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Hoenisch Gravel N, Nelde A, Bauer J, Mühlenbruch L, Schroeder SM, Neidert MC, Scheid J, Lemke S, Dubbelaar ML, Wacker M, Dengler A, Klein R, Mauz PS, Löwenheim H, Hauri-Hohl M, Martin R, Hennenlotter J, Stenzl A, Heitmann JS, Salih HR, Rammensee HG, Walz JS. TOF IMS mass spectrometry-based immunopeptidomics refines tumor antigen identification. Nat Commun 2023; 14:7472. [PMID: 37978195 PMCID: PMC10656517 DOI: 10.1038/s41467-023-42692-7] [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] [Received: 01/12/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for the direct identification and characterization of naturally presented tumor-associated peptides, a key prerequisite for the development of T cell-based immunotherapies. This study reports on the implementation of ion mobility separation-based time-of-flight (TOFIMS) MS for next-generation immunopeptidomics, enabling high-speed and sensitive detection of HLA-presented peptides. Applying TOFIMS-based immunopeptidomics, a novel extensive benignTOFIMS dataset was generated from 94 primary benign samples of solid tissue and hematological origin, which enabled the expansion of benign reference immunopeptidome databases with > 150,000 HLA-presented peptides, the refinement of previously described tumor antigens, as well as the identification of frequently presented self antigens and not yet described tumor antigens comprising low abundant mutation-derived neoepitopes that might serve as targets for future cancer immunotherapy development.
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Affiliation(s)
- Naomi Hoenisch Gravel
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Marian C Neidert
- Neuroscience Center Zürich (ZNZ), University of Zürich and ETH Zürich, Zürich, Switzerland
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zürich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Zürich, Switzerland
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Steffen Lemke
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Marissa L Dubbelaar
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Anna Dengler
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Paul-Stefan Mauz
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zürich, Zürich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University and University Hospital Zürich, Zürich, Switzerland
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- 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
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital 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
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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Medici G, Freudenmann LK, Velz J, Wang SSY, Kapolou K, Paramasivam N, Mühlenbruch L, Kowalewski DJ, Vasella F, Bilich T, Frey BM, Dubbelaar ML, Patterson AB, Zeitlberger AM, Silginer M, Roth P, Weiss T, Wirsching HG, Krayenbühl N, Bozinov O, Regli L, Rammensee HG, Rushing EJ, Sahm F, Walz JS, Weller M, Neidert MC. A T-cell antigen atlas for meningioma: novel options for immunotherapy. Acta Neuropathol 2023; 146:173-190. [PMID: 37368072 PMCID: PMC10329067 DOI: 10.1007/s00401-023-02605-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
Meningiomas are the most common primary intracranial tumors. Although most symptomatic cases can be managed by surgery and/or radiotherapy, a relevant number of patients experience an unfavorable clinical course and additional treatment options are needed. As meningiomas are often perfused by dural branches of the external carotid artery, which is located outside the blood-brain barrier, they might be an accessible target for immunotherapy. However, the landscape of naturally presented tumor antigens in meningioma is unknown. We here provide a T-cell antigen atlas for meningioma by in-depth profiling of the naturally presented immunopeptidome using LC-MS/MS. Candidate target antigens were selected based on a comparative approach using an extensive immunopeptidome data set of normal tissues. Meningioma-exclusive antigens for HLA class I and II are described here for the first time. Top-ranking targets were further functionally characterized by showing their immunogenicity through in vitro T-cell priming assays. Thus, we provide an atlas of meningioma T-cell antigens which will be publicly available for further research. In addition, we have identified novel actionable targets that warrant further investigation as an immunotherapy option for meningioma.
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Affiliation(s)
- Gioele Medici
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland.
