467-020-14862-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/06/2020] [Indexed: 02/08/2023] Open
Abstract
Major Histocompatibility Complex (MHC) class I molecules selectively bind peptides for presentation to cytotoxic T cells. The peptide-free state of these molecules is not well understood. Here, we characterize a disulfide-stabilized version of the human class I molecule HLA-A*02:01 that is stable in the absence of peptide and can readily exchange cognate peptides. We present X-ray crystal structures of the peptide-free state of HLA-A*02:01, together with structures that have dipeptides bound in the A and F pockets. These structural snapshots reveal that the amino acid side chains lining the binding pockets switch in a coordinated fashion between a peptide-free unlocked state and a peptide-bound locked state. Molecular dynamics simulations suggest that the opening and closing of the F pocket affects peptide ligand conformations in adjacent binding pockets. We propose that peptide binding is co-determined by synergy between the binding pockets of the MHC molecule. Major Histocompatibility Complex (MHC) class I molecules present tightly binding peptides on the cell surface for recognition by cytotoxic T cells. Here, the authors present the crystal structures of a disulfide-stabilized human MHC class I molecule in the peptide-free state and bound with dipeptides, and find that peptide binding is accompanied by concerted conformational switches of the amino acid side chains in the binding pockets.
Collapse
|
29
|
Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. Proc Natl Acad Sci U S A 2019; 116:25602-25613. [PMID: 31796585 PMCID: PMC6926029 DOI: 10.1073/pnas.1915562116] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The interplay between a highly polymorphic set of MHC-I alleles and molecular chaperones shapes the repertoire of peptide antigens displayed on the cell surface for T cell surveillance. Here, we demonstrate that the molecular chaperone TAP-binding protein related (TAPBPR) associates with a broad range of partially folded MHC-I species inside the cell. Bimolecular fluorescence complementation and deep mutational scanning reveal that TAPBPR recognition is polarized toward the α2 domain of the peptide-binding groove, and depends on the formation of a conserved MHC-I disulfide epitope in the α2 domain. Conversely, thermodynamic measurements of TAPBPR binding for a representative set of properly conformed, peptide-loaded molecules suggest a narrower MHC-I specificity range. Using solution NMR, we find that the extent of dynamics at "hotspot" surfaces confers TAPBPR recognition of a sparsely populated MHC-I state attained through a global conformational change. Consistently, restriction of MHC-I groove plasticity through the introduction of a disulfide bond between the α1/α2 helices abrogates TAPBPR binding, both in solution and on a cellular membrane, while intracellular binding is tolerant of many destabilizing MHC-I substitutions. Our data support parallel TAPBPR functions of 1) chaperoning unstable MHC-I molecules with broad allele-specificity at early stages of their folding process, and 2) editing the peptide cargo of properly conformed MHC-I molecules en route to the surface, which demonstrates a narrower specificity. Our results suggest that TAPBPR exploits localized structural adaptations, both near and distant to the peptide-binding groove, to selectively recognize discrete conformational states sampled by MHC-I alleles, toward editing the repertoire of displayed antigens.
Collapse
|
30
|
Saini SK, Tamhane T, Anjanappa R, Saikia A, Ramskov S, Donia M, Svane IM, Jakobsen SN, Garcia-Alai M, Zacharias M, Meijers R, Springer S, Hadrup SR. Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells. Sci Immunol 2019; 4:4/37/eaau9039. [DOI: 10.1126/sciimmunol.aau9039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/20/2019] [Indexed: 12/17/2022]
Abstract
The peptide-dependent stability of MHC class I molecules poses a substantial challenge for their use in peptide-MHC multimer–based approaches to comprehensively analyze T cell immunity. To overcome this challenge, we demonstrate the use of functionally empty MHC class I molecules stabilized by a disulfide bond to link the α1and α2helices close to the F pocket. Peptide-loaded disulfide-stabilized HLA-A*02:01 shows complete structural overlap with wild-type HLA-A*02:01. Peptide-MHC multimers prepared using disulfide-stabilized HLA-A*02:01, HLA-A*24:02, and H-2Kbcan be used to identify antigen-specific T cells, and they provide a better staining index for antigen-specific T cell detection compared with multimers prepared with wild-type MHC class I molecules. Disulfide-stabilized MHC class I molecules can be loaded with peptide in the multimerized form without affecting their capacity to stain T cells. We demonstrate the value of empty-loadable tetramers that are converted to antigen-specific tetramers by a single-step peptide addition through their use to identify T cells specific for mutation-derived neoantigens and other cancer-associated antigens in human melanoma.
