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Migueles SA, Nettere DM, Gavil NV, Wang LT, Toulmin SA, Kelly EP, Ward AJ, Lin S, Thompson SA, Peterson BA, Abdeen CS, Sclafani CR, Pryal PF, Leach BG, Ludwig AK, Rogan DC, Przygonska PA, Cattani A, Imamichi H, Sachs A, Cafri G, Huang NN, Patamawenu A, Liang CJ, Hallahan CW, Kambach DM, Han EX, Coupet T, Chen J, Moir SL, Chun TW, Coates EE, Ledgerwood J, Schmidt J, Taillandier-Coindard M, Michaux J, Pak H, Bassani-Sternberg M, Frahm N, McElrath MJ, Connors M. HIV vaccines induce CD8 + T cells with low antigen receptor sensitivity. Science 2023; 382:1270-1276. [PMID: 38096385 DOI: 10.1126/science.adg0514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Current HIV vaccines designed to stimulate CD8+ T cells have failed to induce immunologic control upon infection. The functions of vaccine-induced HIV-specific CD8+ T cells were investigated here in detail. Cytotoxic capacity was significantly lower than in HIV controllers and was not a consequence of low frequency or unaccumulated functional cytotoxic proteins. Low cytotoxic capacity was attributable to impaired degranulation in response to the low antigen levels present on HIV-infected targets. The vaccine-induced T cell receptor (TCR) repertoire was polyclonal and transduction of these TCRs conferred the same reduced functions. These results define a mechanism accounting for poor antiviral activity induced by these vaccines and suggest that an effective CD8+ T cell response may require a vaccination strategy that drives further TCR clonal selection.
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Affiliation(s)
- Stephen A Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Danielle M Nettere
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Noah V Gavil
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence T Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sushila A Toulmin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth P Kelly
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Addison J Ward
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Siying Lin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah A Thompson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bennett A Peterson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cassidy S Abdeen
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carina R Sclafani
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrick F Pryal
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin G Leach
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amanda K Ludwig
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Rogan
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paulina A Przygonska
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cattani
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hiromi Imamichi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Abraham Sachs
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gal Cafri
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ning-Na Huang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andy Patamawenu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - C Jason Liang
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Claire W Hallahan
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | - Susan L Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Coates
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Marie Taillandier-Coindard
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Nicole Frahm
- Vaccine and Infectious Disease Division and the HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division and the HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Ho JNHG, Schmidt D, Lowinus T, Ryoo J, Dopfer EP, Gonzalo Núñez N, Costa-Pereira S, Toffalori C, Punta M, Fetsch V, Wertheimer T, Rittmann MC, Braun LM, Follo M, Briere C, Vinnakota JM, Langenbach M, Koppers F, Shoumariyeh K, Engel H, Rückert T, Märklin M, Holzmayer S, Illert AL, Magon F, Andrieux G, Duquesne S, Pfeifer D, Staniek J, Rizzi M, Miething C, Köhler N, Duyster J, Menssen HD, Boerries M, Buescher JM, Cabezas-Wallscheid N, Blazar BR, Apostolova P, Vago L, Pearce EL, Becher B, Zeiser R. Targeting MDM2 enhances antileukemia immunity after allogeneic transplantation via MHC-II and TRAIL-R1/2 upregulation. Blood 2022; 140:1167-1181. [PMID: 35853161 PMCID: PMC9461473 DOI: 10.1182/blood.2022016082] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with acute myeloid leukemia (AML) often achieve remission after allogeneic hematopoietic cell transplantation (allo-HCT) but subsequently die of relapse driven by leukemia cells resistant to elimination by allogeneic T cells based on decreased major histocompatibility complex II (MHC-II) expression and apoptosis resistance. Here we demonstrate that mouse-double-minute-2 (MDM2) inhibition can counteract immune evasion of AML. MDM2 inhibition induced MHC class I and II expression in murine and human AML cells. Using xenografts of human AML and syngeneic mouse models of leukemia, we show that MDM2 inhibition enhanced cytotoxicity against leukemia cells and improved survival. MDM2 inhibition also led to increases in tumor necrosis factor-related apoptosis-inducing ligand receptor-1 and -2 (TRAIL-R1/2) on leukemia cells and higher frequencies of CD8+CD27lowPD-1lowTIM-3low T cells, with features of cytotoxicity (perforin+CD107a+TRAIL+) and longevity (bcl-2+IL-7R+). CD8+ T cells isolated from leukemia-bearing MDM2 inhibitor-treated allo-HCT recipients exhibited higher glycolytic activity and enrichment for nucleotides and their precursors compared with vehicle control subjects. T cells isolated from MDM2 inhibitor-treated AML-bearing mice eradicated leukemia in secondary AML-bearing recipients. Mechanistically, the MDM2 inhibitor-mediated effects were p53-dependent because p53 knockdown abolished TRAIL-R1/2 and MHC-II upregulation, whereas p53 binding to TRAILR1/2 promotors increased upon MDM2 inhibition. The observations in the mouse models were complemented by data from human individuals. Patient-derived AML cells exhibited increased TRAIL-R1/2 and MHC-II expression on MDM2 inhibition. In summary, we identified a targetable vulnerability of AML cells to allogeneic T-cell-mediated cytotoxicity through the restoration of p53-dependent TRAIL-R1/2 and MHC-II production via MDM2 inhibition.
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Affiliation(s)
- Jenny N H G Ho
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Dominik Schmidt
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Theresa Lowinus
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Jeongmin Ryoo
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Elaine-Pashupati Dopfer
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | | | - Sara Costa-Pereira
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Cristina Toffalori
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Viktor Fetsch
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Tobias Wertheimer
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Marie-Claire Rittmann
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Lukas M Braun
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Marie Follo
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Christelle Briere
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Janaki Manoja Vinnakota
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Marlene Langenbach
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Felicitas Koppers
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Helena Engel
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Tamina Rückert
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Deutsche Forschungsgemeinschaft Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy," University of Tuebingen, Tuebingen, Germany
| | - Samuel Holzmayer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Tuebingen, Germany
- Deutsche Forschungsgemeinschaft Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy," University of Tuebingen, Tuebingen, Germany
| | - Anna L Illert
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Federica Magon
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Julian Staniek
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Centre
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Centre
- Signalling Research Centres BIOSS and CIBSS - Centre for Integrative Biological, Signalling Studies, and
| | - Cornelius Miething
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Natalie Köhler
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Justus Duyster
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | | | - Melanie Boerries
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Joerg M Buescher
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bruce R Blazar
- Division of Blood & Marrow Transplant and Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, MN; and
| | - Petya Apostolova
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Immunology, Transplantation and Infectious Disease, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milano, Italy
| | - Erika L Pearce
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Robert Zeiser
- Clinic of Internal Medicine I, Hematology, Oncology, and Stem Cell Transplantation, Faculty of Medicine, Medical Centre, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research, Center (DKFZ), Heidelberg, Germany
- Signalling Research Centres BIOSS and CIBSS - Centre for Integrative Biological, Signalling Studies, and
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Koning D, Quakkelaar ED, Schellens IMM, Spierings E, van Baarle D. Protective HLA Alleles Recruit Biased and Largely Similar Antigen-Specific T Cell Repertoires across Different Outcomes in HIV Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:3-15. [PMID: 34880106 DOI: 10.4049/jimmunol.2001145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/01/2021] [Indexed: 11/19/2022]
Abstract
CD8+ T cells play an important role in the control of untreated HIV infection. Several studies have suggested a decisive role of TCRs involved in anti-HIV immunity. HLA-B*27 and B*57 are often associated with a delayed HIV disease progression, but the exact correlates that provide superior immunity against HIV are not known. To investigate if the T cell repertoire underlies the protective effect in disease outcome in HLA-B*27 and B*57+ individuals, we analyzed Ag-specific TCR profiles from progressors (n = 13) and slow progressors (n = 11) expressing either B*27 or B*57. Our data showed no differences in TCR diversity between progressors and slow progressors. Both alleles recruit biased T cell repertoires (i.e., TCR populations skewed toward specific TRBV families or CDR3 regions). This bias was unrelated to disease progression and was remarkably profound for HLA-B*57, in which TRBV family usage and CDR3 sequences were shared to some extent even between epitopes. Conclusively, these data suggest that the T cell repertoires recruited by protective HLA alleles are highly similar between progressors and slow progressors in terms of TCR diversity, TCR usage, and cross-reactivity.
