1
|
Dorian D, Gustafson D, Quinn R, Bentley RF, Dorian P, Goodman JM, Fish JE, Connelly KA. Exercise-Dependent Modulation of Immunological Response Pathways in Endurance Athletes With and Without Atrial Fibrillation. J Am Heart Assoc 2024; 13:e033640. [PMID: 38497478 PMCID: PMC11009995 DOI: 10.1161/jaha.123.033640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/12/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Atrial fibrillation (AF) is a common arrhythmia characterized by uncoordinated atrial electrical activity. Lone AF occurs in the absence of traditional risk factors and is frequently observed in male endurance athletes, who face a 2- to 5-fold higher risk of AF compared with healthy, moderately active males. Our understanding of how endurance exercise contributes to the pathophysiology of lone AF remains limited. This study aimed to characterize the circulating protein fluctuations during high-intensity exercise as well as explore potential biomarkers of exercise-associated AF. METHODS AND RESULTS A prospective cohort of 12 male endurance cyclists between the ages of 40 and 65 years, 6 of whom had a history of exercise-associated AF, were recruited to participate using a convenience sampling method. The circulating proteome was subsequently analyzed using multiplex immunoassays and aptamer-based proteomics before, during, and after an acute high-intensity endurance exercise bout to assess temporality and identify potential markers of AF. The endurance exercise bout resulted in significant alterations to proteins involved in immune modulation (eg, growth/differentiation factor 15), skeletal muscle metabolism (eg, α-actinin-2), cell death (eg, histones), and inflammation (eg, interleukin-6). Subjects with AF differed from those without, displaying modulation of proteins previously known to have associations with incident AF (eg, C-reactive protein, insulin-like growth factor-1, and angiopoietin-2), and also with proteins having no previous association (eg, tapasin-related protein and α2-Heremans-Schmid glycoprotein). CONCLUSIONS These findings provide insights into the proteomic response to acute intense exercise, provide mechanistic insights into the pathophysiology behind AF in athletes, and identify targets for future study and validation.
Collapse
Affiliation(s)
- David Dorian
- Department of Medicine, Division of CardiologyUniversity of TorontoTorontoOntarioCanada
| | - Dakota Gustafson
- Department of Laboratory Medicine & PathobiologyUniversity of TorontoTorontoOntarioCanada
- Toronto General Hospital Research InstituteUniversity Health NetworkTorontoOntarioCanada
- Faculty of Health SciencesQueen’s UniversityKingstonOntarioCanada
| | - Ryan Quinn
- Division of CardiologyLi Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoOntarioCanada
| | - Robert F. Bentley
- Faculty of Kinesiology and Physical EducationUniversity of TorontoTorontoOntarioCanada
| | - Paul Dorian
- Department of Medicine, Division of CardiologyUniversity of TorontoTorontoOntarioCanada
- Division of CardiologyLi Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoOntarioCanada
- Department of MedicineUniversity of TorontoTorontoOntarioCanada
- Keenan Research Centre for Biomedical ScienceSt Michael’s Hospital, University of TorontoTorontoOntarioCanada
- Department of PhysiologyUniversity of TorontoTorontoOntarioCanada
- Heart and Stroke Richard Lewar Centre for Research ExcellenceUniversity of TorontoTorontoOntarioCanada
| | - Jack M. Goodman
- Faculty of Kinesiology and Physical EducationUniversity of TorontoTorontoOntarioCanada
- Heart and Stroke Richard Lewar Centre for Research ExcellenceUniversity of TorontoTorontoOntarioCanada
- Division of CardiologySinai Health/University Health NetworkTorontoOntarioCanada
| | - Jason E. Fish
- Department of Laboratory Medicine & PathobiologyUniversity of TorontoTorontoOntarioCanada
- Toronto General Hospital Research InstituteUniversity Health NetworkTorontoOntarioCanada
- Peter Munk Cardiac CentreUniversity Health NetworkTorontoOntarioCanada
| | - Kim A. Connelly
- Department of Medicine, Division of CardiologyUniversity of TorontoTorontoOntarioCanada
- Division of CardiologyLi Ka Shing Knowledge Institute of St. Michael’s HospitalTorontoOntarioCanada
- Department of MedicineUniversity of TorontoTorontoOntarioCanada
- Keenan Research Centre for Biomedical ScienceSt Michael’s Hospital, University of TorontoTorontoOntarioCanada
- Department of PhysiologyUniversity of TorontoTorontoOntarioCanada
- Heart and Stroke Richard Lewar Centre for Research ExcellenceUniversity of TorontoTorontoOntarioCanada
| |
Collapse
|
2
|
Altenburg AF, Morley JL, Bauer J, Walz JS, Boyle LH. Reanalysis of Immunopeptidomics Datasets Provides Mechanistic Insight into TAPBPR-Mediated Peptide Editing on HLA-A, -B and -C Molecules. Wellcome Open Res 2024; 9:113. [PMID: 38800518 PMCID: PMC11126903 DOI: 10.12688/wellcomeopenres.20738.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2024] [Indexed: 05/29/2024] Open
Abstract
Background Major histocompatibility class I (MHC-I, human leukocyte antigen [HLA]-I in humans) molecules present small fragments of the proteome on the cell surface for immunosurveillance, which is pivotal to control infected and malignant cells. Immunogenic peptides are generated and selected in the MHC-I antigen processing and presentation pathway. In this pathway, two homologous molecules, tapasin and TAPBPR, optimise the MHC-I peptide repertoire that is ultimately presented at the plasma membrane. Peptide exchange on HLA-I by human TAPBPR involves the flexible loop region K22-D35, with the leucine at position 30 (L30) involved in mediating peptide dissociation. However, our understanding of the exact molecular mechanisms governing TAPBPR-mediated peptide exchange on HLA-I allotypes remains incomplete. Methods Here, in-depth re-analyses of published immunopeptidomics datasets was used to further examine TAPBPR peptide editing activity and mechanism of action on HLA-I. The role of the TAPBPR editing loop in opening the HLA-I peptide binding groove was assessed using a molecular dynamics simulation. Results We show that TAPBPR shapes the peptide repertoire on HLA-A, -B and -C allotypes. The TAPBPR editing loop was not essential to allow HLA-I to adopt an open state. L30 in the TAPBPR editing loop was typically sufficient to mediate peptide repertoire restriction on the three HLA-I allotypes expressed by HeLa cells. TAPBPR was also able to load peptides onto HLA-I in a loop-dependent manner. Conclusions These results unify the previously hypothesised scoop loop and peptide trap mechanisms of TAPBPR-mediated peptide exchange, with the former involved in peptide filtering and the latter in peptide loading.
