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Middelburg J, Ghaffari S, Schoufour TAW, Sluijter M, Schaap G, Göynük B, Sala BM, Al-Tamimi L, Scheeren F, Franken KLMC, Akkermans JJLL, Cabukusta B, Joosten SA, Derksen I, Neefjes J, van der Burg SH, Achour A, Wijdeven RHM, Weidanz J, van Hall T. The MHC-E peptide ligands for checkpoint CD94/NKG2A are governed by inflammatory signals, whereas LILRB1/2 receptors are peptide indifferent. Cell Rep 2023; 42:113516. [PMID: 38048225 DOI: 10.1016/j.celrep.2023.113516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/23/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023] Open
Abstract
The immune checkpoint NKG2A/CD94 is a promising target for cancer immunotherapy, and its ligand major histocompatibility complex E (MHC-E) is frequently upregulated in cancer. NKG2A/CD94-mediated inhibition of lymphocytes depends on the presence of specific leader peptides in MHC-E, but when and where they are presented in situ is unknown. We apply a nanobody specific for the Qdm/Qa-1b complex, the NKG2A/CD94 ligand in mouse, and find that presentation of Qdm peptide depends on every member of the endoplasmic reticulum-resident peptide loading complex. With a turnover rate of 30 min, the Qdm peptide reflects antigen processing capacity in real time. Remarkably, Qdm/Qa-1b complexes require inflammatory signals for surface expression in situ, despite the broad presence of Qa-1b molecules in homeostasis. Furthermore, we identify LILRB1 as a functional inhibition receptor for MHC-E in steady state. These data provide a molecular understanding of NKG2A blockade in immunotherapy and assign MHC-E as a convergent ligand for multiple immune checkpoints.
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Affiliation(s)
- Jim Middelburg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Soroush Ghaffari
- Department of Biology, College of Science, The University of Texas at Arlington, Arlington, TX, USA
| | - Tom A W Schoufour
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Gaby Schaap
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Büsra Göynük
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Benedetta M Sala
- Science for Life Laboratory, Department of Medicine, Karolinska Institute & Division of Infectious Diseases, Karolinska University Hospital, 171 65 Solna, Sweden
| | - Lejla Al-Tamimi
- Science for Life Laboratory, Department of Medicine, Karolinska Institute & Division of Infectious Diseases, Karolinska University Hospital, 171 65 Solna, Sweden
| | - Ferenc Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kees L M C Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Jimmy J L L Akkermans
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Birol Cabukusta
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Ian Derksen
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute & Division of Infectious Diseases, Karolinska University Hospital, 171 65 Solna, Sweden
| | - Ruud H M Wijdeven
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Jon Weidanz
- Abexxa Biologics, Inc., Arlington, TX, USA; College of Nursing and Health Innovation, The University of Texas at Arlington, Arlington, TX, USA
| | - Thorbald van Hall
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands.
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Hogan MJ, Maheshwari N, Begg BE, Nicastri A, Hedgepeth EJ, Muramatsu H, Pardi N, Miller MA, Reilly SP, Brossay L, Lynch KW, Ternette N, Eisenlohr LC. Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response. Nat Immunol 2023; 24:1933-1946. [PMID: 37828378 DOI: 10.1038/s41590-023-01644-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of 'cryptic' viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.
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Affiliation(s)
- Michael J Hogan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Nikita Maheshwari
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Bridget E Begg
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emma J Hedgepeth
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A Miller
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA
- Century Therapeutics, Philadelphia, PA, USA
| | - Shanelle P Reilly
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Laurent Brossay
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Laurence C Eisenlohr
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Ruibal P, Franken KLMC, van Meijgaarden KE, Walters LC, McMichael AJ, Gillespie GM, Joosten SA, Ottenhoff THM. Discovery of HLA-E-Presented Epitopes: MHC-E/Peptide Binding and T-Cell Recognition. Methods Mol Biol 2022; 2574:15-30. [PMID: 36087196 PMCID: PMC10508831 DOI: 10.1007/978-1-0716-2712-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding the interactions involved during the immunological synapse between peptide, HLA-E molecules, and TCR is crucial to effectively target protective HLA-E-restricted T-cell responses in humans. Here we describe three techniques based on the generation of MHC-E/peptide complexes (MHC-E generically includes HLA-E-like molecules in human and nonhuman species, while HLA-E specifically refers to human molecules), which allow to investigate MHC-E/peptide binding at the molecular level through binding assays and by using peptide loaded HLA-E tetramers, to detect, isolate, and study peptide-specific HLA-E-restricted human T-cells.
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Affiliation(s)
- Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees L M C Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Lucy C Walters
- Nuffield Department of Medicine Research Building, Old Road Campus, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Old Road Campus, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Geraldine M Gillespie
- Nuffield Department of Medicine Research Building, Old Road Campus, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands.