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Affiliation(s)
- Dan Koning
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Esther D Quakkelaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Ingrid M M Schellens
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Debbie van Baarle
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands; and .,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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4
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Patel DN, Yeagley M, Arturo JF, Falasiri S, Chobrutskiy BI, Gozlan EC, Blanck G. A comparison of immune receptor recombination databases sourced from tumour exome or RNAseq files: Verifications of immunological distinctions between primary and metastatic melanoma. Int J Immunogenet 2021; 48:409-418. [PMID: 34298587 DOI: 10.1111/iji.12550] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023]
Abstract
It became apparent several years ago that RNAseq and exome files prepared from tissue could be mined for adaptive immune receptor (IR) recombinations, which has given extra value to datasets originally intended for gene expression or mutation studies. For example, recovery of IR recombination reads from tumour specimen genomics files can correlate with survival rates. In particular, many benchmarking processes have been applied to the two sets of the IR recombination reads obtained from the cancer genome atlas files, but these two sets have never been directly compared. Here we show that both sets largely agree regarding several parameters. For example, recovery of TRB recombination reads from both WXS and RNAseq files representing metastatic melanoma was associated with a better outcome (p < .0004 in both cases); and T-cell receptor recombination read recovery, for both genomics file types, associated very strongly with T-cell gene expression markers. However, the use of CDR3 chemical features for survival distinctions was not consistent. This topic, and the surprising result that both datasets indicated that primary melanoma with recovery of IR recombination reads, in stark contrast to metastatic melanoma, represents a worse outcome, are discussed.
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Affiliation(s)
- Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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5
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Public and private human T-cell clones respond differentially to HCMV antigen when boosted by CD3 copotentiation. Blood Adv 2021; 4:5343-5356. [PMID: 33125463 DOI: 10.1182/bloodadvances.2020002255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) induces long-lasting T-cell immune responses that control but do not clear infection. Typical responses involve private T-cell clones, expressing T-cell antigen receptors (TCRs) unique to a person, and public T-cell clones with identical TCRs active in different people. Here, we report the development of a pretherapeutic immunostimulation modality against HCMV for human T cells, CD3 copotentiation, and the clonal analysis of its effects in recall assays at single-cell resolution. CD3 copotentiation of human T cells required identification of an intrinsically inert anti-CD3 Fab fragment that conditionally augmented signaling only when TCR was coengaged with antigen. When applied in recall assays, CD3 copotentiation enhanced the expansion of both public and private T-cell clones responding to autologous HLA-A2(+) antigen-presenting cells and immunodominant NLVPMVATV (NLV) peptide from HCMV pp65 protein. Interestingly, public vs private TCR expression was associated with distinct clonal expansion signatures in response to recall stimulus. This implied that besides possible differences in their generation and selection in an immune response, public and private T cells may respond differently to pharmacoimmunomodulation. Furthermore, a third clonal expansion profile was observed upon CD3 copotentiation of T-cell clones from HLA-A2(-) donors and 1 HLA-A2(+) presumed-uninfected donor, where NLV was of low intrinsic potency. We conclude that human T-cell copotentiation can increase the expansion of different classes of T-cell clones responding to recall antigens of different strengths, and this may be exploitable for therapeutic development against chronic, persistent infections such as HCMV.
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Elahi S, Shahbaz S, Houston S. Selective Upregulation of CTLA-4 on CD8+ T Cells Restricted by HLA-B*35Px Renders them to an Exhausted Phenotype in HIV-1 infection. PLoS Pathog 2020; 16:e1008696. [PMID: 32760139 PMCID: PMC7410205 DOI: 10.1371/journal.ppat.1008696] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
HLA-B*35Px is associated with HIV-1 disease rapid progression to AIDS. However, the mechanism(s) underlying this deleterious effect of this HLA allele on HIV-1 infection outcome has not fully understood. CD8+ T cells play a crucial role to control the viral replication but impaired CD8+ T cells represent a major hallmark of HIV-1 infection. Here, we examined the effector functions of CD8+ T cells restricted by HLA-B*35Px (HLA-B*35:03 and HLA-B*35:02), HLA-B*27/B57 and non-HLA-B*27/B57 (e.g. HLA-A*01, A*02, A*03, A*11, A*24, A*26, B*40, B*08, B*38, B*44). CD8+ T cells restricted by HLA-B*35Px exhibited an impaired phenotype compared with those restricted by HLA-B*27/B57 and even non-HLA-B*27/B57. CD8+ T cells restricted by non-HLA-B*27/B57 when encountered their cognate epitopes upregulated TIM-3 and thus became suppressed by regulatory T cells (Tregs) via TIM-3: Galectin-9 (Gal-9). Strikingly, CD8+ T cells restricted by HLA-B*35Px expressed fewer TIM-3 and therefore did not get suppressed by Tregs, which was similar to CD8+ T cells restricted by HLA-B*27/B57. Instead, CD8+ T cells restricted by HLA-B*35Px upon recognition of their cognate epitopes upregulated CTLA-4. The transcriptional and impaired phenotype (e.g. poor effector functions) of HIV-specific CD8+ T cells restricted by HLA-B*35 was related to persistent CTLA-4, elevated Eomes and blimp-1 but poor T-bet expression. As such, anti-CTLA-4 antibody, Ipilimumab, reversed the impaired proliferative capacity of antigen-specific CD8+ T cells restricted by HLA-B*35Px but not others. This study supports the concept that CD8+ T resistance to Tregs-mediated suppression is related to allele restriction rather than the epitope specificity. Our results aid to explain a novel mechanism for the inability of HIV-specific CD8+ T cells restricted by HLA-B*35Px to control viral replication. A rare group of HIV-infected individuals with HLA-B*35Px rapidly progress to AIDS but those with HLA-B*27 and HLA-B*57 spare disease progression. Previous studies have suggested that viral mutation may prevent a robust immune response against the virus in these with HLA-B*35Px. However, the functionality of HIV-specific CD8+ T cells restricted by HLA-B*35Px remains unclear. In this study, we demonstrate that HIV-specific CD8+ T cells restricted by HLA-B*35Px (HLA-B*35:03 and HLA-B*35:02) exhibit an impaired phenotype (e.g. low proliferative capacity, poor cytotoxic molecules expression and, poor cytokine production ability). Interestingly, CD8+ T cells restricted by HLA-B*27/B*57 evade regulatory T cells (Tregs) suppression but not those restricted by non-HLA-B*27/B*57. CD8+ T cells restricted by non-HLA-B*27/B*57 when encountering their epitopes upregulate TIM-3 but not those restricted by HLA-B*27/B*57 and HLA-B*35Px. As a result, CD8+ T cells restricted by non-HLA-B*27/B*57 become suppressed by Tregs via TIM-3: Galectin-9 interactions. Strikingly, CD8+ T cells restricted by HLA-B*35Px upregulate CTLA-4 when encountering their epitopes, which render them to an exhausted phenotype. This differential response is linked to the up-regulation of Eomes, Blimp-1 but low T-bet expression in CD8+ T cells restricted by HLA-B*35Px. These results implicate that reinvigoration of these cells might be feasible using an anti-CTLA-4 antibody.
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Affiliation(s)
- Shokrollah Elahi
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Shima Shahbaz
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Stan Houston
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
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7
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Roca AM, Chobrutskiy BI, Callahan BM, Blanck G. T-cell receptor V and J usage paired with specific HLA alleles associates with distinct cervical cancer survival rates. Hum Immunol 2019; 80:237-242. [DOI: 10.1016/j.humimm.2019.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 11/29/2022]
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8
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Li L, Liu Y, Gorny MK. Association of Diverse Genotypes and Phenotypes of Immune Cells and Immunoglobulins With the Course of HIV-1 Infection. Front Immunol 2018; 9:2735. [PMID: 30534128 PMCID: PMC6275200 DOI: 10.3389/fimmu.2018.02735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Disease progression among HIV-1-infected individuals varies widely, but the mechanisms underlying this variability remains unknown. Distinct disease outcomes are the consequences of many factors working in concert, including innate and adaptive immune responses, cell-mediated and humoral immunity, and both genetic and phenotypic factors. Current data suggest that these multifaceted aspects in infected individuals should be considered as a whole, rather than as separate unique elements, and that analyses must be performed in greater detail in order to meet the requirements of personalized medicine and guide optimal vaccine design. However, the wide adoption of antiretroviral therapy (ART) influences the implementation of systematic analyses of the HIV-1-infected population. Consequently, fewer data will be available for acquisition in the future, preventing the comprehensive investigations required to elucidate the underpinnings of variability in disease outcome. This review seeks to recapitulate the distinct genotypic and phenotypic features of the immune system, focusing in particular on comparing the surface proteins of immune cells among individuals with different HIV infection outcomes.