Collapse
Affiliation(s)
- Arwen F Altenburg
- Department of Pathology, University of Cambridge, Cambridge, England, CB2 1QP, UK
| | - Jack L Morley
- Department of Pathology, University of Cambridge, Cambridge, England, CB2 1QP, UK
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, England, CB2 1QP, UK
| |
Collapse
|
3
|
Papadaki GF, Woodward CH, Young MC, Winters TJ, Burslem GM, Sgourakis NG. A Chicken Tapasin ortholog can chaperone empty HLA-B∗37:01 molecules independent of other peptide-loading components. J Biol Chem 2023; 299:105136. [PMID: 37543367 PMCID: PMC10534222 DOI: 10.1016/j.jbc.2023.105136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023] Open
Abstract
Human Tapasin (hTapasin) is the main chaperone of MHC-I molecules, enabling peptide loading and antigen repertoire optimization across HLA allotypes. However, it is restricted to the endoplasmic reticulum (ER) lumen as part of the protein loading complex (PLC), and therefore is highly unstable when expressed in recombinant form. Additional stabilizing co-factors such as ERp57 are required to catalyze peptide exchange in vitro, limiting uses for the generation of pMHC-I molecules of desired antigen specificities. Here, we show that the chicken Tapasin (chTapasin) ortholog can be expressed recombinantly at high yields in a stable form, independent of co-chaperones. chTapasin can bind the human HLA-B∗37:01 with low micromolar-range affinity to form a stable tertiary complex. Biophysical characterization by methyl-based NMR methods reveals that chTapasin recognizes a conserved β2m epitope on HLA-B∗37:01, consistent with previously solved X-ray structures of hTapasin. Finally, we provide evidence that the B∗37:01/chTapasin complex is peptide-receptive and can be dissociated upon binding of high-affinity peptides. Our results highlight the use of chTapasin as a stable scaffold for protein engineering applications aiming to expand the ligand exchange function on human MHC-I and MHC-like molecules.
Collapse
Affiliation(s)
- Georgia F Papadaki
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Claire H Woodward
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael C Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Trenton J Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
4
|
Papadaki GF, Woodward CH, Young MC, Winters TJ, Burslem GM, Sgourakis NG. A Chicken Tapasin ortholog can chaperone empty HLA molecules independently of other peptide-loading components. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546255. [PMID: 37425753 PMCID: PMC10326978 DOI: 10.1101/2023.06.23.546255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Human Tapasin (hTapasin) is the main chaperone of MHC-I molecules, enabling peptide loading and antigen repertoire optimization across HLA allotypes. However, it is restricted to the endoplasmic reticulum (ER) lumen as part of the protein loading complex (PLC) and therefore is highly unstable when expressed in recombinant form. Additional stabilizing co-factors such as ERp57 are required to catalyze peptide exchange in vitro , limiting uses for the generation of pMHC-I molecules of desired antigen specificities. Here, we show that the chicken Tapasin (chTapasin) ortholog can be expressed recombinantly at high yields in stable form, independently of co-chaperones. chTapasin can bind the human HLA-B * 37:01 with low micromolar-range affinity to form a stable tertiary complex. Biophysical characterization by methyl-based NMR methods reveals that chTapasin recognizes a conserved β 2 m epitope on HLA-B * 37:01, consistent with previously solved X-ray structures of hTapasin. Finally, we provide evidence that the B * 37:01/chTapasin complex is peptide-receptive and can be dissociated upon binding of high-affinity peptides. Our results highlight the use of chTapasin as a stable scaffold for future protein engineering applications aiming to expand the ligand exchange function on human MHC-I and MHC-like molecules.
Collapse
|
5
|
Sun Y, Young MC, Woodward CH, Danon JN, Truong HV, Gupta S, Winters TJ, Font-Burgada J, Burslem GM, Sgourakis NG. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. Proc Natl Acad Sci U S A 2023; 120:e2304055120. [PMID: 37310998 PMCID: PMC10288639 DOI: 10.1073/pnas.2304055120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
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 (β2 microglobulin, β2m) subunits for binding to the MHC-I heavy chain (HC) through an engineered disulfide bond bridging conserved epitopes across the HC/β2m interface, to generate conformationally stable, peptide-receptive molecules named "open MHC-I." 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 moderate-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 β2m-interacting sites of the peptide-binding groove to long-range effects on the α2-1 helix and α3 domain. The interchain disulfide bond stabilizes MHC-I molecules in an open conformation to promote peptide exchange across multiple human leukocyte antigen (HLA) allotypes, covering representatives from five HLA-A supertypes, six HLA-B supertypes, and oligomorphic HLA-Ib molecules. Our structure-guided design, combined with conditional β-peptide ligands, provides a universal platform to generate ready-to-load MHC-I systems of enhanced stability, enabling a range of approaches to screen antigenic epitope libraries and probe polyclonal TCR repertoires covering highly polymorphic HLA-I allotypes, as well as oligomorphic nonclassical molecules.
