1
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Hamza H, Ghosh M, Löffler MW, Rammensee HG, Planz O. Identification and relative abundance of naturally presented and cross-reactive influenza A virus MHC class I-restricted T cell epitopes. Emerg Microbes Infect 2024; 13:2306959. [PMID: 38240239 PMCID: PMC10854457 DOI: 10.1080/22221751.2024.2306959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Cytotoxic T lymphocytes are key for controlling viral infection. Unravelling CD8+ T cell-mediated immunity to distinct influenza virus strains and subtypes across prominent HLA types is relevant for combating seasonal infections and emerging new variants. Using an immunopeptidomics approach, naturally presented influenza A virus-derived ligands restricted to HLA-A*24:02, HLA-A*68:01, HLA-B*07:02, and HLA-B*51:01 molecules were identified. Functional characterization revealed multifunctional memory CD8+ T cell responses for nine out of sixteen peptides. Peptide presentation kinetics was optimal around 12 h post infection and presentation of immunodominant epitopes shortly after infection was not always persistent. Assessment of immunogenic epitopes revealed that they are highly conserved across the major zoonotic reservoirs and may contain a single substitution in the vicinity of the anchor residues. These findings demonstrate how the identified epitopes promote T cell pools, possibly cross-protective in individuals and can be potential targets for vaccination.
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Affiliation(s)
- Hazem Hamza
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Virology Laboratory, Environmental Research Division, National Research Centre, Giza, Egypt
| | - Michael Ghosh
- Institute for Immunology, University of Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Institute for Immunology, University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty of Tübingen, Tübingen, Germany
- Centre for Clinical Transfusion 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
| | - Hans-Georg Rammensee
- Institute for 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
- Cluster of Excellence CMFI (EXC2124) "Controlling Microbes to Fight Infections", University of Tübingen, Tübingen, Germany
| | - Oliver Planz
- Institute for Immunology, University of Tübingen, Tübingen, Germany
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2
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Adams VR, Collins LB, Williams TI, Holmes J, Hess P, Atkins HM, Scheidemantle G, Liu X, Lodge M, Johnson AJ, Kennedy A. Myeloid cell MHC I expression drives CD8 + T cell activation in nonalcoholic steatohepatitis. Front Immunol 2024; 14:1302006. [PMID: 38274832 PMCID: PMC10808415 DOI: 10.3389/fimmu.2023.1302006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
Background & aims Activated CD8+ T cells are elevated in Nonalcoholic steatohepatitis (NASH) and are important for driving fibrosis and inflammation. Despite this, mechanisms of CD8+ T cell activation in NASH are largely limited. Specific CD8+ T cell subsets may become activated through metabolic signals or cytokines. However, studies in NASH have not evaluated the impact of antigen presentation or the involvement of specific antigens. Therefore, we determined if activated CD8+ T cells are dependent on MHC class I expression in NASH to regulate fibrosis and inflammation. Methods We used H2Kb and H2Db deficient (MHC I KO), Kb transgenic mice, and myeloid cell Kb deficient mice (LysM Kb KO) to investigate how MHC class I impacts CD8+ T cell function and NASH. Flow cytometry, gene expression, and histology were used to examine hepatic inflammation and fibrosis. The hepatic class I immunopeptidome was evaluated by mass spectrometry. Results In NASH, MHC class I isoform H2Kb was upregulated in myeloid cells. MHC I KO demonstrated protective effects against NASH-induced inflammation and fibrosis. Kb mice exhibited increased fibrosis in the absence of H2Db while LysM Kb KO mice showed protection against fibrosis but not inflammation. H2Kb restricted peptides identified a unique NASH peptide Ncf2 capable of CD8+ T cell activation in vitro. The Ncf2 peptide was not detected during fibrosis resolution. Conclusion These results suggest that activated hepatic CD8+ T cells are dependent on myeloid cell MHC class I expression in diet induced NASH to promote inflammation and fibrosis. Additionally, our studies suggest a role of NADPH oxidase in the production of Ncf2 peptide generation.
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Affiliation(s)
- Victoria R. Adams
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, United States
| | - Leonard B. Collins
- Molecular Education, Technology and Research Innovation Center (METRIC), NC State University, Raleigh, NC, United States
| | - Taufika Islam Williams
- Molecular Education, Technology and Research Innovation Center (METRIC), NC State University, Raleigh, NC, United States
- Department of Chemistry, NC State University, Raleigh, NC, United States
| | - Jennifer Holmes
- College of Veterinary Medicine, NC State University, Raleigh, NC, United States
| | - Paul Hess
- College of Veterinary Medicine, NC State University, Raleigh, NC, United States
| | - Hannah M. Atkins
- Center for Human Health and Environment, NC State University, Raleigh, NC, United States
- Division of Comparative Medicine, UNC Chapel Hill, Chapel Hill, NC, United States
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, United States
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, United States
| | - Mareca Lodge
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, United States
| | - Aaron J. Johnson
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Arion Kennedy
- Department of Molecular and Structural Biochemistry, NC State University, Raleigh, NC, United States
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3
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:820-827. [PMID: 37938771 PMCID: PMC10665195 DOI: 10.1038/s41586-023-06706-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023]
Abstract
The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.
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Affiliation(s)
- Mark Yarmarkovich
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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4
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Buonaguro L, Tagliamonte M. Peptide-based vaccine for cancer therapies. Front Immunol 2023; 14:1210044. [PMID: 37654484 PMCID: PMC10467431 DOI: 10.3389/fimmu.2023.1210044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Different strategies based on peptides are available for cancer treatment, in particular to counter-act the progression of tumor growth and disease relapse. In the last decade, in the context of therapeutic strategies against cancer, peptide-based vaccines have been evaluated in different tumor models. The peptides selected for cancer vaccine development can be classified in two main type: tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs), which are captured, internalized, processed and presented by antigen-presenting cells (APCs) to cell-mediated immunity. Peptides loaded onto MHC class I are recognized by a specific TCR of CD8+ T cells, which are activated to exert their cytotoxic activity against tumor cells presenting the same peptide-MHC-I complex. This process is defined as active immunotherapy as the host's immune system is either de novo activated or restimulated to mount an effective, tumor-specific immune reaction that may ultimately lead to tu-mor regression. However, while the preclinical data have frequently shown encouraging results, therapeutic cancer vaccines clinical trials, including those based on peptides have not provided satisfactory data to date. The limited efficacy of peptide-based cancer vaccines is the consequence of several factors, including the identification of specific target tumor antigens, the limited immunogenicity of peptides and the highly immunosuppressive tumor microenvironment (TME). An effective cancer vaccine can be developed only by addressing all such different aspects. The present review describes the state of the art for each of such factors.
