1
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Stevanović S, Knežević M, Obraz M, Košec A. Successful emergency Lichtenberger lateralisation for immediate bilateral laryngeal immobility after total thyroidectomy: a CARE case report. J Laryngol Otol 2023; 137:1413-1415. [PMID: 37039448 DOI: 10.1017/s0022215123000646] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
OBJECTIVE This case report discusses a successful emergency Lichtenberger lateralisation procedure after immediate bilateral laryngeal immobility, occurring after total thyroidectomy. METHODS A 63-year-old female with right-sided vocal fold paralysis due to compression by a multinodular thyroid goitre underwent total thyroidectomy, which resulted in immediate post-operative bilateral vocal fold immobility. The patient had acute-onset post-operative dyspnoea, was promptly re-intubated, and an emergency lateralisation Lichtenberger suture was placed over the right vocal fold and fixated on the outer surface of the neck. RESULTS After two weeks, her right vocal fold recovered first, with the suture still in place. At four weeks, both vocal folds regained function and the suture was extracted. CONCLUSION The take-away message is that an emergency lateralisation suture may be a viable option in maintaining airway patency, while allowing for normal deglutition, in patients who would otherwise be candidates for prolonged intubation, posterior cordotomy, medial arytenoidectomy or tracheostomy.
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Affiliation(s)
- S Stevanović
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospital Center Sestre Milosrdnice, Zagreb, Croatia
| | - M Knežević
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospital Center Sestre Milosrdnice, Zagreb, Croatia
| | - M Obraz
- Department of Anesthesiology and Intensive Care, University Hospital Center Sestre Milosrdnice, Zagreb, Croatia
| | - A Košec
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospital Center Sestre Milosrdnice, Zagreb, Croatia
- School of Medicine, University of Zagreb, Zagreb, Croatia
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2
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Čukman M, Tkalčec L, Stevanović S, Čupić H, Ivkić PK, Košec A. Accidental laryngeal cancer removal during tracheal intubation. Anaesth Rep 2023; 11:e12247. [PMID: 37736062 PMCID: PMC10511153 DOI: 10.1002/anr3.12247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
- M. Čukman
- Department of Otorhinolaryngology and Head and Neck SurgeryUHC Sestre milosrdniceZagrebCroatia
| | - L. Tkalčec
- School of MedicineUniversity of ZagrebZagrebCroatia
| | - S. Stevanović
- Department of Otorhinolaryngology and Head and Neck SurgeryUniversity Hospital Center Sestre MilosrdniceZagrebCroatia
| | - H. Čupić
- School of MedicineUniversity of ZagrebZagrebCroatia
- Department of PathologyUniversity Hospital Center Sestre MilosrdniceZagrebCroatia
| | - P. K. Ivkić
- Department of OphthalmologyUniversity Hospital Center ZagrebZagrebCroatia
| | - A. Košec
- School of MedicineUniversity of ZagrebZagrebCroatia
- Department of Otorhinolaryngology and Head and Neck SurgeryUniversity Hospital Center Sestre MilosrdniceZagrebCroatia
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3
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Sarango G, Richetta C, Pereira M, Kumari A, Ghosh M, Bertrand L, Pionneau C, Le Gall M, Grégoire S, Jeger‐Madiot R, Rosoy E, Subra F, Delelis O, Faure M, Esclatine A, Graff‐Dubois S, Stevanović S, Manoury B, Ramirez BC, Moris A. The Autophagy Receptor TAX1BP1 (T6BP) improves antigen presentation by MHC-II molecules. EMBO Rep 2022; 23:e55470. [PMID: 36215666 PMCID: PMC9724678 DOI: 10.15252/embr.202255470] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/23/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 12/12/2022] Open
Abstract
CD4+ T lymphocytes play a major role in the establishment and maintenance of immunity. They are activated by antigenic peptides derived from extracellular or newly synthesized (endogenous) proteins presented by the MHC-II molecules. The pathways leading to endogenous MHC-II presentation remain poorly characterized. We demonstrate here that the autophagy receptor, T6BP, influences both autophagy-dependent and -independent endogenous presentation of HIV- and HCMV-derived peptides. By studying the immunopeptidome of MHC-II molecules, we show that T6BP affects both the quantity and quality of peptides presented. T6BP silencing induces the mislocalization of the MHC-II-loading compartments and rapid degradation of the invariant chain (CD74) without altering the expression and internalization kinetics of MHC-II molecules. Defining the interactome of T6BP, we identify calnexin as a T6BP partner. We show that the calnexin cytosolic tail is required for this interaction. Remarkably, calnexin silencing replicates the functional consequences of T6BP silencing: decreased CD4+ T cell activation and exacerbated CD74 degradation. Altogether, we unravel T6BP as a key player of the MHC-II-restricted endogenous presentation pathway, and we propose one potential mechanism of action.
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Affiliation(s)
- Gabriela Sarango
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Clémence Richetta
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance,LBPA, ENS‐Paris Saclay, CNRS UMR8113Université Paris SaclayGif‐sur‐YvetteFrance
| | - Mathias Pereira
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Anita Kumari
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Michael Ghosh
- Department of Immunology, Institute for Cell BiologyUniversity of TübingenTübingenGermany
| | - Lisa Bertrand
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Cédric Pionneau
- Sorbonne UniversitéINSERM, UMS Production et Analyse de Données en Sciences de la vie et en Santé, PASS, Plateforme Post‐génomique de la Pitié SalpêtrièreParisFrance
| | - Morgane Le Gall
- 3P5 proteom'IC facilityUniversité de Paris, Institut Cochin, INSERM U1016, CNRS‐UMR 8104ParisFrance
| | - Sylvie Grégoire
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Raphaël Jeger‐Madiot
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance,Present address:
Sorbonne Université, INSERM U959, Immunology‐Immunopathology‐Immunotherapy (i3)ParisFrance
| | - Elina Rosoy
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Frédéric Subra
- LBPA, ENS‐Paris Saclay, CNRS UMR8113Université Paris SaclayGif‐sur‐YvetteFrance
| | - Olivier Delelis
- LBPA, ENS‐Paris Saclay, CNRS UMR8113Université Paris SaclayGif‐sur‐YvetteFrance
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonLyonFrance,Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM
| | - Audrey Esclatine
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Stéphanie Graff‐Dubois
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance,Present address:
Sorbonne Université, INSERM U959, Immunology‐Immunopathology‐Immunotherapy (i3)ParisFrance
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell BiologyUniversity of TübingenTübingenGermany
| | - Bénédicte Manoury
- Institut Necker Enfants Malades, INSERM U1151‐CNRS UMR 8253, Faculté de médecine NeckerUniversité de ParisParisFrance
| | - Bertha Cecilia Ramirez
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Arnaud Moris
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
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4
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Bittner ZA, Liu X, Mateo Tortola M, Tapia-Abellán A, Shankar S, Andreeva L, Mangan M, Spalinger M, Kalbacher H, Düwell P, Lovotti M, Bosch K, Dickhöfer S, Marcu A, Stevanović S, Herster F, Cardona Gloria Y, Chang TH, Bork F, Greve CL, Löffler MW, Wolz OO, Schilling NA, Kümmerle-Deschner JB, Wagner S, Delor A, Grimbacher B, Hantschel O, Scharl M, Wu H, Latz E, Weber ANR. BTK operates a phospho-tyrosine switch to regulate NLRP3 inflammasome activity. J Exp Med 2021; 218:212658. [PMID: 34554188 PMCID: PMC8480672 DOI: 10.1084/jem.20201656] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 03/18/2021] [Accepted: 08/05/2021] [Indexed: 12/18/2022] Open
Abstract
Activity of the NLRP3 inflammasome, a critical mediator of inflammation, is controlled by accessory proteins, posttranslational modifications, cellular localization, and oligomerization. How these factors relate is unclear. We show that a well-established drug target, Bruton’s tyrosine kinase (BTK), affects several levels of NLRP3 regulation. BTK directly interacts with NLRP3 in immune cells and phosphorylates four conserved tyrosine residues upon inflammasome activation, in vitro and in vivo. Furthermore, BTK promotes NLRP3 relocalization, oligomerization, ASC polymerization, and full inflammasome assembly, probably by charge neutralization, upon modification of a polybasic linker known to direct NLRP3 Golgi association and inflammasome nucleation. As NLRP3 tyrosine modification by BTK also positively regulates IL-1β release, we propose BTK as a multifunctional positive regulator of NLRP3 regulation and BTK phosphorylation of NLRP3 as a novel and therapeutically tractable step in the control of inflammation.
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Affiliation(s)
- Zsófia Agnes Bittner
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Xiao Liu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Maria Mateo Tortola
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Ana Tapia-Abellán
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sangeetha Shankar
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Liudmila Andreeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Matthew Mangan
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Marianne Spalinger
- Department for Gastroenterology and Hepatology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Peter Düwell
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany
| | - Marta Lovotti
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany
| | - Karlotta Bosch
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sabine Dickhöfer
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Franziska Herster
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Yamel Cardona Gloria
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Tzu-Hsuan Chang
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Francesca Bork
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Carsten L Greve
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence 2180, Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany
| | - Olaf-Oliver Wolz
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Jasmin B Kümmerle-Deschner
- Division of Pediatric Rheumatology and Autoinflammation Reference Center Tübingen, Department of Pediatrics, University Hospital Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 2124, Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Anita Delor
- Centre of Chronic Immunodeficiency, University Hospital Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Centre of Chronic Immunodeficiency, University Hospital Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs University, Freiburg, Germany.,German Center for Infection Research, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, Albert-Ludwigs University, Freiburg, Germany.,Cluster of Excellence 2155, Resolving Infection Susceptibility, Hanover Medical School, Freiburg, Germany
| | - Oliver Hantschel
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps University of Marburg, Marburg, Germany
| | - Michael Scharl
- Department for Gastroenterology and Hepatology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, Bonn, Germany.,Division of Infectious Diseases and Immunology, University of Massachusetts, Worcester, MA
| | - Alexander N R Weber
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 2180, Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 2124, Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany.,German Cancer Consortium, Tübingen, Germany
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5
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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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6
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Bilich T, Nelde A, Heitmann JS, Maringer Y, Roerden M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Rachfalski D, Märklin M, Stevanović S, Rammensee HG, Salih HR, Walz JS. T cell and antibody kinetics delineate SARS-CoV-2 peptides mediating long-term immune responses in COVID-19 convalescent individuals. Sci Transl Med 2021; 13:eabf7517. [PMID: 33723016 PMCID: PMC8128286 DOI: 10.1126/scitranslmed.abf7517] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [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: 11/17/2020] [Revised: 01/14/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Long-term immunological memory to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for the development of population-level immunity, which is the aim of vaccination approaches. Reports on rapidly decreasing antibody titers have led to questions regarding the efficacy of humoral immunity alone. The relevance of T cell memory after coronavirus disease 2019 (COVID-19) remains unclear. Here, we investigated SARS-CoV-2 antibody and T cell responses in matched samples of COVID-19 convalescent individuals up to 6 months after infection. Longitudinal analysis revealed decreasing and stable spike- and nucleocapsid-specific antibody responses, respectively. In contrast, functional T cell responses remained robust, and even increased, in both frequency and intensity. Single peptide mapping of T cell diversity over time identified open reading frame-independent, dominant T cell epitopes mediating long-term SARS-CoV-2 T cell responses. Identification of these epitopes may be fundamental for COVID-19 vaccine design.
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Affiliation(s)
- Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - David Rachfalski
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), 70376 Stuttgart, Germany
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7
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Marcu A, Bichmann L, Kuchenbecker L, Kowalewski DJ, Freudenmann LK, Backert L, Mühlenbruch L, Szolek A, Lübke M, Wagner P, Engler T, Matovina S, Wang J, Hauri-Hohl M, Martin R, Kapolou K, Walz JS, Velz J, Moch H, Regli L, Silginer M, Weller M, Löffler MW, Erhard F, Schlosser A, Kohlbacher O, Stevanović S, Rammensee HG, Neidert MC. HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. J Immunother Cancer 2021; 9:e002071. [PMID: 33858848 PMCID: PMC8054196 DOI: 10.1136/jitc-2020-002071] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level. METHODS Human tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing. RESULTS The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference. CONCLUSION Given that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org .
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Affiliation(s)
- Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Daniel Johannes Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Linus Backert
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - András Szolek
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Philipp Wagner
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Tobias Engler
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Sabine Matovina
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Konstantina Kapolou
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Juliane Sarah Walz
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital of Tübingen, Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology (IKP) and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Julia Velz
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Luca Regli
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Manuela Silginer
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus W Löffler
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University of Hospital Tübingen, Tübingen, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Bayern, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center - Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Marian Christoph Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich and ETH Zurich, Zurich, Switzerland
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8
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Halabi S, Ghosh M, Stevanović S, Rammensee HG, Bertzbach LD, Kaufer BB, Moncrieffe MC, Kaspers B, Härtle S, Kaufman J. The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek's disease virus peptides by using an unprecedented binding motif. PLoS Biol 2021; 19:e3001057. [PMID: 33901176 PMCID: PMC8101999 DOI: 10.1371/journal.pbio.3001057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/07/2020] [Revised: 05/06/2021] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek's disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek's disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek's disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek's disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.