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Affiliation(s)
- Liuzhe Li
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Yan Liu
- Institute of Pathogenic Biology, Medical College, University of South China, Hengyang, China
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
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9
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Mathew NR, Baumgartner F, Braun L, O’Sullivan D, Thomas S, Waterhouse M, Müller TA, Hanke K, Taromi S, Apostolova P, Illert AL, Melchinger W, Duquesne S, Schmitt-Graeff A, Osswald L, Yan KL, Weber A, Tugues S, Spath S, Pfeifer D, Follo M, Claus R, Lübbert M, Rummelt C, Bertz H, Wäsch R, Haag J, Schmidts A, Schultheiss M, Bettinger D, Thimme R, Ullrich E, Tanriver Y, Vuong GL, Arnold R, Hemmati P, Wolf D, Ditschkowski M, Jilg C, Wilhelm K, Leiber C, Gerull S, Halter J, Lengerke C, Pabst T, Schroeder T, Kobbe G, Rösler W, Doostkam S, Meckel S, Stabla K, Metzelder SK, Halbach S, Brummer T, Hu Z, Dengjel J, Hackanson B, Schmid C, Holtick U, Scheid C, Spyridonidis A, Stölzel F, Ordemann R, Müller LP, Sicre-de-Fontbrune F, Ihorst G, Kuball J, Ehlert JE, Feger D, Wagner EM, Cahn JY, Schnell J, Kuchenbauer F, Bunjes D, Chakraverty R, Richardson S, Gill S, Kröger N, Ayuk F, Vago L, Ciceri F, Müller AM, Kondo T, Teshima T, Klaeger S, Kuster B, Kim D(DH, Weisdorf D, van der Velden W, Dörfel D, Bethge W, Hilgendorf I, Hochhaus A, Andrieux G, Börries M, Busch H, Magenau J, Reddy P, Labopin M, Antin JH, Henden AS, Hill GR, Kennedy GA, Bar M, Sarma A, McLornan D, Mufti G, Oran B, Rezvani K, Sha O, Negrin RS, Nagler A, Prinz M, Burchert A, Neubauer A, Beelen D, Mackensen A, von Bubnoff N, Herr W, Becher B, Socié G, Caligiuri MA, Ruggiero E, Bonini C, Häcker G, Duyster J, Finke J, Pearce E, Blazar BR, Zeiser R. Sorafenib promotes graft-versus-leukemia activity in mice and humans through IL-15 production in FLT3-ITD-mutant leukemia cells. Nat Med 2018; 24:282-291. [PMID: 29431743 PMCID: PMC6029618 DOI: 10.1038/nm.4484] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/05/2018] [Indexed: 12/28/2022]
Abstract
Individuals with acute myeloid leukemia (AML) harboring an internal tandem duplication (ITD) in the gene encoding Fms-related tyrosine kinase 3 (FLT3) who relapse after allogeneic hematopoietic cell transplantation (allo-HCT) have a 1-year survival rate below 20%. We observed that sorafenib, a multitargeted tyrosine kinase inhibitor, increased IL-15 production by FLT3-ITD+ leukemia cells. This synergized with the allogeneic CD8+ T cell response, leading to long-term survival in six mouse models of FLT3-ITD+ AML. Sorafenib-related IL-15 production caused an increase in CD8+CD107a+IFN-γ+ T cells with features of longevity (high levels of Bcl-2 and reduced PD-1 levels), which eradicated leukemia in secondary recipients. Mechanistically, sorafenib reduced expression of the transcription factor ATF4, thereby blocking negative regulation of interferon regulatory factor 7 (IRF7) activation, which enhanced IL-15 transcription. Both IRF7 knockdown and ATF4 overexpression in leukemia cells antagonized sorafenib-induced IL-15 production in vitro. Human FLT3-ITD+ AML cells obtained from sorafenib responders following sorafenib therapy showed increased levels of IL-15, phosphorylated IRF7, and a transcriptionally active IRF7 chromatin state. The mitochondrial spare respiratory capacity and glycolytic capacity of CD8+ T cells increased upon sorafenib treatment in sorafenib responders but not in nonresponders. Our findings indicate that the synergism of T cells and sorafenib is mediated via reduced ATF4 expression, causing activation of the IRF7-IL-15 axis in leukemia cells and thereby leading to metabolic reprogramming of leukemia-reactive T cells in humans. Therefore, sorafenib treatment has the potential to contribute to an immune-mediated cure of FLT3-ITD-mutant AML relapse, an otherwise fatal complication after allo-HCT.
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Affiliation(s)
- Nimitha R. Mathew
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Francis Baumgartner
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lukas Braun
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - David O’Sullivan
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Simone Thomas
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Germany
| | - Miguel Waterhouse
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tony A. Müller
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kathrin Hanke
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Sanaz Taromi
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Petya Apostolova
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna L. Illert
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang Melchinger
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Lena Osswald
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kai-Li Yan
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Arnim Weber
- Department of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany
| | - Sonia Tugues
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sabine Spath
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Dietmar Pfeifer
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marie Follo
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rainer Claus
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Rummelt
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hartmut Bertz
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ralph Wäsch
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johanna Haag
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrea Schmidts
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Schultheiss
- Department of Medicine II, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany
| | - Dominik Bettinger
- Department of Medicine II, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany
| | - Evelyn Ullrich
- University Hospital Frankfurt, Department for Children and Adolescents Medicine, Division of Stem Cell Transplantation and Immunology, Goethe-University, Frankfurt, Germany
| | - Yakup Tanriver
- Department of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany
- Department of Nephrology, University Medical Center Freiburg, Freiburg, Germany
| | - Giang Lam Vuong
- Department of Stem Cell Transplantation, Charité University Medicine Berlin, Germany
| | - Renate Arnold
- Department of Stem Cell Transplantation, Charité University Medicine Berlin, Germany
| | - Philipp Hemmati
- Department of Stem Cell Transplantation, Charité University Medicine Berlin, Germany
| | - Dominik Wolf
- Medical Clinic III, Oncology, Hematology, Immunooncology and Rheumatology, University Hospital Bonn (UKB), Bonn, Germany
| | - Markus Ditschkowski
- Department of Bone Marrow Transplantation, West German Cancer Center, University Hospital Essen, Germany
| | - Cordula Jilg
- Department of Urology, University Medical Center Freiburg, Freiburg, Germany
| | - Konrad Wilhelm
- Department of Urology, University Medical Center Freiburg, Freiburg, Germany
| | - Christian Leiber
- Department of Urology, University Medical Center Freiburg, Freiburg, Germany
| | - Sabine Gerull
- Division of Hematology, University Hospital Basel, Basel, Switzerland
| | - Jörg Halter
- Division of Hematology, University Hospital Basel, Basel, Switzerland
| | - Claudia Lengerke
- Division of Hematology, University Hospital Basel, Basel, Switzerland
| | - Thomas Pabst
- Inselspital/Universitätsspital Bern, CH-3010 Bern, Switzerland
| | - Thomas Schroeder
- Department of Hematology, Oncology and Clinical Immunology, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Guido Kobbe
- Department of Hematology, Oncology and Clinical Immunology, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Wolf Rösler
- Department of Hematology and Oncology, University of Erlangen, Germany
| | | | - Stephan Meckel
- Department of Neuroradiology, University Medical Center Freiburg, Freiburg, Germany
| | - Kathleen Stabla
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, and University Medical Center Giessen and Marburg, Marburg, Germany
| | - Stephan K. Metzelder
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, and University Medical Center Giessen and Marburg, Marburg, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg; and German Cancer Research Center (DKFZ), Heidelberg, Germany, Freiburg, Germany
- Center for Biological signaling studies (BIOSS) - University of Freiburg, Germany
| | - Zehan Hu
- Department of Dermatology, Medical Center - University of Freiburg, Germany; and Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joern Dengjel
- Department of Dermatology, Medical Center - University of Freiburg, Germany; and Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Björn Hackanson
- Interdisziplinäres Cancer Center Augsburg (ICCA), II. Medizinische Klinik, Augsburg, Germany
| | - Christoph Schmid
- Interdisziplinäres Cancer Center Augsburg (ICCA), II. Medizinische Klinik, Augsburg, Germany
| | - Udo Holtick
- Department of Internal Medicine I, University Hospital Cologne, Germany
| | - Christof Scheid
- Department of Internal Medicine I, University Hospital Cologne, Germany
| | | | - Friedrich Stölzel
- Department of Hematology and Oncology, Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden, Germany
| | - Rainer Ordemann
- Department of Hematology and Oncology, Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden, Germany
| | - Lutz P. Müller
- Department of Hematology and Oncology, Universitätsklinikum Halle, Halle, Germany
| | - Flore Sicre-de-Fontbrune
- APHP, Saint Louis Hospital, Hematology Stem cell transplantation, & Inserm UMR 1160, Paris, France
| | - Gabriele Ihorst
- Clinical Trials Unit, Faculty of Medicine and Medical Center - University of Freiburg, Germany
| | - Jürgen Kuball
- Department of Hematology, University Medical Center Utrecht, The Netherlands
| | | | | | - Eva-Maria Wagner