Collapse
Affiliation(s)
- Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Michael C. Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Claire H. Woodward
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Julia N. Danon
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Hau V. Truong
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Sagar Gupta
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Trenton J. Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Joan Font-Burgada
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA19111
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| |
Collapse
|
6
|
Margulies DH, Jiang J, Ahmad J, Boyd LF, Natarajan K. Chaperone function in antigen presentation by MHC class I molecules-tapasin in the PLC and TAPBPR beyond. Front Immunol 2023; 14:1179846. [PMID: 37398669 PMCID: PMC10308438 DOI: 10.3389/fimmu.2023.1179846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Peptide loading of MHC-I molecules plays a critical role in the T cell response to infections and tumors as well as to interactions with inhibitory receptors on natural killer (NK) cells. To facilitate and optimize peptide acquisition, vertebrates have evolved specialized chaperones to stabilize MHC-I molecules during their biosynthesis and to catalyze peptide exchange favoring high affinity or optimal peptides to permit transport to the cell surface where stable peptide/MHC-I (pMHC-I) complexes are displayed and are available for interaction with T cell receptors and any of a host of inhibitory and activating receptors. Although components of the endoplasmic reticulum (ER) resident peptide loading complex (PLC) were identified some 30 years ago, the detailed biophysical parameters that govern peptide selection, binding, and surface display have recently been understood better with advances in structural methods including X-ray crystallography, cryogenic electron microscopy (cryo-EM), and computational modeling. These approaches have provided refined mechanistic illustration of the molecular events involved in the folding of the MHC-I heavy chain, its coordinate glycosylation, assembly with its light chain, β2-microglobulin (β2m), its association with the PLC, and its binding of peptides. Our current view of this important cellular process as it relates to antigen presentation to CD8+ T cells is based on many different approaches: biochemical, genetic, structural, computational, cell biological, and immunological. In this review, taking advantage of recent X-ray and cryo-EM structural evidence and molecular dynamics simulations, examined in the context of past experiments, we attempt a dispassionate evaluation of the details of peptide loading in the MHC-I pathway. By critical evaluation of several decades of investigation, we outline aspects of the peptide loading process that are well-understood and indicate those that demand further detailed investigation. Further studies should contribute not only to basic understanding, but also to applications for immunization and therapy of tumors and infections.
Collapse
|
7
|
Satti R, Morley JL, Boyle LH. Get into the groove! The influence of TAPBPR on cargo selection. Curr Opin Immunol 2023; 83:102346. [PMID: 37295041 DOI: 10.1016/j.coi.2023.102346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/12/2023]
Abstract
Since the discovery of Transporter associated with antigen processing-binding protein-related (TAPBPR) over two decades ago, extensive studies have explored its function in the context of the major histocompatibility complex class-I (MHC-I) antigen processing and presentation pathway. As a chaperone and peptide editor, TAPBPR was recently revealed to have overlapping structural features when resolved with peptide-receptive MHC-I molecules compared with the two newly solved tapasin:MHC-I structures. Despite this, the two chaperones seem to have a unique criteria for loading high-affinity peptides on MHC-I molecules. Yet, the mechanism of action of how TAPBPR creates its distinct filter in cargo selection for peptide-receptive MHC-I molecules continues to be a subject of debate.
Collapse
Affiliation(s)
- Reem Satti
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP , UK
| | - Jack L Morley
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP , UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP , UK.
| |
Collapse
|
8
|
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: 11] [Impact Index Per Article: 11.0] [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
|
9
|
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: 1.0] [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
|
10
|
Sun Y, Papadaki GF, Devlin CA, Danon JN, Young MC, Winters TJ, Burslem GM, Procko E, Sgourakis NG. Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes. SCIENCE ADVANCES 2023; 9:eade7151. [PMID: 36827371 PMCID: PMC9956121 DOI: 10.1126/sciadv.ade7151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/19/2023] [Indexed: 06/01/2023]
Abstract
Immunological chaperones tapasin and TAP binding protein, related (TAPBPR) play key roles in antigenic peptide optimization and quality control of nascent class I major histocompatibility complex (MHC-I) molecules. The polymorphic nature of MHC-I proteins leads to a range of allelic dependencies on chaperones for assembly and cell-surface expression, limiting chaperone-mediated peptide exchange to a restricted set of human leukocyte antigen (HLA) allotypes. Here, we demonstrate and characterize xeno interactions between a chicken TAPBPR ortholog and a complementary repertoire of HLA allotypes, relative to its human counterpart. We find that TAPBPR orthologs recognize empty MHC-I with broader allele specificity and facilitate peptide exchange by maintaining a reservoir of receptive molecules. Deep mutational scanning of human TAPBPR further identifies gain-of-function mutants, resembling the chicken sequence, which can enhance HLA-A*01:01 expression in situ and promote peptide exchange in vitro. These results highlight that polymorphic sites on MHC-I and chaperone surfaces can be engineered to manipulate their interactions, enabling chaperone-mediated peptide exchange on disease-relevant HLA alleles.