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Affiliation(s)
- Samer Halabi
- University of Cambridge, Department of Pathology, Cambridge, United Kingdom
- University of Edinburgh, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
| | - Michael Ghosh
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | | | | | | | - Bernd Kaspers
- Ludwig Maximillians University, Veterinary Faculty, Planegg, Germany
| | - Sonja Härtle
- Ludwig Maximillians University, Veterinary Faculty, Planegg, Germany
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Cambridge, United Kingdom
- University of Edinburgh, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
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9
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Schöllhorn A, Schuhmacher J, Besedovsky L, Fendel R, Jensen ATR, Stevanović S, Lange T, Rammensee HG, Born J, Gouttefangeas C, Dimitrov S. Integrin Activation Enables Sensitive Detection of Functional CD4 + and CD8 + T Cells: Application to Characterize SARS-CoV-2 Immunity. Front Immunol 2021; 12:626308. [PMID: 33854501 PMCID: PMC8040333 DOI: 10.3389/fimmu.2021.626308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/05/2020] [Accepted: 02/09/2021] [Indexed: 01/28/2023] Open
Abstract
We have previously shown that conformational change in the β2-integrin is a very early activation marker that can be detected with fluorescent multimers of its ligand intercellular adhesion molecule (ICAM)-1 for rapid assessment of antigen-specific CD8+ T cells. In this study, we describe a modified protocol of this assay for sensitive detection of functional antigen-specific CD4+ T cells using a monoclonal antibody (clone m24 Ab) specific for the open, high-affinity conformation of the β2-integrin. The kinetics of β2-integrin activation was different on CD4+ and CD8+ T cells (several hours vs. few minutes, respectively); however, m24 Ab readily stained both cell types 4–6 h after antigen stimulation. With this protocol, we were able to monitor ex vivo effector and memory CD4+ and CD8+ T cells specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cytomegalovirus (CMV), Epstein–Barr virus (EBV), and hepatitis B virus (HBV) in whole blood or cryopreserved peripheral blood mononuclear cells (PBMCs) of infected or vaccinated individuals. By costaining β2-integrin with m24 and CD154 Abs, we assessed extremely low frequencies of polyfunctional CD4+ T cell responses. The novel assay used in this study allows very sensitive and simultaneous screening of both CD4+ and CD8+ T cell reactivities, with versatile applicability in clinical and vaccination studies.
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Affiliation(s)
- Anna Schöllhorn
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Juliane Schuhmacher
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Luciana Besedovsky
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Anja T R Jensen
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - 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
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, 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
| | - Jan Born
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the University of Tübingen (IDM), Tübingen, Germany
| | - Cécile Gouttefangeas
- 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
| | - Stoyan Dimitrov
- Institute of Medical Psychology and Behavioral Neurobiology, University of Tübingen, Tübingen, Germany
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10
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Ghosh M, Hartmann H, Jakobi M, März L, Bichmann L, Freudenmann LK, Mühlenbruch L, Segan S, Rammensee HG, Schneiderhan-Marra N, Shipp C, Stevanović S, Joos TO. The Impact of Biomaterial Cell Contact on the Immunopeptidome. Front Bioeng Biotechnol 2021; 8:571294. [PMID: 33392160 PMCID: PMC7773052 DOI: 10.3389/fbioe.2020.571294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 06/10/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Biomaterials play an increasing role in clinical applications and regenerative medicine. A perfectly designed biomaterial should restore the function of damaged tissue without triggering an undesirable immune response, initiate self-regeneration of the surrounding tissue and gradually degrade after implantation. The immune system is well recognized to play a major role in influencing the biocompatibility of implanted medical devices. To obtain a better understanding of the effects of biomaterials on the immune response, we have developed a highly sensitive novel test system capable of examining changes in the immune system by biomaterial. Here, we evaluated for the first time the immunopeptidome, a highly sensitive system that reflects cancer transformation, virus or drug influences and passes these cellular changes directly to T cells, as a test system to examine the effects of contact with materials. Since monocytes are one of the first immune cells reacting to biomaterials, we have tested the influence of different materials on the immunopeptidome of the monocytic THP-1 cell line. The tested materials included stainless steel, aluminum, zinc, high-density polyethylene, polyurethane films containing zinc diethyldithiocarbamate, copper, and zinc sulfate. The incubation with all material types resulted in significantly modulated peptides in the immunopeptidome, which were material-associated. The magnitude of induced changes in the immunopeptidome after the stimulation appeared comparable to that of bacterial lipopolysaccharides (LPS). The source proteins of many detected peptides are associated with cytotoxicity, fibrosis, autoimmunity, inflammation, and cellular stress. Considering all tested materials, it was found that the LPS-induced cytotoxicity-, inflammation- and cellular stress-associated HLA class I peptides were mainly induced by aluminum, whereas HLA class II peptides were mainly induced by stainless steel. These findings provide the first insights into the effects of biomaterials on the immunopeptidome. A more thorough understanding of these effects may enable the design of more biocompatible implant materials using in vitro models in future. Such efforts will provide a deeper understanding of possible immune responses induced by biomaterials such as fibrosis, inflammation, cytotoxicity, and autoimmune reactions.
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Affiliation(s)
- Michael Ghosh
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.,Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hanna Hartmann
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Meike Jakobi
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Léo März
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Applied Bioinformatics, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Lena K Freudenmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Sören Segan
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | | | - Christopher Shipp
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
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11
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Sturm T, Sautter B, Wörner TP, Stevanović S, Rammensee HG, Planz O, Heck AJR, Aebersold R. Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome. J Proteome Res 2020; 20:289-304. [PMID: 33141586 PMCID: PMC7786382 DOI: 10.1021/acs.jproteome.0c00386] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
To
understand and treat immunology-related diseases, a comprehensive,
unbiased characterization of major histocompatibility complex (MHC)
peptide ligands is of key importance. Preceding the analysis by mass
spectrometry, MHC class I peptide ligands are typically isolated by
MHC immunoaffinity chromatography (MHC-IAC) and less often by mild
acid elution (MAE). MAE may provide a cheap alternative to MHC-IAC
for suspension cells but has been hampered by the high number of contaminating,
MHC-unrelated peptides. Here, we optimized MAE, yielding MHC peptide
ligand purities of more than 80%. When compared with MHC-IAC, obtained
peptides were similar in numbers, identities, and to a large extent
intensities, while the percentage of cysteinylated peptides was 5
times higher in MAE. The latter benefitted the discovery of MHC-allotype-specific,
distinct cysteinylation frequencies at individual positions of MHC
peptide ligands. MAE revealed many MHC ligands with unmodified, N-terminal
cysteine residues which get lost in MHC-IAC workflows. The results
support the idea that MAE might be particularly valuable for the high-confidence
analysis of post-translational modifications by avoiding the exposure
of the investigated peptides to enzymes and reactive molecules in
the cell lysate. Our improved and carefully documented MAE workflow
represents a high-quality, cost-effective alternative to MHC-IAC for
suspension cells.
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Affiliation(s)
- Theo Sturm
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands.,Philochem AG, 8112 Otelfingen, Switzerland
| | - Benedikt Sautter
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias P Wörner
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Planz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.,Faculty of Science, University of Zurich, 8057 Zürich, Switzerland
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12
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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: 383] [Impact Index Per Article: 95.8] [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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13
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Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E. Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy. Genome Med 2020; 12:32. [PMID: 32228647 PMCID: PMC7106651 DOI: 10.1186/s13073-020-00731-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 10/23/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. Methods We analyzed HLA-presented peptides by MS-based ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues, and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate targets with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from The Cancer Genome Atlas (TCGA KIRC, n = 452). DNA methylation (TCGA KIRC, n = 273), somatic mutations (TCGA KIRC, n = 392), and gene ontology (GO) and correlations with tumor metabolites (cohort 1, n = 30) and immune-oncological markers (cohort 1, n = 37) were analyzed to characterize regulatory and functional involvements. CD8+ T cell priming assays were used to identify immunogenic peptides. The candidate gene EGLN3 was functionally investigated in cell culture. Results A total of 34,226 HLA class I- and 19,325 class II-presented peptides were identified in ccRCC tissue, of which 443 class I and 203 class II peptides were ccRCC-specific and presented in ≥ 3 tumors. One hundred eighty-five of the 499 corresponding source genes were involved in pathways activated by ccRCC tumors. After validation in the independent cohort from TCGA, 113 final candidate genes remained. Candidates were involved in extracellular matrix organization, hypoxic signaling, immune processes, and others. Nine of the 12 peptides assessed by immunogenicity analysis were able to activate naïve CD8+ T cells, including peptides derived from EGLN3. Functional analysis of EGLN3 revealed possible tumor-promoting functions. Conclusions Integration of HLA ligandomics, transcriptomics, genetic, and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is recommended to expand the treatment landscape of ccRCC.
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Affiliation(s)
- Anna Reustle
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Carolin Meyerhoff
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Siahei Kandabarau
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Florian Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Steffen Rausch
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Viktoria Stühler
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcus Scharpf
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany. .,University of Tuebingen, Tuebingen, Germany. .,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany. .,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany. .,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany.
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
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14
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Lübke M, Spalt S, Kowalewski DJ, Zimmermann C, Bauersfeld L, Nelde A, Bichmann L, Marcu A, Peper JK, Kohlbacher O, Walz JS, Le-Trilling VTK, Hengel H, Rammensee HG, Stevanović S, Halenius A. Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models. J Exp Med 2020; 217:e20191164. [PMID: 31869419 PMCID: PMC7062530 DOI: 10.1084/jem.20191164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/25/2019] [Revised: 10/24/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022] Open
Abstract
In healthy individuals, immune control of persistent human cytomegalovirus (HCMV) infection is effectively mediated by virus-specific CD4+ and CD8+ T cells. However, identifying the repertoire of T cell specificities for HCMV is hampered by the immense protein coding capacity of this betaherpesvirus. Here, we present a novel approach that employs HCMV deletion mutant viruses lacking HLA class I immunoevasins and allows direct identification of naturally presented HCMV-derived HLA ligands by mass spectrometry. We identified 368 unique HCMV-derived HLA class I ligands representing an unexpectedly broad panel of 123 HCMV antigens. Functional characterization revealed memory T cell responses in seropositive individuals for a substantial proportion (28%) of these novel peptides. Multiple HCMV-directed specificities in the memory T cell pool of single individuals indicate that physiologic anti-HCMV T cell responses are directed against a broad range of antigens. Thus, the unbiased identification of naturally presented viral epitopes enabled a comprehensive and systematic assessment of the physiological repertoire of anti-HCMV T cell specificities in seropositive individuals.
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Affiliation(s)
- Maren Lübke
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Stefanie Spalt
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium, Partner Site Tübingen, Tübingen, Germany
| | - Daniel J. Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Cosima Zimmermann
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annika Nelde
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Janet Kerstin Peper
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | | | - Hartmut Hengel
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium, Partner Site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium, Partner Site Tübingen, Tübingen, Germany
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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15
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Ghosh M, Gauger M, Marcu A, Nelde A, Denk M, Schuster H, Rammensee HG, Stevanović S. Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies. Mol Cell Proteomics 2020; 19:432-443. [PMID: 31937595 PMCID: PMC7050110 DOI: 10.1074/mcp.c119.001652] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/09/2020] [Indexed: 12/30/2022] Open
Abstract
For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. To support clinical trials based on HLA-presented tumor-associated antigens, in this study the sensitive LC-MS/MS HLA class I antigen identification pipeline was fully validated for our technical equipment according to the current US Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines.The immunopeptidomes of JY cells with or without spiked-in, isotope labeled peptides, of peripheral blood mononuclear cells of healthy volunteers as well as a chronic lymphocytic leukemia and a bladder cancer sample were reliably identified using a data-dependent acquisition method. As the LC-MS/MS pipeline is used for identification purposes, the validation parameters include accuracy, precision, specificity, limit of detection and robustness.
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Affiliation(s)
- Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; Natural and Medical Science Institute at the University of Tübingen (NMI), Reutlingen, Germany
| | - Marion Gauger
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Monika Denk
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; German Cancer Research Center (DKFZ) partner site and German Cancer Consortium (DKTK) Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; German Cancer Research Center (DKFZ) partner site and German Cancer Consortium (DKTK) Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; German Cancer Research Center (DKFZ) partner site and German Cancer Consortium (DKTK) Tübingen, Tübingen, Germany.