Collapse
|
31
|
Thomas C, Tampé R. MHC I chaperone complexes shaping immunity. Curr Opin Immunol 2019; 58:9-15. [DOI: 10.1016/j.coi.2019.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/16/2018] [Accepted: 01/04/2019] [Indexed: 01/21/2023]
|
32
|
Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Front Immunol 2019; 10:966. [PMID: 31130956 PMCID: PMC6509175 DOI: 10.3389/fimmu.2019.00966] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/15/2019] [Indexed: 11/21/2022] Open
Abstract
T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures of TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both the peptide and the MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for peptide presentation, the physical properties of class I MHC proteins are tuned by different peptides in ways that are not always structurally visible. These include MHC protein motions, or dynamics, which are believed to influence interactions with a variety of MHC-binding proteins, including not only TCRs, but other activating and inhibitory receptors as well as components of the peptide loading machinery. Here, we investigated the mechanisms by which peptides tune the dynamics of the common class I MHC protein HLA-A2. By examining more than 50 lengthy molecular dynamics simulations of HLA-A2 presenting different peptides, we identified regions susceptible to dynamic tuning, including regions in the peptide binding domain as well as the distal α3 domain. Further analyses of the simulations illuminated mechanisms by which the influences of different peptides are communicated throughout the protein, and involve regions of the peptide binding groove, the β2-microglobulin subunit, and the α3 domain. Overall, our results demonstrate that the class I MHC protein is a highly tunable peptide sensor whose physical properties vary considerably with bound peptide. Our data provides insight into the underlying principles and suggest a role for dynamically driven allostery in the immunological function of MHC proteins.
Collapse
Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Alistair Bailey
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Christian Abraham
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Tim Elliott
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| |
Collapse
|
33
|
Goncu B, Yucesan E, Aysan E, Kandas NO. HLA Class I Expression Changes in Different Types of Cultured Parathyroid Cells. EXP CLIN TRANSPLANT 2019; 20:854-862. [PMID: 30995898 DOI: 10.6002/ect.2018.0388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Tissue-specific immunogenicity can be characterized by the determination of human leukocyte antigens (HLA). Parathyroid hyperplasia tissue cells are presumed to have the ability to lose HLA class I expression profile during cultivation, whereas healthy parathyroid cells are presumed to already express HLA class I molecules at low levels. However, there are conflicting results about the expression of HLA class I antigens. In this study, our aim was to evaluate different patterns of HLA class I expression in different parathyroid tissue cells. MATERIALS AND METHODS Parathyroid tissue cells were isolated enzymatically and cultured in vitro. Expression of HLA class I (HLA-A, HLA-B, HLA-C) mRNA and protein levels were studied in 7 parathyroid adenomas and 9 parathyroid hyperplasia tissue samples by reverse transcriptase-polymerase chain reaction and Western blot analyses. RESULTS HLA-A protein expression remained stable in parathyroid adenoma and hyperplasia tissue, but HLA-A mRNA expression decreased in adenoma tissue. In parathyroid hyperplasia tissue, HLA-B protein expression remained stable, although mRNA expres-sion levels decreased during cultivation. HLA-C mRNA expression was steady in parathyroid adenoma yet significantly decreased in hyperplasia tissue samples. HLA-C protein expression levels were below 30 pg for both types of parathyroid tissue during cultivation. CONCLUSIONS HLA class I expression levels of para-thyroid hyperplasia and adenoma tissue were not found to be similar. Parathyroid hyperplasia tissue is the donor tissue for the treatment of permanent hypoparathyroidism. Therefore, expression patterns of HLA class I are directly relevant to the transplant process. In particular, the HLA region is highly polymorphic, and, as a consequence of this, heterogeneous correlations among HLA-A, HLA-B, and HLA-C expression patterns of parathyroid tissue should be evaluated in detail before transplant for future studies.