Collapse
Affiliation(s)
- Yi Sun
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Georgia F. Papadaki
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Christine A. Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61820, USA
| | - Julia N. Danon
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Michael C. Young
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Trenton J. Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61820, USA
| | - Nikolaos G. Sgourakis
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| |
Collapse
|
11
|
McShan AC, Devlin CA, Papadaki GF, Sun Y, Green AI, Morozov GI, Burslem GM, Procko E, Sgourakis NG. TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules. Nat Chem Biol 2022; 18:859-868. [PMID: 35725941 PMCID: PMC9703140 DOI: 10.1038/s41589-022-01049-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/28/2022] [Indexed: 11/08/2022]
Abstract
Chaperones tapasin and transporter associated with antigen processing (TAP)-binding protein related (TAPBPR) associate with the major histocompatibility complex (MHC)-related protein 1 (MR1) to promote trafficking and cell surface expression. However, the binding mechanism and ligand dependency of MR1/chaperone interactions remain incompletely characterized. Here in vitro, biochemical and computational studies reveal that, unlike MHC-I, TAPBPR recognizes MR1 in a ligand-independent manner owing to the absence of major structural changes in the MR1 α2-1 helix between empty and ligand-loaded molecules. Structural characterization using paramagnetic nuclear magnetic resonance experiments combined with restrained molecular dynamics simulations reveals that TAPBPR engages conserved surfaces on MR1 to induce similar adaptations to those seen in MHC-I/TAPBPR co-crystal structures. Finally, nuclear magnetic resonance relaxation dispersion experiments using 19F-labeled diclofenac show that TAPBPR can affect the exchange kinetics of noncovalent metabolites with the MR1 groove, serving as a catalyst. Our results support a role of chaperones in stabilizing nascent MR1 molecules to enable loading of endogenous or exogenous cargo.
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
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine A Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Georgia F Papadaki
- 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
| | - Yi Sun
- 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
| | - Adam I Green
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 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
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 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
|
12
|
Meraviglia-Crivelli D, Zheleva A, Barainka M, Moreno B, Villanueva H, Pastor F. Therapeutic Strategies to Enhance Tumor Antigenicity: Making the Tumor Detectable by the Immune System. Biomedicines 2022; 10:biomedicines10081842. [PMID: 36009389 PMCID: PMC9405394 DOI: 10.3390/biomedicines10081842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/12/2022] [Accepted: 07/27/2022] [Indexed: 12/22/2022] Open
Abstract
Cancer immunotherapy has revolutionized the oncology field, but many patients still do not respond to current immunotherapy approaches. One of the main challenges in broadening the range of responses to this type of treatment is the limited source of tumor neoantigens. T cells constitute a main line of defense against cancer, and the decisive step to trigger their activation is mediated by antigen recognition. Antigens allow the immune system to differentiate between self and foreign, which constitutes a critical step in recognition of cancer cells and the consequent development or control of the malignancy. One of the keystones to achieving a successful antitumor response is the presence of potent tumor antigens, known as neoantigens. However, tumors develop strategies to evade the immune system and resist current immunotherapies, and many tumors present a low tumor mutation burden limiting the presence of tumor antigenicity. Therefore, new approaches must be taken into consideration to overcome these shortcomings. The possibility of making tumors more antigenic represents a promising front to further improve the success of immunotherapy in cancer. Throughout this review, we explored different state-of-the-art tools to induce the presentation of new tumor antigens by intervening at protein, mRNA or genomic levels in malignant cells.
Collapse
Affiliation(s)
- Daniel Meraviglia-Crivelli
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Angelina Zheleva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Martin Barainka
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Beatriz Moreno
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
| | - Helena Villanueva
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
| | - Fernando Pastor
- Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain; (D.M.-C.); (A.Z.); (M.B.); (B.M.); (H.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
- Correspondence:
| |
Collapse
|
13
|
D’Amico S, Tempora P, Melaiu O, Lucarini V, Cifaldi L, Locatelli F, Fruci D. Targeting the antigen processing and presentation pathway to overcome resistance to immune checkpoint therapy. Front Immunol 2022; 13:948297. [PMID: 35936007 PMCID: PMC9352877 DOI: 10.3389/fimmu.2022.948297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the significant clinical advances with the use of immune checkpoint inhibitors (ICIs) in a wide range of cancer patients, response rates to the therapy are variable and do not always result in long-term tumor regression. The development of ICI-resistant disease is one of the pressing issue in clinical oncology, and the identification of new targets and combination therapies is a crucial point to improve response rates and duration. Antigen processing and presentation (APP) pathway is a key element for an efficient response to ICI therapy. Indeed, malignancies that do not express tumor antigens are typically poor infiltrated by T cells and unresponsive to ICIs. Therefore, improving tumor immunogenicity potentially increases the success rate of ICI therapy. In this review, we provide an overview of the key elements of the APP machinery that can be exploited to enhance tumor immunogenicity and increase the efficacy of ICI-based immunotherapy.