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16
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Bilich T, Nelde A, Bauer J, Walz S, Roerden M, Salih HR, Weisel K, Besemer B, Marcu A, Lübke M, Schuhmacher J, Neidert MC, Rammensee HG, Stevanović S, Walz JS. Mass spectrometry-based identification of a B-cell maturation antigen-derived T-cell epitope for antigen-specific immunotherapy of multiple myeloma. Blood Cancer J 2020; 10:24. [PMID: 32111817 PMCID: PMC7048774 DOI: 10.1038/s41408-020-0288-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023] Open
Abstract
The B-cell maturation antigen (BCMA) is currently being evaluated as promising tumor-associated surface antigen for T-cell-based immunotherapy approaches, such as CAR T cells and bispecific antibodies, in multiple myeloma (MM). Cytotoxic T cells bearing BCMA-specific T-cell receptors might further allow targeting HLA-presented antigens derived from the intracellular domain of BCMA. By analyzing a mass spectrometry-acquired immunopeptidome dataset of primary MM samples and MM cell lines for BCMA-derived HLA ligands, we identified the naturally presented HLA-B*18-restricted ligand P(BCMA)B*18. Additionally, P(BCMA)B*18 was identified on primary CLL samples, thereby expanding the range for possible applications. P(BCMA)B*18 induced multifunctional BCMA-specific cells de novo from naïve CD8+ T cells of healthy volunteers. These T cells exhibited antigen-specific lysis of autologous peptide-loaded cells. Even in the immunosuppressive context of MM, we detected spontaneous memory T-cell responses against P(BCMA)B*18 in patients. By applying CTLA-4 and PD-1 inhibition in vitro we induced multifunctional P(BCMA)B*18-specific CD8+ T cells in MM patients lacking preexisting BCMA-directed immune responses. Finally, we could show antigen-specific lysis of autologous peptide-loaded target cells and even MM.1S cells naturally presenting P(BCMA)B*18 using patient-derived P(BCMA)B*18-specific T cells. Hence, this BCMA-derived T-cell epitope represents a promising target for T-cell-based immunotherapy and monitoring following immunotherapy in B-cell malignancy patients.
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Affiliation(s)
- Tatjana Bilich
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Annika Nelde
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Jens Bauer
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Simon Walz
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
- University Hospital Tübingen, Department of Urology, Tübingen, Germany
| | - Malte Roerden
- University Hospital Tübingen, Department of Hematology and Oncology, Tübingen, Germany
| | - Helmut R Salih
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Katja Weisel
- University Hospital Tübingen, Department of Hematology and Oncology, Tübingen, Germany
- University Hospital Hamburg-Eppendorf, Department of Oncology, Hamburg-Eppendorf, Germany
| | - Britta Besemer
- University Hospital Tübingen, Department of Hematology and Oncology, Tübingen, Germany
| | - Ana Marcu
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Maren Lübke
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Juliane Schuhmacher
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Marian C Neidert
- University Hospital Zurich and University of Zurich, Department of Neurosurgery, Clinical Neuroscience Center, Zurich, Switzerland
| | - Hans-Georg Rammensee
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany.
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17
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Löffler MW, Nussbaum B, Jäger G, Jurmeister PS, Budczies J, Pereira PL, Clasen S, Kowalewski DJ, Mühlenbruch L, Königsrainer I, Beckert S, Ladurner R, Wagner S, Bullinger F, Gross TH, Schroeder C, Sipos B, Königsrainer A, Stevanović S, Denkert C, Rammensee HG, Gouttefangeas C, Haen SP. A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer. Front Immunol 2019; 10:2526. [PMID: 31803175 PMCID: PMC6877671 DOI: 10.3389/fimmu.2019.02526] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 03/18/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Radiofrequency ablation (RFA) is an established treatment option for malignancies located in the liver. RFA-induced irreversible coagulation necrosis leads to the release of danger signals and cellular content. Hence, RFA may constitute an endogenous in situ tumor vaccination, stimulating innate and adaptive immune responses, including tumor-antigen specific T cells. This may explain a phenomenon termed abscopal effect, namely tumor regression in untreated lesions evidenced after distant thermal ablation or irradiation. In this study, we therefore assessed systemic and local immune responses in individual patients treated with RFA. Methods: For this prospective clinical trial, patients with liver metastasis from colorectal carcinoma (mCRC) receiving RFA and undergoing metachronous liver surgery for another lesion were recruited (n = 9) during a 5-year period. Tumor and non-malignant liver tissue samples from six patients were investigated by whole transcriptome sequencing and tandem-mass spectrometry, characterizing naturally presented HLA ligands. Tumor antigen-derived HLA-restricted peptides were selected by different predefined approaches. Further, candidate HLA ligands were manually curated. Peripheral blood mononuclear cells were stimulated in vitro with epitope candidate peptides, and functional T cell responses were assessed by intracellular cytokine staining. Immunohistochemical markers were additionally investigated in surgically resected mCRC from patients treated with (n = 9) or without RFA (n = 7). Results: In all six investigated patients, either induced immune responses and/or pre-existing T cell immunity against the selected targets were observed. Multi-cytokine responses were inter alia directed against known tumor antigens such as cyclin D1 but also against a (predicted) mutation contained in ERBB3. Immunohistochemistry did not show a relevant influx of immune cells into distant malignant lesions after RFA treatment (n = 9) as compared to the surgery only mCRC group (n = 7). Conclusions: Using an individualized approach for target selection, RFA induced and/or boosted T cell responses specific for individual tumor antigens were more frequently detectable as compared to previously published observations with well-characterized tumor antigens. However, the witnessed modest RFA-induced immunological effects alone may not be sufficient for the rejection of established tumors. Therefore, these findings warrant further clinical investigation including the assessment of RFA combination therapies e.g., with immune stimulatory agents, cancer vaccination, and/or immune checkpoint inhibitors.
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Affiliation(s)
- Markus W Löffler
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Bianca Nussbaum
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Günter Jäger
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | | | - Jan Budczies
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Philippe L Pereira
- Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen, Germany.,Department of Radiology, Minimally Invasive Therapies and Nuclear Medicine, SLK-Hospital Heilbronn GmbH, Heilbronn, Germany
| | - Stephan Clasen
- Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Ingmar Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Beckert
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Ruth Ladurner
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Silvia Wagner
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Florian Bullinger
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Thorben H Gross
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany.,Department Medical Oncology and Pneumology, University Hospital Tübingen, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Bence Sipos
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty 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 (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Institute of Pathology, University Hospital Marburg (UKGM) and Philipps-University Marburg, Marburg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty 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 (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Cécile Gouttefangeas
- Department of Immunology, Interfaculty 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 (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Sebastian P Haen
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany.,Department of Oncology, Hematology and Bone Marrow Transplantation With Division of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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18
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Rammensee HG, Wiesmüller KH, Chandran PA, Zelba H, Rusch E, Gouttefangeas C, Kowalewski DJ, Di Marco M, Haen SP, Walz JS, Gloria YC, Bödder J, Schertel JM, Tunger A, Müller L, Kießler M, Wehner R, Schmitz M, Jakobi M, Schneiderhan-Marra N, Klein R, Laske K, Artzner K, Backert L, Schuster H, Schwenck J, Weber ANR, Pichler BJ, Kneilling M, la Fougère C, Forchhammer S, Metzler G, Bauer J, Weide B, Schippert W, Stevanović S, Löffler MW. A new synthetic toll-like receptor 1/2 ligand is an efficient adjuvant for peptide vaccination in a human volunteer. J Immunother Cancer 2019; 7:307. [PMID: 31730025 PMCID: PMC6858783 DOI: 10.1186/s40425-019-0796-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 06/10/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND We previously showed that the bacterial lipopeptide Pam3Cys-Ser-Ser, meanwhile established as a toll-like receptor (TLR) 1/2 ligand, acts as a strong adjuvant for the induction of virus specific CD8+ T cells in mice, when covalently coupled to a synthetic peptide. CASE PRESENTATION We now designed a new water-soluble synthetic Pam3Cys-derivative, named XS15 and characterized it in vitro by a TLR2 NF-κB luciferase reporter assay. Further, the capacity of XS15 to activate immune cells and stimulate peptide-specific CD8+ T and NK cells by 6-sulfo LacNAc+ monocytes was assessed by flow cytometry as well as cytokine induction using immunoassays. The induction of a functional immune response after vaccination of a volunteer with viral peptides was assessed by ELISpot assay and flow cytometry in peripheral blood cells and infiltrating cells at the vaccination site, as well as by immunohistochemistry and imaging. XS15 induced strong ex vivo CD8+ and TH1 CD4+ responses in a human volunteer upon a single injection of XS15 mixed to uncoupled peptides in a water-in-oil emulsion (Montanide™ ISA51 VG). A granuloma formed locally at the injection site containing highly activated functional CD4+ and CD8+ effector memory T cells. The total number of vaccine peptide-specific functional T cells was experimentally assessed and estimated to be 3.0 × 105 in the granuloma and 20.5 × 106 in peripheral blood. CONCLUSION Thus, in one volunteer we show a granuloma forming by peptides combined with an efficient adjuvant in a water-in-oil-emulsion, inducing antigen specific T cells detectable in circulation and at the vaccination site, after one single vaccination only. The ex vivo T cell responses in peripheral blood were detectable for more than one year and could be strongly boosted by a second vaccination. Hence, XS15 is a promising adjuvant candidate for peptide vaccination, in particular for tumor peptide vaccines in a personalized setting.
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Affiliation(s)
- Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, 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, Tubingen, Germany.
| | | | - P Anoop Chandran
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Henning Zelba
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Elisa Rusch
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, 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, Tubingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.,Present address: Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Sebastian P Haen
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany.,Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University Hospital of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, 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, Tubingen, Germany.,Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University Hospital of Tübingen, Tübingen, Germany
| | - Yamel Cardona Gloria
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Johanna Bödder
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Jill-Marie Schertel
- Faculty of Medicine Carl Gustav Carus, Institute of Immunology, Technische Universität Dresden, Dresden, Germany
| | - Antje Tunger
- Faculty of Medicine Carl Gustav Carus, Institute of Immunology, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany and Helmholtz Association/ Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Luise Müller
- Faculty of Medicine Carl Gustav Carus, Institute of Immunology, Technische Universität Dresden, Dresden, Germany
| | - Maximilian Kießler
- Faculty of Medicine Carl Gustav Carus, Institute of Immunology, Technische Universität Dresden, Dresden, Germany
| | - Rebekka Wehner
- Faculty of Medicine Carl Gustav Carus, Institute of Immunology, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany and Helmholtz Association/ Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Schmitz
- Faculty of Medicine Carl Gustav Carus, Institute of Immunology, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany and Helmholtz Association/ Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Meike Jakobi
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | - Reinhild Klein
- Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University Hospital of Tübingen, Tübingen, Germany
| | - Karoline Laske
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Kerstin Artzner
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.,Present address: Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.,Present address: Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Johannes Schwenck
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tubingen, Germany.,Department of Nuclear Medicine and Clinical Molecular Imaging, University Hospital of Tübingen, Tübingen, Germany.,Werner Siemens Imaging Center, Medical Faculty, University of Tübingen, Tübingen, Germany
| | - Alexander N R Weber
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tubingen, Germany
| | - Bernd J Pichler
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tubingen, Germany.,Werner Siemens Imaging Center, Medical Faculty, University of Tübingen, Tübingen, Germany
| | - Manfred Kneilling
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tubingen, Germany.,Werner Siemens Imaging Center, Medical Faculty, University of Tübingen, Tübingen, Germany.,Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
| | - Christian la Fougère
- 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, Tubingen, Germany.,Department of Nuclear Medicine and Clinical Molecular Imaging, University Hospital of Tübingen, Tübingen, Germany
| | - Stephan Forchhammer
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
| | - Gisela Metzler
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
| | - Jürgen Bauer
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
| | - Benjamin Weide
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
| | - Wilfried Schippert
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, 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, Tubingen, Germany
| | - Markus W Löffler
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, 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, Tubingen, Germany. .,Department of General, Visceral and Transplant Surgery, University Hospital of Tübingen, Tübingen, Germany. .,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany.