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland.
| | - Lena K Freudenmann
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Julia Velz
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Sophie Shih-Yüng Wang
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery and Neurotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Konstantina Kapolou
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Roche Diagnostics International Ltd, Rotkreuz, Switzerland
| | - Nagarajan Paramasivam
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Lena Mühlenbruch
- 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 Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
| | - Daniel J Kowalewski
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Flavio Vasella
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Tatjana Bilich
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Beat M Frey
- Blood Transfusion Service, Swiss Red Cross, Schlieren, Switzerland
| | - Marissa L Dubbelaar
- 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 Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, 72076, Tübingen, Baden-Württemberg, Germany
| | | | - Anna Maria Zeitlberger
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007, St. Gallen, Switzerland
| | - Manuela Silginer
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Patrick Roth
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Tobias Weiss
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Hans-Georg Wirsching
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Niklaus Krayenbühl
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Oliver Bozinov
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007, St. Gallen, Switzerland
| | - Luca Regli
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Elisabeth Jane Rushing
- Department of Neuropathology, University Hospital and University of Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane S Walz
- 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 Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Marian C Neidert
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007, St. Gallen, Switzerland
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3
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Mühlenbruch L, Abou-Kors T, Dubbelaar ML, Bichmann L, Kohlbacher O, Bens M, Thomas J, Ezić J, Kraus JM, Kestler HA, von Witzleben A, Mytilineos J, Fürst D, Engelhardt D, Doescher J, Greve J, Schuler PJ, Theodoraki MN, Brunner C, Hoffmann TK, Rammensee HG, Walz JS, Laban S. The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination. Br J Cancer 2023; 128:1777-1787. [PMID: 36823366 PMCID: PMC9949688 DOI: 10.1038/s41416-023-02197-y] [Citation(s) in RCA: 2] [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: 09/13/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND The immune peptidome of OPSCC has not previously been studied. Cancer-antigen specific vaccination may improve clinical outcome and efficacy of immune checkpoint inhibitors such as PD1/PD-L1 antibodies. METHODS Mapping of the OPSCC HLA ligandome was performed by mass spectrometry (MS) based analysis of naturally presented HLA ligands isolated from tumour tissue samples (n = 40) using immunoaffinity purification. The cohort included 22 HPV-positive (primarily HPV-16) and 18 HPV-negative samples. A benign reference dataset comprised of the HLA ligandomes of benign haematological and tissue datasets was used to identify tumour-associated antigens. RESULTS MS analysis led to the identification of naturally HLA-presented peptides in OPSCC tumour tissue. In total, 22,769 peptides from 9485 source proteins were detected on HLA class I. For HLA class II, 15,203 peptides from 4634 source proteins were discovered. By comparative profiling against the benign HLA ligandomic datasets, 29 OPSCC-associated HLA class I ligands covering 11 different HLA allotypes and nine HLA class II ligands were selected to create a peptide warehouse. CONCLUSION Tumour-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi)personalised strategies.
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Affiliation(s)
- Lena Mühlenbruch
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,German Cancer Consortium (DKTK), Partner Site Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Tsima Abou-Kors
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marissa L. Dubbelaar
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Leon Bichmann
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Oliver Kohlbacher
- grid.10392.390000 0001 2190 1447Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence Machine Learning in the Sciences (EXC2064), Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.411544.10000 0001 0196 8249Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Institute for Bioinformatics and Medical Informatics, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Martin Bens
- grid.418245.e0000 0000 9999 5706Leibniz-Institute on Aging, Fritz-Lipmann-Institute, 07745 Jena, Thüringen Germany
| | - Jaya Thomas
- grid.5491.90000 0004 1936 9297CRUK and NIHR Experimental Cancer Medicine Center & School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
| | - Jasmin Ezić
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johann M. Kraus
- grid.6582.90000 0004 1936 9748Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Hans A. Kestler
- grid.6582.90000 0004 1936 9748Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Adrian von Witzleben
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Joannis Mytilineos
- grid.410712.10000 0004 0473 882XInstitute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden–Württemberg–Hessen, and University Hospital Ulm, Ulm, Germany ,grid.6582.90000 0004 1936 9748Institute of Transfusion Medicine, Ulm University, Ulm, Germany ,German Stem Cell Donor Registry, German Red Cross Blood Transfusion Service, Ulm, Germany
| | - Daniel Fürst
- grid.410712.10000 0004 0473 882XInstitute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden–Württemberg–Hessen, and University Hospital Ulm, Ulm, Germany ,grid.6582.90000 0004 1936 9748Institute of Transfusion Medicine, Ulm University, Ulm, Germany
| | - Daphne Engelhardt
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johannes Doescher
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Jens Greve
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Patrick J. Schuler
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marie-Nicole Theodoraki
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Cornelia Brunner
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Thomas K. Hoffmann
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Hans-Georg Rammensee
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,German Cancer Consortium (DKTK), Partner Site Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Juliane S. Walz
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.411544.10000 0001 0196 8249Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Baden-Württemberg 72076 Germany
| | - Simon Laban
- Department of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany.
