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Grauwet K, Berger T, Kann MC, Silva H, Larson R, Leick MB, Bailey SR, Bouffard AA, Millar D, Gallagher K, Turtle CJ, Frigault MJ, Maus MV. Stealth transgenes enable CAR-T cells to evade host immune responses. J Immunother Cancer 2024; 12:e008417. [PMID: 38724463 PMCID: PMC11086422 DOI: 10.1136/jitc-2023-008417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Adoptive cell therapy, such as chimeric antigen receptor (CAR)-T cell therapy, has improved patient outcomes for hematological malignancies. Currently, four of the six FDA-approved CAR-T cell products use the FMC63-based αCD19 single-chain variable fragment, derived from a murine monoclonal antibody, as the extracellular binding domain. Clinical studies demonstrate that patients develop humoral and cellular immune responses to the non-self CAR components of autologous CAR-T cells or donor-specific antigens of allogeneic CAR-T cells, which is thought to potentially limit CAR-T cell persistence and the success of repeated dosing. METHODS In this study, we implemented a one-shot approach to prevent rejection of engineered T cells by simultaneously reducing antigen presentation and the surface expression of both Classes of the major histocompatibility complex (MHC) via expression of the viral inhibitors of transporter associated with antigen processing (TAPi) in combination with a transgene coding for shRNA targeting class II MHC transactivator (CIITA). The optimal combination was screened in vitro by flow cytometric analysis and mixed lymphocyte reaction assays and was validated in vivo in mouse models of leukemia and lymphoma. Functionality was assessed in an autologous setting using patient samples and in an allogeneic setting using an allogeneic mouse model. RESULTS The combination of the Epstein-Barr virus TAPi and an shRNA targeting CIITA was efficient and effective at reducing cell surface MHC classes I and II in αCD19 'stealth' CAR-T cells while retaining in vitro and in vivo antitumor functionality. Mixed lymphocyte reaction assays and IFNγ ELISpot assays performed with T cells from patients previously treated with autologous αCD19 CAR-T cells confirm that CAR T cells expressing the stealth transgenes evade allogeneic and autologous anti-CAR responses, which was further validated in vivo. Importantly, we noted anti-CAR-T cell responses in patients who had received multiple CAR-T cell infusions, and this response was reduced on in vitro restimulation with autologous CARs containing the stealth transgenes. CONCLUSIONS Together, these data suggest that the proposed stealth transgenes may reduce the immunogenicity of autologous and allogeneic cellular therapeutics. Moreover, patient data indicate that repeated doses of autologous FMC63-based αCD19 CAR-T cells significantly increased the anti-CAR T cell responses in these patients.
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Affiliation(s)
- Korneel Grauwet
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Trisha Berger
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - Michael C Kann
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - Harrison Silva
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - Rebecca Larson
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mark B Leick
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stefanie R Bailey
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amanda A Bouffard
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - David Millar
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kathleen Gallagher
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Cameron J Turtle
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Matthew J Frigault
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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2
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Rein AF, Lauruschkat CD, Muchsin I, Köchel C, Tischer-Zimmermann S, Bauersfeld L, Nelde A, Lübke M, Prusty BK, Schlosser A, Halenius A, Eiz-Vesper B, Dölken L, Grigoleit GU, Einsele H, Erhard F, Kraus S. Identification of novel canonical and cryptic HCMV-specific T-cell epitopes for HLA-A∗03 and HLA-B∗15 via peptide-PRISM. Blood Adv 2024; 8:712-724. [PMID: 38127299 PMCID: PMC10845030 DOI: 10.1182/bloodadvances.2023011120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
ABSTRACT Human cytomegalovirus (HCMV) reactivation poses a substantial risk to patients receiving tranplants. Effective risk stratification and vaccine development is hampered by a lack of HCMV-derived immunogenic peptides in patients with common HLA-A∗03:01 and HLA-B∗15:01 haplotypes. This study aimed to discover novel HCMV immunogenic peptides for these haplotypes by combining ribosome sequencing (Ribo-seq) and mass spectrometry with state-of-the-art computational tools, Peptide-PRISM and Probabilistic Inference of Codon Activities by an EM Algorithm. Furthermore, using machine learning, an algorithm was developed to predict immunogenicity based on translational activity, binding affinity, and peptide localization within small open reading frames to identify the most promising peptides for in vitro validation. Immunogenicity of these peptides was subsequently tested by analyzing peptide-specific T-cell responses of HCMV-seropositive and -seronegative healthy donors as well as patients with transplants. This resulted in the direct identification of 3 canonical and 1 cryptic HLA-A∗03-restricted immunogenic peptides as well as 5 canonical and 1 cryptic HLA-B∗15-restricted immunogenic peptide, with a specific interferon gamma-positive (IFN-γ+)/CD8+ T-cell response of ≥0.02%. High T-cell responses were detected against 2 HLA-A∗03-restricted and 3 HLA-B∗15-restricted canonical peptides with frequencies of up to 8.77% IFN-γ+/CD8+ T cells in patients after allogeneic stem cell transplantation. Therefore, our comprehensive strategy establishes a framework for efficient identification of novel immunogenic peptides from both existing and novel Ribo-seq data sets.