Collapse
Affiliation(s)
- Beyza Goncu
- From the Experimental Research Center, Bezmialem Vakif University, Istanbul, Turkey
| | | | | | | |
Collapse
|
34
|
Dirscherl C, Hein Z, Ramnarayan VR, Jacob-Dolan C, Springer S. A two-hybrid antibody micropattern assay reveals specific in cis interactions of MHC I heavy chains at the cell surface. eLife 2018; 7:e34150. [PMID: 30180933 PMCID: PMC6125123 DOI: 10.7554/elife.34150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/24/2018] [Indexed: 12/22/2022] Open
Abstract
We demonstrate a two-hybrid assay based on antibody micropatterns to study protein-protein interactions at the cell surface of major histocompatibility complex class I (MHC I) proteins. Anti-tag and conformation-specific antibodies are used for individual capture of specific forms of MHC I proteins that allow for location- and conformation-specific analysis by fluorescence microscopy. The assay is used to study the in cis interactions of MHC I proteins at the cell surface under controlled conditions and to define the involved protein conformations. Our results show that homotypic in cis interactions occur exclusively between MHC I free heavy chains, and we identify the dissociation of the light chain from the MHC I protein complex as a condition for MHC I in cis interactions. The functional role of these MHC I protein-protein interactions at the cell surface needs further investigation. We propose future technical developments of our two-hybrid assay for further analysis of MHC I protein-protein interactions.
Collapse
Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and ChemistryJacobs UniversityBremenGermany
| | - Zeynep Hein
- Department of Life Sciences and ChemistryJacobs UniversityBremenGermany
| | | | | | | |
Collapse
|
35
|
Hein Z, Borchert B, Tolba Abualrous E, Springer S. Distinct mechanisms survey the structural integrity of HLA-B*27:05 intracellularly and at the surface. PLoS One 2018; 13:e0200811. [PMID: 30071035 PMCID: PMC6071996 DOI: 10.1371/journal.pone.0200811] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/03/2018] [Indexed: 02/06/2023] Open
Abstract
HLA-B*27:05 is associated with the development of autoimmune spondyloarthropathies, but the precise causal relationship between the MHC haplotype and disease pathogenesis is yet to be elucidated. Studies focusing on the structure and cellular trafficking of HLA-B*27:05 implicate several links between the onset of inflammation and the unusual conformations of the molecule inside and at the surface of antigen presenting cells. Several lines of evidence emphasize the emergence of those unnatural protein conformations under conditions where peptide loading onto B*27:05 is impaired. To understand how cellular factors distinguish between poorly loaded molecules from the optimally loaded ones, we have investigated the intracellular transport, folding, and cell surface expression of this particular B27 subtype. Our findings show that B*27:05 is structurally unstable in the absence of peptide, and that an artificially introduced disulfide bond between residues 84 and 139 conferred enhanced conformational stability to the suboptimally loaded molecules. Empty or suboptimally loaded B*27:05 can escape intracellular retention and arrive at the cell surface leading to the appearance of increased number of β2m-free heavy chains. Our study reveals a general mechanism found in the early secretory pathways of murine and human cells that apply to the quality control of MHC class I molecules, and it highlights the allotype-specific structural features of HLA-B*27:05 that can be associated with aberrant antigen presentation and that might contribute to the etiology of disease.