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Affiliation(s)
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - “Fond G. Pascale”, Naples, Italy
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5
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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] [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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6
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Burbage M, Rocañín-Arjó A, Baudon B, Arribas YA, Merlotti A, Rookhuizen DC, Heurtebise-Chrétien S, Ye M, Houy A, Burgdorf N, Suarez G, Gros M, Sadacca B, Carrascal M, Garmilla A, Bohec M, Baulande S, Lombard B, Loew D, Waterfall JJ, Stern MH, Goudot C, Amigorena S. Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements. Sci Immunol 2023; 8:eabm6360. [PMID: 36735776 DOI: 10.1126/sciimmunol.abm6360] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Oncogenesis often implicates epigenetic alterations, including derepression of transposable elements (TEs) and defects in alternative splicing. Here, we explore the possibility that noncanonical splice junctions between exons and TEs represent a source of tumor-specific antigens. We show that mouse normal tissues and tumor cell lines express wide but distinct ranges of mRNA junctions between exons and TEs, some of which are tumor specific. Immunopeptidome analyses in tumor cell lines identified peptides derived from exon-TE splicing junctions associated to MHC-I molecules. Exon-TE junction-derived peptides were immunogenic in tumor-bearing mice. Both prophylactic and therapeutic vaccinations with junction-derived peptides delayed tumor growth in vivo. Inactivation of the TE-silencing histone 3-lysine 9 methyltransferase Setdb1 caused overexpression of new immunogenic junctions in tumor cells. Our results identify exon-TE splicing junctions as epigenetically controlled, immunogenic, and protective tumor antigens in mice, opening possibilities for tumor targeting and vaccination in patients with cancer.
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Affiliation(s)
- Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Derek C Rookhuizen
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | | | - Mengliang Ye
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Alexandre Houy
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Nina Burgdorf
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Guadalupe Suarez
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Marine Gros
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Andrea Garmilla
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Mylène Bohec
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Sylvain Baulande
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
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7
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Schwarz S, Schmitz J, Löffler MW, Ghosh M, Rammensee HG, Olshvang E, Markel M, Mockel-Tenbrinck N, Dzionek A, Krake S, Arslan B, Kampe KD, Wendt A, Bauer P, Mullins CS, Schlosser A, Linnebacher M. T cells of colorectal cancer patients' stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells. J Immunother Cancer 2022; 10:jitc-2022-005651. [PMID: 36460334 PMCID: PMC9723954 DOI: 10.1136/jitc-2022-005651] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Patients with cancers that exhibit extraordinarily high somatic mutation numbers are ideal candidates for immunotherapy and enable identifying tumor-specific peptides through stimulation of tumor-reactive T cells (Tc). METHODS Colorectal cancers (CRC) HROC113 and HROC285 were selected based on high TMB, microsatellite instability and HLA class I expression. Their HLA ligandome was characterized using mass spectrometry, compared with the HLA ligand atlas and HLA class I-binding affinity was predicted. Cryptic peptides were identified using Peptide-PRISM. Patients' Tc were isolated from either peripheral blood (pTc) or tumor material (tumor-infiltrating Tc, TiTc) and expanded. In addition, B-lymphoblastoid cells (B-LCL) were generated and used as antigen-presenting cells. pTc and TiTc were stimulated twice for 7 days using peptide pool-loaded B-LCL. Subsequently, interferon gamma (IFNγ) release was quantified by ELISpot. Finally, cytotoxicity against autologous tumor cells was assessed in a degranulation assay. RESULTS 100 tumor-specific candidate peptides-97 cryptic peptides and 3 classically mutated neoantigens-were selected. The neoantigens originated from single nucleotide substitutions in the genes IQGAP1, CTNNB1, and TRIT1. Cryptic and neoantigenic peptides inducing IFNγ secretion of Tc were further investigated. Stimulation of pTc and TiTc with neoantigens and selected cryptic peptides resulted in increased release of cytotoxic granules in the presence of autologous tumor cells, substantiating their improved tumor cell recognition. Tetramer staining showed an enhanced number of pTc and TiTc specific for the IQGAP1 neoantigen. Subpopulation analysis prior to peptide stimulation revealed that pTc mainly consisted of memory Tc, whereas TiTc constituted primarily of effector and effector memory Tc. This allows to infer that TiTc reacting to neoantigens and cryptic peptides must be present within the tumor microenvironment. CONCLUSION These results prove that the analyzed CRC present both mutated neoantigenic and cryptic peptides on their HLA class I molecules. Moreover, stimulation with these peptides significantly strengthened tumor cell recognition by Tc. Since the overall number of neoantigenic peptides identifiable by HLA ligandome analysis hitherto is small, our data emphasize the relevance of increasing the target scope for cancer vaccines by the cryptic peptide category.
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Affiliation(s)
- Sandra Schwarz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Johanna Schmitz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Markus W Löffler
- Department of General, Visceral and Transplant Surgery, Universitätsklinikum Tübingen, Tubingen, Germany,Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany
| | | | - Marvin Markel
- Miltenyi Biotec BV & Co KG, Bergisch Gladbach, Germany
| | | | | | | | | | | | | | | | - Christina S Mullins
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Andreas Schlosser
- Center for Integrative and Translational Bioimaging, Rudolf-Virchow Center, University of Würzburg, Würzburg, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
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8
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Chow DT, Rardin MJ. Identification and Mitigation of Defensins in the Immunopurification of Peptide MHC-I Antigens from Lung Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1590-1597. [PMID: 34645265 DOI: 10.1021/jasms.1c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The class I major histocompatibility (MHC-I) complex is a set of diverse cell surface receptors encoded by the human leukocyte antigen gene complex. These receptors present intracellular antigens to cytotoxic T cells providing information on the state and health of cells. Changes in the immunopeptidome during cancer may provide novel targets for therapeutic intervention. To understand how the tumor immunopeptidome is altered, we developed a mass spectrometry (MS) based platform for isolating and identifying MHC-I peptide antigens in lung tumors. In the course of our work, we encountered several large unknown peptide contaminants which had not been previously reported. To understand the source of these major contaminants, we isolated them using offline fractionation and identified them by liquid chromatography-tandem mass spectrometry (LC-MS/MS) as members of the host defense protein family known as the defensins. To mitigate their detrimental effects, we modified our "Original" data-dependent acquisition (DDA) MS method to narrowly target the MHC-I peptides based on their physical properties including charge state and molecular weight ("z state" DDA), evaluated field asymmetric ion mobility spectrometry to attempt gas-phase separation prior to MS analysis, and developed an immunodepletion approach using defensin specific antibodies. This modified approach improves peptide identification and reduces the impact of defensin contamination in lung tissue samples.
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Affiliation(s)
- David T Chow
- Amgen Research, Discovery Attribute Sciences Amgen, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Amgen Research, Discovery Attribute Sciences Amgen, South San Francisco, California 94080, United States
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9
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Hernández-Malmierca P, Vonficht D, Schnell A, Uckelmann HJ, Bollhagen A, Mahmoud MAA, Landua SL, van der Salm E, Trautmann CL, Raffel S, Grünschläger F, Lutz R, Ghosh M, Renders S, Correia N, Donato E, Dixon KO, Hirche C, Andresen C, Robens C, Werner PS, Boch T, Eisel D, Osen W, Pilz F, Przybylla A, Klein C, Buchholz F, Milsom MD, Essers MAG, Eichmüller SB, Hofmann WK, Nowak D, Hübschmann D, Hundemer M, Thiede C, Bullinger L, Müller-Tidow C, Armstrong SA, Trumpp A, Kuchroo VK, Haas S. Antigen presentation safeguards the integrity of the hematopoietic stem cell pool. Cell Stem Cell 2022; 29:760-775.e10. [PMID: 35523139 PMCID: PMC9202612 DOI: 10.1016/j.stem.2022.04.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/08/2021] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are responsible for the production of blood and immune cells. Throughout life, HSPCs acquire oncogenic aberrations that can cause hematological cancers. Although molecular programs maintaining stem cell integrity have been identified, safety mechanisms eliminating malignant HSPCs from the stem cell pool remain poorly characterized. Here, we show that HSPCs constitutively present antigens via major histocompatibility complex class II. The presentation of immunogenic antigens, as occurring during malignant transformation, triggers bidirectional interactions between HSPCs and antigen-specific CD4+ T cells, causing stem cell proliferation, differentiation, and specific exhaustion of aberrant HSPCs. This immunosurveillance mechanism effectively eliminates transformed HSPCs from the hematopoietic system, thereby preventing leukemia onset. Together, our data reveal a bidirectional interaction between HSPCs and CD4+ T cells, demonstrating that HSPCs are not only passive receivers of immunological signals but also actively engage in adaptive immune responses to safeguard the integrity of the stem cell pool.