Collapse
Affiliation(s)
- Silvia D’Amico
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Patrizia Tempora
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ombretta Melaiu
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Valeria Lucarini
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Loredana Cifaldi
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Rome, Italy
- Academic Department of Pediatrics (DPUO), Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology and of Cell and Gene Therapy, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Doriana Fruci,
| |
Collapse
|
14
|
Rosales TJ, Baker BM. Chaperoning the dance of antigen presentation. Nat Chem Biol 2022; 18:796-797. [PMID: 35725942 DOI: 10.1038/s41589-022-01069-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tatiana J Rosales
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
| |
Collapse
|
15
|
Xu H, Song K, Da LT. Dynamics of peptide loading into major histocompatibility complex class I molecules chaperoned by TAPBPR. Phys Chem Chem Phys 2022; 24:12397-12409. [PMID: 35575131 DOI: 10.1039/d2cp00423b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Major histocompatibility complex class I (MHC-I) molecules display antigenic peptides on the cell surface for T cell receptor scanning, thereby activating the immune response. Peptide loading into MHC-I molecules is thus a critical step during the antigen presentation process. Chaperone TAP-binding protein related (TAPBPR) plays a critical role in promoting high-affinity peptide loading into MHC-I, by discriminating against the low-affinity ones. However, the complete peptide loading dynamics into TAPBPR-bound MHC-I is still elusive. Here, we constructed kinetic network models based on hundreds of short-time MD simulations with an aggregated simulation time of ∼21.7 μs, and revealed, at atomic level, four key intermediate states of one antigenic peptide derived from melanoma-associated MART-1/Melan-A protein during its loading process into TAPBPR-bound MHC-I. We find that the TAPBPR binding at the MHC-I pocket-F can substantially reshape the distant pocket-B via allosteric regulations, which in turn promotes the following peptide N-terminal loading. Intriguingly, the partially loaded peptide could profoundly weaken the TAPBPR-MHC stability, promoting the dissociation of the TAPBPR scoop-loop (SL) region from the pocket-F to a more solvent-exposed conformation. Structural inspections further indicate that the peptide loading could remotely affect the SL binding site through both allosteric perturbations and direct contacts. In addition, another structural motif of TAPBPR, the jack hairpin region, was also found to participate in mediating the peptide editing. Our study sheds light on the detailed molecular mechanisms underlying the peptide loading process into TAPBPR-bound MHC-I and pinpoints the key structural factors responsible for dictating the peptide-loading dynamics.
Collapse
Affiliation(s)
- Honglin Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Kaiyuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| |
Collapse
|
16
|
Ilca FT, Boyle LH. The glycosylation status of MHC class I molecules impacts their interactions with TAPBPR. Mol Immunol 2021; 139:168-176. [PMID: 34543843 PMCID: PMC8524320 DOI: 10.1016/j.molimm.2021.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/16/2021] [Accepted: 09/11/2021] [Indexed: 11/20/2022]
Abstract
Glycosylation plays a crucial role in the folding, structure, quality control and trafficking of glycoproteins. Here, we explored whether the glycosylation status of MHC class I (MHC-I) molecules impacts their affinity for the peptide editor, TAPBPR. We demonstrate that the interaction between TAPBPR and MHC-I is stronger when MHC-I lacks a glycan. Subsequently, TAPBPR can dissociate peptides, even those of high affinity, more easily from non-glycosylated MHC-I compared to their glycosylated counterparts. In addition, TAPBPR is more resistant to peptide-mediated allosteric release from non-glycosylated MHC-I compared to species with a glycan attached. Consequently, we find the glycosylation status of HLA-A*68:02, -A*02:01 and -B*27:05 influences their ability to undergo TAPBPR-mediated peptide exchange. The discovery that the glycan attached to MHC-I significantly influences the affinity of their interactions with TAPBPR has important implications, on both an experimental level and in a biological context.
Collapse
Affiliation(s)
- F Tudor Ilca
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
| |
Collapse
|
17
|
Aflalo A, Boyle LH. Polymorphisms in MHC class I molecules influence their interactions with components of the antigen processing and presentation pathway. Int J Immunogenet 2021; 48:317-325. [PMID: 34176210 DOI: 10.1111/iji.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
MHC class I (MHC-I) molecules undergo an intricate folding process in order to pick up antigenic peptide to present to the immune system. In recent years, the discovery of a new peptide editor for MHC-I has added an extra level of complexity in our understanding of how peptide presentation is regulated. On top of this, the incredible diversity in MHC-I molecules leads to significant variation in the interaction between MHC-I and components of the antigen processing and presentation pathway. Here, we review our current understanding regarding how polymorphisms in human leukocyte antigen class I molecules influence their interactions with key components of the antigen processing and presentation pathway. A deeper understanding of this may offer new insights regarding how apparently subtle variation in MHC-I can have a significant impact on susceptibility to disease.
Collapse
Affiliation(s)
- Aure Aflalo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, UK
| |
Collapse
|
18
|
Hafstrand I, Aflalo A, Boyle LH. Why TAPBPR? Implications of an additional player in MHC class I peptide presentation. Curr Opin Immunol 2021; 70:90-94. [PMID: 34052734 DOI: 10.1016/j.coi.2021.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The peptide editor TAPBPR is the newest member of the major histocompatibility complex class I (MHC-I) antigen processing and presentation pathway. Since 2013, studies have explored the functions and mechanisms of action of this tapasin homolog. Here, we review the key insights gained from structural studies of the TAPBPR:MHC-I complex and the involvement of the TAPBPR loop in peptide exchange. However, despite recent advances, the question still remains: why do we need TAPBPR? The recent appreciation that different MHC-I allotypes vary in their ability to interact with TAPBPR, together with a role for TAPBPR in alternative presentation pathways highlights that much remains unknown concerning the biological need for TAPBPR.