Collapse
Affiliation(s)
- Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Britta Borchert
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Esam Tolba Abualrous
- Department of Mathematics and Computer Science, Freie Universität, Berlin, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
- * E-mail:
| |
Collapse
|
36
|
Geng J, Zaitouna AJ, Raghavan M. Selected HLA-B allotypes are resistant to inhibition or deficiency of the transporter associated with antigen processing (TAP). PLoS Pathog 2018; 14:e1007171. [PMID: 29995954 PMCID: PMC6056074 DOI: 10.1371/journal.ppat.1007171] [Citation(s) in RCA: 25] [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: 01/23/2018] [Revised: 07/23/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules present antigenic peptides to CD8+ T cells, and are also important for natural killer (NK) cell immune surveillance against infections and cancers. MHC-I molecules are assembled via a complex assembly pathway in the endoplasmic reticulum (ER) of cells. Peptides present in the cytosol of cells are transported into the ER via the transporter associated with antigen processing (TAP). In the ER, peptides are assembled with MHC-I molecules via the peptide-loading complex (PLC). Components of the MHC-I assembly pathway are frequently targeted by viruses, in order to evade host immunity. Many viruses encode inhibitors of TAP, which is thought to be a central source of peptides for the assembly of MHC-I molecules. However, human MHC-I (HLA-I) genes are highly polymorphic, and it is conceivable that several variants can acquire peptides via TAP-independent pathways, thereby conferring resistance to pathogen-derived inhibitors of TAP. To broadly assess TAP-independent expression within the HLA-B locus, expression levels of 27 frequent HLA-B alleles were tested in cells with deficiencies in TAP. Approximately 15% of tested HLA-B allotypes are expressed at relatively high levels on the surface of TAP1 or TAP2-deficient cells and occur in partially peptide-receptive forms and Endoglycosidase H sensitive forms on the cell surface. Synergy between high peptide loading efficiency, broad specificity for peptides prevalent within unconventional sources and high intrinsic stability of the empty form allows for deviations from the conventional HLA-I assembly pathway for some HLA-B*35, HLA-B*57 and HLA-B*15 alleles. Allotypes that display higher expression in TAP-deficient cells are more resistant to viral TAP inhibitor-induced HLA-I down-modulation, and HLA-I down-modulation-induced NK cell activation. Conversely, the same allotypes are expected to mediate stronger CD8+ T cell responses under TAP-inhibited conditions. Thus, the degree of resistance to TAP inhibition functionally separates specific HLA-B allotypes. Human leukocyte antigen (HLA) class I molecules present pathogen-derived components (peptides) to cytotoxic T cells, thereby inducing the T cells to kill virus-infected cells. A complex cellular pathway involving the transporter associated with antigen processing (TAP) is typically required for the loading of peptides onto HLA class I molecules, and for effective anti-viral immunity mediated by cytotoxic T cells. Many viruses encode inhibitors of TAP as a means to evade anti-viral immunity by cytotoxic T cells. In humans, there are three sets of genes encoding HLA class I molecules, which are the HLA-A, HLA-B and HLA-C genes. These genes are highly variable, with thousands of allelic variants in human populations. Most individuals typically express two variants of each gene, one inherited from each parent. We demonstrate that about 15% of tested HLA-B allotypes have higher resistance to viral inhibitors of TAP or deficiency of TAP, compared to other HLA-B variants. HLA-B allotypes that are more resistant to TAP inhibition are expected to induce stronger CD8+ T cell responses against pathogens that inhibit TAP. Thus, unconventional TAP-independent assembly pathways are broadly prevalent among HLA-B variants. Such pathways provide mechanisms to effectively combat viruses that evade the conventional TAP-dependent HLA-B assembly pathway.
Collapse
Affiliation(s)
- Jie Geng
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anita J. Zaitouna
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
37
|
McShan AC, Natarajan K, Kumirov VK, Flores-Solis D, Jiang J, Badstübner M, Toor JS, Bagshaw CR, Kovrigin EL, Margulies DH, Sgourakis NG. Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle. Nat Chem Biol 2018; 14:811-820. [PMID: 29988068 PMCID: PMC6202177 DOI: 10.1038/s41589-018-0096-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 05/02/2018] [Accepted: 05/21/2018] [Indexed: 01/09/2023]
Abstract
Chaperones TAPBPR and tapasin associate with class-I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR, and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product, and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, where the lifetime and structural features of transiently bound peptides controls the regulation of a conformational switch, located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex.
