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Voogd L, Ruibal P, Ottenhoff TH, Joosten SA. Antigen presentation by MHC-E: a putative target for vaccination? Trends Immunol 2022; 43:355-365. [PMID: 35370095 PMCID: PMC9058203 DOI: 10.1016/j.it.2022.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 12/30/2022]
Abstract
The essentially monomorphic human antigen presentation molecule HLA-E is an interesting candidate target to enable vaccination irrespective of genetic diversity. Predictive HLA-E peptide-binding motifs have been refined to facilitate HLA-E peptide discovery. HLA-E can accommodate structurally divergent peptides of both self and microbial origin. Intracellular processing and presentation pathways for peptides by HLA-E for T cell receptor (TCR) recognition remain to be elucidated. Recent studies show that, unlike canonical peptides, inhibition of the transporter associated with antigen presentation (TAP) is essential to allow HLA-E antigen presentation in cytomegalovirus (CMV) infection and possibly also of other non-canonical peptides. We propose three alternative and TAP-independent MHC-E antigen-presentation pathways, including for Mycobacterium tuberculosis infections. These insights may help in designing potential HLA-E targeting vaccines against tumors and pathogens.
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2
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Abdulhaqq S, Ventura AB, Reed JS, Bashirova AA, Bateman KB, McDonald E, Wu HL, Greene JM, Schell JB, Morrow D, Wisskirchen K, Martin JN, Deeks SG, Carrington M, Protzer U, Früh K, Hansen SG, Picker LJ, Sacha JB, Bimber BN. Identification and Characterization of Antigen-Specific CD8 + T Cells Using Surface-Trapped TNF-α and Single-Cell Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2913-2921. [PMID: 34810222 PMCID: PMC9124229 DOI: 10.4049/jimmunol.2100535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 12/31/2022]
Abstract
CD8+ T cells are key mediators of antiviral and antitumor immunity. The isolation and study of Ag-specific CD8+ T cells, as well as mapping of their MHC restriction, has practical importance to the study of disease and the development of therapeutics. Unfortunately, most experimental approaches are cumbersome, owing to the highly variable and donor-specific nature of MHC-bound peptide/TCR interactions. Here we present a novel system for rapid identification and characterization of Ag-specific CD8+ T cells, particularly well suited for samples with limited primary cells. Cells are stimulated ex vivo with Ag of interest, followed by live cell sorting based on surface-trapped TNF-α. We take advantage of major advances in single-cell sequencing to generate full-length sequence data from the paired TCR α- and β-chains from these Ag-specific cells. The paired TCR chains are cloned into retroviral vectors and used to transduce donor CD8+ T cells. These TCR transductants provide a virtually unlimited experimental reagent, which can be used for further characterization, such as minimal epitope mapping or identification of MHC restriction, without depleting primary cells. We validated this system using CMV-specific CD8+ T cells from rhesus macaques, characterizing an immunodominant Mamu-A1*002:01-restricted epitope. We further demonstrated the utility of this system by mapping a novel HLA-A*68:02-restricted HIV Gag epitope from an HIV-infected donor. Collectively, these data validate a new strategy to rapidly identify novel Ags and characterize Ag-specific CD8+ T cells, with applications ranging from the study of infectious disease to immunotherapeutics and precision medicine.
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Affiliation(s)
- Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Katherine B Bateman
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Eric McDonald
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - John B Schell
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - David Morrow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Karin Wisskirchen
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum Munich, Munich, Germany
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Steven G Deeks
- HIV/AIDS Program, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA; and
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum Munich, Munich, Germany
| | - Klaus Früh
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR;
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
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Bansal A, Gehre MN, Qin K, Sterrett S, Ali A, Dang Y, Abraham S, Costanzo MC, Venegas LA, Tang J, Manjunath N, Brockman MA, Yang OO, Kan-Mitchell J, Goepfert PA. HLA-E-restricted HIV-1-specific CD8+ T cell responses in natural infection. J Clin Invest 2021; 131:148979. [PMID: 34228645 PMCID: PMC8363272 DOI: 10.1172/jci148979] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/01/2021] [Indexed: 01/07/2023] Open
Abstract
CD8+ T cell responses restricted by MHC-E, a nonclassical MHC molecule, have been associated with protection in an SIV/rhesus macaque model. The biological relevance of HLA-E-restricted CD8+ T cell responses in HIV infection, however, remains unknown. In this study, CD8+ T cells responding to HIV-1 Gag peptides presented by HLA-E were analyzed. Using in vitro assays, we observed HLA-E-restricted T cell responses to what we believe to be a newly identified subdominant Gag-KL9 as well as a well-described immunodominant Gag-KF11 epitope in T cell lines derived from chronically HIV-infected patients and also primed from healthy donors. Blocking of the HLA-E/KF11 binding by the B7 signal peptide resulted in decreased CD8+ T cell responses. KF11 presented via HLA-E in HIV-infected cells was recognized by antigen-specific CD8+ T cells. Importantly, bulk CD8+ T cells obtained from HIV-infected individuals recognized infected cells via HLA-E presentation. Ex vivo analyses at the epitope level showed a higher responder frequency of HLA-E-restricted responses to KF11 compared with KL9. Taken together, our findings of HLA-E-restricted HIV-specific immune responses offer intriguing and possibly paradigm-shifting insights into factors that contribute to the immunodominance of CD8+ T cell responses in HIV infection.