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Affiliation(s)
- Pablo Hernández-Malmierca
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hannah J Uckelmann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA; Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alina Bollhagen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mohamed A A Mahmoud
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Sophie-Luise Landua
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Elise van der Salm
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christine L Trautmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Simon Raffel
- Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Florian Grünschläger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Raphael Lutz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Simon Renders
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Nádia Correia
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Elisa Donato
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Karin O Dixon
- Evergrande Center for Immunologic Diseases, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christoph Hirche
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Carolin Andresen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Claudia Robens
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Paula S Werner
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Tobias Boch
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany; Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Eisel
- Research Group GMP & T Cell Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Wolfram Osen
- Research Group GMP & T Cell Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Franziska Pilz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Adriana Przybylla
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Corinna Klein
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Frank Buchholz
- Medical Faculty, University Hospital Carl Gustav Carus, NCT/UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany
| | - Michael D Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Experimental Hematology, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marieke A G Essers
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefan B Eichmüller
- Research Group GMP & T Cell Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany; Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany; Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Hundemer
- Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Christian Thiede
- German Cancer Consortium (DKTK), Heidelberg, Germany; Medical Department 1, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Lars Bullinger
- German Cancer Consortium (DKTK), Heidelberg, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Cancer Immunology, Berlin, Germany
| | - Carsten Müller-Tidow
- Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA; Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Cancer Immunology, Berlin, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
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10
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Löffler MW, Gori S, Izzo F, Mayer-Mokler A, Ascierto P, Königsrainer A, Ma YT, Sangro B, Francque S, Vonghia L, Inno A, Avallone A, Ludwig J, Alcoba DD, Flohr C, Aslan K, Mendrzyk R, Schuster H, Borrelli M, Valmori D, Chaumette T, Heidenreich R, Gouttefangeas C, Forlani G, Tagliamonte M, Fusco C, Penta R, Iñarrairaegui M, Gnad-Vogt U, Reinhardt C, Weinschenk T, Accolla RS, Singh H, Rammensee HG, Buonaguro L. Phase I/II multicenter trial of a novel therapeutic cancer vaccine, HepaVac-101, for hepatocellular carcinoma. Clin Cancer Res 2022; 28:2555-2566. [PMID: 35421231 DOI: 10.1158/1078-0432.ccr-21-4424] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/25/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Immunotherapy for hepatocellular carcinoma (HCC) shows considerable promise in improving clinical outcomes. HepaVac-101 represents a single-arm, first-in-man Phase I/II multicenter cancer vaccine trial for HCC (NCT03203005). It combines multi-peptide antigens (IMA970A) with the TLR7/8/RIG I agonist CV8102. IMA970A includes 5 HLA-A*24 and 7 HLA-A*02 as well as 4 HLA-DR restricted peptides selected after mass spectrometric identification in human HCC tissues or cell lines. CV8102 is an RNA-based immunostimulator inducing a balanced Th1/Th2 immune response. EXPERIMENTAL DESIGN 82 patients with very early to intermediate stage HCCs were enrolled and screened for suitable HLA haplotypes and 22 put on study treatment. This consisted in a single infusion of low-dose cyclophosphamide followed by 9 intradermal coadministrations of IMA970A and CV8102. Only patients with no disease relapse after standard of care treatments were vaccinated. Primary endpoints of HepaVac-101 clinical trial were safety, tolerability and antigen-specific T-cell responses. Secondary or exploratory endpoints included additional immunological parameters and survival endpoints. RESULTS The vaccination showed a good safety profile. Transient mild-to-moderate injection-site reactions were the most frequent IMA970A/CV8102-related side effects. Immune responses against {greater than or equal to}1 vaccinated HLA class I tumor-associated peptide (TAA) and {greater than or equal to}1 vaccinated HLA class II TAA were respectively induced in 37% and 53% of the vaccinees. CONCLUSION Immunotherapy may provide a great improvement in treatment options for HCC. HepaVac-101 is a first-in-man clinical vaccine trial with multiple novel HLA class I- and class II-restricted TAAs against HCC. The results are initial evidence for safety and immunogenicity of the vaccine. Further clinical evaluations are warranted.
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Affiliation(s)
| | - Stefania Gori
- IRCCS Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - Francesco Izzo
- Istituto Nazionale per lo Studio e la Cura dei Tumori, Napoli, Italy
| | | | - Paolo Ascierto
- Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | | | - Yuk Ting Ma
- University of Birmingham, Birmingham, United Kingdom
| | - Bruno Sangro
- Clínica Universidad de Navarra and CIBEREHD, Pamplona, Navarra, Spain
| | | | | | - Alessandro Inno
- IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Verona, Italy
| | | | - Jörg Ludwig
- Immatics Biotechnologies (Germany), Tuebingen, Germany
| | | | | | | | | | | | - Marco Borrelli
- ISTITUTO NAZIONALE TUMORI IRCCS - Fondazione Pascale, napoli, napoli, Italy
| | - Danila Valmori
- Institut National de la Sante et de la Recherche Medicale, Nantes-Saint Herblain, France
| | | | | | | | | | | | | | - Roberta Penta
- AORN Santobono-Pausilipon Children's Hospital, Naples, Italy
| | | | | | | | | | | | | | | | - Luigi Buonaguro
- ISTITUTO NAZIONALE TUMORI IRCCS - Fondazione Pascale, NAPLES, Italy
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11
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Kim Y, Konda P, Murphy JP, Paulo JA, Gygi SP, Gujar S. Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities. Mol Cell Proteomics 2022; 21:100182. [PMID: 34922008 PMCID: PMC8864471 DOI: 10.1016/j.mcpro.2021.100182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/14/2021] [Accepted: 12/05/2021] [Indexed: 02/08/2023] Open
Abstract
The combination cancer immunotherapies with oncolytic virus (OV) and immune checkpoint blockade (ICB) reinstate otherwise dysfunctional antitumor CD8 T cell responses. One major mechanism that aids such reinstatement of antitumor CD8 T cells involves the availability of new class I major histocompatibility complex (MHC-I)-bound tumor epitopes following therapeutic intervention. Thus, therapy-induced changes within the MHC-I peptidome hold the key to understanding the clinical implications for therapy-reinstated CD8 T cell responses. Here, using mass spectrometry-based immuno-affinity methods and tumor-bearing animals treated with OV and ICB (alone or in combination), we captured the therapy-induced alterations within the tumor MHC-I peptidome, which were then tested for their CD8 T cell response-stimulating activity. We found that the oncolytic reovirus monotherapy drives up- as well as downexpression of tumor MHC-I peptides in a cancer type and oncolysis susceptibility dependent manner. Interestingly, the combination of reovirus + ICB results in higher numbers of differentially expressed MHC-I-associated peptides (DEMHCPs) relative to either monotherapies. Most importantly, OV+ICB-driven DEMHCPs contain biologically active epitopes that stimulate interferon-gamma responses in cognate CD8 T cells, which may mediate clinically desired antitumor attack and cancer immunoediting. These findings highlight that the therapy-induced changes to the MHC-I peptidome contribute toward the reinstated antitumor CD8 T cell attack established following OV + ICB combination cancer immunotherapy.