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Affiliation(s)
- Alice Felicitas Rein
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | | | - Ihsan Muchsin
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Carolin Köchel
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Sabine Tischer-Zimmermann
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Liane Bauersfeld
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Bhupesh Kumar Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center - Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Anne Halenius
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Götz Ulrich Grigoleit
- Department of Hematology, Oncology and Immunology, Helios Hospital Duisburg, Duisburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
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3
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Schroeder SM, Nelde A, Walz JS. Viral T-cell epitopes - Identification, characterization and clinical application. Semin Immunol 2023; 66:101725. [PMID: 36706520 DOI: 10.1016/j.smim.2023.101725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
T-cell immunity, mediated by CD4+ and CD8+ T cells, represents a cornerstone in the control of viral infections. Virus-derived T-cell epitopes are represented by human leukocyte antigen (HLA)-presented viral peptides on the surface of virus-infected cells. They are the prerequisite for the recognition of infected cells by T cells. Knowledge of viral T-cell epitopes provides on the one hand a diagnostic tool to decipher protective T-cell immune responses in the human population and on the other hand various prophylactic and therapeutic options including vaccination approaches and the transfer of virus-specific T cells. Such approaches have already been proven to be effective against various viral infections, particularly in immunocompromised patients lacking sufficient humoral, antibody-based immune response. This review provides an overview on the state of the art as well as current studies regarding the identification and characterization of viral T-cell epitopes and approaches of clinical application. In the first chapter in silico prediction tools and direct, mass spectrometry-based identification of viral T-cell epitopes is compared. The second chapter provides an overview of commonly used assays for further characterization of T-cell responses and phenotypes. The final chapter presents an overview of clinical application of viral T-cell epitopes with a focus on human immunodeficiency virus (HIV), human cytomegalovirus (HCMV) and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), being representatives of relevant viruses.
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Affiliation(s)
- Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Department for Otorhinolaryngology, Head, and Neck Surgery, University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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4
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Meyer S, Blaas I, Bollineni RC, Delic-Sarac M, Tran TT, Knetter C, Dai KZ, Madssen TS, Vaage JT, Gustavsen A, Yang W, Nissen-Meyer LSH, Douvlataniotis K, Laos M, Nielsen MM, Thiede B, Søraas A, Lund-Johansen F, Rustad EH, Olweus J. Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants. Cell Rep 2023; 42:111995. [PMID: 36656713 PMCID: PMC9826989 DOI: 10.1016/j.celrep.2023.111995] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOC) is driven by mutations that mediate escape from neutralizing antibodies. There is also evidence that mutations can cause loss of T cell epitopes. However, studies on viral escape from T cell immunity have been hampered by uncertain estimates of epitope prevalence. Here, we map and quantify CD8 T cell responses to SARS-CoV-2-specific minimal epitopes in blood drawn from April to June 2020 from 83 COVID-19 convalescents. Among 37 HLA ligands eluted from five prevalent alleles and an additional 86 predicted binders, we identify 29 epitopes with an immunoprevalence ranging from 3% to 100% among individuals expressing the relevant HLA allele. Mutations in VOC are reported in 10.3% of the epitopes, while 20.6% of the non-immunogenic peptides are mutated in VOC. The nine most prevalent epitopes are conserved in VOC. Thus, comprehensive mapping of epitope prevalence does not provide evidence that mutations in VOC are driven by escape of T cell immunity.