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Ruibal P, Franken KLMC, van Meijgaarden KE, van Loon JJF, van der Steen D, Heemskerk MHM, Ottenhoff THM, Joosten SA. Peptide Binding to HLA-E Molecules in Humans, Nonhuman Primates, and Mice Reveals Unique Binding Peptides but Remarkably Conserved Anchor Residues. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:2861-2872. [PMID: 33020145 PMCID: PMC7653511 DOI: 10.4049/jimmunol.2000810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022]
Abstract
Ag presentation via the nonclassical MHC class Ib molecule HLA-E, with nearly complete identity between the two alleles expressed in humans, HLA-E*01:01 and HLA-E*01:03, can lead to the activation of unconventional T cells in humans. Despite this virtual genetic monomorphism, differences in peptide repertoires binding to the two allelic variants have been reported. To further dissect and compare peptide binding to HLA-E*01:01 and HLA-E*01:03, we used an UV-mediated peptide exchange binding assay and an HPLC-based competition binding assay. In addition, we investigated binding of these same peptides to Mamu-E, the nonhuman primate homologue of human HLA-E, and to the HLA-E-like molecule Qa-1b in mice. We next exploited the differences and homologies in the peptide binding pockets of these four molecules to identify allele specific as well as common features of peptide binding motifs across species. Our results reveal differences in peptide binding preferences and intensities for each human HLA-E variant compared with Mamu-E and Qa-1b Using extended peptide libraries, we identified and refined the peptide binding motifs for each of the four molecules and found that they share main anchor positions, evidenced by conserved amino acid preferences across the four HLA-E molecules studied. In addition, we also identified differences in peptide binding motifs, which could explain the observed variations in peptide binding preferences and affinities for each of the four HLA-E-like molecules. Our results could help with guiding the selection of candidate pathogen-derived peptides with the capacity to target HLA-E-restricted T cells that could be mobilized in vaccination and immunotherapeutic strategies.
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Affiliation(s)
- Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Kees L M C Franken
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Krista E van Meijgaarden
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Joeri J F van Loon
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Dirk van der Steen
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
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5
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Ying G, Wang J, Mallevaey T, Van Calenbergh S, Zajonc DM. Structural basis of NKT cell inhibition using the T-cell receptor-blocking anti-CD1d antibody 1B1. J Biol Chem 2019; 294:12947-12956. [PMID: 31296659 PMCID: PMC6721955 DOI: 10.1074/jbc.ra119.009403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
Natural killer T (NKT) cells are a subset of T lymphocytes that recognize glycolipid antigens presented by the CD1d molecule (CD1d). They rapidly respond to antigen challenge and can activate both innate and adaptive immune cells. To study the role of antigen presentation in NKT cell activation, previous studies have developed several anti-CD1d antibodies that block CD1d binding to T-cell receptors (TCRs). Antibodies that are specific to both CD1d and the presented antigen can only be used to study the function of only a limited number of antigens. In contrast, antibodies that bind CD1d and block TCR binding regardless of the presented antigen can be widely used to assess the role of TCR-mediated NKT cell activation in various disease models. Here, we report the crystal structure of the widely used anti-mouse CD1d antibody 1B1 bound to CD1d at a resolution of 2.45 Å and characterized its binding to CD1d-presented glycolipids. We observed that 1B1 uses a long hydrophobic H3 loop that is inserted deep into the binding groove of CD1d where it makes intimate nonpolar contacts with the lipid backbone of an incorporated spacer lipid. Using an NKT cell agonist that has a modified sphingosine moiety, we further demonstrate that 1B1 in its monovalent form cannot block TCR-mediated NKT cell activation, because 1B1 fails to bind with high affinity to mCD1d. Our results suggest potential limitations of using 1B1 to assess antigen recognition by NKT cells, especially when investigating antigens that do not follow the canonical two alkyl-chain rule.
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Affiliation(s)
- Ge Ying
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California 92037
| | - Jing Wang
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California 92037
| | - Thierry Mallevaey
- Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dirk M. Zajonc
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California 92037,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium, To whom correspondence should be addressed:
Cancer Immunology Discovery, Pfizer, San Diego, CA 92121. E-mail:
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6
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Evidence of functional Cd94 polymorphism in a free-living house mouse population. Immunogenetics 2018; 71:321-333. [PMID: 30535636 DOI: 10.1007/s00251-018-01100-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023]
Abstract
The CD94 receptor, expressed on natural killer (NK) and CD8+ T cells, is known as a relatively non-polymorphic receptor with orthologues in humans, other primates, cattle, and rodents. In the house mouse (Mus musculus), a single allele is highly conserved among laboratory strains, and reports of allelic variation in lab- or wild-living mice are lacking, except for deficiency in one lab strain (DBA/2J). The non-classical MHC-I molecule Qa-1b is the ligand for mouse CD94/NKG2A, presenting alternative non-americ fragment of leader peptides (Qa-1 determinant modifier (Qdm)) from classical MHC-I molecules. Here, we report a novel allele identified in free-living house mice captured in Norway, living among individuals carrying the canonical Cd94 allele. The novel Cd94LocA allele encodes 12 amino acid substitutions in the extracellular lectin-like domain. Flow cytometric analysis of primary NK cells and transfected cells indicates that the substitutions prevent binding of CD94 mAb and Qa-1b/Qdm tetramers. Our data further indicate correlation of Cd94 polymorphism with the two major subspecies of house mice in Europe. Together, these findings suggest that the Cd94LocA/NKG2A heterodimeric receptor is widely expressed among M. musculus subspecies musculus, with ligand-binding properties different from mice of subspecies domesticus, such as the C57BL/6 strain.
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