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Affiliation(s)
- Youra Kim
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Prathyusha Konda
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - J Patrick Murphy
- Department of Biology, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shashi Gujar
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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12
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2021; 599:477-484. [PMID: 34732890 PMCID: PMC8599005 DOI: 10.1038/s41586-021-04061-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022]
Abstract
The majority of oncogenic drivers are intracellular proteins, thus constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient to generate responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins that are essential for tumourigenesis and focus on targeting the unmutated peptide QYNPIRTTF, discovered on HLA-A*24:02, which is derived from the neuroblastoma dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (CARs) using a counter-panning strategy with predicted potentially cross-reactive peptides. We further hypothesized that peptide-centric CARs could recognize peptides on additional HLA allotypes when presented in a similar manner. Informed by computational modelling, we showed that PHOX2B peptide-centric CARs also recognize QYNPIRTTF presented by HLA-A*23:01 and the highly divergent HLA-B*14:02. Finally, we demonstrated potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that peptide-centric CARs have the potential to vastly expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and widen the population of patients who would benefit from such therapy by breaking conventional HLA restriction.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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13
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Watts E, Potts GK, Ready DB, George Thompson AM, Lee J, Escobar EE, Patterson MJ, Brodbelt JS. Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2021; 93:13134-13142. [PMID: 34553926 DOI: 10.1021/acs.analchem.1c01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying major histocompatibility complex (MHC) class I immunopeptide antigens represents a key step in the development of immune-based targeted therapeutics and vaccines. However, the complete characterization of these antigens by tandem mass spectrometry remains challenging due to their short sequence length, high degree of hydrophobicity, and/or lack of sufficiently basic amino acids. This study seeks to address the potential for 193 nm ultraviolet photodissociation (UVPD) to improve the analysis of MHC class I immunopeptides by offering enhanced characterization of these sequences in lower charge states and differentiation of prominent isomeric leucine and isoleucine residues in the HLA-A*02:01 motif. Although electron transfer dissociation-higher energy collisional dissociation (EThcD) offered some success in the differentiation of leucine and isoleucine, 193 nm UVPD was able to confirm the identity of nearly 60% of leucine and isoleucine residues in a synthetic peptide mixture. Furthermore, 193 nm UVPD led to significantly more peptide identifications and higher scoring metrics than EThcD for peptides obtained from immunoprecipitation of MHC class I immunopeptides from in vitro cell culture. Additionally, 193 nm UVPD represents a promising complementary technique to higher-energy collisional dissociation (HCD), in which 424 of the 2593 peptides identified by 193 nm UVPD were not identified by HCD in HLA-A*02:01-specific immunoprecipitation and 804 of the 3300 peptides identified by 193 nm UVPD were not identified by HCD for pan HLA-A, -B, and -C immunoprecipitation. These results highlight that 193 nm UVPD offers an option for the characterization of immunopeptides, including differentiation of leucine and isoleucine residues.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | - Gregory K Potts
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Damien B Ready
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | | | - Janice Lee
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
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14
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Hirama T, Tokita S, Nakatsugawa M, Murata K, Nannya Y, Matsuo K, Inoko H, Hirohashi Y, Hashimoto S, Ogawa S, Takemasa I, Sato N, Hata F, Kanaseki T, Torigoe T. Proteogenomic identification of an immunogenic HLA class I neoantigen in mismatch repair-deficient colorectal cancer tissue. JCI Insight 2021; 6:e146356. [PMID: 34185709 PMCID: PMC8410045 DOI: 10.1172/jci.insight.146356] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/16/2021] [Indexed: 12/21/2022] Open
Abstract
Although CD8+ T cells recognize neoantigens that arise from somatic mutations in cancer, only a small fraction of nonsynonymous mutations give rise to clinically relevant neoantigens. In this study, HLA class I ligandomes of a panel of human colorectal cancer (CRC) and matched normal tissues were analyzed using mass spectrometry–based proteogenomic analysis. Neoantigen presentation was rare; however, the analysis detected a single neoantigen in a mismatch repair–deficient CRC (dMMR-CRC) tissue sample carrying 3967 nonsynonymous mutations, where abundant tumor-infiltrating lymphocytes (TILs) and inflamed gene expression status were observed in the tumor microenvironment (TME). Using the HLA class I ligandome data and gene expression profiles, a set of nonmutated tumor-associated antigen (TAA) candidates was concomitantly identified. Interestingly, CD8+ TILs predominantly recognized the detected neoantigen over the array of TAA candidates. Neoantigen-reactive CD8+ TILs showed PD-1 positivity and exhibited functional and specific responses. Moreover, T cell receptor (TCR) profiling identified the sequence of the neoantigen-reactive TCR clonotype and showed its expansion in the TME. Transduction of the sequenced TCR conferred neoantigen specificity and cytotoxicity to peripheral blood lymphocytes. The proteogenomic approach revealed the antigenic and reactive T cell landscape in dMMR-CRC, demonstrating the presence of an immunogenic neoantigen and its potential therapeutic applications.