Collapse
Affiliation(s)
- Andrew C McShan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Vlad K Kumirov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David Flores-Solis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Mareike Badstübner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Clive R Bagshaw
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
38
|
Chen Z, Zhang N, Qi J, Chen R, Dijkstra JM, Li X, Wang Z, Wang J, Wu Y, Xia C. The Structure of the MHC Class I Molecule of Bony Fishes Provides Insights into the Conserved Nature of the Antigen-Presenting System. THE JOURNAL OF IMMUNOLOGY 2017; 199:3668-3678. [PMID: 29055007 DOI: 10.4049/jimmunol.1600229] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/15/2017] [Indexed: 01/02/2023]
Abstract
MHC molecules evolved with the descent of jawed fishes some 350-400 million years ago. However, very little is known about the structural features of primitive MHC molecules. To gain insight into these features, we focused on the MHC class I Ctid-UAA of the evolutionarily distant grass carp (Ctenopharyngodon idella). The Ctid-UAA H chain and β2-microglobulin (Ctid-β2m) were refolded in vitro in the presence of peptides from viruses that infect carp. The resulting peptide-Ctid-UAA (p/Ctid-UAA) structures revealed the classical MHC class I topology with structural variations. In comparison with known mammalian and chicken peptide-MHC class I (p/MHC I) complexes, p/Ctid-UAA structure revealed several distinct features. Notably, 1) although the peptide ligand conventionally occupied all six pockets (A-F) of the Ag-binding site, the binding mode of the P3 side chain to pocket D was not observed in other p/MHC I structures; 2) the AB loop between β strands of the α1 domain of p/Ctid-UAA complex comes into contact with Ctid-β2m, an interaction observed only in chicken p/BF2*2101-β2m complex; and 3) the CD loop of the α3 domain, which in mammals forms a contact with CD8, has a unique position in p/Ctid-UAA that does not superimpose with the structures of any known p/MHC I complexes, suggesting that the p/Ctid-UAA to Ctid-CD8 binding mode may be distinct. This demonstration of the structure of a bony fish MHC class I molecule provides a foundation for understanding the evolution of primitive class I molecules, how they present peptide Ags, and how they might control T cell responses.
Collapse
Affiliation(s)
- Zhaosan Chen
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Jianxun Qi
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Rong Chen
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan; and
| | - Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Zhenbao Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Junya Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Yanan Wu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; .,Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, Haidian District, Beijing 100094, China
| |
Collapse
|
39
|
Ayres CM, Corcelli SA, Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Front Immunol 2017; 8:935. [PMID: 28824655 PMCID: PMC5545744 DOI: 10.3389/fimmu.2017.00935] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 01/28/2023] Open
Abstract
Structural biology of peptides presented by class I and class II MHC proteins has transformed immunology, impacting our understanding of fundamental immune mechanisms and allowing researchers to rationalize immunogenicity and design novel vaccines. However, proteins are not static structures as often inferred from crystallographic structures. Their components move and breathe individually and collectively over a range of timescales. Peptides bound within MHC peptide-binding grooves are no exception and their motions have been shown to impact recognition by T cell and other receptors in ways that influence function. Furthermore, peptides tune the motions of MHC proteins themselves, which impacts recognition of peptide/MHC complexes by other proteins. Here, we review the motional properties of peptides in MHC binding grooves and discuss how peptide properties can influence MHC motions. We briefly review theoretical concepts about protein motion and highlight key data that illustrate immunological consequences. We focus primarily on class I systems due to greater availability of data, but segue into class II systems as the concepts and consequences overlap. We suggest that characterization of the dynamic “energy landscapes” of peptide/MHC complexes and the resulting functional consequences is one of the next frontiers in structural immunology.
Collapse
Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| |
Collapse
|
40
|
Fisette O, Wingbermühle S, Schäfer LV. Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHCI Binding Groove. Front Immunol 2017; 8:408. [PMID: 28458665 PMCID: PMC5394104 DOI: 10.3389/fimmu.2017.00408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/29/2022] Open
Abstract
Antigen processing on MHCI involves the exchange of low-affinity peptides by high-affinity, immunodominant ones. This peptide editing process is mediated by tapasin and ERAAP at the peptide C- and N-terminus, respectively. Since tapasin does not contact the peptide directly, a sensing mechanism involving conformational changes likely allows tapasin to distinguish antigen-loaded MHCI molecules from those occupied by weakly bound, non-specific peptides. To understand this mechanism at the atomic level, we performed molecular dynamics simulations of MHCI allele B*44:02 loaded with peptides truncated or modified at the C- or N-terminus. We show that the deletion of peptide anchor residues leads to reversible, partial dissociation of the peptide from MHCI on the microsecond timescale. Fluctuations in the MHCI α2-1 helix segment, bordering the binding groove and cradled by tapasin in the PLC, are influenced by the peptide C-terminus occupying the nearby F-pocket. Simulations of tapasin complexed with MHCI bound to a low-affinity peptide show that tapasin widens the MHCI binding groove near the peptide C-terminus and weakens the attractive forces between MHCI and the peptide. Our simulations thus provide a detailed, spatially resolved picture of MHCI plasticity, revealing how peptide loading status can affect key structural regions contacting tapasin.