- Dept. of Hematology and Oncology, Universitaetsmedizin Mainz, Mainz, Germany
| | - Jean-Yves Cahn
- Clinique Universitaire Hématologie, Université Grenoble Alpes, France
| | - Jacqueline Schnell
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Florian Kuchenbauer
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Donald Bunjes
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Ronjon Chakraverty
- Cancer Institute and Institute of Immunity and Transplantation, Royal Free Hospital, London, UK
| | - Simon Richardson
- Cancer Institute and Institute of Immunity and Transplantation, Royal Free Hospital, London, UK
| | - Saar Gill
- Hospital of the University of Pennsylvania, Smilow Translational Research Center, Philadelphia, PA, USA
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Hospital Hamburg-Eppendorf, Germany
| | - Francis Ayuk
- Department of Stem Cell Transplantation, University Hospital Hamburg-Eppendorf, Germany
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Unit of Hematology and Bone Marrow Transplantation, San Raffaele Scientific Institute, and University Vita-Salute San Raffaele Milano, Italy
| | - Fabio Ciceri
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Unit of Hematology and Bone Marrow Transplantation, San Raffaele Scientific Institute, and University Vita-Salute San Raffaele Milano, Italy
| | - Antonia M. Müller
- Department of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Takeshi Kondo
- Department of Hematology, Hokkaido University, Sapporo, Japan
| | | | - Susan Klaeger
- German Cancer Consortium (DKTK), partner site Freiburg; and German Cancer Research Center (DKFZ), Heidelberg, Germany, Freiburg, Germany
- Proteomics and Bioanalytics, Technische Universitaet Muenchen, Partner Site of the German Cancer Consortium, Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Technische Universitaet Muenchen, Partner Site of the German Cancer Consortium, Freising, Germany
| | - Dennis (Dong Hwan) Kim
- Department of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University of Toronto, Ontario, Canada
| | - Daniel Weisdorf
- Hematology, Oncology and Transplantation University of Minnesota, Minneapolis, USA
| | | | - Daniela Dörfel
- Medizinische Klinik II, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Wolfgang Bethge
- Medizinische Klinik II, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Inken Hilgendorf
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Geoffroy Andrieux
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Börries
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - John Magenau
- Department of Hematology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Pavan Reddy
- Department of Hematology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Myriam Labopin
- EBMT Statistical Unit, Hôpital Saint Antoine Paris, France
| | - Joseph H. Antin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Andrea S. Henden
- Bone Marrow Transplant Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia & Department of Haematology, Royal Brisbane Hospital, Brisbane, Australia
| | - Geoffrey R. Hill
- Bone Marrow Transplant Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia & Department of Haematology, Royal Brisbane Hospital, Brisbane, Australia
- Department of Haematology, Royal Brisbane and Womens Hospital, Brisbane, Australia
| | - Glen A. Kennedy
- Department of Haematology, Royal Brisbane and Womens Hospital, Brisbane, Australia
| | - Merav Bar
- Division of Blood and Marrow Transplantation, Fred Hutchinson Cancer Research Center, University of WA Seattle, USA
| | - Anita Sarma
- Department of Haematological Medicine, King’s College Hospital NHS Foundation Trust, London, UK
| | - Donal McLornan
- Department of Haematological Medicine, King’s College Hospital NHS Foundation Trust, London, UK
| | - Ghulam Mufti
- Department of Haematological Medicine, King’s College Hospital NHS Foundation Trust, London, UK
| | - Betul Oran
- Division of BMT, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Omid Sha
- Division of Blood and Marrow Transplantation, Stanford University Medical School, Stanford, CA, USA
| | - Robert S. Negrin
- Division of Blood and Marrow Transplantation, Stanford University Medical School, Stanford, CA, USA
| | - Arnon Nagler
- Division of Hematology, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Marco Prinz
- Department of Neuroradiology, University Medical Center Freiburg, Freiburg, Germany
- Center for Biological signaling studies (BIOSS) - University of Freiburg, Germany
| | - Andreas Burchert
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University Freiburg, Germany
| | - Andreas Neubauer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University Freiburg, Germany
| | - Dietrich Beelen
- Department of Urology, University Medical Center Freiburg, Freiburg, Germany
| | | | - Nikolas von Bubnoff
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Gerard Socié
- APHP, Saint Louis Hospital, Hematology Stem cell transplantation, & Inserm UMR 1160, Paris, France
| | | | - Eliana Ruggiero
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Unit of Hematology and Bone Marrow Transplantation, San Raffaele Scientific Institute, and University Vita-Salute San Raffaele Milano, Italy
| | - Chiara Bonini
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Unit of Hematology and Bone Marrow Transplantation, San Raffaele Scientific Institute, and University Vita-Salute San Raffaele Milano, Italy
| | - Georg Häcker
- Department of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany
| | - Justus Duyster
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Finke
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Erika Pearce
- Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Bruce R. Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robert Zeiser
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Biological signaling studies (BIOSS) - University of Freiburg, Germany
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10
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Leitman EM, Palmer CD, Buus S, Chen F, Riddell L, Sims S, Klenerman P, Sáez-Cirión A, Walker BD, Hess PR, Altfeld M, Matthews PC, Goulder PJR. Saporin-conjugated tetramers identify efficacious anti-HIV CD8+ T-cell specificities. PLoS One 2017; 12:e0184496. [PMID: 29020090 PMCID: PMC5636067 DOI: 10.1371/journal.pone.0184496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Antigen-specific T-cells are highly variable, spanning potent antiviral efficacy and damaging auto-reactivity. In virus infections, identifying the most efficacious responses is critical to vaccine design. However, current methods depend on indirect measures or on ex vivo expanded CTL clones. We here describe a novel application of cytotoxic saporin-conjugated tetramers to kill antigen-specific T-cells without significant off-target effects. The relative efficacy of distinct antiviral CD8+ T-cell specificity can be directly assessed via antigen-specific CD8+ T-cell depletion. The utility of these reagents is demonstrated here in identifying the CD8+ T-cell specificity most effective in preventing HIV progression in HIV-infected HLA-B*27-positive immune controllers.
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Affiliation(s)
- Ellen M. Leitman
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christine D. Palmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Lynn Riddell
- Integrated Sexual Health Services, Northamptonshire Healthcare NHS Trust, Northampton, United Kingdom
| | - Stuart Sims
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Paul Klenerman
- NIHR Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV, Inflammation et Persistance, Paris, France
| | - Bruce D. Walker
- Harvard Medical School, Boston, Massachusetts, United States of America
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Paul R. Hess
- Immunology Program, Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Marcus Altfeld
- Harvard Medical School, Boston, Massachusetts, United States of America
- Virus Immunology Unit, Heinrich-Pette-Institut, Hamburg, Germany
| | - Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Philip J. R. Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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11
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Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet 2017; 49:659-665. [DOI: 10.1038/ng.3822] [Citation(s) in RCA: 302] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/28/2017] [Indexed: 12/16/2022]
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12
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TCR clonotypes: molecular determinants of T-cell efficacy against HIV. Curr Opin Virol 2016; 16:77-85. [PMID: 26874617 DOI: 10.1016/j.coviro.2016.01.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 01/02/2023]
Abstract
Because of the enormous complexity and breadth of the overall HIV-specific CD8(+) T-cell response, invaluable information regarding important aspects of T-cell efficacy against HIV can be sourced from studies performed on individual clonotypes. Data gathered from ex vivo and in vitro analyses of T-cell responses and viral evolution bring us one step closer towards deciphering the correlates of protection against HIV. HIV-responsive CD8(+) T-cell populations are characterized by specific clonotypic immunodominance patterns and public TCRs. The TCR endows T-cells with two key features, important for the effective control of HIV: avidity and crossreactivity. While TCR avidity is a major determinant of CD8(+) T-cell functional efficacy against the virus, crossreactivity towards wildtype and mutant viral epitopes is crucial for adaptation to HIV evolution. The properties of CD4(+) T-cell responses in HIV controllers appear also to be shaped by high avidity public TCR clonotypes. The molecular nature of the TCR, together with the clonotypic composition of the HIV-specific T-cell response, emerge as major determinants of anti-viral efficacy.