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Affiliation(s)
- Tomomi Hirama
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Munehide Nakatsugawa
- Department of Pathology, Tokyo Medical University Hachioji Medical Center, Tokyo, Japan
| | - Kenji Murata
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | | | - Shinichi Hashimoto
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,The World Premier International Research Center Initiative and Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ichiro Takemasa
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
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15
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Walter B, Canjuga D, Yüz SG, Ghosh M, Bozko P, Przystal JM, Govindarajan P, Anderle N, Keller A, Tatagiba M, Schenke‐Layland K, Rammensee H, Stevanovic S, Malek NP, Schmees C, Tabatabai G. Argyrin F Treatment‐Induced Vulnerabilities Lead to a Novel Combination Therapy in Experimental Glioma. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202100078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bianca Walter
- Department of Neurology and Interdisciplinary Neuro‐Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research Eberhard Karls University Tübingen Hoppe‐Seyler‐Strasse 3 72076 Tübingen Germany
| | - Denis Canjuga
- Department of Neurology and Interdisciplinary Neuro‐Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research Eberhard Karls University Tübingen Hoppe‐Seyler‐Strasse 3 72076 Tübingen Germany
| | - Simge G. Yüz
- NMI Natural and Medical Sciences Institute at the University Tübingen Markwiesenstraße 55 72770 Reutlingen Germany
| | - Michael Ghosh
- Department of Immunology, Interfaculty Institute for Cell Biology Eberhard Karls University Tübingen Auf der Morgenstelle 15/3 72076 Tübingen Germany
| | - Przemyslaw Bozko
- Department of Internal Medicine I University Hospital Tübingen, Eberhard Karls University Tübingen Otfried‐Müller‐Str. 10 72076 Tübingen Germany
| | - Justyna M. Przystal
- Department of Neurology and Interdisciplinary Neuro‐Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research Eberhard Karls University Tübingen Hoppe‐Seyler‐Strasse 3 72076 Tübingen Germany
- German Cancer Consortium (DKTK) DKFZ Partner Site Tübingen 69117 Heidelberg Germany
| | - Parameswari Govindarajan
- Department of Neurology and Interdisciplinary Neuro‐Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research Eberhard Karls University Tübingen Hoppe‐Seyler‐Strasse 3 72076 Tübingen Germany
| | - Nicole Anderle
- NMI Natural and Medical Sciences Institute at the University Tübingen Markwiesenstraße 55 72770 Reutlingen Germany
| | - Anna‐Lena Keller
- NMI Natural and Medical Sciences Institute at the University Tübingen Markwiesenstraße 55 72770 Reutlingen Germany
| | - Marcos Tatagiba
- Department of Neurosurgery University Hospital Tübingen, Eberhard Karls University Tübingen Hoppe‐Seyler‐Strasse 3 72076 Tübingen Germany
| | - Katja Schenke‐Layland
- NMI Natural and Medical Sciences Institute at the University Tübingen Markwiesenstraße 55 72770 Reutlingen Germany
- Cluster of excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen 72076 Tübingen Germany
- Department of Biomedical Engineering Eberhard Karls University Tübingen Calwerstraße 7 72076 Tübingen Germany
- Department of Medicine/Cardiology University of California Los Angeles 100 UCLA Medical Plaza, Suite 630 Los Angeles CA 90095 USA
| | - Hans‐Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology Eberhard Karls University Tübingen Auf der Morgenstelle 15/3 72076 Tübingen Germany
- German Cancer Consortium (DKTK) DKFZ Partner Site Tübingen 69117 Heidelberg Germany
- Cluster of excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen 72076 Tübingen Germany
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology Eberhard Karls University Tübingen Auf der Morgenstelle 15/3 72076 Tübingen Germany
- German Cancer Consortium (DKTK) DKFZ Partner Site Tübingen 69117 Heidelberg Germany
- Cluster of excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen 72076 Tübingen Germany
| | - Nisar P. Malek
- Department of Internal Medicine I University Hospital Tübingen, Eberhard Karls University Tübingen Otfried‐Müller‐Str. 10 72076 Tübingen Germany
- German Cancer Consortium (DKTK) DKFZ Partner Site Tübingen 69117 Heidelberg Germany
- Cluster of excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen 72076 Tübingen Germany
| | - Christian Schmees
- NMI Natural and Medical Sciences Institute at the University Tübingen Markwiesenstraße 55 72770 Reutlingen Germany
- Cluster of excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen 72076 Tübingen Germany
| | - Ghazaleh Tabatabai
- Department of Neurology and Interdisciplinary Neuro‐Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research Eberhard Karls University Tübingen Hoppe‐Seyler‐Strasse 3 72076 Tübingen Germany
- German Cancer Consortium (DKTK) DKFZ Partner Site Tübingen 69117 Heidelberg Germany
- Cluster of excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen 72076 Tübingen Germany
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16
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Shinkawa T, Tokita S, Nakatsugawa M, Kikuchi Y, Kanaseki T, Torigoe T. Characterization of CD8 + T-cell responses to non-anchor-type HLA class I neoantigens with single amino-acid substitutions. Oncoimmunology 2021; 10:1870062. [PMID: 33537174 PMCID: PMC7833734 DOI: 10.1080/2162402x.2020.1870062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
CD8+ T cells are capable of recognizing mutation-derived neoantigens displayed by HLA class I molecules, thereby exhibiting the ability to distinguish between cancer and normal cells. However, accumulating evidence has shown that only a small fraction of nonsynonymous somatic mutations give rise to clinically relevant neoantigens. The properties of such neoantigens, which must be presented by HLA and immunogenic to induce a T-cell response, remain elusive. In this study, we explored the HLA class I ligandome of a human cancer cell line with microsatellite instability using a proteogenomic approach. The results demonstrated that neoantigens accounted for only 0.34% of the HLA class I ligandome, and most neoantigens were encoded by genes with abundant expression. Thereafter, T-cell responses were prioritized, and immunodominant neoantigens were defined using naive CD8+ T cells derived from healthy donors. AKF9, an immunogenic neoantigen with a mutation at a non-anchor position, formed a stable peptide-HLA complex. T-cell responses were analyzed against a panel of AKF9 variants with single amino-acid substitutions, in which mutations did not alter the high HLA-binding affinity and stability. The responses varied across individuals, demonstrating the impact of heterogeneous T-cell repertoires in this human cancer model. Moreover, responses were biased toward a variant group with large structural changes compared to the wild-type peptide. Thus, naive T-cell induction can be attributed to multiple determinants. Combining structural dissimilarity with gene-expression levels, HLA-binding affinity, and stability may further help prioritize the immunogenicity of non-anchor-type neoantigens.
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Affiliation(s)
- Tomoyo Shinkawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Serina Tokita
- Academic center, Sapporo Dohto Hospital, Sapporo, Japan.,Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Munehide Nakatsugawa
- Department of Pathology, Tokyo Medical University Hachioji Medical Center, Tokyo, Japan.,Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Yasuhiro Kikuchi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
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17
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Kuznetsov A, Voronina A, Govorun V, Arapidi G. Critical Review of Existing MHC I Immunopeptidome Isolation Methods. Molecules 2020; 25:E5409. [PMID: 33228004 PMCID: PMC7699222 DOI: 10.3390/molecules25225409] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
Major histocompatibility complex class I (MHC I) plays a crucial role in the development of adaptive immune response in vertebrates. MHC molecules are cell surface protein complexes loaded with short peptides and recognized by the T-cell receptors (TCR). Peptides associated with MHC are named immunopeptidome. The MHC I immunopeptidome is produced by the proteasome degradation of intracellular proteins. The knowledge of the immunopeptidome repertoire facilitates the creation of personalized antitumor or antiviral vaccines. A huge number of publications on the immunopeptidome diversity of different human and mouse biological samples-plasma, peripheral blood mononuclear cells (PBMCs), and solid tissues, including tumors-appeared in the scientific journals in the last decade. Significant immunopeptidome identification efficiency was achieved by advances in technology: the immunoprecipitation of MHC and mass spectrometry-based approaches. Researchers optimized common strategies to isolate MHC-associated peptides for individual tasks. They published many protocols with differences in the amount and type of biological sample, amount of antibodies, type and amount of insoluble support, methods of post-fractionation and purification, and approaches to LC-MS/MS identification of immunopeptidome. These parameters have a large impact on the final repertoire of isolated immunopeptidome. In this review, we summarize and compare immunopeptidome isolation techniques with an emphasis on the results obtained.