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19
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Kapolou K, Katharina Freudenmann L, Friebel E, Bichmann L, Becher B, Stevanović S, Rammensee HG, Weller M, Christoph Neidert M. IMMU-08. THE ANTIGENIC LANDSCAPE OF GLIOBLASTOMA - REFINING THE TARGETS FOR IMMUNOTHERAPY. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
We provide a comprehensive analysis of the antigenic landscape of glioblastoma using a multi-omics approach including ligandome mapping of the Human Leukocyte Antigen (HLA) ligandome, next generation sequencing (NGS) as well as an in-depth characterization of tumor-infiltrating lymphocytes (TIL) using mass cytometry and ultra-deep sequencing of the T-cell receptor (TCR). Tumor-exclusive HLA class I and class II ligands (immune precipitation and LC-MS/MS) of 24 isocitrate dehydrogenase 1 wild type glioblastoma samples and 10 autologous primary glioblastoma cell lines were defined in comparison to an HLA ligandome normal tissue reference database (n > 418). We found 11,496 glioblastoma exclusive HLA class I ligands (2,064 shared with cell lines; 3,754 on ≥ 2 glioblastoma samples). On the source protein level, 239 glioblastoma exclusive proteins were identified; among them 54 were also found in cell lines. For HLA class II ligands the analysis revealed 11,870 glioblastoma exclusive peptides (444 shared with cell lines; 3,420 on ≥ 2 glioblastoma samples) and 278 glioblastoma exclusive proteins; among which 18 were present also in cell lines. Moreover, whole-exome sequencing and whole RNA sequencing of 13 tumor samples was performed with the aim to predict neoantigens. On average 5,662 somatic missense effects were identified per patient (min: 4,258; max: 7,479). Candidate peptides are grouped into (i) in silico predicted neoepitopes, (ii) tumor-exclusivity on HLA, (iii) gene expression (e.g. cancer testis antigens). Top-ranking candidates from each group will be tested with regards to their immunogenicity in an autologous setting (TIL, peripheral blood mononuclear cells, patient derived tumor cells). Finally, the peptide and immunogenicity data is correlated with the immune phenotype of the TIL compartment as well as the TCR repertoire of the sample.
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Affiliation(s)
- Konstantina Kapolou
- University Hospital and University of Zurich, Department of Neurology, Laboratory of Molecular Neuro-Oncology, Zurich, Switzerland
| | | | | | - Leon Bichmann
- Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | | | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Hans-Georg Rammensee
- Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
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20
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Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O. MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. J Proteome Res 2019; 18:3876-3884. [DOI: 10.1021/acs.jproteome.9b00313] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Stefan Stevanović
- German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen 72076, Germany
| | | | - Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
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21
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Ivić MA, Lović J, Stevanović S, Nikolić N, Trišović N, Lađarević J, Vuković D, Drmanić S, Mladenović A, Jadranin M, Petrović S, Mijin D. Electrochemical behavior of esomeprazole: Its determination at Au electrode as standard and in injection powder combined with the study of its degradation. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.113303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Audehm S, Glaser M, Pecoraro M, Bräunlein E, Mall S, Klar R, Effenberger M, Albers J, Bianchi HDO, Peper J, Yusufi N, Busch DH, Stevanović S, Mann M, Antes I, Krackhardt AM. Key Features Relevant to Select Antigens and TCR From the MHC-Mismatched Repertoire to Treat Cancer. Front Immunol 2019; 10:1485. [PMID: 31316521 PMCID: PMC6611213 DOI: 10.3389/fimmu.2019.01485] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 11/27/2018] [Accepted: 06/13/2019] [Indexed: 11/13/2022] Open
Abstract
Adoptive transfer of T cells transgenic for tumor-reactive T-cell receptors (TCR) is an attractive immunotherapeutic approach. However, clinical translation is so far limited due to challenges in the identification of suitable target antigens as well as TCRs that are concurrent safe and efficient. Definition of key characteristics relevant for effective and specific tumor rejection is essential to improve current TCR-based adoptive T-cell immunotherapies. We here characterized in-depth two TCRs derived from the human leukocyte antigen (HLA)-mismatched allogeneic repertoire targeting two different myeloperoxidase (MPO)-derived peptides presented by the same HLA-restriction element side by side comprising state of the art biochemical and cellular in vitro, in vivo, and in silico experiments. In vitro experiments reveal comparable functional avidities, off-rates, and cytotoxic activities for both TCRs. However, we observed differences especially with respect to cytokine secretion and cross-reactivity as well as in vivo activity. Biochemical and in silico analyses demonstrate different binding qualities of MPO-peptides to the HLA-complex determining TCR qualities. We conclude from our biochemical and in silico analyses of peptide-HLA-binding that rigid and high-affinity binding of peptides is one of the most important factors for isolation of TCRs with high specificity and tumor rejection capacity from the MHC-mismatched repertoire. Based on our results, we developed a workflow for selection of such TCRs with high potency and safety profile suitable for clinical translation.
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Affiliation(s)
- Stefan Audehm
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Manuel Glaser
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Freising, Germany
| | - Matteo Pecoraro
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Eva Bräunlein
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sabine Mall
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Richard Klar
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Manuel Effenberger
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Julian Albers
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Henrique de Oliveira Bianchi
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Janet Peper
- Eberhard Karls University Tübingen, Interfaculty Institute for Cell Biology, Tübingen, Germany
| | - Nahid Yusufi
- Nuklearmedizin, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Dirk H Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Stefan Stevanović
- Eberhard Karls University Tübingen, Interfaculty Institute for Cell Biology, Tübingen, Germany.,Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Iris Antes
- Center for Integrated Protein Science at the Department for Biosciences, Technische Universität München, Freising, Germany
| | - Angela M Krackhardt
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,Partner Site Munich, German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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23
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Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A, Rammensee HG. Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome Med 2019; 11:28. [PMID: 31039795 PMCID: PMC6492406 DOI: 10.1186/s13073-019-0636-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs. METHODS In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data. RESULTS The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations. CONCLUSIONS This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.
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Affiliation(s)
- Markus W. Löffler
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
| | - Christopher Mohr
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Leon Bichmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- Center for Bioinformatics, University of Tübingen, Sand 14, D-72076 Tübingen, Germany
- Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076 Tübingen, Germany
| | - Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Mathias Walzer
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- Center for Bioinformatics, University of Tübingen, Sand 14, D-72076 Tübingen, Germany
- Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076 Tübingen, Germany
- Present address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Christopher M. Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076 Tübingen, Germany
| | - Nico Trautwein
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
| | - Franz J. Hilke
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076 Tübingen, Germany
| | - Raphael S. Zinser
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
| | - Lena Mühlenbruch
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
| | - Daniel J. Kowalewski
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076 Tübingen, Germany
| | - Heiko Schuster
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076 Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076 Tübingen, Germany
| | - Jakob Matthes
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076 Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Stefan Czemmel
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Ingmar Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
| | - Karolin Thiel
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
| | - Silvio Nadalin
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
| | - Stefan Beckert
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
- Present address: Department of General and Visceral Surgery, Schwarzwald-Baar Hospital, Klinikstr. 11, D-78052 Villingen-Schwenningen, Germany
| | - Hans Bösmüller
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, D-72076 Tübingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, D-72076 Tübingen, Germany
| | - Ana Velic
- Interfaculty Institute for Cell Biology, Proteome Center Tübingen (PCT), University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Boris Maček
- Interfaculty Institute for Cell Biology, Proteome Center Tübingen (PCT), University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Sebastian P. Haen
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
- Internal Medicine, Department for Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University of Tübingen, Otfried-Müller-Str. 10, D-72076 Tübingen, Germany
| | - Luigi Buonaguro
- Cancer Immunoregulation Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, “Fondazione Pascale” – IRCCS, 80131 Naples, Italy
| | - Oliver Kohlbacher
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
- Center for Bioinformatics, University of Tübingen, Sand 14, D-72076 Tübingen, Germany
- Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- Max Planck Institute for Developmental Biology, Biomolecular Interactions, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - HEPAVAC Consortium
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076 Tübingen, Germany
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076 Tübingen, Germany
- Center for Bioinformatics, University of Tübingen, Sand 14, D-72076 Tübingen, Germany
- Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076 Tübingen, Germany
- Present address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076 Tübingen, Germany
- Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- Present address: Department of General and Visceral Surgery, Schwarzwald-Baar Hospital, Klinikstr. 11, D-78052 Villingen-Schwenningen, Germany
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, D-72076 Tübingen, Germany
- Interfaculty Institute for Cell Biology, Proteome Center Tübingen (PCT), University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
- Internal Medicine, Department for Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University of Tübingen, Otfried-Müller-Str. 10, D-72076 Tübingen, Germany
- Cancer Immunoregulation Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, “Fondazione Pascale” – IRCCS, 80131 Naples, Italy
- Max Planck Institute for Developmental Biology, Biomolecular Interactions, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
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24
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Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A, Rammensee HG. Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome Med 2019. [PMID: 31039795 DOI: 10.1186/s13073-019-0636-8.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs. METHODS In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data. RESULTS The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations. CONCLUSIONS This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.
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Affiliation(s)
- Markus W Löffler
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076, Tübingen, Germany. .,Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany. .,Department of Clinical Pharmacology, University Hospital Tübingen, Auf der Morgenstelle 8, D-72076, Tübingen, Germany.
| | - Christopher Mohr
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.,Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076, Tübingen, Germany
| | - Leon Bichmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,Center for Bioinformatics, University of Tübingen, Sand 14, D-72076, Tübingen, Germany.,Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Mathias Walzer
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,Center for Bioinformatics, University of Tübingen, Sand 14, D-72076, Tübingen, Germany.,Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076, Tübingen, Germany.,Present address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,, United Kingdom
| | - Christopher M Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076, Tübingen, Germany
| | - Nico Trautwein
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany
| | - Franz J Hilke
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076, Tübingen, Germany
| | - Raphael S Zinser
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany
| | - Lena Mühlenbruch
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany
| | - Daniel J Kowalewski
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076, Tübingen, Germany
| | - Heiko Schuster
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076, Tübingen, Germany
| | - Jakob Matthes
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Calwerstr. 7, D-72076, Tübingen, Germany.,NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Stefan Czemmel
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076, Tübingen, Germany
| | - Ingmar Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076, Tübingen, Germany
| | - Karolin Thiel
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076, Tübingen, Germany
| | - Silvio Nadalin
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076, Tübingen, Germany
| | - Stefan Beckert
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076, Tübingen, Germany.,Present address: Department of General and Visceral Surgery, Schwarzwald-Baar Hospital, Klinikstr. 11, D-78052, Villingen-Schwenningen, Germany
| | - Hans Bösmüller
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, D-72076, Tübingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Liebermeisterstr. 8, D-72076, Tübingen, Germany
| | - Ana Velic
- Interfaculty Institute for Cell Biology, Proteome Center Tübingen (PCT), University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Boris Maček
- Interfaculty Institute for Cell Biology, Proteome Center Tübingen (PCT), University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Sebastian P Haen
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Internal Medicine, Department for Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University of Tübingen, Otfried-Müller-Str. 10, D-72076, Tübingen, Germany
| | - Luigi Buonaguro
- Cancer Immunoregulation Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale" - IRCCS, 80131, Naples, Italy
| | - Oliver Kohlbacher
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.,Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, D-72076, Tübingen, Germany.,Center for Bioinformatics, University of Tübingen, Sand 14, D-72076, Tübingen, Germany.,Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076, Tübingen, Germany.,NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany.,Max Planck Institute for Developmental Biology, Biomolecular Interactions, Spemannstr. 35, D-72076, Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Hoppe-Seyler-Str. 3, D-72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | | | - Hans-Georg Rammensee
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
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25
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Ahmetlić F, Riedel T, Hömberg N, Bauer V, Trautwein N, Geishauser A, Sparwasser T, Stevanović S, Röcken M, Mocikat R. Regulatory T Cells in an Endogenous Mouse Lymphoma Recognize Specific Antigen Peptides and Contribute to Immune Escape. Cancer Immunol Res 2019; 7:600-608. [PMID: 30894379 DOI: 10.1158/2326-6066.cir-18-0419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/13/2018] [Accepted: 01/29/2019] [Indexed: 11/16/2022]
Abstract
Foxp3+ regulatory T cells (Tregs) sustain immune homeostasis and may contribute to immune escape in malignant disease. As a prerequisite for developing immunologic approaches in cancer therapy, it is necessary to understand the ontogeny and the antigenic specificities of tumor-infiltrating Tregs. We addressed this question by using a λ-MYC transgenic mouse model of endogenously arising B-cell lymphoma, which mirrors key features of human Burkitt lymphoma. We show that Foxp3+ Tregs suppress antitumor responses in endogenous lymphoma. Ablation of Foxp3+ Tregs significantly delayed tumor development. The ratio of Treg to effector T cells was elevated in growing tumors, which could be ascribed to differential proliferation. The Tregs detected were mainly natural Tregs that apparently recognized self-antigens. We identified MHC class II-restricted nonmutated self-epitopes, which were more prevalent in lymphoma than in normal B cells and could be recognized by Tregs. These epitopes were derived from proteins that are associated with cellular processes related to malignancy and may be overexpressed in the tumor.