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13
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Cukalac T, Kan WT, Dash P, Guan J, Quinn KM, Gras S, Thomas PG, La Gruta NL. Paired TCRαβ analysis of virus-specific CD8(+) T cells exposes diversity in a previously defined 'narrow' repertoire. Immunol Cell Biol 2015; 93:804-14. [PMID: 25804828 DOI: 10.1038/icb.2015.44] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023]
Abstract
T-cell receptor (TCR) usage has an important role in determining the outcome of CD8(+) cytotoxic T-lymphocyte responses to viruses and other pathogens. However, the characterization of TCR usage from which such conclusions are drawn is based on exclusive analysis of either the TCRα chain or, more commonly, the TCRβ chain. Here, we have used a multiplexed reverse transcription-PCR protocol to analyse the CDR3 regions of both TCRα and β chains from single naive or immune epitope-specific cells to provide a comprehensive picture of epitope-specific TCR usage and selection into the immune response. Analysis of TCR repertoires specific for three influenza-derived epitopes (D(b)NP(366), D(b)PA(224) and D(b)PB1-F2(62)) showed preferential usage of particular TCRαβ proteins in the immune repertoire relative to the naive repertoire, in some cases, resulting in a complete shift in TRBV preference or CDR3 length, and restricted repertoire diversity. The NP(366)-specific TCRαβ repertoire, previously defined as clonally restricted based on TCRβ analysis, was similarly diverse as the PA(224)- and PB1-F2(62)-specific repertoires. Intriguingly, preferred TCR characteristics (variable gene usage, CDR3 length and junctional gene usage) appeared to be able to confer specificity either independently or in concert with one another, depending on the epitope specificity. These data have implications for established correlations between the nature of the TCR repertoire and response outcomes after infection, and suggest that analysis of a subset of cells or a single TCR chain does not accurately depict the nature of the antigen-specific TCRαβ repertoire.
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Affiliation(s)
- Tania Cukalac
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Wan-Ting Kan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Guan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Kylie M Quinn
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
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14
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Complex T-cell receptor repertoire dynamics underlie the CD8+ T-cell response to HIV-1. J Virol 2014; 89:110-9. [PMID: 25320304 DOI: 10.1128/jvi.01765-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Although CD8(+) T cells are important for the control of HIV-1 in vivo, the precise correlates of immune efficacy remain unclear. In this study, we conducted a comprehensive analysis of viral sequence variation and T-cell receptor (TCR) repertoire composition across multiple epitope specificities in a group of antiretroviral treatment-naive individuals chronically infected with HIV-1. A negative correlation was detected between changes in antigen-specific TCR repertoire diversity and CD8(+) T-cell response magnitude, reflecting clonotypic expansions and contractions related to alterations in cognate viral epitope sequences. These patterns were independent of the individual, as evidenced by discordant clonotype-specific transitions directed against different epitopes in single subjects. Moreover, long-term asymptomatic HIV-1 infection was characterized by evolution of the TCR repertoire in parallel with viral replication. Collectively, these data suggest a continuous bidirectional process of adaptation between HIV-1 and virus-specific CD8(+) T-cell clonotypes orchestrated at the TCR-antigen interface. IMPORTANCE We describe a relation between viral epitope mutation, antigen-specific T-cell expansion, and the repertoire of responding clonotypes in chronic HIV-1 infection. This work provides insights into the process of coadaptation between the human immune system and a rapidly evolving lentivirus.
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15
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Sun X, Fujiwara M, Shi Y, Kuse N, Gatanaga H, Appay V, Gao GF, Oka S, Takiguchi M. Superimposed epitopes restricted by the same HLA molecule drive distinct HIV-specific CD8+ T cell repertoires. THE JOURNAL OF IMMUNOLOGY 2014; 193:77-84. [PMID: 24899498 DOI: 10.4049/jimmunol.1400375] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Superimposed epitopes, in which a shorter epitope is embedded within a longer one, can be presented by the same HLA class I molecule. CD8(+) CTL responses against such epitopes and the contribution of this phenomenon to immune control are poorly characterized. In this study, we examined HLA-A*24:02-restricted CTLs specific for the superimposed HIV Nef epitopes RYPLTFGWCF (RF10) and RYPLTFGW (RW8). Unexpectedly, RF10-specific and RW8-specific CTLs from HIV-1-infected HLA-A*24:02+ individuals had no overlapping Ag reactivity or clonotypic compositions. Single-cell TCR sequence analyses demonstrated that RF10-specific T cells had a more diverse TCR repertoire than did RW8-specific T cells. Furthermore, RF10-specific CTLs presented a higher Ag sensitivity and HIV suppressive capacity compared with RW8-specific CTLs. Crystallographic analyses revealed important structural differences between RF10- and RW8-HLA-A*24:02 complexes as well, with featured and featureless conformations, respectively, providing an explanation for the induction of distinct T cell responses against these epitopes. The present study shows that a single viral sequence containing superimposed epitopes restricted by the same HLA molecule could elicit distinct CD8+ T cell responses, therefore enhancing the control of HIV replication. This study also showed that a featured epitope (e.g., RF10) could drive the induction of T cells with high TCR diversity and affinity.
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Affiliation(s)
- Xiaoming Sun
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mamoru Fujiwara
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yi Shi
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Nozomi Kuse
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; and
| | - Victor Appay
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; INSERM, Unité Mixte de Recherche 1135, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Centre d'Immunologie et des Maladies Infectieuses-Paris, 75013, Paris, France
| | - George F Gao
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan; AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; and
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan;
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16
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The impact of viral evolution and frequency of variant epitopes on primary and memory human immunodeficiency virus type 1-specific CD8⁺ T cell responses. Virology 2013; 450-451:34-48. [PMID: 24503065 DOI: 10.1016/j.virol.2013.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/11/2013] [Accepted: 10/08/2013] [Indexed: 12/18/2022]
Abstract
It is unclear if HIV-1 variants lose the ability to prime naïve CD8(+) cytotoxic T lymphocytes (CTL) during progressive, untreated infection. We conducted a comprehensive longitudinal analysis of viral evolution and its impact on primary and memory CD8(+) T cell responses pre-seroconversion (SC), post-SC, and during combination antiretroviral therapy (cART). Memory T cell responses targeting autologous virus variants reached a nadir by 8 years post-SC with development of AIDS, followed by a transient enhancement of anti-HIV-1 CTL responses upon initiation of cART. We show broad and high magnitude primary T cell responses to late variants in pre-SC T cells, comparable to primary anti-HIV-1 responses induced in T cells from uninfected persons. Despite evolutionary changes, CD8(+) T cells could still be primed to HIV-1 variants. Hence, vaccination against late, mutated epitopes could be successful in enhancing primary reactivity of T cells for control of the residual reservoir of HIV-1 during cART.
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17
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Iancu EM, Gannon PO, Laurent J, Gupta B, Romero P, Michielin O, Romano E, Speiser DE, Rufer N. Persistence of EBV antigen-specific CD8 T cell clonotypes during homeostatic immune reconstitution in cancer patients. PLoS One 2013; 8:e78686. [PMID: 24205294 PMCID: PMC3808305 DOI: 10.1371/journal.pone.0078686] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/15/2013] [Indexed: 11/19/2022] Open
Abstract
Persistent viruses are kept in check by specific lymphocytes. The clonal T cell receptor (TCR) repertoire against Epstein-Barr virus (EBV), once established following primary infection, exhibits a robust stability over time. However, the determinants contributing to this long-term persistence are still poorly characterized. Taking advantage of an in vivo clinical setting where lymphocyte homeostasis was transiently perturbed, we studied EBV antigen-specific CD8 T cells before and after non-myeloablative lympho-depleting chemotherapy of melanoma patients. Despite more advanced T cell differentiation, patients T cells showed clonal composition comparable to healthy individuals, sharing a preference for TRBV20 and TRBV29 gene segment usage and several co-dominant public TCR clonotypes. Moreover, our data revealed the presence of relatively few dominant EBV antigen-specific T cell clonotypes, which mostly persisted following transient lympho-depletion (TLD) and lymphocyte recovery, likely related to absence of EBV reactivation and de novo T cell priming in these patients. Interestingly, persisting clonotypes frequently co-expressed memory/homing-associated genes (CD27, IL7R, EOMES, CD62L/SELL and CCR5) supporting the notion that they are particularly important for long-lasting CD8 T cell responses. Nevertheless, the clonal composition of EBV-specific CD8 T cells was preserved over time with the presence of the same dominant clonotypes after non-myeloablative chemotherapy. The observed clonotype persistence demonstrates high robustness of CD8 T cell homeostasis and reconstitution.