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Affiliation(s)
- Alexandr Kuznetsov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
| | - Alice Voronina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Georgij Arapidi
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
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18
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Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process. Cancers (Basel) 2020; 12:cancers12061660. [PMID: 32585818 PMCID: PMC7352969 DOI: 10.3390/cancers12061660] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/11/2020] [Accepted: 06/20/2020] [Indexed: 12/14/2022] Open
Abstract
According to the latest available data, cancer is the second leading cause of death, highlighting the need for novel cancer therapeutic approaches. In this context, immunotherapy is emerging as a reliable first-line treatment for many cancers, particularly metastatic melanoma. Indeed, cancer immunotherapy has attracted great interest following the recent clinical approval of antibodies targeting immune checkpoint molecules, such as PD-1, PD-L1, and CTLA-4, that release the brakes of the immune system, thus reviving a field otherwise poorly explored. Cancer immunotherapy mainly relies on the generation and stimulation of cytotoxic CD8 T lymphocytes (CTLs) within the tumor microenvironment (TME), priming T cells and establishing efficient and durable anti-tumor immunity. Therefore, there is a clear need to define and identify immunogenic T cell epitopes to use in therapeutic cancer vaccines. Naturally presented antigens in the human leucocyte antigen-1 (HLA-I) complex on the tumor surface are the main protagonists in evocating a specific anti-tumor CD8+ T cell response. However, the methodologies for their identification have been a major bottleneck for their reliable characterization. Consequently, the field of antigen discovery has yet to improve. The current review is intended to define what are today known as tumor antigens, with a main focus on CTL antigenic peptides. We also review the techniques developed and employed to date for antigen discovery, exploring both the direct elution of HLA-I peptides and the in silico prediction of epitopes. Finally, the last part of the review analyses the future challenges and direction of the antigen discovery field.
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19
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Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire. Nat Rev Clin Oncol 2020; 17:595-610. [PMID: 32572208 PMCID: PMC7306938 DOI: 10.1038/s41571-020-0387-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2020] [Indexed: 12/21/2022]
Abstract
Immune-checkpoint inhibition provides an unmatched level of durable clinical efficacy in various malignancies. Such therapies promote the activation of antigen-specific T cells, although the precise targets of these T cells remain unknown. Exploiting these targets holds great potential to amplify responses to treatment, such as by combining immune-checkpoint inhibition with therapeutic vaccination or other antigen-directed treatments. In this scenario, the pivotal hurdle remains the definition of valid HLA-restricted tumour antigens, which requires several levels of evidence before targets can be established with sufficient confidence. Suitable antigens might include tumour-specific antigens with alternative or wild-type sequences, tumour-associated antigens and cryptic antigens that exceed exome boundaries. Comprehensive antigen classification is required to enable future clinical development and the definition of innovative treatment strategies. Furthermore, clinical development remains challenging with regard to drug manufacturing and regulation, as well as treatment feasibility. Despite these challenges, treatments based on diligently curated antigens combined with a suitable therapeutic platform have the potential to enable optimal antitumour efficacy in patients, either as monotherapies or in combination with other established immunotherapies. In this Review, we summarize the current state-of-the-art approaches for the identification of candidate tumour antigens and provide a structured terminology based on their underlying characteristics. Immune-checkpoint inhibition has transformed the treatment of patients with advanced-stage cancers. Nonetheless, the specific antigens targeted by T cells that are activated or reactivated by these agents remain largely unknown. In this Review, the authors describe the characterization and classification of tumour antigens including descriptions of the most appropriate detection methods, and discuss potential regulatory issues regarding the use of tumour antigen-based therapeutics. Immune-checkpoint inhibition has profoundly changed the paradigm for the care of several malignancies. Although these therapies activate antigen-specific T cells, the precise mechanisms of action and their specific targets remain largely unknown. Anticancer immunotherapies encompass two fundamentally different therapeutic principles based on knowledge of their therapeutic targets, that either have been characterized (antigen-aware) or have remained elusive (antigen-unaware). HLA-presented tumour antigens of potential therapeutic relevance can comprise alternative or wild-type amino acid sequences and can be subdivided into different categories based on their mechanisms of formation. The available methods for the detection of HLA-presented antigens come with intrinsic challenges and limitations and, therefore, warrant multiple lines of evidence of robust tumour specificity before being considered for clinical use. Knowledge obtained using various antigen-detection strategies can be combined with different therapeutic platforms to create individualized therapies that hold great promise, including when combined with already established immunotherapies. Tailoring immunotherapies while taking into account the substantial heterogeneity of malignancies as well as that of HLA loci not only requires innovative science, but also demands innovative approaches to trial design and drug regulation.
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20
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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] [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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21
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Teck AT, Urban S, Quass P, Nelde A, Schuster H, Letsch A, Busse A, Walz JS, Keilholz U, Ochsenreither S. Cancer testis antigen Cyclin A1 harbors several HLA-A*02:01-restricted T cell epitopes, which are presented and recognized in vivo. Cancer Immunol Immunother 2020; 69:1217-1227. [PMID: 32157447 PMCID: PMC8222032 DOI: 10.1007/s00262-020-02519-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/12/2020] [Indexed: 01/22/2023]
Abstract
Cyclin A1 is a promising antigen for T cell therapy being selectively expressed in high-grade ovarian cancer (OC) and acute myeloid leukemia (AML) stem cells. For adoptive T cell therapy, a single epitope has to be selected, with high affinity to MHC class I and adequate processing and presentation by malignant cells to trigger full activation of specific T cells. In silico prediction with three algorithms indicated 13 peptides of Cyclin A1 9 to 11 amino acids of length to have high affinity to HLA-A*02:01. Ten of them proved to be affine in an HLA stabilization assay using TAP-deficient T2 cells. Their immunogenicity was assessed by repetitive stimulation of CD8+ T cells from two healthy donors with single-peptide-pulsed dendritic cells or monocytes. Intracellular cytokine staining quantified the enrichment of peptide-specific functional T cells. Seven peptides were immunogenic, three of them against both donors. Specific cell lines were cloned and used in killing assays to demonstrate recognition of endogenous Cyclin A1 in the HLA-A*02:01-positive AML cell line THP-1. Immunopeptidome analysis based on direct isolation of HLA-presented peptides by mass spectrometry of primary AML and OC samples identified four naturally presented epitopes of Cyclin A1. The immunopeptidome of HeLa cells transfected with Cyclin A1 and HLA-A*02:01 revealed six Cyclin A1-derived HLA ligands. Epitope p410–420 showed high affinity to HLA-A*02:01 and immunogenicity in both donors. It proved to be naturally presented on primary AML blast and provoked spontaneous functional response of T cells from treatment naïve OC and, therefore, warrants further development for clinical application.
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Affiliation(s)
- Anja Tatjana Teck
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany
| | - Sabrina Urban
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany
| | - Petra Quass
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany.,Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika Nelde
- Department of Immunology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Anne Letsch
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Antonia Busse
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane Sarah Walz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Ochsenreither
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany. .,Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany.