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Affiliation(s)
- Fatima Ahmetlić
- Helmholtz-Zentrum München, Eigenständige Forschungseinheit Translationale Molekulare Immunologie, München, Germany.,Helmholtz-Zentrum München, Institut für Molekulare Immunologie, München, Germany
| | - Tanja Riedel
- Helmholtz-Zentrum München, Institut für Molekulare Immunologie, München, Germany
| | - Nadine Hömberg
- Helmholtz-Zentrum München, Eigenständige Forschungseinheit Translationale Molekulare Immunologie, München, Germany.,Helmholtz-Zentrum München, Institut für Molekulare Immunologie, München, Germany
| | - Vera Bauer
- Helmholtz-Zentrum München, Eigenständige Forschungseinheit Translationale Molekulare Immunologie, München, Germany
| | - Nico Trautwein
- Eberhard-Karls-Universität, Interfakultäres Institut für Zellbiologie, Tübingen, Germany
| | - Albert Geishauser
- Helmholtz-Zentrum München, Eigenständige Forschungseinheit Translationale Molekulare Immunologie, München, Germany.,Helmholtz-Zentrum München, Institut für Molekulare Immunologie, München, Germany
| | - Tim Sparwasser
- Institut für Infektionsimmunologie, Twincore, Zentrum für Experimentelle und Klinische Infektionsforschung, Hannover, and Institut für Medizinische Mikrobiologie und Hygiene, Johannes-Gutenberg-Universität, Mainz, Germany
| | - Stefan Stevanović
- Eberhard-Karls-Universität, Interfakultäres Institut für Zellbiologie, Tübingen, Germany
| | - Martin Röcken
- Eberhard-Karls-Universität, Universitäts-Hautklinik, Tübingen, Germany
| | - Ralph Mocikat
- Helmholtz-Zentrum München, Eigenständige Forschungseinheit Translationale Molekulare Immunologie, München, Germany. .,Helmholtz-Zentrum München, Institut für Molekulare Immunologie, München, Germany
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26
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Hilf N, Kuttruff-Coqui S, Frenzel K, Bukur V, Stevanović S, Gouttefangeas C, Platten M, Tabatabai G, Dutoit V, van der Burg SH, Straten PT, Martinez-Ricarte F, Ponsati B, Okada H, Lassen U, Admon A, Ottensmeier CH, Ulges A, Kreiter S, von Deimling A, Skardelly M, Migliorini D, Kroep JR, Idorn M, Rodon J, Piro J, Poulsen HS, Shraibman B, McCann K, Mendrzyk R, Lower M, Stieglbauer M, Britten CM, Capper D, Welters MJP, Sahuquillo J, Kiesel K, Derhovanessian E, Rusch E, Bunse L, Song C, Heesch S, Wagner C, Kemmer-Bruck A, Ludwig J, Castle JC, Schoor O, Tadmor AD, Green E, Fritsche J, Meyer M, Pawlowski N, Dorner S, Hoffgaard F, Rossler B, Maurer D, Weinschenk T, Reinhardt C, Huber C, Rammensee HG, Singh-Jasuja H, Sahin U, Dietrich PY, Wick W. Publisher Correction: Actively personalized vaccination trial for newly diagnosed glioblastoma. Nature 2019; 566:E13. [PMID: 30733620 DOI: 10.1038/s41586-019-0959-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The additional author support information was erroneously omitted from the Supplementary Information. This has been corrected online.
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Affiliation(s)
- Norbert Hilf
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | - Stefan Stevanović
- Eberhard Karls Universität Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany
| | - Cecile Gouttefangeas
- Eberhard Karls Universität Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany.,CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Michael Platten
- University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany.,Medical Faculty Mannheim, Mannheim, Germany
| | - Ghazaleh Tabatabai
- Eberhard Karls Universität Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany.,University Hospital Tübingen, Tübingen, Germany
| | | | - Sjoerd H van der Burg
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany.,Leiden University Medical Center, Leiden, The Netherlands
| | - Per Thor Straten
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany.,Center for Cancer Immune Therapy (CCIT), Department of Hematology, University Hospital Herlev, Herlev, Denmark.,Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Hideho Okada
- University of California, San Francisco, San Francisco, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Arie Admon
- Technion - Israel Institute of Technology, Haifa, Israel
| | | | | | - Sebastian Kreiter
- BioNTech AG, Mainz, Germany.,CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Andreas von Deimling
- University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | | | | | - Judith R Kroep
- Leiden University Medical Center, Leiden, The Netherlands
| | - Manja Idorn
- Center for Cancer Immune Therapy (CCIT), Department of Hematology, University Hospital Herlev, Herlev, Denmark.,Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jordi Rodon
- Vall d'Hebron University Hospital, Barcelona, Spain.,M. D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | | | | | | | | | | | | | - Monika Stieglbauer
- Eberhard Karls Universität Tübingen, Tübingen, Germany.,CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Cedrik M Britten
- BioNTech AG, Mainz, Germany.,CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany.,Oncology R&D, GlaxoSmithKline, Stevenage, UK
| | - David Capper
- University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany.,Charité, University Medicine Berlin, Berlin, Germany
| | - Marij J P Welters
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany.,Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Elisa Rusch
- Eberhard Karls Universität Tübingen, Tübingen, Germany.,CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Lukas Bunse
- University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Colette Song
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | - Jorg Ludwig
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | - John C Castle
- BioNTech AG, Mainz, Germany.,Agenus Inc, Lexington, KY, USA
| | | | - Arbel D Tadmor
- TRON GmbH - Translational Oncology at the University Medical Center of Johannes Gutenberg University, Mainz, Germany
| | - Edward Green
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany.,Medical Faculty Mannheim, Mannheim, Germany
| | | | - Miriam Meyer
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | - Sonja Dorner
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | | | | | | | - Hans-Georg Rammensee
- Eberhard Karls Universität Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany
| | | | | | | | - Wolfgang Wick
- University Hospital Heidelberg, Heidelberg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany.
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27
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Hilf N, Kuttruff-Coqui S, Frenzel K, Bukur V, Stevanović S, Gouttefangeas C, Platten M, Tabatabai G, Dutoit V, van der Burg SH, Thor Straten P, Martínez-Ricarte F, Ponsati B, Okada H, Lassen U, Admon A, Ottensmeier CH, Ulges A, Kreiter S, von Deimling A, Skardelly M, Migliorini D, Kroep JR, Idorn M, Rodon J, Piró J, Poulsen HS, Shraibman B, McCann K, Mendrzyk R, Löwer M, Stieglbauer M, Britten CM, Capper D, Welters MJP, Sahuquillo J, Kiesel K, Derhovanessian E, Rusch E, Bunse L, Song C, Heesch S, Wagner C, Kemmer-Brück A, Ludwig J, Castle JC, Schoor O, Tadmor AD, Green E, Fritsche J, Meyer M, Pawlowski N, Dorner S, Hoffgaard F, Rössler B, Maurer D, Weinschenk T, Reinhardt C, Huber C, Rammensee HG, Singh-Jasuja H, Sahin U, Dietrich PY, Wick W. Actively personalized vaccination trial for newly diagnosed glioblastoma. Nature 2019; 565:240-245. [PMID: 30568303 DOI: 10.1038/s41586-018-0810-y] [Citation(s) in RCA: 546] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/19/2018] [Indexed: 12/24/2022]
Abstract
Patients with glioblastoma currently do not sufficiently benefit from recent breakthroughs in cancer treatment that use checkpoint inhibitors1,2. For treatments using checkpoint inhibitors to be successful, a high mutational load and responses to neoepitopes are thought to be essential3. There is limited intratumoural infiltration of immune cells4 in glioblastoma and these tumours contain only 30-50 non-synonymous mutations5. Exploitation of the full repertoire of tumour antigens-that is, both unmutated antigens and neoepitopes-may offer more effective immunotherapies, especially for tumours with a low mutational load. Here, in the phase I trial GAPVAC-101 of the Glioma Actively Personalized Vaccine Consortium (GAPVAC), we integrated highly individualized vaccinations with both types of tumour antigens into standard care to optimally exploit the limited target space for patients with newly diagnosed glioblastoma. Fifteen patients with glioblastomas positive for human leukocyte antigen (HLA)-A*02:01 or HLA-A*24:02 were treated with a vaccine (APVAC1) derived from a premanufactured library of unmutated antigens followed by treatment with APVAC2, which preferentially targeted neoepitopes. Personalization was based on mutations and analyses of the transcriptomes and immunopeptidomes of the individual tumours. The GAPVAC approach was feasible and vaccines that had poly-ICLC (polyriboinosinic-polyribocytidylic acid-poly-L-lysine carboxymethylcellulose) and granulocyte-macrophage colony-stimulating factor as adjuvants displayed favourable safety and strong immunogenicity. Unmutated APVAC1 antigens elicited sustained responses of central memory CD8+ T cells. APVAC2 induced predominantly CD4+ T cell responses of T helper 1 type against predicted neoepitopes.
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Affiliation(s)
- Norbert Hilf
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | - Stefan Stevanović
- Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany
| | - Cécile Gouttefangeas
- Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Michael Platten
- University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
- Medical Faculty Mannheim, Mannheim, Germany
| | - Ghazaleh Tabatabai
- Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany
- University Hospital Tübingen, Tübingen, Germany
| | | | - Sjoerd H van der Burg
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
- Leiden University Medical Center, Leiden, The Netherlands
| | - Per Thor Straten
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
- Center for Cancer Immune Therapy (CCIT), Department of Hematology, University Hospital Herlev, Herlev, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Hideho Okada
- University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Arie Admon
- Technion - Israel Institute of Technology, Haifa, Israel
| | | | | | - Sebastian Kreiter
- BioNTech AG, Mainz, Germany
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Andreas von Deimling
- University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | | | | | - Judith R Kroep
- Leiden University Medical Center, Leiden, The Netherlands
| | - Manja Idorn
- Center for Cancer Immune Therapy (CCIT), Department of Hematology, University Hospital Herlev, Herlev, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jordi Rodon
- Vall d'Hebron University Hospital, Barcelona, Spain
- M. D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | | | | | | | | | | | | | - Monika Stieglbauer
- Eberhard Karls Universität Tübingen, Tübingen, Germany
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Cedrik M Britten
- BioNTech AG, Mainz, Germany
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
- Oncology R&D, GlaxoSmithKline, Stevenage, UK
| | - David Capper
- University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
- Charité, University Medicine Berlin, Berlin, Germany
| | - Marij J P Welters
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
- Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Elisa Rusch
- Eberhard Karls Universität Tübingen, Tübingen, Germany
- CIMT/CIP - Association for Cancer Immunotherapy, working group Cancer Immunoguiding Program, Mainz, Germany
| | - Lukas Bunse
- University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Colette Song
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | - Jörg Ludwig
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | - John C Castle
- BioNTech AG, Mainz, Germany
- Agenus Inc., Lexington, KY, USA
| | | | - Arbel D Tadmor
- TRON GmbH - Translational Oncology at the University Medical Center of Johannes Gutenberg University, Mainz, Germany
| | - Edward Green
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
- Medical Faculty Mannheim, Mannheim, Germany
| | | | - Miriam Meyer
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | - Sonja Dorner
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | | | | | | | - Hans-Georg Rammensee
- Eberhard Karls Universität Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center Partner Site Tübingen, Tübingen, Germany
| | | | | | | | - Wolfgang Wick
- University Hospital Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany.
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28
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Abstract
MHC class I peptide motifs are used on a regular basis to identify and predict MHC class I ligands and CD8+ T cell epitopes. This approach is above all an invaluable tool for the identification of disease-associated epitopes ranging from pathogen associated epitopes, tumor associated natural and neoepitopes to autoimmune disease associated epitopes. As a matter of fact, the vast majority of T cell epitopes discovered during the past two decades was identified by means of epitope prediction and MHC ligand identification. Here we describe the steps which are necessary to identify MHC epitopes from monoallelic and multiallelic cells and establish MHC class I peptide motifs to compose a reliable scoring matrix for epitope prediction. As an example, the ligands of monoallelic C1R cells and multiallelic peripheral blood mononuclear cell tissue will be identified and a scoring matrix for the prediction of HLA-C*01:02-presented T cell epitopes will be developed.
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Affiliation(s)
- Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
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29
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Abstract
The large-scale and in-depth identification of MHC class I- and II-presented peptides is indispensable for gaining insight into the fundamental rules of immune recognition as well as for developing innovative immunotherapeutic approaches against cancer and other diseases. In this chapter we briefly review the existing strategies for the isolation of MHC-restricted peptides and provide a detailed protocol for the immunoaffinity purification of MHC class I- and II-presented peptides from primary tissues or cells.
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Affiliation(s)
- Annika Nelde
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.
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30
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Ilca FT, Neerincx A, Hermann C, Marcu A, Stevanović S, Deane JE, Boyle LH. TAPBPR mediates peptide dissociation from MHC class I using a leucine lever. eLife 2018; 7:40126. [PMID: 30484775 PMCID: PMC6307860 DOI: 10.7554/elife.40126] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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: 07/15/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022] Open
Abstract
Tapasin and TAPBPR are known to perform peptide editing on major histocompatibility complex class I (MHC I) molecules; however, the precise molecular mechanism(s) involved in this process remain largely enigmatic. Here, using immunopeptidomics in combination with novel cell-based assays that assess TAPBPR-mediated peptide exchange, we reveal a critical role for the K22-D35 loop of TAPBPR in mediating peptide exchange on MHC I. We identify a specific leucine within this loop that enables TAPBPR to facilitate peptide dissociation from MHC I. Moreover, we delineate the molecular features of the MHC I F pocket required for TAPBPR to promote peptide dissociation in a loop-dependent manner. These data reveal that chaperone-mediated peptide editing on MHC I can occur by different mechanisms dependent on the C-terminal residue that the MHC I accommodates in its F pocket and provide novel insights that may inform the therapeutic potential of TAPBPR manipulation to increase tumour immunogenicity.