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Affiliation(s)
- Emanuela M. Iancu
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Philippe O. Gannon
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Julien Laurent
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Bhawna Gupta
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Pedro Romero
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Olivier Michielin
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Emanuela Romano
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Daniel E. Speiser
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Lausanne, Switzerland
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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18
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La Gruta NL, Thomas PG. Interrogating the relationship between naïve and immune antiviral T cell repertoires. Curr Opin Virol 2013; 3:447-51. [PMID: 23849601 DOI: 10.1016/j.coviro.2013.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/22/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022]
Abstract
Understanding how naïve virus-specific CD8+ T cells influence the type of immune response generated after virus infection is critical for the development of enhanced therapeutic and vaccination strategies to exploit CD8+ T cell-mediated immunity. Recent technological advances in T cell isolation and T receptor sequencing have allowed for greater understanding of the basic structure of immune T cell repertoires, the diversity of responses within and between individuals, and changes in repertoires over time and in response to infection conditions. In this review, we discuss the current understanding of how T cell repertoires contribute to potent antiviral responses. Additionally we compare the state of the art in receptor sequencing, highlighting the advantages and disadvantages of the three most common approaches: next-generation sequencing, template-switch anchored RT-PCR, and multiplex single cell PCR. Finally, we describe how TCR sequencing has delineated the relationship between naïve and immune T cell repertoires.
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Affiliation(s)
- Nicole L La Gruta
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC 3010, Australia.
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19
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Zaunders J, van Bockel D. Innate and Adaptive Immunity in Long-Term Non-Progression in HIV Disease. Front Immunol 2013; 4:95. [PMID: 23630526 PMCID: PMC3633949 DOI: 10.3389/fimmu.2013.00095] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 04/09/2013] [Indexed: 12/20/2022] Open
Abstract
Long-term non-progressors (LTNP) were identified after 10-15 years of the epidemic, and have been the subject of intense investigation ever since. In a small minority of cases, infection with nef/3'LTR deleted attenuated viral strains allowed control over viral replication. A common feature of LTNP is the readily detected proliferation of CD4 T-cells in vitro, in response to p24. In some cases, the responding CD4 T-cells have cytotoxic effector function and may target conserved p24 epitopes, similar to the CD8 T-cells described below. LTNP may also carry much lower HIV DNA burden in key CD4 subsets, presumably resulting from lower viral replication during primary infection. Some studies, but not others, suggest that LTNP have CD4 T-cells that are relatively resistant to HIV infection in vitro. One possible mechanism may involve up-regulation of the cell cycle regulator p21/waf in CD4 T-cells from LTNP. Delayed progression in Caucasian LTNP is also partly associated with heterozygosity of the Δ32 CCR5 allele, probably through decreased expression of CCR5 co-receptor on CD4 T-cells. However, in approximately half of Caucasian LTNP, two host genotypes, namely HLA-B57 and HLA-B27, are associated with viral control. Immunodominant CD8 T-cells from these individuals target epitopes in p24 that are highly conserved, and escape mutations have significant fitness costs to the virus. Furthermore, recent studies have suggested that these CD8 T-cells from LTNP, but not from HLA-B27 or HLA-B57 progressors, can cross-react with intermediate escape mutations, preventing full escape via compensatory mutations. Humoral immunity appears to play little part in LTNP subjects, since broadly neutralizing antibodies are rare, even amongst slow progressors. Recent genome-wide comparisons between LTNP and progressors have confirmed the HLA-B57, HLA-B27, and delta32 CCR5 allelic associations, plus indicated a role for HLA-C/KIR interactions, but have not revealed any new genotypes so far. Nevertheless, it is hoped that studying the mechanisms of intracellular restriction factors, such as the recently identified SAMHD1, will lead to a better understanding of non-progression.
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Affiliation(s)
- John Zaunders
- Centre for Applied Medical Research, St Vincent's Hospital Darlinghurst, NSW, Australia
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20
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Imami N, Westrop SJ, Grageda N, Herasimtschuk AA. Long-Term Non-Progression and Broad HIV-1-Specific Proliferative T-Cell Responses. Front Immunol 2013; 4:58. [PMID: 23459797 PMCID: PMC3585435 DOI: 10.3389/fimmu.2013.00058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/17/2013] [Indexed: 12/30/2022] Open
Abstract
Complex mechanisms underlying the maintenance of fully functional, proliferative, HIV-1-specific T-cell responses involve processes from early T-cell development through to the final stages of T-cell differentiation and antigen recognition. Virus-specific proliferative CD4 and CD8 T-cell responses, important for the control of infection, are observed in some HIV-1(+) patients during early stages of disease, and are maintained in long-term non-progressing subjects. In the vast majority of HIV-1(+) patients, full immune functionality is lost when proliferative HIV-1-specific T-cell responses undergo a variable progressive decline throughout the course of chronic infection. This appears irreparable despite administration of potent combination antiretroviral therapy, which to date is non-curative, necessitating life-long administration and the development of effective, novel, therapeutic interventions. While a sterilizing cure, involving clearance of virus from the host, remains a primary aim, a "functional cure" may be a more feasible goal with considerable impact on worldwide HIV-1 infection. Such an approach would enable long-term co-existence of host and virus in the absence of toxic and costly drugs. Effective immune homeostasis coupled with a balanced response appropriately targeting conserved viral antigens, in a manner that avoids hyperactivation and exhaustion, may prove to be the strongest correlate of durable viral control. This review describes novel concepts underlying full immune functionality in the context of HIV-1 infection, which may be utilized in future strategies designed to improve upon existing therapy. The aim will be to induce long-term non-progressor or elite controller status in every infected host, through immune-mediated control of viremia and reduction of viral reservoirs, leading to lower HIV-1 transmission rates.
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Affiliation(s)
- Nesrina Imami
- Department of Medicine, Imperial College LondonLondon, UK
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21
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A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8+ T Cells. Immunity 2013; 38:425-36. [DOI: 10.1016/j.immuni.2012.11.021] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 11/05/2012] [Indexed: 12/11/2022]
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22
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Yin L, Scott-Browne J, Kappler JW, Gapin L, Marrack P. T cells and their eons-old obsession with MHC. Immunol Rev 2013; 250:49-60. [PMID: 23046122 PMCID: PMC3963424 DOI: 10.1111/imr.12004] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
T cells bearing receptors made up of α and β chains (TCRs) usually react with peptides bound to major histocompatibility complex proteins (MHC). This bias could be imposed by positive selection, the phenomenon that selects thymocytes to mature into T cells only if the TCRs they bear react with low but appreciable affinity with MHC + peptide combinations in the thymus cortex. However, it is also possible that the polypeptides of TCRs themselves do not have random specificities but rather are biased toward reaction with MHC. Evolution would therefore have selected for a collection of TCR variable elements that are prone to react with MHC. If this were to be so, positive selection would act on thymocytes bearing a pre biased collection of TCRs to pick out those that react to some extent, but not too well, with self MHC + self-peptides. A problem with studies of this evolutionary idea is the fact that there are many TCR variable elements and that these differ considerably in the amino acids with which they contact MHC. However, recent experiments by our group and others suggest that one group of TCR variable elements, those related to the mouse Vβ8 family, has amino acids in their CDR2 regions that consistently bind a particular site on an MHC α-helix. Other groups of variable elements may use different patterns of amino acids to achieve the same goal. Mutation of these amino acids reduces the ability of T cells and thymocytes to react with MHC. These amino acids are present in the variable regions of distantly related species such as sharks and human. Overall the data indicate that TCR elements have indeed been selected by evolution to react with MHC proteins. Many mysteries about TCRs remain to be solved, including the nature of auto-recognition, the basis of MHC allele specificity, and the very nature and complexity of TCRs on mature T cells.
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Affiliation(s)
- Lei Yin
- Integrated Department of Immunology, HHMI, National Jewish Health, Denver, CO, USA
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Autologous HIV-1 clade-B Nef peptides elicit increased frequency, breadth and function of CD8+ T-cells compared to consensus peptides. PLoS One 2012. [PMID: 23185362 PMCID: PMC3501503 DOI: 10.1371/journal.pone.0049562] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To determine the function and phenotype of CD8(+) T-cells targeting consensus and autologous sequences of entire HIV-1 Nef protein. METHODS Multiparameter flow cytometry-based analysis was used to evaluate the responses of two treatment naïve HIV-infected individuals, during primary and the chronic phases of infection. RESULTS A greater breadth and magnitude of CD8 IFN-γ responses to autologous compared to clade-B consensus peptides was observed in both subjects. Cross recognition between autologous and consensus peptides decreased in both subjects during progression from primary to chronic infection. The frequencies of TEMRA and TEM CD8(+) T-cells targeting autologous peptides were higher than those targeting consensus peptides and were more polyfunctional (IFN-γ(+) Gr-B(+) CD107a(+)). CONCLUSIONS Our data indicate superior sensitivity and specificity of autologous peptides. The functional and maturational aspects of "real" versus "cross-recognized" responses were also found to differ, highlighting the importance of a sequence-specific approach towards understanding HIV immune response.