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22
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Yarmarkovich M, Farrel A, Sison A, di Marco M, Raman P, Parris JL, Monos D, Lee H, Stevanovic S, Maris JM. Immunogenicity and Immune Silence in Human Cancer. Front Immunol 2020; 11:69. [PMID: 32256484 PMCID: PMC7092187 DOI: 10.3389/fimmu.2020.00069] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Despite recent advances in cancer immunotherapy, the process of immunoediting early in tumorigenesis remains obscure. Here, we employ a mathematical model that utilizes the Cancer Genome Atlas (TCGA) data to elucidate the contribution of individual mutations and HLA alleles to the immunoediting process. We find that common cancer mutations including BRAF-V600E and KRAS-G12D are predicted to bind none of the common HLA alleles, and are thus “immunogenically silent” in the human population. We identify regions of proteins that are not presented by HLA at a population scale, coinciding with frequently mutated hotspots in cancer, and other protein regions broadly presented across the population in which few mutations occur. We also find that 9/29 common HLA alleles contribute disproportionately to the immunoediting of early oncogenic mutations. These data provide insights into immune evasion of common driver mutations and a molecular basis for the association of particular HLA genotypes with cancer susceptibility.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Artemio Sison
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Moreno di Marco
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Pichai Raman
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,The Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joshua L Parris
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Dimitrios Monos
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hongzhe Lee
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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23
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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] [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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24
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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] [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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25
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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] [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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26
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Alspach E, Lussier DM, Miceli AP, Kizhvatov I, DuPage M, Luoma AM, Meng W, Lichti CF, Esaulova E, Vomund AN, Runci D, Ward JP, Gubin MM, Medrano RFV, Arthur CD, White JM, Sheehan KCF, Chen A, Wucherpfennig KW, Jacks T, Unanue ER, Artyomov MN, Schreiber RD. MHC-II neoantigens shape tumour immunity and response to immunotherapy. Nature 2019; 574:696-701. [PMID: 31645760 PMCID: PMC6858572 DOI: 10.1038/s41586-019-1671-8] [Citation(s) in RCA: 520] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/12/2019] [Indexed: 12/11/2022]
Abstract
The ability of the immune system to eliminate and shape the immunogenicity of tumours defines the process of cancer immunoediting1. Immunotherapies such as those that target immune checkpoint molecules can be used to augment immune-mediated elimination of tumours and have resulted in durable responses in patients with cancer that did not respond to previous treatments. However, only a subset of patients benefit from immunotherapy and more knowledge about what is required for successful treatment is needed2-4. Although the role of tumour neoantigen-specific CD8+ T cells in tumour rejection is well established5-9, the roles of other subsets of T cells have received less attention. Here we show that spontaneous and immunotherapy-induced anti-tumour responses require the activity of both tumour-antigen-specific CD8+ and CD4+ T cells, even in tumours that do not express major histocompatibility complex (MHC) class II molecules. In addition, the expression of MHC class II-restricted antigens by tumour cells is required at the site of successful rejection, indicating that activation of CD4+ T cells must also occur in the tumour microenvironment. These findings suggest that MHC class II-restricted neoantigens have a key function in the anti-tumour response that is nonoverlapping with that of MHC class I-restricted neoantigens and therefore needs to be considered when identifying patients who will most benefit from immunotherapy.
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Affiliation(s)
- Elise Alspach
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Danielle M Lussier
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Alexander P Miceli
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Ilya Kizhvatov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Michel DuPage
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Anthony N Vomund
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniele Runci
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey P Ward
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Matthew M Gubin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Ruan F V Medrano
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Cora D Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - J Michael White
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kathleen C F Sheehan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Alex Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA. .,The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA. .,The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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27
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Zimmermann C, Kowalewski D, Bauersfeld L, Hildenbrand A, Gerke C, Schwarzmüller M, Le-Trilling VTK, Stevanovic S, Hengel H, Momburg F, Halenius A. HLA-B locus products resist degradation by the human cytomegalovirus immunoevasin US11. PLoS Pathog 2019; 15:e1008040. [PMID: 31527904 PMCID: PMC6764698 DOI: 10.1371/journal.ppat.1008040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 09/27/2019] [Accepted: 08/22/2019] [Indexed: 12/27/2022] Open
Abstract
To escape CD8+ T-cell immunity, human cytomegalovirus (HCMV) US11 redirects MHC-I for rapid ER-associated proteolytic degradation (ERAD). In humans, classical MHC-I molecules are encoded by the highly polymorphic HLA-A, -B and -C gene loci. While HLA-C resists US11 degradation, the specificity for HLA-A and HLA-B products has not been systematically studied. In this study we analyzed the MHC-I peptide ligands in HCMV-infected cells. A US11-dependent loss of HLA-A ligands was observed, but not of HLA-B. We revealed a general ability of HLA-B to assemble with β2m and exit from the ER in the presence of US11. Surprisingly, a low-complexity region between the signal peptide sequence and the Ig-like domain of US11, was necessary to form a stable interaction with assembled MHC-I and, moreover, this region was also responsible for changing the pool of HLA-B ligands. Our data suggest a two-pronged strategy by US11 to escape CD8+ T-cell immunity, firstly, by degrading HLA-A molecules, and secondly, by manipulating the HLA-B ligandome. The human immune system can cover the presentation of a wide array of pathogen derived antigens owing to the three extraordinary polymorphic MHC class I (MHC-I) gene loci, called HLA-A, -B and -C in humans. Studying the HLA peptide ligands of human cytomegalovirus (HCMV) infected cells, we realized that the HCMV encoded glycoprotein US11 targeted different HLA gene products in distinct manners. More than 20 years ago the first HCMV encoded MHC-I inhibitors were identified, including US11, targeting MHC-I for proteasomal degradation. Here, we describe that the prime target for US11-mediated degradation is HLA-A, whereas HLA-B can resist degradation. Our further mechanistic analysis revealed that US11 uses various domains for distinct functions. Remarkably, the ability of US11 to interact with assembled MHC-I and modify peptide loading of degradation-resistant HLA-B was dependent on a low-complexity region (LCR) located between the signal peptide and the immunoglobulin-like domain of US11. To redirect MHC-I for proteasomal degradation the LCR was dispensable. These findings now raise the intriguing question why US11 has evolved to target HLA-A and -B differentially. Possibly, HLA-B molecules are spared in order to dampen NK cell attack against infected cells.
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Affiliation(s)
- Cosima Zimmermann
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Hildenbrand
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carolin Gerke
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Magdalena Schwarzmüller
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hartmut Hengel
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Momburg
- Clinical Cooperation Unit Applied Tumor Immunity, Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center, Heidelberg, Germany
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- * E-mail:
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28
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Kanaseki T, Tokita S, Torigoe T. Proteogenomic discovery of cancer antigens: Neoantigens and beyond. Pathol Int 2019; 69:511-518. [PMID: 31397525 DOI: 10.1111/pin.12841] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/07/2019] [Indexed: 12/24/2022]
Abstract
Host T cells infiltrate the cancer lesion and contribute to patient survival. T cells recognize antigen peptides displayed by the cancer cell human leukocyte antigen (HLA) system. Cancer antigens constitute an essential element of T-cell discrimination and play an indispensable role in anti-cancer responses. HLA ligandome analysis directly and comprehensively detects the peptides that are naturally presented by HLA of given cells, leading to discovery of cancer antigens. A proteogenomic approach, which combines conventional proteomics with genomic information, has further deciphered the landscape of the cancer HLA ligandome. Neoantigens that arise from somatic mutations are arguably the major type of peptides patient T cells recognize. Moreover, cancer cells present peptides derived from alleged noncoding regions, which also elicit T-cell responses thereby serving as cancer antigens. The diversity of newly discovered antigen sources implies that T cells are capable of sensing a variety of genomic aberrations in cancer.