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Affiliation(s)
- Anju Bansal
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Mika N. Gehre
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Kai Qin
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Sarah Sterrett
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Ayub Ali
- Department of Medicine and AIDS Institute, UCLA, Los Angeles, California, USA
| | - Ying Dang
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Sojan Abraham
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | - Margaret C. Costanzo
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Leon A. Venegas
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - N. Manjunath
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, Paul L. Foster School of Medicine, El Paso, Texas, USA
| | | | - Otto O. Yang
- Department of Medicine and AIDS Institute, UCLA, Los Angeles, California, USA
| | - June Kan-Mitchell
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Paul A. Goepfert
- Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
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4
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Verweij MC, Hansen SG, Iyer R, John N, Malouli D, Morrow D, Scholz I, Womack J, Abdulhaqq S, Gilbride RM, Hughes CM, Ventura AB, Ford JC, Selseth AN, Oswald K, Shoemaker R, Berkemeier B, Bosche WJ, Hull M, Shao J, Sacha JB, Axthelm MK, Edlefsen PT, Lifson JD, Picker LJ, Früh K. Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy. Science 2021; 372:eabe9233. [PMID: 33766941 PMCID: PMC8354429 DOI: 10.1126/science.abe9233] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/15/2021] [Indexed: 12/15/2022]
Abstract
Strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens elicit CD8+ T cells recognizing epitopes presented by major histocompatibility complex II (MHC-II) and MHC-E but not MHC-Ia. These immune responses mediate replication arrest of SIV in 50 to 60% of monkeys. We show that the peptide VMAPRTLLL (VL9) embedded within the RhCMV protein Rh67 promotes intracellular MHC-E transport and recognition of RhCMV-infected fibroblasts by MHC-E-restricted CD8+ T cells. Deletion or mutation of viral VL9 abrogated MHC-E-restricted CD8+ T cell priming, resulting in CD8+ T cell responses exclusively targeting MHC-II-restricted epitopes. These responses were comparable in magnitude and differentiation to responses elicited by 68-1 vectors but did not protect against SIV. Thus, Rh67-enabled direct priming of MHC-E-restricted T cells is crucial for RhCMV/SIV vaccine efficacy.
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Affiliation(s)
- Marieke C Verweij
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Ravi Iyer
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Nessy John
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - David Morrow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Isabel Scholz
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jennie Womack
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Julia C Ford
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Andrea N Selseth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Kelli Oswald
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Rebecca Shoemaker
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Brian Berkemeier
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | - William J Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Michael Hull
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Jason Shao
- Population Sciences and Computational Biology Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Paul T Edlefsen
- Population Sciences and Computational Biology Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
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Del Val M, Antón LC, Ramos M, Muñoz-Abad V, Campos-Sánchez E. Endogenous TAP-independent MHC-I antigen presentation: not just the ER lumen. Curr Opin Immunol 2020; 64:9-14. [PMID: 31935516 DOI: 10.1016/j.coi.2019.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/11/2019] [Indexed: 11/30/2022]
Abstract
Altered and infected cells are eliminated by CD8+ cytotoxic T lymphocytes. This requires production of antigenic peptides mostly in the cytosol, transport to the endoplasmic reticulum (ER) by the transporter associated with antigen processing (TAP), and cell surface presentation by major histocompatibility complex class I (MHC-I). Strikingly, antigen presentation occurs without TAP, although it is inefficient and associated to human pathology. TAP-independent peptides derive both from membrane and secreted proteins, as well as cytosolic ones. The efficiency of TAP-independent presentation may be impacted by the availability of receptive MHC-I, and in turn by the functional presence in the ER of the peptide-loading complex, itself anchored on TAP. Without TAP, surface expression of human leukocyte antigen (HLA)-B allotypes varies widely, with those presenting a broader peptide repertoire among the most TAP-independent. Much remains to be learned on the alternative cellular pathways for antigen presentation in the absence of TAP.
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Affiliation(s)
- Margarita Del Val
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
| | - Luis C Antón
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Manuel Ramos
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Víctor Muñoz-Abad
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Elena Campos-Sánchez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
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