Collapse
Affiliation(s)
- Ida Hafstrand
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Aure Aflalo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom.
| |
Collapse
|
19
|
Thomas C, Tampé R. MHC I assembly and peptide editing - chaperones, clients, and molecular plasticity in immunity. Curr Opin Immunol 2021; 70:48-56. [PMID: 33689959 DOI: 10.1016/j.coi.2021.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/07/2021] [Indexed: 11/24/2022]
Abstract
Peptides presented on MHC I molecules allow the immune system to detect diseased cells. The displayed peptides typically stem from proteasomal degradation of cytoplasmic proteins and are translocated into the ER lumen where they are trimmed and loaded onto MHC I. Peptide translocation is carried out by the transporter associated with antigen processing, which forms the central building block of a dynamic assembly called the peptide-loading complex (PLC). By coordinating peptide transfer with MHC I loading and peptide optimization, the PLC is a linchpin in the adaptive immune system. Peptide loading and optimization is catalyzed by the PLC component tapasin and the PLC-independent TAPBPR, two MHC I-dedicated enzymes chaperoning empty or suboptimally loaded MHC I and selecting stable peptide-MHC I complexes in a process called peptide editing or proofreading. Recent structural and functional studies of peptide editing have dramatically improved our understanding of this pivotal event in antigen processing/presentation. This review is dedicated to Vincenzo Cerundolo (1959-2020) for his pioneering work in the field of antigen processing/presentation.
Collapse
Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
| |
Collapse
|
20
|
Mpakali A, Stratikos E. The Role of Antigen Processing and Presentation in Cancer and the Efficacy of Immune Checkpoint Inhibitor Immunotherapy. Cancers (Basel) 2021; 13:E134. [PMID: 33406696 PMCID: PMC7796214 DOI: 10.3390/cancers13010134] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
Recent clinical successes of cancer immunotherapy using immune checkpoint inhibitors (ICIs) are rapidly changing the landscape of cancer treatment. Regardless of initial impressive clinical results though, the therapeutic benefit of ICIs appears to be limited to a subset of patients and tumor types. Recent analyses have revealed that the potency of ICI therapies depends on the efficient presentation of tumor-specific antigens by cancer cells and professional antigen presenting cells. Here, we review current knowledge on the role of antigen presentation in cancer. We focus on intracellular antigen processing and presentation by Major Histocompatibility class I (MHCI) molecules and how it can affect cancer immune evasion. Finally, we discuss the pharmacological tractability of manipulating intracellular antigen processing as a complementary approach to enhance tumor immunogenicity and the effectiveness of ICI immunotherapy.
Collapse
Affiliation(s)
- Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15784 Athens, Greece
| |
Collapse
|
21
|
Qi T, Qu J, Tu C, Lu Q, Li G, Wang J, Qu Q. Super-Enhancer Associated Five-Gene Risk Score Model Predicts Overall Survival in Multiple Myeloma Patients. Front Cell Dev Biol 2020; 8:596777. [PMID: 33344452 PMCID: PMC7744621 DOI: 10.3389/fcell.2020.596777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Multiple myeloma (MM) is a malignant plasma cell tumor with high heterogeneity, characterized by anemia, hypercalcemia, renal failure, and lytic bone lesions. Although various powerful prognostic factors and models have been exploited, the development of more accurate prognosis and treatment for MM patients is still facing many challenges. Given the essential roles of super-enhancer (SE) associated genes in the tumorigenesis of MM, we tried to initially screen and identify the significant prognostic factors from SE associated genes in MM by the least absolute shrinkage and selection operator (Lasso) penalized Cox regression, univariate and multivariate Cox regression analysis using GSE24080 and GSE9782 datasets. Risk score model of five genes including CSGALNACT1, FAM53B, TAPBPL, REPIN1, and DDX11, was further constructed and the Kaplan-Meier (K-M) curves showed that the low-risk group seems to have better clinical outcome of survival compared to the high-risk group. Time-dependent receiver operating characteristic (ROC) curves presented the favorable performance of the model. An interactive nomogram consisting of the five-gene risk group and eleven clinical traits was established and identified by calibration curves. Therefore, the risk score model of SE associated five genes developed here could be used to predict the prognosis of MM patients, which may assist the clinical treatment of MM patients in the future.
Collapse
Affiliation(s)
- Tingting Qi
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiong Lu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Guohua Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Jiaojiao Wang
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacy, Central South University, Changsha, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
22
|
Linker SB, Randolph-Moore L, Kottilil K, Qiu F, Jaeger BN, Barron J, Gage FH. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. Genome Res 2020; 30:1643-1654. [PMID: 33122305 PMCID: PMC7605253 DOI: 10.1101/gr.262196.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
Abstract
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5′ gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type–specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.
Collapse
Affiliation(s)
- Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lynne Randolph-Moore
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kalyani Kottilil
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Fan Qiu
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculty of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Jerika Barron
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California 94143, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| |
Collapse
|
23
|
Zaitoua AJ, Kaur A, Raghavan M. Variations in MHC class I antigen presentation and immunopeptidome selection pathways. F1000Res 2020; 9. [PMID: 33014341 PMCID: PMC7525337 DOI: 10.12688/f1000research.26935.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Major histocompatibility class I (MHC-I) proteins mediate immunosurveillance against pathogens and cancers by presenting antigenic or mutated peptides to antigen receptors of CD8+ T cells and by engaging receptors of natural killer (NK) cells. In humans, MHC-I molecules are highly polymorphic. MHC-I variations permit the display of thousands of distinct peptides at the cell surface. Recent mass spectrometric studies have revealed unique and shared characteristics of the peptidomes of individual MHC-I variants. The cell surface expression of MHC-I–peptide complexes requires the functions of many intracellular assembly factors, including the transporter associated with antigen presentation (TAP), tapasin, calreticulin, ERp57, TAP-binding protein related (TAPBPR), endoplasmic reticulum aminopeptidases (ERAPs), and the proteasomes. Recent studies provide important insights into the structural features of these factors that govern MHC-I assembly as well as the mechanisms underlying peptide exchange. Conformational sensing of MHC-I molecules mediates the quality control of intracellular MHC-I assembly and contributes to immune recognition by CD8 at the cell surface. Recent studies also show that several MHC-I variants can follow unconventional assembly routes to the cell surface, conferring selective immune advantages that can be exploited for immunotherapy.