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Affiliation(s)
- Saskia Meyer
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Isaac Blaas
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Marina Delic-Sarac
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Trung T. Tran
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Cathrine Knetter
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Ke-Zheng Dai
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | | | - John T. Vaage
- Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Alice Gustavsen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
| | - Weiwen Yang
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | | | - Karolos Douvlataniotis
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Maarja Laos
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Morten Milek Nielsen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Arne Søraas
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway,ImmunoLingo Convergence Center, University of Oslo, 0372 Oslo, Norway
| | - Even H. Rustad
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway,Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway,Corresponding author
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5
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Yu B, Shi Q, Belk JA, Yost KE, Parker KR, Li R, Liu BB, Huang H, Lingwood D, Greenleaf WJ, Davis MM, Satpathy AT, Chang HY. Engineered cell entry links receptor biology with single-cell genomics. Cell 2022; 185:4904-4920.e22. [PMID: 36516854 PMCID: PMC9789208 DOI: 10.1016/j.cell.2022.11.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/31/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
Cells communicate with each other via receptor-ligand interactions. Here, we describe lentiviral-mediated cell entry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell type, and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter-clonal vs. intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.
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Affiliation(s)
- Bingfei Yu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Betty B Liu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Huang Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | | | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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6
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Jiang S, Nan F, Zhang S, Zhang X, Li Z, Yu Z, Liu F, Li J, Zhou X, Niu D, Wang H, Zhang X, Liu W, Yang X, Wang Y, Wang B. CRM197-conjugated multi antigen dominant epitope for effective human cytomegalovirus vaccine development. Int J Biol Macromol 2022; 224:79-93. [DOI: 10.1016/j.ijbiomac.2022.10.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C. Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- *Correspondence: Katherine Kedzierska,
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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8
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Marcu A, Schlosser A, Keupp A, Trautwein N, Johann P, Wölfl M, Lager J, Monoranu CM, Walz JS, Henkel LM, Krauß J, Ebinger M, Schuhmann M, Thomale UW, Pietsch T, Klinker E, Schlegel PG, Oyen F, Reisner Y, Rammensee HG, Eyrich M. Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors. J Immunother Cancer 2021; 9:jitc-2021-003404. [PMID: 34599019 PMCID: PMC8488729 DOI: 10.1136/jitc-2021-003404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 12/30/2022] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS tumors of infancy and early childhood. Hallmark is the surprisingly simple genome with inactivating mutations or deletions in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expanded T cells. However, it is unclear which epitopes T cells might recognize on AT/RT cells. Methods Here, we report a comprehensive mass spectrometry (MS)-based analysis of naturally presented human leukocyte antigen (HLA) class I and class II ligands on 23 AT/RTs. MS data were validated by matching with a human proteome dataset and exclusion of peptides that are part of the human benignome. Cryptic peptide ligands were identified using Peptide-PRISM. Results Comparative HLA ligandome analysis of the HLA ligandome revealed 55 class I and 139 class II tumor-exclusive peptides. No peptide originated from the SMARCB1 region. In addition, 61 HLA class I tumor-exclusive peptide sequences derived from non-canonically translated proteins. Combination of peptides from natural and cryptic class I and class II origin gave optimal representation of tumor cell compartments. Substantial overlap existed with the cryptic immunopeptidome of glioblastomas, but no concordance was found with extracranial tumors. More than 80% of AT/RT exclusive peptides were able to successfully prime CD8+ T cells, whereas naturally occurring memory responses in AT/RT patients could only be detected for class II epitopes. Interestingly, >50% of AT/RT exclusive class II ligands were also recognized by T cells from glioblastoma patients but not from healthy donors. Conclusions These findings highlight that AT/RTs, potentially paradigmatic for other pediatric tumors with a low mutational load, present a variety of highly immunogenic HLA class I and class II peptides from canonical as well as non-canonical protein sources. Inclusion of such cryptic peptides into therapeutic vaccines would enable an optimized mapping of the tumor cell surface, thereby reducing the likelihood of immune evasion.