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Affiliation(s)
- F Tudor Ilca
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Neerincx
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Clemens Hermann
- Department of Integrative Biomedical Sciences, Division of Chemical and Systems Biology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium, Tübingen, Germany
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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31
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Marijt KA, Blijleven L, Verdegaal EME, Kester MG, Kowalewski DJ, Rammensee HG, Stevanović S, Heemskerk MHM, van der Burg SH, van Hall T. Identification of non-mutated neoantigens presented by TAP-deficient tumors. J Exp Med 2018; 215:2325-2337. [PMID: 30115740 PMCID: PMC6122969 DOI: 10.1084/jem.20180577] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 12/29/2022] Open
Abstract
A hybrid forward-reversed immunological screen is performed to identify 16 novel HLA-A2 presented cancer antigens. These peptides are selectively presented by immune-escaped cancer cells with defects in the peptide transporter TAP. In contrast to mutated neoantigens, these “self” neoantigens are universally presented across different cancer types. Most T cell–based immunotherapies of cancer depend on intact antigen presentation by HLA class I molecules (HLA-I). However, defects in the antigen-processing machinery can cause downregulation of HLA-I, rendering tumor cells resistant to CD8+ T cells. Previously, we demonstrated that a unique category of cancer antigens is selectively presented by tumor cells deficient for the peptide transporter TAP, enabling a specific attack of such tumors without causing immunopathology in mouse models. With a novel combinatorial screening approach, we now identify 16 antigens of this category in humans. These HLA-A*02:01 presented peptides do not derive from the mutanome of cancers, but are of “self” origin and therefore constitute universal neoantigens. Indeed, CD8+ T cells specific for the leader peptide of the ubiquitously expressed LRPAP1 protein recognized TAP-deficient, HLA-Ilow lymphomas, melanomas, and renal and colon carcinomas, but not healthy counterparts. In contrast to personalized mutanome-targeted therapies, these conserved neoantigens and their cognate receptors can be exploited for immune-escaped cancers across diverse histological origins.
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Affiliation(s)
- Koen A Marijt
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Laura Blijleven
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Els M E Verdegaal
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Michel G Kester
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Daniel J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium, German Cancer Research Center, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium, German Cancer Research Center, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium, German Cancer Research Center, Tübingen, Germany
| | | | - Sjoerd H van der Burg
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
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32
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Neidert MC, Kowalewski DJ, Silginer M, Kapolou K, Backert L, Freudenmann LK, Peper JK, Marcu A, Wang SSY, Walz JS, Wolpert F, Rammensee HG, Henschler R, Lamszus K, Westphal M, Roth P, Regli L, Stevanović S, Weller M, Eisele G. The natural HLA ligandome of glioblastoma stem-like cells: antigen discovery for T cell-based immunotherapy. Acta Neuropathol 2018; 135:923-938. [PMID: 29557506 DOI: 10.1007/s00401-018-1836-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 01/27/2023]
Abstract
Glioblastoma is the most frequent malignant primary brain tumor. In a hierarchical tumor model, glioblastoma stem-like cells (GSC) play a major role in tumor initiation and maintenance as well as in therapy resistance and recurrence. Thus, targeting this cellular subset may be key to effective immunotherapy. Here, we present a mass spectrometry-based analysis of HLA-presented peptidomes of GSC and glioblastoma patient specimens. Based on the analysis of patient samples (n = 9) and GSC (n = 3), we performed comparative HLA peptidome profiling against a dataset of normal human tissues. Using this immunopeptidome-centric approach we could clearly delineate a subset of naturally presented, GSC-associated HLA ligands, which might serve as highly specific targets for T cell-based immunotherapy. In total, we identified 17 antigens represented by 41 different HLA ligands showing natural and exclusive presentation both on GSC and patient samples. Importantly, in vitro immunogenicity and antigen-specific target cell killing assays suggest these peptides to be epitopes of functional CD8+ T cell responses, thus rendering them prime candidates for antigen-specific immunotherapy of glioblastoma.
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33
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Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanović S, Haen SP. Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation. Cancer Res 2018; 78:4627-4641. [PMID: 29789417 DOI: 10.1158/0008-5472.can-17-1745] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/15/2017] [Accepted: 05/16/2018] [Indexed: 11/16/2022]
Abstract
Immune cell infiltrates have proven highly relevant for colorectal carcinoma prognosis, making colorectal cancer a promising candidate for immunotherapy. Because tumors interact with the immune system via HLA-presented peptide ligands, exact knowledge of the peptidome constitution is fundamental for understanding this relationship. Here, we comprehensively describe the naturally presented HLA ligandome of colorectal carcinoma and corresponding nonmalignant colon (NMC) tissue. Mass spectrometry identified 35,367 and 28,132 HLA class I ligands on colorectal carcinoma and NMC, attributable to 7,684 and 6,312 distinct source proteins, respectively. Cancer-exclusive peptides were assessed on source protein level using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein analysis through evolutionary relationships (PANTHER), revealing pathognomonic colorectal carcinoma-associated pathways, including Wnt, TGFβ, PI3K, p53, and RTK-RAS. Relative quantitation of peptide presentation on paired colorectal carcinoma and NMC tissue further identified source proteins from cancer- and infection-associated pathways to be overrepresented merely within the colorectal carcinoma ligandome. From the pool of tumor-exclusive peptides, a selected HLA-ligand subset was assessed for immunogenicity, with the majority exhibiting an existing T-cell repertoire. Overall, these data show that the HLA ligandome reflects cancer-associated pathways implicated in colorectal carcinoma oncogenesis, suggesting that alterations in tumor cell metabolism could result in cancer-specific, albeit not mutation-derived, tumor antigens. Hence, a defined pool of unique tumor peptides, attributable to complex cellular alterations that are exclusive to malignant cells, might comprise promising candidates for immunotherapeutic applications.Significance: Cancer-associated pathways are reflected in the antigenic landscape of colorectal cancer, suggesting that tumor-specific antigens do not necessarily have to be mutation-derived but may also originate from other alterations in cancer cells. Cancer Res; 78(16); 4627-41. ©2018 AACR.
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Affiliation(s)
- Markus W Löffler
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Tübingen, Germany
| | - Daniel J Kowalewski
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Linus Backert
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany.,University of Tübingen, Center for Bioinformatics, Tübingen, Germany
| | - Jörg Bernhardt
- University of Greifswald, Institute of Microbiology, Greifswald, Germany
| | | | - Heiko Schuster
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Florian Dengler
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany.,University Hospital Tübingen, Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, Tübingen, Germany
| | - Daniel Backes
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany.,University Hospital Tübingen, Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, Tübingen, Germany
| | - Hans-Georg Kopp
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,University Hospital Tübingen, Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, Tübingen, Germany
| | - Stefan Beckert
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Tübingen, Germany
| | - Silvia Wagner
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Tübingen, Germany
| | - Ingmar Königsrainer
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Tübingen, Germany
| | - Oliver Kohlbacher
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,University of Tübingen, Center for Bioinformatics, Tübingen, Germany.,University of Tübingen, Quantitative Biology Center (QBiC), Tübingen, Germany.,Max Planck Institute for Developmental Biology, Biomolecular Interactions, Tübingen, Germany
| | - Lothar Kanz
- University Hospital Tübingen, Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, Tübingen, Germany
| | - Alfred Königsrainer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Sebastian P Haen
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany.,University Hospital Tübingen, Department of Oncology, Hematology, Immunology, Rheumatology and Pulmonology, Tübingen, Germany
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Freudenmann LK, Marcu A, Stevanović S. Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. Immunology 2018; 154:331-345. [PMID: 29658117 DOI: 10.1111/imm.12936] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/13/2022] Open
Abstract
The entirety of human leukocyte antigen (HLA)-presented peptides is referred to as the HLA ligandome of a cell or tissue, in tumours often termed immunopeptidome. Mapping the tumour immunopeptidome by mass spectrometry (MS) comprehensively views the pathophysiologically relevant antigenic signature of human malignancies. MS is an unbiased approach stringently filtering the candidates to be tested as opposed to epitope prediction algorithms. In the setting of peptide-specific immunotherapies, MS-based strategies significantly diminish the risk of lacking clinical benefit, as they yield highly enriched amounts of truly presented peptides. Early immunopeptidomic efforts were severely limited by technical sensitivity and manual spectra interpretation. The technological progress with development of orbitrap mass analysers and enhanced chromatographic performance led to vast improvements in mass accuracy, sensitivity, resolution, and speed. Concomitantly, bioinformatic tools were developed to process MS data, integrate sequencing results, and deconvolute multi-allelic datasets. This enabled the immense advancement of tumour immunopeptidomics. Studying the HLA-presented peptide repertoire bears high potential for both answering basic scientific questions and translational application. Mapping the tumour HLA ligandome has started to significantly contribute to target identification for the design of peptide-specific cancer immunotherapies in clinical trials and compassionate need treatments. In contrast to prediction algorithms, rare HLA allotypes and HLA class II can be adequately addressed when choosing MS-guided target identification platforms. Herein, we review the identification of tumour HLA ligands focusing on sources, methods, bioinformatic data analysis, translational application, and provide an outlook on future developments.
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Affiliation(s)
- Lena Katharina Freudenmann
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Ana Marcu
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
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35
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Gravett AM, Trautwein N, Stevanović S, Dalgleish AG, Copier J. Gemcitabine alters the proteasome composition and immunopeptidome of tumour cells. Oncoimmunology 2018; 7:e1438107. [PMID: 29930882 PMCID: PMC5990974 DOI: 10.1080/2162402x.2018.1438107] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 01/05/2023] Open
Abstract
The antigenic makeup of tumour cells can have a profound effect on the progression of cancer and success of immunotherapies. Therefore, one strategy to improve the efficacy of cancer treatments is to augment the antigens displayed by tumours. The present study explores how the recognition of tumour cells may be altered by non-cytotoxic concentrations of gemcitabine (GEM). Testing a panel of chemotherapeutics in human cancer cell lines in vitro, it was found that GEM increased surface expression of HLA-A,B,C and that underlying this were specific increases in β-2-microglobulin and immunoproteasome subunit proteins. Furthermore, the peptide antigen repertoire displayed on HLA class I was altered, revealing a number of novel antigens, many of which that were derived from proteins involved in the DNA-damage response. Changes in the nature of the peptide antigens eluted from HLA-A,B,C after GEM treatment consisted of amino acid anchor-residue modifications and changes in peptide length which rendered peptides likely to favour alternative HLA-alleles and increased their predicted immunogenicity. Signalling through the MAPK/ERK and NFκB/RelB pathways was associated with these changes. These data may explain observations made in previous in vivo studies, advise as to which antigens should be used in future vaccination protocols and reinforce the idea that chemotherapy and immunotherapy could be used in combination.
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Affiliation(s)
- A M Gravett
- Institute for infection and immunity, St George's, University of London, London, UK
| | - N Trautwein
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - S Stevanović
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - A G Dalgleish
- Institute for infection and immunity, St George's, University of London, London, UK
| | - J Copier
- Institute for infection and immunity, St George's, University of London, London, UK
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36
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Nelde A, Kowalewski DJ, Backert L, Schuster H, Werner JO, Klein R, Kohlbacher O, Kanz L, Salih HR, Rammensee HG, Stevanović S, Walz JS. HLA ligandome analysis of primary chronic lymphocytic leukemia (CLL) cells under lenalidomide treatment confirms the suitability of lenalidomide for combination with T-cell-based immunotherapy. Oncoimmunology 2018; 7:e1316438. [PMID: 29632711 DOI: 10.1080/2162402x.2017.1316438] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 02/06/2023] Open
Abstract
Recent studies suggest that CLL is an immunogenic disease, which might be effectively targeted by antigen-specific T-cell-based immunotherapy. However, CLL is associated with a profound immune defect, which might represent a critical limitation for mounting clinically effective antitumor immune responses. As several studies have demonstrated that lenalidomide can reinforce effector T-cell responses in CLL, the combination of T-cell-based immunotherapy with the immunomodulatory drug lenalidomide represents a promising approach to overcome the immunosuppressive state in CLL. Antigen-specific immunotherapy also requires the robust presentation of tumor-associated HLA-presented antigens on target cells. We thus performed a longitudinal study of the effect of lenalidomide on the HLA ligandome of primary CLL cells in vitro. We showed that lenalidomide exposure does not affect absolute HLA class I and II surface expression levels on primary CLL cells. Importantly, semi-quantitative mass spectrometric analyses of the HLA peptidome of three CLL patient samples found only minor qualitative and quantitative effects of lenalidomide on HLA class I- and II-restricted peptide presentation. Furthermore, we confirmed stable presentation of previously described CLL-associated antigens under lenalidomide treatment. Strikingly, among the few HLA ligands showing significant modulation under lenalidomide treatment, we identified upregulated IKZF-derived peptides, which may represent a direct reflection of the cereblon-mediated effect of lenalidomide on CLL cells. Since we could not observe any relevant influence of lenalidomide on the established CLL-associated antigen targets of anticancer T-cell responses, this study validates the suitability of lenalidomide for the combination with antigen-specific T-cell-based immunotherapies.