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High frequency of herpesvirus-specific clonotypes in the human T cell repertoire can remain stable over decades with minimal turnover. J Virol 2012; 87:697-700. [PMID: 23077319 DOI: 10.1128/jvi.02180-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
High-throughput T cell receptor sequencing on sequentially banked blood samples from healthy individuals has shown that high-frequency clonotypes can remain relatively stable for up to 18 years, with minimal inflation, deflation, or turnover. These populations included T cell expansions specific for Epstein-Barr virus. Thus, in spite of exposure to a barrage of microorganisms over the course of life, the dominant clonotypes in the mature peripheral T cell repertoire can alter surprisingly little.
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Chen H, Ndhlovu ZM, Liu D, Porter LC, Fang JW, Darko S, Brockman MA, Miura T, Brumme ZL, Schneidewind A, Piechocka-Trocha A, Cesa KT, Sela J, Cung TD, Toth I, Pereyra F, Yu XG, Douek DC, Kaufmann DE, Allen TM, Walker BD. TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection. Nat Immunol 2012; 13:691-700. [PMID: 22683743 DOI: 10.1038/ni.2342] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/11/2012] [Indexed: 12/17/2022]
Abstract
The human leukocyte antigens HLA-B27 and HLA-B57 are associated with protection against progression of disease that results from infection with human immunodeficiency virus type 1 (HIV-1), yet most people with alleles encoding HLA-B27 and HLA-B57 are unable to control HIV-1. Here we found that HLA-B27-restricted CD8(+) T cells in people able to control infection with HIV-1 (controllers) and those who progress to disease after infection with HIV-1 (progressors) differed in their ability to inhibit viral replication through targeting of the immunodominant epitope of group-associated antigen (Gag) of HIV-1. This was associated with distinct T cell antigen receptor (TCR) clonotypes, characterized by superior control of HIV-1 replication in vitro, greater cross-reactivity to epitope variants and enhanced loading and delivery of perforin. We also observed clonotype-specific differences in antiviral efficacy for an immunodominant HLA-B57-restricted response in controllers and progressors. Thus, the efficacy of such so-called 'protective alleles' is modulated by specific TCR clonotypes selected during natural infection, which provides a functional explanation for divergent HIV-1 outcomes.
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Affiliation(s)
- Huabiao Chen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, USA
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26
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A novel tuberculosis DNA vaccine in an HIV-1 p24 protein backbone confers protection against Mycobacterium tuberculosis and simultaneously elicits robust humoral and cellular responses to HIV-1. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2012; 19:723-30. [PMID: 22461526 DOI: 10.1128/cvi.05700-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis remains a major infectious disease worldwide. Moreover, latent M. tuberculosis infection is more likely to progress to active TB and eventually leads to death when HIV infection is involved. Thus, it is urgent to develop a novel TB vaccine with immunogenicity to both M. tuberculosis and HIV. In this study, four uncharacterized T cell epitopes from MPT64, Ag85A, Ag85B, and TB10.4 antigens of M. tuberculosis were predicted, and HIV-1-derived p24, an immunodominant protein that can induce protective responses to HIV-1, was used as an immunogenic backbone. M. tuberculosis epitopes were incorporated separately into the gene backbone of p24, forming a pP24-Mtb DNA vaccine. We demonstrated that pP24-Mtb immunization induced a strong M. tuberculosis-specific cellular response as evidenced by T cell proliferation, cytotoxicity, and elevated frequency of gamma interferon (IFN-γ)-secreting T cells. Interestingly, a p24-specific cellular response and high levels of p24-specific IgG were also induced by pP24-Mtb immunization. When the protective effect was assessed after mycobacterial challenge, pP24-Mtb vaccination significantly reduced tissue bacterial loads and profoundly attenuated the mycobacterial infection-related lung inflammation and injury. Our findings demonstrated that the pP24-Mtb tuberculosis vaccine confers effective protection against mycobacterial challenge with simultaneously elicited robust immune responses to HIV-1, which may provide clues for developing novel vaccines to prevent dual infections.
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Janbazian L, Price DA, Canderan G, Filali-Mouhim A, Asher TE, Ambrozak DR, Scheinberg P, Boulassel MR, Routy JP, Koup RA, Douek DC, Sekaly RP, Trautmann L. Clonotype and repertoire changes drive the functional improvement of HIV-specific CD8 T cell populations under conditions of limited antigenic stimulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 188:1156-67. [PMID: 22210916 PMCID: PMC3262882 DOI: 10.4049/jimmunol.1102610] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Persistent exposure to cognate Ag leads to the functional impairment and exhaustion of HIV-specific CD8 T cells. Ag withdrawal, attributable either to antiretroviral treatment or the emergence of epitope escape mutations, causes HIV-specific CD8 T cell responses to wane over time. However, this process does not continue to extinction, and residual CD8 T cells likely play an important role in the control of HIV replication. In this study, we conducted a longitudinal analysis of clonality, phenotype, and function to define the characteristics of HIV-specific CD8 T cell populations that persist under conditions of limited antigenic stimulation. Ag decay was associated with dynamic changes in the TCR repertoire, increased expression of CD45RA and CD127, decreased expression of programmed death-1, and the emergence of polyfunctional HIV-specific CD8 T cells. High-definition analysis of individual clonotypes revealed that the Ag loss-induced gain of function within HIV-specific CD8 T cell populations could be attributed to two nonexclusive mechanisms: 1) functional improvement of persisting clonotypes; and 2) recruitment of particular clonotypes endowed with superior functional capabilities.
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Affiliation(s)
- Loury Janbazian
- Laboratory of Immunology, Department of Microbiology and Immunology, Université de Montréal, Montreal, H2X 1P1, Canada
| | - David A. Price
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of InfectionandImmunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, Wales, UK
| | - Glenda Canderan
- Vaccine and Gene Therapy Institute - Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
| | - Abdelali Filali-Mouhim
- Laboratory of Immunology, Department of Microbiology and Immunology, Université de Montréal, Montreal, H2X 1P1, Canada
| | - Tedi E. Asher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R. Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phillip Scheinberg
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohamad Rachid Boulassel
- Division of Hematology, Royal Victoria Hospital, McGill University Health Centre, Montreal, H3A 1A1, Canada
| | - Jean-Pierre Routy
- Division of Hematology, Royal Victoria Hospital, McGill University Health Centre, Montreal, H3A 1A1, Canada
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafick-Pierre Sekaly
- Laboratory of Immunology, Department of Microbiology and Immunology, Université de Montréal, Montreal, H2X 1P1, Canada
- Vaccine and Gene Therapy Institute - Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
- Faculty of Medicine, Department of Microbiology and Immunology, McGill University, Montreal, H3A 2B4, Canada
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Lydie Trautmann
- Vaccine and Gene Therapy Institute - Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
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28
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HLA B*5701-positive long-term nonprogressors/elite controllers are not distinguished from progressors by the clonal composition of HIV-specific CD8+ T cells. J Virol 2012; 86:4014-8. [PMID: 22278241 DOI: 10.1128/jvi.06982-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To better understand the qualitative features of effective human immunodeficiency virus (HIV)-specific immunity, we examined the TCR clonal composition of CD8(+) T cells recognizing conserved HIV p24-derived epitopes in HLA-B*5701-positive long-term nonprogressors/elite controllers (LTNP/EC) and HLA-matched progressors. Both groups displayed oligoclonal HLA-B5701-restricted p24-specific CD8(+) T-cell responses with similar levels of diversity and few public clonotypes. Thus, HIV-specific CD8(+) T-cell responses in LTNP/EC are not differentiated from those of progressors on the basis of clonal diversity or TCR sharing.
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29
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Antiretroviral therapy reduces the magnitude and T cell receptor repertoire diversity of HIV-specific T cell responses without changing T cell clonotype dominance. J Virol 2012; 86:4213-21. [PMID: 22258246 DOI: 10.1128/jvi.06000-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After initiation of antiretroviral therapy (ART), HIV loads and frequencies of HIV epitope-specific immune responses decrease. A diverse virus-specific T cell receptor (TCR) repertoire allows the host to respond to viral epitope diversity, but the effect of antigen reduction as a result of ART on the TCR repertoire of epitope-specific CD8(+) T cell populations has not been well defined. We determined the TCR repertoires of 14 HIV-specific CD8(+) T cell responses from 8 HIV-positive individuals before and after initiation of ART. We used multiparameter flow cytometry to measure the distribution of memory T cell subsets and the surface expression of PD-1 on T cell populations and T cell clonotypes within epitope-specific responses from these individuals. Post-ART, we noted decreases in the frequency of circulating epitope-specific T cells (P = 0.02), decreases in the number of T-cell clonotypes found within epitope-specific T cell receptor repertoires (P = 0.024), and an overall reduction in the amino acid diversity within these responses (P < 0.0001). Despite this narrowing of the T cell response to HIV, the overall hierarchy of dominant T cell receptor clonotypes remained stable compared to that pre-ART. CD8(+) T cells underwent redistributions in memory phenotypes and a reduction in CD38 and PD-1 expression post-ART. Despite extensive remodeling at the structural and phenotypic levels, PD-1 was expressed at higher levels on dominant clonotypes within epitope-specific responses before and after initiation of ART. These data suggest that the antigen burden may maintain TCR diversity and that dominant clonotypes are sensitive to antigen even after dramatic reductions after initiation of ART.