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4
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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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5
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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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6
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Wang J, Jelcic I, Mühlenbruch L, Haunerdinger V, Toussaint NC, Zhao Y, Cruciani C, Faigle W, Naghavian R, Foege M, Binder TMC, Eiermann T, Opitz L, Fuentes-Font L, Reynolds R, Kwok WW, Nguyen JT, Lee JH, Lutterotti A, Münz C, Rammensee HG, Hauri-Hohl M, Sospedra M, Stevanovic S, Martin R. HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis. Cell 2020; 183:1264-1281.e20. [PMID: 33091337 PMCID: PMC7707104 DOI: 10.1016/j.cell.2020.09.054] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [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: 02/21/2020] [Revised: 08/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
The HLA-DR15 haplotype is the strongest genetic risk factor for multiple sclerosis (MS), but our understanding of how it contributes to MS is limited. Because autoreactive CD4+ T cells and B cells as antigen-presenting cells are involved in MS pathogenesis, we characterized the immunopeptidomes of the two HLA-DR15 allomorphs DR2a and DR2b of human primary B cells and monocytes, thymus, and MS brain tissue. Self-peptides from HLA-DR molecules, particularly from DR2a and DR2b themselves, are abundant on B cells and thymic antigen-presenting cells. Furthermore, we identified autoreactive CD4+ T cell clones that can cross-react with HLA-DR-derived self-peptides (HLA-DR-SPs), peptides from MS-associated foreign agents (Epstein-Barr virus and Akkermansia muciniphila), and autoantigens presented by DR2a and DR2b. Thus, both HLA-DR15 allomorphs jointly shape an autoreactive T cell repertoire by serving as antigen-presenting structures and epitope sources and by presenting the same foreign peptides and autoantigens to autoreactive CD4+ T cells in MS. HLA-DR15 present abundant HLA-DR-derived self-peptides on B cells Autoreactive T cells in MS recognize HLA-DR-derived self-peptides/DR15 complexes Foreign peptides/DR15 complexes trigger potential autoreactive T cells in MS HLA-DR15 shape an autoreactive T cell repertoire by cross-reactivity/restriction
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Affiliation(s)
- Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Ivan Jelcic
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Lena Mühlenbruch
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Veronika Haunerdinger
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich 8093, Switzerland; Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD 20850, USA
| | - Carolina Cruciani
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Reza Naghavian
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Magdalena Foege
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Thomas M C Binder
- HLA Laboratory of the Stefan Morsch Foundation (SMS), Birkenfeld 55765, Germany
| | - Thomas Eiermann
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich 8057, Switzerland
| | - Laura Fuentes-Font
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Richard Reynolds
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Julie T Nguyen
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Jar-How Lee
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Andreas Lutterotti
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Mireia Sospedra
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Stefan Stevanovic
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland.
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7
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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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8
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Laban S, Eziç J, Bichmann L, Mytilineos D, Fürstberger A, Kestler H, Schuler P, Hoffmann T, Rammensee HG, Stevanovic S, Mühlenbruch L. HLA-ligandome analysis reveals target antigens of oropharyngeal squamous cell carcinoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz252.043] [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: 11/15/2022] Open
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9
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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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10
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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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