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Affiliation(s)
- Annika Nelde
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - Daniel J Kowalewski
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Linus Backert
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Jan-Ole Werner
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lothar Kanz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.,Clinical Cooperation Unit Translational Immunology, German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
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37
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Walz JS, Kowalewski DJ, Backert L, Nelde A, Kohlbacher O, Weide B, Kanz L, Salih HR, Rammensee HG, Stevanović S. Favorable immune signature in CLL patients, defined by antigen-specific T-cell responses, might prevent second skin cancers. Leuk Lymphoma 2018; 59:1949-1958. [DOI: 10.1080/10428194.2017.1403022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Juliane Sarah Walz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | | | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Benjamin Weide
- Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Lothar Kanz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - Helmut Rainer Salih
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany
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38
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Di Marco M, Schuster H, Backert L, Ghosh M, Rammensee HG, Stevanović S. Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices. J Immunol 2017; 199:2639-2651. [PMID: 28904123 DOI: 10.4049/jimmunol.1700938] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2023]
Abstract
The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles both in the innate and adaptive immune system. Starting already during embryogenesis and continuing throughout our lives, these three Ags exert major functions in immune tolerance, defense against infections, and anticancer immune responses. Despite these important roles, identification and characterization of the peptides presented by these molecules has been lacking behind the more abundant HLA-A and HLA-B gene products. In this study, we elucidated the peptide specificities of these HLA molecules using a comprehensive analysis of naturally presented peptides. To that end, the 15 most frequently expressed HLA-C alleles as well as HLA-E*01:01 and HLA-G*01:01 were transfected into lymphoblastoid C1R cells expressing low endogenous HLA. Identification of naturally presented peptides was performed by immunoprecipitation of HLA and subsequent analysis of HLA-bound peptides by liquid chromatographic tandem mass spectrometry. Peptide motifs of HLA-C unveil anchors in position 2 or 3 with high variances between allotypes, and a less variable anchor at the C-terminal end. The previously reported small ligand repertoire of HLA-E was confirmed within our analysis, and we could show that HLA-G combines a large ligand repertoire with distinct features anchoring peptides at positions 3 and 9, supported by an auxiliary anchor in position 1 and preferred residues in positions 2 and 7. The wealth of HLA ligands resulted in prediction matrices for octa-, nona-, and decamers. Matrices were validated in terms of their binding prediction and compared with the latest NetMHC prediction algorithm NetMHCpan-3.0, which demonstrated their predictive power.
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Affiliation(s)
- Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Immatics Biotechnologies GmbH, 72076 Tübingen, Germany; and
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany;
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39
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Neerincx A, Hermann C, Antrobus R, van Hateren A, Cao H, Trautwein N, Stevanović S, Elliott T, Deane JE, Boyle LH. TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway. eLife 2017; 6:e23049. [PMID: 28425917 PMCID: PMC5441866 DOI: 10.7554/elife.23049] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 04/14/2017] [Indexed: 11/24/2022] Open
Abstract
Recently, we revealed that TAPBPR is a peptide exchange catalyst that is important for optimal peptide selection by MHC class I molecules. Here, we asked whether any other co-factors associate with TAPBPR, which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle that is known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex, dependent on a conserved cysteine at position 94 in TAPBPR, in which TAPBPR promotes the association of UGT1 with peptide-receptive MHC class I molecules. We reveal that the interaction between TAPBPR and UGT1 facilities the reglucosylation of the glycan on MHC class I molecules, promoting their recognition by calreticulin. Our results suggest that in addition to being a peptide editor, TAPBPR improves peptide optimisation by promoting peptide-receptive MHC class I molecules to associate with the peptide-loading complex.
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Affiliation(s)
- Andreas Neerincx
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Clemens Hermann
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Andy van Hateren
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Science, University of Southampton, Southampton, United Kingdom
| | - Huan Cao
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Nico Trautwein
- Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Tim Elliott
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Science, University of Southampton, Southampton, United Kingdom
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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40
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Löffler MW, Chandran PA, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yañez VA, Mohr C, Sturm M, Nguyen HP, Riess O, Bauer P, Nahnsen S, Nadalin S, Zieker D, Glatzle J, Thiel K, Schneiderhan-Marra N, Clasen S, Bösmüller H, Fend F, Kohlbacher O, Gouttefangeas C, Stevanović S, Königsrainer A, Rammensee HG. Erratum to "Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient". J Hepatol 2017; 66:252-253. [PMID: 27863814 PMCID: PMC6880294 DOI: 10.1016/j.jhep.2016.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Markus W. Löffler
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany,University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany,Corresponding author. Address: University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany. Tel.: +49 7071 29 80992; fax: +49 7071 29 5653.
| | - P. Anoop Chandran
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Karoline Laske
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany,Current address: Immatics Biotechnologies GmbH, Paul Ehrlich Str. 15, 72076 Tübingen, Germany
| | - Christopher Schroeder
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Irina Bonzheim
- University Hospital Tübingen, Institute of Pathology, Liebermeisterstr. 8, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
| | - Mathias Walzer
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany,University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany,University of Tübingen, Dept. of Computer Science, Sand 14, 72076 Tübingen, Germany
| | - Franz J. Hilke
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Nico Trautwein
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Daniel J. Kowalewski
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany,Current address: Immatics Biotechnologies GmbH, Paul Ehrlich Str. 15, 72076 Tübingen, Germany
| | - Heiko Schuster
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Marc Günder
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Viviana A. Carcamo Yañez
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Christopher Mohr
- University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany,University of Tübingen, Dept. of Computer Science, Sand 14, 72076 Tübingen, Germany
| | - Marc Sturm
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Huu-Phuc Nguyen
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Olaf Riess
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Peter Bauer
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
| | - Sven Nahnsen
- University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany,University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Silvio Nadalin
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Derek Zieker
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Jörg Glatzle
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany,Current address: Klinikum Konstanz, Luisenstr. 7, 78464 Konstanz, Germany
| | - Karolin Thiel
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Nicole Schneiderhan-Marra
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Stephan Clasen
- University Hospital Tübingen, Department of Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Hans Bösmüller
- University Hospital Tübingen, Institute of Pathology, Liebermeisterstr. 8, 72076 Tübingen, Germany
| | - Falko Fend
- University Hospital Tübingen, Institute of Pathology, Liebermeisterstr. 8, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
| | - Oliver Kohlbacher
- University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany,University of Tübingen, Dept. of Computer Science, Sand 14, 72076 Tübingen, Germany,University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, 72076 Tübingen, Germany,Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
| | - Cécile Gouttefangeas
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
| | - Alfred Königsrainer
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site, Tübingen, Germany
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Nelde A, Walz JS, Kowalewski DJ, Schuster H, Wolz OO, Peper JK, Cardona Gloria Y, Langerak AW, Muggen AF, Claus R, Bonzheim I, Fend F, Salih HR, Kanz L, Rammensee HG, Stevanović S, Weber ANR. HLA class I-restricted MYD88 L265P-derived peptides as specific targets for lymphoma immunotherapy. Oncoimmunology 2016; 6:e1219825. [PMID: 28405493 PMCID: PMC5384368 DOI: 10.1080/2162402x.2016.1219825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 04/01/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 12/28/2022] Open
Abstract
Genome sequencing has uncovered an array of recurring somatic mutations in different non-Hodgkin lymphoma (NHL) subtypes. If affecting protein-coding regions, such mutations may yield mutation-derived peptides that may be presented by HLA class I proteins and recognized by cytotoxic T cells. A recurring somatic and oncogenic driver mutation of the Toll-like receptor adaptor protein MYD88, Leu265Pro (L265P) was identified in up to 90% of different NHL subtype patients. We therefore screened the potential of MYD88L265P-derived peptides to elicit cytotoxic T cell responses as tumor-specific neoantigens. Based on in silico predictions, we identified potential MYD88L265P-containing HLA ligands for several HLA class I restrictions. A set of HLA class I MYD88L265P-derived ligands elicited specific cytotoxic T cell responses for HLA-B*07 and -B*15. These data highlight the potential of MYD88L265P mutation-specific peptide-based immunotherapy as a novel personalized treatment approach for patients with MYD88L265P+ NHLs that may complement pharmacological approaches targeting oncogenic MyD88 L265P signaling.
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Affiliation(s)
- Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Juliane Sarah Walz
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | | | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Olaf-Oliver Wolz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Janet Kerstin Peper
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Yamel Cardona Gloria
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Anton W. Langerak
- Department of Immunology, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Alice F. Muggen
- Department of Immunology, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Rainer Claus
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
| | - Irina Bonzheim
- Department of Pathology, University Hospital Tübingen, Tübingen, Germany
| | - Falko Fend
- Department of Pathology, University Hospital Tübingen, Tübingen, Germany
| | - Helmut Rainer Salih
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
- Clinical Cooperation Unit Translational Immunology, German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany
| | - Lothar Kanz
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany
| | - Alexander N. R. Weber
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
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Barth SM, Schreitmüller CM, Proehl F, Oehl K, Lumpp LM, Kowalewski DJ, Di Marco M, Sturm T, Backert L, Schuster H, Stevanović S, Rammensee HG, Planz O. Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy. PLoS One 2016; 11:e0167017. [PMID: 27893789 PMCID: PMC5125661 DOI: 10.1371/journal.pone.0167017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 08/26/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022] Open
Abstract
There are limitations in pre-clinical settings using mice as a basis for clinical development in humans. In cancer, similarities exist between humans and dogs; thus, the dog patient can be a link in the transition from laboratory research on mouse models to clinical trials in humans. Knowledge of the peptides presented on MHC molecules is fundamental for the development of highly specific T cell-based immunotherapies. This information is available for human MHC molecules but is absent for the canine MHC. In the present study, we characterized the binding motif of dog leukocyte antigen (DLA) class I allele DLA-88*50101, using human C1R and K562 transfected cells expressing the DLA-88*50101 heavy chain. MHC class I immunoaffinity-purification revealed 3720 DLA-88*50101 derived peptides, which enabled the determination of major anchor positions. The characterized binding motif of DLA-88*50101 was similar to HLA-A*02:01. Peptide binding analyses on HLA-A*02:01 and DLA-88*50101 via flow cytometry showed weak binding of DLA-88*50101 derived peptides to HLA-A*02:01, and vice versa. Our results present for the first time a detailed peptide binding motif of the canine MHC class I allelic product DLA-88*50101. These data support the goal of establishing dogs as a suitable animal model for the evaluation and development of T cell-based cancer immunotherapies, benefiting both dog and human patients.
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Affiliation(s)
- Sharon M. Barth
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | | | - Franziska Proehl
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Kathrin Oehl
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Institute for Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Leonie M. Lumpp
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Daniel J. Kowalewski
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Immatics, Biotechnologies GmbH, Tuebingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Theo Sturm
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Linus Backert
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Applied Bioinformatics, Center of Bioinformatics and Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- Institute for Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Stevanović
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Oliver Planz
- Department of Immunology, Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
- * E-mail:
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Löffler MW, Chandran PA, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yañez VA, Mohr C, Sturm M, Nguyen HP, Riess O, Bauer P, Nahnsen S, Nadalin S, Zieker D, Glatzle J, Thiel K, Schneiderhan-Marra N, Clasen S, Bösmüller H, Fend F, Kohlbacher O, Gouttefangeas C, Stevanović S, Königsrainer A, Rammensee HG. Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient. J Hepatol 2016; 65:849-855. [PMID: 27397612 PMCID: PMC5756536 DOI: 10.1016/j.jhep.2016.06.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/16/2016] [Accepted: 06/29/2016] [Indexed: 01/06/2023]
Abstract
BACKGROUND & AIMS We report a novel experimental immunotherapeutic approach in a patient with metastatic intrahepatic cholangiocarcinoma. In the 5year course of the disease, the initial tumor mass, two local recurrences and a lung metastasis were surgically removed. Lacking alternative treatment options, aiming at the induction of anti-tumor T cells responses, we initiated a personalized multi-peptide vaccination, based on in-depth analysis of tumor antigens (immunopeptidome) and sequencing. METHODS Tumors were characterized by immunohistochemistry, next-generation sequencing and mass spectrometry of HLA ligands. RESULTS Although several tumor-specific neo-epitopes were predicted in silico, none could be validated by mass spectrometry. Instead, a personalized multi-peptide vaccine containing non-mutated tumor-associated epitopes was designed and applied. Immunomonitoring showed vaccine-induced T cell responses to three out of seven peptides administered. The pulmonary metastasis resected after start of vaccination showed strong immune cell infiltration and perforin positivity, in contrast to the previous lesions. The patient remains clinically healthy, without any radiologically detectable tumors since March 2013 and the vaccination is continued. CONCLUSIONS This remarkable clinical course encourages formal clinical studies on adjuvant personalized peptide vaccination in cholangiocarcinoma. LAY SUMMARY Metastatic cholangiocarcinomas, cancers that originate from the liver bile ducts, have very limited treatment options and a fatal prognosis. We describe a novel therapeutic approach in such a patient using a personalized multi-peptide vaccine. This vaccine, developed based on the characterization of the patient's tumor, evoked detectable anti-tumor immune responses, associating with long-term tumor-free survival.