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Affiliation(s)
- Ana Marcu
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany
| | | | - Anne Keupp
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Nico Trautwein
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Pascal Johann
- Swabian Children's Cancer Center, Augsburg, Germany.,DKFZ Heidelberg, Heidelberg, Germany
| | - Matthias Wölfl
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Johanna Lager
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Camelia Maria Monoranu
- Department of Neuropathology, Institute for Pathology, University of Würzburg, Würzburg, Germany
| | - Juliane S Walz
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany.,Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital of Tübingen, Tübingen, Germany
| | - Lisa M Henkel
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Jürgen Krauß
- Department of Neurosurgery, University Medical Center Würzburg, Würzburg, Germany
| | - Martin Ebinger
- University Children's Hospital, University Medical Center Tübingen, Tübingen, Germany
| | - Martin Schuhmann
- Department of Neurosurgery, University Medical Center Tübingen, Tübingen, Germany
| | | | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Erdwine Klinker
- Institute for Transfusion Medicine, University Medical Center Würzburg, Würzburg, Germany
| | - Paul G Schlegel
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Florian Oyen
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yair Reisner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Matthias Eyrich
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
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9
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Höttler A, März L, Lübke M, Rammensee HG, Stevanović S. Broad and Efficient Activation of Memory CD4 + T Cells by Novel HAdV- and HCMV-Derived Peptide Pools. Front Immunol 2021; 12:700438. [PMID: 34322126 PMCID: PMC8312486 DOI: 10.3389/fimmu.2021.700438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 12/03/2022] Open
Abstract
Reactivation of Human Cytomegalovirus (HCMV) and Human Adenovirus (HAdV) in immunocompromised patients following stem cell transplantation (SCT) or solid organ transplantation (SOT) is associated with high morbidity and mortality. The adoptive transfer of virus-specific CD8+ and CD4+ T cells has been shown to re-establish the antiviral T-cell response and improve clinical outcome. The viral load in immunocompromised patients can efficiently be reduced solely by the infusion of virus-specific CD4+ T cells. The identification of CD4+ T-cell epitopes has mainly focused on a limited number of viral proteins that were characterized as immunodominant. Here, we used in silico prediction to determine promiscuous CD4+ T-cell epitopes from the entire proteomes of HCMV and HAdV. Immunogenicity testing with enzyme-linked immuno spot (ELISpot) assays and intracellular cytokine staining (ICS) revealed numerous novel CD4+ T-cell epitopes derived from a broad spectrum of viral antigens. We identified 17 novel HCMV-derived and seven novel HAdV-derived CD4+ T-cell epitopes that were recognized by > 50% of the assessed peripheral blood mononuclear cell (PBMC) samples. The newly identified epitopes were pooled with previously published, retested epitopes to stimulate virus-specific memory T cells in PBMCs from numerous randomly selected blood donors. Our peptide pools induced strong IFNγ secretion in 46 out of 48 (HCMV) and 31 out of 31 (HAdV) PBMC cultures. In conclusion, we applied an efficient method to screen large viral proteomes for promiscuous CD4+ T-cell epitopes to improve the detection and isolation of virus-specific T cells in a clinical setting.
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Affiliation(s)
- Alexander Höttler
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Léo März
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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10
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Klatt MG, Mack KN, Bai Y, Aretz ZEH, Nathan LI, Mun SS, Dao T, Scheinberg DA. Solving an MHC allele-specific bias in the reported immunopeptidome. JCI Insight 2020; 5:141264. [PMID: 32897882 PMCID: PMC7566711 DOI: 10.1172/jci.insight.141264] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
Identification of MHC class I–bound peptides by immunopurification of MHC complexes and subsequent analysis by mass spectrometry is crucial for understanding T cell immunology and immunotherapy. Investigation of the steps for the MHC ligand isolation process revealed biases in widely used isolation techniques toward peptides of lower hydrophobicity. As MHC ligand hydrophobicity correlates positively with immunogenicity, identification of more hydrophobic MHC ligands could potentially lead to more effective isolation of immunogenic peptides as targets for immunotherapies. We solved this problem by use of higher concentrations of acetonitrile for the separation of MHC ligands and their respective complexes. This increased overall MHC ligand identifications by 2-fold, increased detection of cancer germline antigen–derived peptides by 50%, and resulted in profound variations in isolation efficacy between different MHC alleles correlating with the hydrophobicity of their anchor residues. Overall, these insights enabled a more complete view of the immunopeptidome and overcame a systematic underrepresentation of these critical MHC ligands of high hydrophobicity. An approach is identified to prevent bias in the immunopeptidome towards MHC ligands of lower hydrophobicity and therefore immunogenicity.