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30
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Abstract
Historically, sharing T cell receptors (TCRs) between individuals has been speculated to be impossible, considering the dramatic discrepancy between the potential enormity of the TCR repertoire and the limited number of T cells generated in each individual. However, public T cell response, in which multiple individuals share identical TCRs in responding to a same antigenic epitope, has been extensively observed in a variety of immune responses across many species. Public T cell responses enable individuals within a population to generate similar antigen-specific TCRs against certain ubiquitous pathogens, leading to favorable biological outcomes. However, the relatively concentrated feature of TCR repertoire may limit T cell response in a population to some other pathogens. It could be a great benefit for human health if public T cell responses can be manipulated. Therefore, the mechanistic insight of public TCR generation is important to know. Recently, high-throughput DNA sequencing has revolutionized the study of immune receptor repertoires, which allows a much better understanding of the factors that determine the overlap of TCR repertoire among individuals. Here, we summarize the current knowledge on public T-cell response and discuss future challenges in this field.
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Affiliation(s)
- Hanjie Li
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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31
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32
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Berger CT, Frahm N, Price DA, Mothe B, Ghebremichael M, Hartman KL, Henry LM, Brenchley JM, Ruff LE, Venturi V, Pereyra F, Sidney J, Sette A, Douek DC, Walker BD, Kaufmann DE, Brander C. High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control. J Virol 2011; 85:9334-45. [PMID: 21752903 PMCID: PMC3165743 DOI: 10.1128/jvi.00460-11] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/30/2011] [Indexed: 12/20/2022] Open
Abstract
Virus-specific cytotoxic T lymphocytes (CTL) with high levels of functional avidity have been associated with viral clearance in hepatitis C virus infection and with enhanced antiviral protective immunity in animal models. However, the role of functional avidity as a determinant of HIV-specific CTL efficacy remains to be assessed. Here we measured the functional avidities of HIV-specific CTL responses targeting 20 different, optimally defined CTL epitopes restricted by 13 different HLA class I alleles in a cohort comprising 44 HIV controllers and 68 HIV noncontrollers. Responses restricted by HLA-B alleles and responses targeting epitopes located in HIV Gag exhibited significantly higher functional avidities than responses restricted by HLA-A or HLA-C molecules (P = 0.0003) or responses targeting epitopes outside Gag (P < 0.0001). The functional avidities of Gag-specific and HLA-B-restricted responses were higher in HIV controllers than in noncontrollers (P = 0.014 and P = 0.018) and were not restored in HIV noncontrollers initiating antiretroviral therapy. T-cell receptor (TCR) analyses revealed narrower TCR repertoires in higher-avidity CTL populations, which were dominated by public TCR sequences in HIV controllers. Together, these data link the presence of high-avidity Gag-specific and HLA-B-restricted CTL responses with viral suppression in vivo and provide new insights into the immune parameters that mediate spontaneous control of HIV infection.
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Affiliation(s)
- Christoph T. Berger
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Nicole Frahm
- Fred Hutchinson Cancer Research Center/NIAID HIV Vaccine Trials Network (HVTN), Seattle, Washington
| | - David A. Price
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
- Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
| | - Beatriz Mothe
- Lluita contra la Sida Foundation, Hospital Germans Trias i Pujol, Universitat Autònoma de Badalona, Barcelona, Spain
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Musie Ghebremichael
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kari L. Hartman
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Leah M. Henry
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Laura E. Ruff
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Daniel E. Kaufmann
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Christian Brander
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
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33
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Iglesias MC, Almeida JR, Fastenackels S, van Bockel DJ, Hashimoto M, Venturi V, Gostick E, Urrutia A, Wooldridge L, Clement M, Gras S, Wilmann PG, Autran B, Moris A, Rossjohn J, Davenport MP, Takiguchi M, Brander C, Douek DC, Kelleher AD, Price DA, Appay V. Escape from highly effective public CD8+ T-cell clonotypes by HIV. Blood 2011; 118:2138-49. [PMID: 21734237 PMCID: PMC3162351 DOI: 10.1182/blood-2011-01-328781] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 06/20/2011] [Indexed: 11/20/2022] Open
Abstract
Mapping the precise determinants of T-cell efficacy against viruses in humans is a public health priority with crucial implications for vaccine design. To inform this effort, we performed a comprehensive analysis of the effective CD8(+) T-cell clonotypes that constitute responses specific for the HIV p24 Gag-derived KK10 epitope (KRWIILGLNK; residues 263-272) restricted by HLA-B*2705, which are known to confer superior control of viral replication in HIV-infected individuals. Particular KK10-specific CD8(+) T-cell clonotypes, characterized by TRBV4-3/TRBJ1-3 gene rearrangements, were found to be preferentially selected in vivo and shared between individuals. These "public" clonotypes exhibit high levels of TCR avidity and Ag sensitivity, which impart functional advantages and enable effective suppression of HIV replication. The early L(268)M mutation at position 6 of the KK10 epitope enables the virus to avoid recognition by these highly effective CD8(+) T-cell clonotypes. However, alternative clonotypes with variant reactivity provide flexibility within the overall KK10-specific response. These findings provide refined mechanistic insights into the workings of an effective CD8(+) T-cell response against HIV.
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Affiliation(s)
- Maria Candela Iglesias
- Inserm UMR S 945, Infections and Immunity, Université Pierre et Marie Curie-Paris 6, Hôpital Pitié-Salpêtrière, Paris, France
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34
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Conrad JA, Ramalingam RK, Smith RM, Barnett L, Lorey SL, Wei J, Simons BC, Sadagopal S, Meyer-Olson D, Kalams SA. Dominant clonotypes within HIV-specific T cell responses are programmed death-1high and CD127low and display reduced variant cross-reactivity. THE JOURNAL OF IMMUNOLOGY 2011; 186:6871-85. [PMID: 21562156 DOI: 10.4049/jimmunol.1004234] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
HIV epitope-specific T cell responses are often comprised of clonotypic expansions with distinct functional properties. In HIV(+) individuals, we measured programmed death-1 (PD-1) and IL-7Rα expression, MHC class I tetramer binding, cytokine production, and proliferation profiles of dominant and subdominant TCR clonotypes to evaluate the relationship between the composition of the HIV-specific T cell repertoire and clonotypic phenotype and function. Dominant clonotypes are characterized by higher PD-1 expression and lower C127 expression compared with subdominant clonotypes, and TCR avidity positively correlates with PD-1 expression. At low peptide concentrations, dominant clonotypes fail to survive in culture. In response to stimulation with peptides representing variant epitopes, subdominant clonotypes produce higher relative levels of cytokines and display greater capacity for cross-recognition compared with dominant clonotypes. These data indicate that dominant clonotypes within HIV-specific T cell responses display a phenotype consistent with ongoing exposure to cognate viral epitopes and suggest that cross-reactive, subdominant clonotypes may retain greater capacity to suppress replication of viral variants as well as to survive in the absence of strong antigenic signaling.
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Affiliation(s)
- Joseph A Conrad
- Department of Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232, USA
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35
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Miles JJ, Douek DC, Price DA. Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol Cell Biol 2011; 89:375-87. [PMID: 21301479 DOI: 10.1038/icb.2010.139] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The naïve T-cell repertoire is vast, containing millions of unique T-cell receptor (TCR) structures. Faced with such diversity, the mobilization of TCR structures from this enormous pool was once thought to be a stochastic, even chaotic, process. However, steady and systematic dissection over the last 20 years has revealed that this is not the case. Instead, the TCR repertoire deployed against individual antigens is routinely ordered and biased. Often, identical and near-identical TCR repertoires can be observed across different individuals, suggesting that the system encompasses an element of predictability. This review provides a catalog of αβ TCR bias by disease and by species, and discusses the mechanisms that govern this inherent and widespread phenomenon.
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Affiliation(s)
- John J Miles
- T Cell Modulation Laboratory, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, UK.
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