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Affiliation(s)
- Markus W Löffler
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany; University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany.
| | - P Anoop Chandran
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Karoline Laske
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany; Current address: Immatics Biotechnologies GmbH, Paul Ehrlich Str. 15, 72076 Tübingen, Germany
| | - Christopher Schroeder
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Irina Bonzheim
- University Hospital Tübingen, Institute of Pathology, Liebermeisterstr. 8, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
| | - Mathias Walzer
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany; University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany; University of Tübingen, Dept. of Computer Science, Sand 14, 72076 Tübingen, Germany
| | - Franz J Hilke
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Nico Trautwein
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Daniel J Kowalewski
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany; Current address: Immatics Biotechnologies GmbH, Paul Ehrlich Str. 15, 72076 Tübingen, Germany
| | - Heiko Schuster
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Marc Günder
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Viviana A Carcamo Yañez
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Christopher Mohr
- University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany; University of Tübingen, Dept. of Computer Science, Sand 14, 72076 Tübingen, Germany
| | - Marc Sturm
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Huu-Phuc Nguyen
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Olaf Riess
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Peter Bauer
- University Hospital Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
| | - Sven Nahnsen
- University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany; University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Silvio Nadalin
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Derek Zieker
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Jörg Glatzle
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany; Current address: Klinikum Konstanz, Luisenstr. 7, 78464 Konstanz, Germany
| | - Karolin Thiel
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Nicole Schneiderhan-Marra
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Stephan Clasen
- University Hospital Tübingen, Department of Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
| | - Hans Bösmüller
- University Hospital Tübingen, Institute of Pathology, Liebermeisterstr. 8, 72076 Tübingen, Germany
| | - Falko Fend
- University Hospital Tübingen, Institute of Pathology, Liebermeisterstr. 8, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
| | - Oliver Kohlbacher
- University of Tübingen, Center for Bioinformatics, Sand 14, 72076 Tübingen, Germany; University of Tübingen, Dept. of Computer Science, Sand 14, 72076 Tübingen, Germany; University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, 72076 Tübingen, Germany; Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
| | - Cécile Gouttefangeas
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
| | - Alfred Königsrainer
- University Hospital Tübingen, Department of General, Visceral and Transplant Surgery, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Auf der Morgenstelle 15, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Germany
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Klatt MG, Kowalewski DJ, Schuster H, Di Marco M, Hennenlotter J, Stenzl A, Rammensee HG, Stevanović S. Carcinogenesis of renal cell carcinoma reflected in HLA ligands: A novel approach for synergistic peptide vaccination design. Oncoimmunology 2016; 5:e1204504. [PMID: 27622074 DOI: 10.1080/2162402x.2016.1204504] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 01/08/2023] Open
Abstract
Despite recent advances in immunotherapy of renal cell carcinoma (RCC), peptide vaccination strategies still lack an approach for personalized peptide vaccination that takes intra- and inter-tumoral heterogeneity and biological characteristics into account. In this study, we use an immunoprecipitation and mass spectrometry-based approach supplemented by network analysis of HLA ligands to target this goal. By analyzing HLA-presented peptides for HLA class I and II of 11 malignant and 6 non-malignant kidney tissue samples, more than 2,700 peptides and 1,600 corresponding source proteins were identified. A high overlap with HLA ligands derived from peripheral blood mononuclear cells (PBMCs) was detected most likely due to tumor-infiltrating inflammatory cells and therefore excluded from network analysis. Subsequent biological function analysis of HLA ligands by the GeneMANIA online platform showed enrichment for well established, but also novel, pathways and biological processes involved in carcinogenesis of RCC almost exclusively in malignant tissue samples. By exploring source proteins involved in these overrepresented pathways, we verified various known tumor-associated antigens (TAAs) for RCC (e.g., CA9, EGLN3, IGFBP3, MMP7, PAX2, VEGFA, or EGFR) but could also detect novel TAAs for RCC (e.g., PLOD2, LOX, ENPEP, or TGFBI). Some of these new TAAs had already been shown to elicit a T cell response in cancer patients. Thus, network analysis of HLA ligands provided a new platform for implementing personalized, multipeptide vaccines with potentially synergistic antitumor effects.
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Affiliation(s)
- Martin G Klatt
- Department of Hematology and Oncology, University of Tübingen , Tübingen, Germany
| | - Daniel J Kowalewski
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - Heiko Schuster
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - Moreno Di Marco
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | | | - Arnulf Stenzl
- Department of Urology, University of Tübingen , Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen , Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen , Tübingen, Germany
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45
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Kowalewski DJ, Walz S, Backert L, Schuster H, Kohlbacher O, Weisel K, Rittig SM, Kanz L, Salih HR, Rammensee HG, Stevanović S, Stickel JS. Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini. Blood Cancer J 2016; 6:e411. [PMID: 27058226 PMCID: PMC4855252 DOI: 10.1038/bcj.2016.14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 02/03/2023] Open
Abstract
Recent studies suggest that multiple myeloma is an immunogenic disease, which might be effectively targeted by antigen-specific T-cell immunotherapy. As standard of care in myeloma includes proteasome inhibitor therapy, it is of great importance to characterize the effects of this treatment on HLA-restricted antigen presentation and implement only robustly presented targets for immunotherapeutic intervention. Here, we present a study that longitudinally and semi-quantitatively maps the effects of the proteasome inhibitor carfilzomib on HLA-restricted antigen presentation. The relative presentation levels of 4780 different HLA ligands were quantified in an in vitro model employing carfilzomib treatment of MM.1S and U266 myeloma cells, which revealed significant modulation of a substantial fraction of the HLA-presented peptidome. Strikingly, we detected selective down-modulation of HLA ligands with aromatic C-terminal anchor amino acids. This particularly manifested as a marked reduction in the presentation of HLA ligands through the HLA allotypes A*23:01 and A*24:02 on MM.1S cells. These findings implicate that carfilzomib mediates a direct, peptide motif-specific inhibitory effect on HLA ligand processing and presentation. As a substantial proportion of HLA allotypes present peptides with aromatic C-termini, our results may have broad implications for the implementation of antigen-specific treatment approaches in patients undergoing carfilzomib treatment.
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Affiliation(s)
- D J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - S Walz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - L Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - H Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - O Kohlbacher
- Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Tübingen, Germany.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - K Weisel
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - S M Rittig
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - L Kanz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - H R Salih
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.,Clinical Cooperation Unit Translational Immunology, German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - H-G Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - S Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - J S Stickel
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
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46
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Prokop L, Souczek S, Peper J, Rammensee HG, Stevanović S. Abstract B057: Optimizing the high throughput in vitro priming of tumor specific T cells. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-b057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Peptide-based vaccines are a promising strategy for immunotherapy against cancer. Our group has characterized large numbers of HLA ligands from tumor cells; among them many that might be used for in vivo induction of tumor-specific immune responses. For the development of peptide-based immunotherapies such peptides should be able to induce in vivo tumor-directed immune responses, especially by CD8+ T cells that have a key role in inducing death of tumor cells. The aim of our work is to establish a fast and efficient workflow for immunogenicity testing of tumor-extracted HLA ligands. T cells usually depend on professional antigen presenting cells such as autologous dendritic cells (DCs) for specific induction and expansion. Since the generation of dendritic cells is expensive and time consuming with varying quality and amount of differentiated DCs, we established an artificial system to replace cell-based in vitro priming of T cells, streptavidin-coated artificial antigen presenting cells loaded with defined amounts of recombinant HLA molecules and costimulatory antibodies such as anti-CD28. Using the standard protocol, CD8+ T cells are stimulated three times with artificial antigen presenting cells in weekly intervals in the presence of IL-2 and IL-12. Peptide-specific CD8+ T cells are identified by tetramer staining. Our group started to vary different parameters of this protocol to increase the frequency and number of antigen specific T cells. Alternate costimulatory antibodies and cytokines proved successful to reach that goal. Employing artificial APCs for in vitro priming of tumor-reactive T cells will foster immunogenicity analysis of novel peptides for immunotherapy.
Citation Format: Lea Prokop, Stefanie Souczek, Janet Peper, Hans-Georg Rammensee, Stefan Stevanović. Optimizing the high throughput in vitro priming of tumor specific T cells. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B057.
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Affiliation(s)
- Lea Prokop
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Baden-Württemberg, Germany
| | - Stefanie Souczek
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Baden-Württemberg, Germany
| | - Janet Peper
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Baden-Württemberg, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Baden-Württemberg, Germany
| | - Stefan Stevanović
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Baden-Württemberg, Germany
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47
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Hermann C, van Hateren A, Trautwein N, Neerincx A, Duriez PJ, Stevanović S, Trowsdale J, Deane JE, Elliott T, Boyle LH. TAPBPR alters MHC class I peptide presentation by functioning as a peptide exchange catalyst. eLife 2015; 4:e09617. [PMID: 26439010 PMCID: PMC4718805 DOI: 10.7554/elife.09617] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/05/2015] [Indexed: 12/29/2022] Open
Abstract
Our understanding of the antigen presentation pathway has recently been enhanced with the identification that the tapasin-related protein TAPBPR is a second major histocompatibility complex (MHC) class I-specific chaperone. We sought to determine whether, like tapasin, TAPBPR can also influence MHC class I peptide selection by functioning as a peptide exchange catalyst. We show that TAPBPR can catalyse the dissociation of peptides from peptide-MHC I complexes, enhance the loading of peptide-receptive MHC I molecules, and discriminate between peptides based on affinity in vitro. In cells, the depletion of TAPBPR increased the diversity of peptides presented on MHC I molecules, suggesting that TAPBPR is involved in restricting peptide presentation. Our results suggest TAPBPR binds to MHC I in a peptide-receptive state and, like tapasin, works to enhance peptide optimisation. It is now clear there are two MHC class I specific peptide editors, tapasin and TAPBPR, intimately involved in controlling peptide presentation to the immune system.
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Affiliation(s)
- Clemens Hermann
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andy van Hateren
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, United Kingdom
| | - Nico Trautwein
- Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas Neerincx
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Patrick J Duriez
- Cancer Research UK Protein Core Facility, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stefan Stevanović
- Department of Immunology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Tim Elliott
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Peper JK, Stevanović S. A combined approach of human leukocyte antigen ligandomics and immunogenicity analysis to improve peptide-based cancer immunotherapy. Cancer Immunol Immunother 2015; 64:1295-303. [PMID: 25822767 PMCID: PMC11029747 DOI: 10.1007/s00262-015-1682-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/10/2015] [Indexed: 11/30/2022]
Abstract
The breakthrough development of immune checkpoint inhibitors as clinically effective novel therapies demonstrates the potential of cancer immunotherapy. The identification of suitable targets for specific immunotherapy, however, remains a challenging task. Most peptides previously used for vaccination in clinical trials were able to elicit strong immunological responses but failed with regard to clinical benefit. This might, at least partly, be caused by an inadequate peptide selection, usually derived from established tumor-associated antigens which are not necessarily presented as human leukocyte antigen (HLA) ligands. Recently, HLA ligandome analysis revealed cancer-associated peptides, which have been used in clinical trials showing encouraging impact on survival. To improve peptide-based cancer immunotherapy, our group established a combined approach of HLA ligandomics and immunogenicity analysis for the identification of vaccine peptides. This approach is based on the identification of naturally presented HLA ligands on tumor samples, the selection of tumor-associated/tumor-specific HLA ligands and their subsequent testing for immunogenicity in vitro. In this review, we want to present our pipeline for the identification of vaccine peptides, focusing on ovarian cancer, and want to discuss differences to other approaches. Furthermore, we want to give a short outlook of a potential multi-peptide vaccination trial using the novel identified peptides.
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Affiliation(s)
- Janet Kerstin Peper
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany,
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Stevanović S. III. Auripigment von Allchar in Macédonien. Z KRIST-CRYST MATER 2015. [DOI: 10.1524/zkri.1904.39.1.14] [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] [Indexed: 11/24/2022]
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