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Affiliation(s)
- Martin G Klatt
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kyeara N Mack
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Pharmacology Department and
| | - Yang Bai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Pharmacology Department and
| | - Zita E H Aretz
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Physiology Biophysics and Systems Biology Program, Weill Cornell Medicine, New York, New York, USA
| | - Levy I Nathan
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sung Soo Mun
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tao Dao
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Scheinberg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Pharmacology Department and
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11
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Nelde A, Bilich T, Heitmann JS, Maringer Y, Salih HR, Roerden M, Lübke M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Traenkle B, Kaiser PD, Rothbauer U, Becker M, Junker D, Krause G, Strengert M, Schneiderhan-Marra N, Templin MF, Joos TO, Kowalewski DJ, Stos-Zweifel V, Fehr M, Rabsteyn A, Mirakaj V, Karbach J, Jäger E, Graf M, Gruber LC, Rachfalski D, Preuß B, Hagelstein I, Märklin M, Bakchoul T, Gouttefangeas C, Kohlbacher O, Klein R, Stevanović S, Rammensee HG, Walz JS. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nat Immunol 2020; 22:74-85. [PMID: 32999467 DOI: 10.1038/s41590-020-00808-x] [Citation(s) in RCA: 385] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022]
Abstract
T cell immunity is central for the control of viral infections. To characterize T cell immunity, but also for the development of vaccines, identification of exact viral T cell epitopes is fundamental. Here we identify and characterize multiple dominant and subdominant SARS-CoV-2 HLA class I and HLA-DR peptides as potential T cell epitopes in COVID-19 convalescent and unexposed individuals. SARS-CoV-2-specific peptides enabled detection of post-infectious T cell immunity, even in seronegative convalescent individuals. Cross-reactive SARS-CoV-2 peptides revealed pre-existing T cell responses in 81% of unexposed individuals and validated similarity with common cold coronaviruses, providing a functional basis for heterologous immunity in SARS-CoV-2 infection. Diversity of SARS-CoV-2 T cell responses was associated with mild symptoms of COVID-19, providing evidence that immunity requires recognition of multiple epitopes. Together, the proposed SARS-CoV-2 T cell epitopes enable identification of heterologous and post-infectious T cell immunity and facilitate development of diagnostic, preventive and therapeutic measures for COVID-19.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Maren Lübke
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Bjoern Traenkle
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Philipp D Kaiser
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.,Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Matthias Becker
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | | | - Markus F Templin
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Thomas O Joos
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | | | - Michael Fehr
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Armin Rabsteyn
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,Department of General Pediatrics, Oncology/Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Valbona Mirakaj
- Department of Anesthesia and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Julia Karbach
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Elke Jäger
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Michael Graf
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena-Christin Gruber
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - David Rachfalski
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Beate Preuß
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Ilona Hagelstein
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Tamam Bakchoul
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Cécile Gouttefangeas
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max-Planck-Institute for Developmental Biology, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany. .,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.
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12
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Reguzova A, Ghosh M, Müller M, Rziha HJ, Amann R. Orf Virus-Based Vaccine Vector D1701-V Induces Strong CD8+ T Cell Response against the Transgene but Not against ORFV-Derived Epitopes. Vaccines (Basel) 2020; 8:E295. [PMID: 32531997 PMCID: PMC7349966 DOI: 10.3390/vaccines8020295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/14/2023] Open
Abstract
The potency of viral vector-based vaccines depends on their ability to induce strong transgene-specific immune response without triggering anti-vector immunity. Previously, Orf virus (ORFV, Parapoxvirus) strain D1701-V was reported as a novel vector mediating protection against viral infections. The short-lived ORFV-specific immune response and the absence of virus neutralizing antibodies enables repeated immunizations and enhancement of humoral immune responses against the inserted antigens. However, only limited information exists about the D1701-V induced cellular immunity. In this study we employed major histocompatibility complex (MHC) ligandomics and immunogenicity analysis to identify ORFV-specific epitopes. Using liquid chromatography-tandem mass spectrometry we detected 36 ORFV-derived MHC I peptides, originating from various proteins. Stimulated splenocytes from ORFV-immunized mice did not exhibit specific CD8+ T cell responses against the tested peptides. In contrast, immunization with ovalbumin-expressing ORFV recombinant elicited strong SIINFEKL-specific CD8+ T lymphocyte response. In conclusion, our data indicate that cellular immunity to the ORFV vector is negligible, while strong CD8+ T cell response is induced against the inserted transgene. These results further emphasize the ORFV strain D1701-V as an attractive vector for vaccine development. Moreover, the presented experiments describe prerequisites for the selection of T cell epitopes exploitable for generation of ORFV-based vaccines by reverse genetics.
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Affiliation(s)
| | | | | | | | - Ralf Amann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.G.); (M.M.); (H.-J.R.)
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