Collapse
Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Sebastian Wingbermühle
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| |
Collapse
|
41
|
Wieczorek M, Abualrous ET, Sticht J, Álvaro-Benito M, Stolzenberg S, Noé F, Freund C. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front Immunol 2017. [PMID: 28367149 DOI: 10.3389/fimmu.2017.00292.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins is essential for adaptive immunity. Prior to presentation, peptides need to be generated from proteins that are either produced by the cell's own translational machinery or that are funneled into the endo-lysosomal vesicular system. The prolonged interaction between a T cell receptor and specific pMHC complexes, after an extensive search process in secondary lymphatic organs, eventually triggers T cells to proliferate and to mount a specific cellular immune response. Once processed, the peptide repertoire presented by MHC proteins largely depends on structural features of the binding groove of each particular MHC allelic variant. Additionally, two peptide editors-tapasin for class I and HLA-DM for class II-contribute to the shaping of the presented peptidome by favoring the binding of high-affinity antigens. Although there is a vast amount of biochemical and structural information, the mechanism of the catalyzed peptide exchange for MHC class I and class II proteins still remains controversial, and it is not well understood why certain MHC allelic variants are more susceptible to peptide editing than others. Recent studies predict a high impact of protein intermediate states on MHC allele-specific peptide presentation, which implies a profound influence of MHC dynamics on the phenomenon of immunodominance and the development of autoimmune diseases. Here, we review the recent literature that describe MHC class I and II dynamics from a theoretical and experimental point of view and we highlight the similarities between MHC class I and class II dynamics despite the distinct functions they fulfill in adaptive immunity.
Collapse
Affiliation(s)
- Marek Wieczorek
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | | | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| |
Collapse
|
42
|
Wieczorek M, Abualrous ET, Sticht J, Álvaro-Benito M, Stolzenberg S, Noé F, Freund C. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front Immunol 2017; 8:292. [PMID: 28367149 PMCID: PMC5355494 DOI: 10.3389/fimmu.2017.00292] [Citation(s) in RCA: 645] [Impact Index Per Article: 80.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/28/2017] [Indexed: 11/21/2022] Open
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins is essential for adaptive immunity. Prior to presentation, peptides need to be generated from proteins that are either produced by the cell’s own translational machinery or that are funneled into the endo-lysosomal vesicular system. The prolonged interaction between a T cell receptor and specific pMHC complexes, after an extensive search process in secondary lymphatic organs, eventually triggers T cells to proliferate and to mount a specific cellular immune response. Once processed, the peptide repertoire presented by MHC proteins largely depends on structural features of the binding groove of each particular MHC allelic variant. Additionally, two peptide editors—tapasin for class I and HLA-DM for class II—contribute to the shaping of the presented peptidome by favoring the binding of high-affinity antigens. Although there is a vast amount of biochemical and structural information, the mechanism of the catalyzed peptide exchange for MHC class I and class II proteins still remains controversial, and it is not well understood why certain MHC allelic variants are more susceptible to peptide editing than others. Recent studies predict a high impact of protein intermediate states on MHC allele-specific peptide presentation, which implies a profound influence of MHC dynamics on the phenomenon of immunodominance and the development of autoimmune diseases. Here, we review the recent literature that describe MHC class I and II dynamics from a theoretical and experimental point of view and we highlight the similarities between MHC class I and class II dynamics despite the distinct functions they fulfill in adaptive immunity.