Collapse
Affiliation(s)
- Anita J Zaitoua
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amanpreet Kaur
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
24
|
Ilca FT, Drexhage LZ, Brewin G, Peacock S, Boyle LH. Distinct Polymorphisms in HLA Class I Molecules Govern Their Susceptibility to Peptide Editing by TAPBPR. Cell Rep 2020; 29:1621-1632.e3. [PMID: 31693900 PMCID: PMC7057265 DOI: 10.1016/j.celrep.2019.09.074] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/28/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Understanding how peptide selection is controlled on different major histocompatibility complex class I (MHC I) molecules is pivotal for determining how variations in these proteins influence our predisposition to infectious diseases, cancer, and autoinflammatory conditions. Although the intracellular chaperone TAPBPR edits MHC I peptides, it is unclear which allotypes are subjected to TAPBPR-mediated peptide editing. Here, we examine the ability of 97 different human leukocyte antigen (HLA) class I allotypes to interact with TAPBPR. We reveal a striking preference of TAPBPR for HLA-A, particularly for supertypes A2 and A24, over HLA-B and -C molecules. We demonstrate that the increased propensity of these HLA-A molecules to undergo TAPBPR-mediated peptide editing is determined by molecular features of the HLA-A F pocket, specifically residues H114 and Y116. This work reveals that specific polymorphisms in MHC I strongly influence their susceptibility to chaperone-mediated peptide editing, which may play a significant role in disease predisposition.
Collapse
Affiliation(s)
- F Tudor Ilca
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Linnea Z Drexhage
- Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
| | - Gemma Brewin
- Tissue Typing Laboratory, Box 209, Level 6 ATC, Cambridge University Hospitals, NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Box 209, Level 6 ATC, Cambridge University Hospitals, NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.
| |
Collapse
|
25
|
Ilca T, Boyle LH. The Ins and Outs of TAPBPR. Curr Opin Immunol 2020; 64:146-151. [PMID: 32814254 DOI: 10.1016/j.coi.2020.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/25/2020] [Indexed: 11/26/2022]
Abstract
Peptide presentation on MHC class I molecules (MHC-I) is central to mounting effective antiviral and antitumoral immune responses. The tapasin-related protein TAPBPR is an MHC-I peptide editor which shapes the final peptide repertoire displayed on the cell surface. Here, we review recent findings which further elucidate the mechanisms by which TAPBPR performs peptide editing on a molecular level, and how glycosylation on MHC-I influences the interaction with TAPBPR and the peptide loading complex. We also explore how the function of TAPBPR can be utilized to promote exogenous peptide loading directly onto plasma-membrane expressed MHC-I. This has led to the development of new assays to investigate TAPBPR-mediated peptide editing and uncovered translational opportunities of utilizing TAPBPR to treat human disease.
Collapse
Affiliation(s)
- Tudor Ilca
- Department of Pathology, University of Cambridge, UK
| | | |
Collapse
|
26
|
Jing L, Ott M, Church CD, Kulikauskas RM, Ibrani D, Iyer JG, Afanasiev OK, Colunga A, Cook MM, Xie H, Greninger AL, Paulson KG, Chapuis AG, Bhatia S, Nghiem P, Koelle DM. Prevalent and Diverse Intratumoral Oncoprotein-Specific CD8 + T Cells within Polyomavirus-Driven Merkel Cell Carcinomas. Cancer Immunol Res 2020; 8:648-659. [PMID: 32179557 DOI: 10.1158/2326-6066.cir-19-0647] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/16/2019] [Accepted: 03/09/2020] [Indexed: 12/16/2022]
Abstract
Merkel cell carcinoma (MCC) is often caused by persistent expression of Merkel cell polyomavirus (MCPyV) T-antigen (T-Ag). These non-self proteins comprise about 400 amino acids (AA). Clinical responses to immune checkpoint inhibitors, seen in about half of patients, may relate to T-Ag-specific T cells. Strategies to increase CD8+ T-cell number, breadth, or function could augment checkpoint inhibition, but vaccines to augment immunity must avoid delivery of oncogenic T-antigen domains. We probed MCC tumor-infiltrating lymphocytes (TIL) with an artificial antigen-presenting cell (aAPC) system and confirmed T-Ag recognition with synthetic peptides, HLA-peptide tetramers, and dendritic cells (DC). TILs from 9 of 12 (75%) subjects contained CD8+ T cells recognizing 1-8 MCPyV epitopes per person. Analysis of 16 MCPyV CD8+ TIL epitopes and prior TIL data indicated that 97% of patients with MCPyV+ MCC had HLA alleles with the genetic potential that restrict CD8+ T-cell responses to MCPyV T-Ag. The LT AA 70-110 region was epitope rich, whereas the oncogenic domains of T-Ag were not commonly recognized. Specific recognition of T-Ag-expressing DCs was documented. Recovery of MCPyV oncoprotein-specific CD8+ TILs from most tumors indicated that antigen indifference was unlikely to be a major cause of checkpoint inhibition failure. The myriad of epitopes restricted by diverse HLA alleles indicates that vaccination can be a rational component of immunotherapy if tumor immune suppression can be overcome, and the oncogenic regions of T-Ag can be modified without impacting immunogenicity.