Collapse
Affiliation(s)
- Marek Wieczorek
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | | | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| |
Collapse
|
43
|
Moody PR, Sayers EJ, Magnusson JP, Alexander C, Borri P, Watson P, Jones AT. Receptor Crosslinking: A General Method to Trigger Internalization and Lysosomal Targeting of Therapeutic Receptor:Ligand Complexes. Mol Ther 2015; 23:1888-98. [PMID: 26412588 PMCID: PMC4700114 DOI: 10.1038/mt.2015.178] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/01/2015] [Indexed: 02/06/2023] Open
Abstract
A major unmet clinical need is a universal method for subcellular targeting of bioactive molecules to lysosomes. Delivery to this organelle enables either degradation of oncogenic receptors that are overexpressed in cancers, or release of prodrugs from antibody–drug conjugates. Here, we describe a general method that uses receptor crosslinking to trigger endocytosis and subsequently redirect trafficking of receptor:cargo complexes from their expected route, to lysosomes. By incubation of plasma membrane receptors with biotinylated cargo and subsequent addition of streptavidin to crosslink receptor:cargo–biotin complexes, we achieved rapid and selective lysosomal targeting of transferrin, an anti-MHC class I antibody, and the clinically approved anti-Her2 antibody trastuzumab. These three protein ligands each target a receptor with a distinct cellular function and intracellular trafficking profile. Importantly, we confirmed that crosslinking of trastuzumab increased lysosomal degradation of its cognate oncogenic receptor Her2 in breast cancer cell lines SKBR3 and BT474. These data suggest that crosslinking could be exploited for a wide range of target receptors, for navigating therapeutics through the endolysosomal pathway, for significant therapeutic benefit.
Collapse
Affiliation(s)
- Paul R Moody
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales
| | - Edward J Sayers
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales
| | | | | | - Paola Borri
- School of Biosciences, Cardiff University, Cardiff, Wales
| | - Peter Watson
- School of Biosciences, Cardiff University, Cardiff, Wales
| | - Arwyn T Jones
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales
| |
Collapse
|
44
|
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
|
45
|
Montealegre S, Venugopalan V, Fritzsche S, Kulicke C, Hein Z, Springer S. Dissociation of β2-microglobulin determines the surface quality control of major histocompatibility complex class I molecules. FASEB J 2015; 29:2780-8. [PMID: 25782992 DOI: 10.1096/fj.14-268094] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/25/2015] [Indexed: 11/11/2022]
Abstract
Major histocompatibility complex class I proteins, which present antigenic peptides to cytotoxic T lymphocytes at the surface of all nucleated cells, are endocytosed and destroyed rapidly once their peptide ligand has dissociated. The molecular mechanism of this cellular quality control process, which prevents rebinding of exogenous peptides and thus erroneous immune responses, is unknown. To identify the nature of the decisive step in endocytic sorting of class I molecules and its location, we have followed the removal of optimally and suboptimally peptide-loaded murine H-2K(b) class I proteins from the cell surface. We find that the binding of their light chain, β2-microglobulin (β2m), protects them from endocytic destruction. Thus, the extended survival of suboptimally loaded K(b) molecules at 25°C is attributed to decreased dissociation of β2m. Because all forms of K(b) are constantly internalized but little β2m-receptive heavy chain is present at the cell surface, it is likely that β2m dissociation and recognition of the heavy chain for lysosomal degradation take place in an endocytic compartment.
Collapse
Affiliation(s)
- Sebastián Montealegre
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Vaishnavi Venugopalan
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Susanne Fritzsche
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Corinna Kulicke
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| |
Collapse
|
46
|
Transport and quality control of MHC class I molecules in the early secretory pathway. Curr Opin Immunol 2015; 34:83-90. [PMID: 25771183 DOI: 10.1016/j.coi.2015.02.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 02/21/2015] [Accepted: 02/24/2015] [Indexed: 12/26/2022]
Abstract
Folding and peptide binding of major histocompatibility complex (MHC) class I molecules have been thoroughly researched, but the mechanistic connection between these biochemical events and the progress of class I through the early secretory pathway is much less well understood. This review focuses on the question how the partially assembled forms of class I (which lack high-affinity peptide and/or the light chain beta-2 microglobulin) are retained inside the cell. Such investigations offer researchers exciting chances to understand the connections between class I structure, conformational dynamics, peptide binding kinetics and thermodynamics, intracellular transport, and antigen presentation.
Collapse
|
47
|
Abualrous ET, Fritzsche S, Hein Z, Al-Balushi MS, Reinink P, Boyle LH, Wellbrock U, Antoniou AN, Springer S. F pocket flexibility influences the tapasin dependence of two differentially disease-associated MHC Class I proteins. Eur J Immunol 2015; 45:1248-57. [PMID: 25615938 DOI: 10.1002/eji.201445307] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/06/2014] [Accepted: 01/19/2015] [Indexed: 01/01/2023]
Abstract
The human MHC class I protein HLA-B*27:05 is statistically associated with ankylosing spondylitis, unlike HLA-B*27:09, which differs in a single amino acid in the F pocket of the peptide-binding groove. To understand how this unique amino acid difference leads to a different behavior of the proteins in the cell, we have investigated the conformational stability of both proteins using a combination of in silico and experimental approaches. Here, we show that the binding site of B*27:05 is conformationally disordered in the absence of peptide due to a charge repulsion at the bottom of the F pocket. In agreement with this, B*27:05 requires the chaperone protein tapasin to a greater extent than the conformationally stable B*27:09 in order to remain structured and to bind peptide. Taken together, our data demonstrate a method to predict tapasin dependence and physiological behavior from the sequence and crystal structure of a particular class I allotype. Also watch the Video Abstract.
Collapse
Affiliation(s)
- Esam T Abualrous
- Department of Life Science and Chemistry, Jacobs University Bremen, Bremen, Germany; Department of Physics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
The first step of peptide selection in antigen presentation by MHC class I molecules. Proc Natl Acad Sci U S A 2015; 112:1505-10. [PMID: 25605945 DOI: 10.1073/pnas.1416543112] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MHC class I molecules present a variable but limited repertoire of antigenic peptides for T-cell recognition. Understanding how peptide selection is achieved requires mechanistic insights into the interactions between the MHC I and candidate peptides. We find that, at first encounter, MHC I H-2K(b) considers a wide range of peptides, including those with expanded N termini and unfitting anchor residues. Discrimination occurs in the second step, when noncanonical peptides dissociate with faster exchange rates. This second step exhibits remarkable temperature sensitivity, as illustrated by numerous noncanonical peptides presented by H-2K(b) in cells cultured at 26 °C relative to 37 °C. Crystallographic analyses of H-2K(b)-peptide complexes suggest that a conformational adaptation of H-2K(b) drives the decisive step in peptide selection. We propose that MHC class I molecules consider initially a large peptide pool, subsequently refined by a temperature-sensitive induced-fit mechanism to retain the canonical peptide repertoire.
Collapse
|
49
|
Janßen L, Ramnarayan VR, Aboelmagd M, Iliopoulou M, Hein Z, Majoul I, Fritzsche S, Halenius A, Springer S. The murine cytomegalovirus immunoevasin gp40 binds MHC class I molecules to retain them in the early secretory pathway. J Cell Sci 2015; 129:219-27. [DOI: 10.1242/jcs.175620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/26/2015] [Indexed: 12/30/2022] Open
Abstract
In the presence of the murine cytomegalovirus (mCMV) gp40 (m152) protein, murine major histocompatibility complex (MHC) class I molecules do not reach the cell surface but are retained in an early compartment of the secretory pathway. We find that gp40 does not impair folding or high-affinity peptide binding of class I molecules but binds to them to retain them in the endoplasmic reticulum (ER), the ER-Golgi intermediate compartment (ERGIC), and the cis-Golgi, most likely by retrieval from the cis-Golgi to the ER. We identify a sequence in gp40 that is required for both its own retention in the early secretory pathway and for that of class I molecules.
Collapse
Affiliation(s)
- Linda Janßen
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | | | - Mohamed Aboelmagd
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Maria Iliopoulou
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Irina Majoul
- Institute of Biology, University of Lübeck, Germany
| | - Susanne Fritzsche
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Anne Halenius
- Institute of Virology, University of Freiburg, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| |
Collapse
|