Collapse
Affiliation(s)
- Lichen Jing
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
| | - Mariliis Ott
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
| | - Candice D Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Rima M Kulikauskas
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Dafina Ibrani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Jayasri G Iyer
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Olga K Afanasiev
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Aric Colunga
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Maclean M Cook
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Kelly G Paulson
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, Washington.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Aude G Chapuis
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, Washington.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Shailender Bhatia
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, Washington.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David M Koelle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington. .,Department of Laboratory Medicine, University of Washington, Seattle, Washington.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington.,Benaroya Research Institute, Seattle, Washington
| |
Collapse
|
27
|
Briquez PS, Hauert S, de Titta A, Gray LT, Alpar AT, Swartz MA, Hubbell JA. Engineering Targeting Materials for Therapeutic Cancer Vaccines. Front Bioeng Biotechnol 2020; 8:19. [PMID: 32117911 PMCID: PMC7026271 DOI: 10.3389/fbioe.2020.00019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/10/2020] [Indexed: 12/24/2022] Open
Abstract
Therapeutic cancer vaccines constitute a valuable tool to educate the immune system to fight tumors and prevent cancer relapse. Nevertheless, the number of cancer vaccines in the clinic remains very limited to date, highlighting the need for further technology development. Recently, cancer vaccines have been improved by the use of materials, which can strongly enhance their intrinsic properties and biodistribution profile. Moreover, vaccine efficacy and safety can be substantially modulated through selection of the site at which they are delivered, which fosters the engineering of materials capable of targeting cancer vaccines to specific relevant sites, such as within the tumor or within lymphoid organs, to further optimize their immunotherapeutic effects. In this review, we aim to give the reader an overview of principles and current strategies to engineer therapeutic cancer vaccines, with a particular focus on the use of site-specific targeting materials. We will first recall the goal of therapeutic cancer vaccination and the type of immune responses sought upon vaccination, before detailing key components of cancer vaccines. We will then present how materials can be engineered to enhance the vaccine's pharmacokinetic and pharmacodynamic properties. Finally, we will discuss the rationale for site-specific targeting of cancer vaccines and provide examples of current targeting technologies.
Collapse
Affiliation(s)
- Priscilla S. Briquez
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | - Sylvie Hauert
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | | | - Laura T. Gray
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | - Aaron T. Alpar
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
| | - Melody A. Swartz
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, United States
- Committee on Immunology, The University of Chicago, Chicago, IL, United States
| | - Jeffrey A. Hubbell
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, United States
- Committee on Immunology, The University of Chicago, Chicago, IL, United States
| |
Collapse
|
28
|
O’Rourke SM, Morozov GI, Roberts JT, Barb AW, Sgourakis NG. Production of soluble pMHC-I molecules in mammalian cells using the molecular chaperone TAPBPR. Protein Eng Des Sel 2019; 32:525-532. [PMID: 32725167 PMCID: PMC7451022 DOI: 10.1093/protein/gzaa015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Current approaches for generating major histocompatibility complex (MHC) Class-I proteins with desired bound peptides (pMHC-I) for research, diagnostic and therapeutic applications are limited by the inherent instability of empty MHC-I molecules. Using the properties of the chaperone TAP-binding protein related (TAPBPR), we have developed a robust method to produce soluble, peptide-receptive MHC-I molecules in Chinese Hamster Ovary cells at high yield, completely bypassing the requirement for laborious refolding from inclusion bodies expressed in E.coli. Purified MHC-I/TAPBPR complexes can be prepared for multiple human allotypes, and exhibit complex glycan modifications at the conserved Asn 86 residue. As a proof of concept, we demonstrate both HLA allele-specific peptide binding and MHC-restricted antigen recognition by T cells for two relevant tumor-associated antigens. Our system provides a facile, high-throughput approach for generating pMHC-I antigens to probe and expand TCR specificities present in polyclonal T cell repertoires.
Collapse
Affiliation(s)
- Sara M O’Rourke
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Giora I Morozov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jacob T Roberts
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Adam W Barb
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center University of Georgia, Athens, GA 30602, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| |
Collapse
|
29
|
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: 3.8] [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]
|
30
|
Ilca FT, Neerincx A, Hermann C, Marcu A, Stevanović S, Deane JE, Boyle LH. TAPBPR mediates peptide dissociation from MHC class I using a leucine lever. eLife 2018; 7:40126. [PMID: 30484775 PMCID: PMC6307860 DOI: 10.7554/elife.40126] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022] Open
Abstract
Tapasin and TAPBPR are known to perform peptide editing on major histocompatibility complex class I (MHC I) molecules; however, the precise molecular mechanism(s) involved in this process remain largely enigmatic. Here, using immunopeptidomics in combination with novel cell-based assays that assess TAPBPR-mediated peptide exchange, we reveal a critical role for the K22-D35 loop of TAPBPR in mediating peptide exchange on MHC I. We identify a specific leucine within this loop that enables TAPBPR to facilitate peptide dissociation from MHC I. Moreover, we delineate the molecular features of the MHC I F pocket required for TAPBPR to promote peptide dissociation in a loop-dependent manner. These data reveal that chaperone-mediated peptide editing on MHC I can occur by different mechanisms dependent on the C-terminal residue that the MHC I accommodates in its F pocket and provide novel insights that may inform the therapeutic potential of TAPBPR manipulation to increase tumour immunogenicity.
Collapse
Affiliation(s)
- F Tudor Ilca
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Neerincx
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Clemens Hermann
- Department of Integrative Biomedical Sciences, Division of Chemical and Systems Biology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium, Tübingen, Germany
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|