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Affiliation(s)
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
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29
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Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S. Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy. J Proteome Res 2019; 18:2666-2675. [PMID: 31095916 DOI: 10.1021/acs.jproteome.9b00173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Oncolytic viruses (OVs), known for their cancer-killing characteristics, also overturn tumor-associated defects in antigen presentation through the MHC class I pathway and induce protective neo-antitumor CD8 T cell responses. Nonetheless, whether OVs shape the tumor MHC-I ligandome remains unknown. Here, we investigated if an OV induces the presentation of novel MHC I-bound tumor antigens (termed tumor MHC-I ligands). Using comparative mass spectrometry (MS)-based MHC-I ligandomics, we determined differential tumor MHC-I ligand expression following treatment with oncolytic reovirus in a murine ovarian cancer model. In vitro, we found that reovirus changes the tumor ligandome of cancer cells. Concurrent multiplexed quantitative proteomics revealed that the reovirus-induced changes in tumor MHC-I ligand presentation were mostly independent of their source proteins. In an in vivo model, tumor MHC-I ligands induced by reovirus were detectable not only in tumor tissues but also the spleens (a source of antigen-presenting cells) of tumor-bearing mice. Most importantly, therapy-induced MHC-I ligands stimulated antigen-specific IFNγ responses in antitumor CD8 T cells from mice treated with reovirus. These data show that therapy-induced MHC-I ligands may shape underlying neo-antitumor CD8 T cell responses. As such, they should be considered in strategies promoting the efficacy of OV-based cancer immunotherapies.
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Affiliation(s)
| | | | | | | | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72074 Tübingen , Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen , Germany
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72074 Tübingen , Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen , Germany
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | | | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72074 Tübingen , Germany
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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30
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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: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [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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31
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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] [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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32
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Belnoue E, Mayol JF, Carboni S, Di Berardino Besson W, Dupuychaffray E, Nelde A, Stevanovic S, Santiago-Raber ML, Walker PR, Derouazi M. Targeting self and neo-epitopes with a modular self-adjuvanting cancer vaccine. JCI Insight 2019; 5:127305. [PMID: 31013258 DOI: 10.1172/jci.insight.127305] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Induction of a potent CD4 and CD8 T-cell response against tumor-specific and tumor-associated antigen is critical for eliminating tumor cells. Recent vaccination strategies have been hampered by an inefficacious and low amplitude immune response. Here we describe a self-adjuvanted chimeric protein vaccine platform to address these challenges, characterized by a multidomain construction incorporating (i) a cell penetrating peptide (CPP) allowing internalization of several multiantigenic Major Histocompatibility Complex (MHC)-restricted peptides within (ii) the multiantigenic domain (Mad) and (iii) a TLR2/4 agonist domain (TLRag). Functionality of the resulting chimeric protein is based on the combined effect of the above-mentioned three different domains for simultaneous activation of antigen presenting cells and antigen cross-presentation, leading to an efficacious multiantigenic and multiallelic cellular immune response. Helper and cytotoxic T-cell responses were observed against model-, neo- and self-antigens, and were highly potent in several murine tumor models. The safety and the immunogenicity of a human vaccine candidate designed for colorectal cancer treatment was demonstrated in a non-human primate model. This newly engineered therapeutic vaccine approach is promising for the treatment of poorly infiltrated tumors that do not respond to currently marketed immunotherapies.
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Affiliation(s)
| | | | | | | | | | - Annika Nelde
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tubingen, Germany
| | - Stefan Stevanovic
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tubingen, Germany
| | | | - Paul R Walker
- Centre for Translational Research in Onco-Hematology, Department of Internal Medicine Specialties, University of Geneva and Division of Oncology, Geneva University Hospitals, Geneva, Switzerland
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33
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The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy. Blood 2019; 133:550-565. [DOI: 10.1182/blood-2018-07-866830] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/01/2018] [Indexed: 12/30/2022] Open
Abstract
Abstract
Antileukemia immunity plays an important role in disease control and maintenance of tyrosine kinase inhibitor (TKI)-free remission in chronic myeloid leukemia (CML). Thus, antigen-specific immunotherapy holds promise for strengthening immune control in CML but requires the identification of CML-associated targets. In this study, we used a mass spectrometry–based approach to identify naturally presented HLA class I– and class II–restricted peptides in primary CML samples. Comparative HLA ligandome profiling using a comprehensive dataset of different hematological benign specimens and samples from CML patients in deep molecular remission delineated a panel of novel frequently presented CML-exclusive peptides. These nonmutated target antigens are of particular relevance because our extensive data-mining approach suggests the absence of naturally presented BCR-ABL– and ABL-BCR–derived HLA-restricted peptides and the lack of frequent tumor-exclusive presentation of known cancer/testis and leukemia-associated antigens. Functional characterization revealed spontaneous T-cell responses against the newly identified CML-associated peptides in CML patient samples and their ability to induce multifunctional and cytotoxic antigen-specific T cells de novo in samples from healthy volunteers and CML patients. Thus, these antigens are prime candidates for T-cell–based immunotherapeutic approaches that may prolong TKI-free survival and even mediate cure of CML patients.
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34
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Marino F, Chong C, Michaux J, Bassani-Sternberg M. High-Throughput, Fast, and Sensitive Immunopeptidomics Sample Processing for Mass Spectrometry. Methods Mol Biol 2019; 1913:67-79. [PMID: 30666599 DOI: 10.1007/978-1-4939-8979-9_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Comprehensive knowledge of the HLA class I and class II peptides presented to T cells is crucial for designing innovative therapeutics against cancer and other diseases. So far, methodologies for recovery of HLA class I and II peptides for subsequent mass spectrometry-based analysis have been a major limitation. In this chapter we describe a detailed protocol for a high-throughput, reproducible, and sensitive immunoaffinity-purification of HLA-I and HLA-II peptides from up to 96 samples in a plate format, suitable for tissue samples and cell lines. Our methodology reduces sample handling, has a competitive peptide yield, and can be completed within 5 h. This simplified pipeline is applicable for basic and clinical applications.
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Affiliation(s)
- Fabio Marino
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Chloe Chong
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland. .,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.
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35
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Rajaraman S, Canjuga D, Ghosh M, Codrea MC, Sieger R, Wedekink F, Tatagiba M, Koch M, Lauer UM, Nahnsen S, Rammensee HG, Mühlebach MD, Stevanovic S, Tabatabai G. Measles Virus-Based Treatments Trigger a Pro-inflammatory Cascade and a Distinctive Immunopeptidome in Glioblastoma. MOLECULAR THERAPY-ONCOLYTICS 2018; 12:147-161. [PMID: 30775418 PMCID: PMC6365369 DOI: 10.1016/j.omto.2018.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 12/26/2022]
Abstract
Glioblastoma is an aggressive primary brain tumor with bad prognosis. On the other hand, oncolytic measles virus (MeV) therapy is an experimental glioma treatment strategy with clinical safety and first evidence of anti-tumoral efficacy. Therefore, we investigated the combination of MeV with conventional therapies by cytotoxic survival assays in long-term glioma cell lines LN229, LNZ308, and glioma stem-like GS8 cells, as well as the basal viral infectivity in primary glioblastoma cultures T81/16, T1094/17, and T708/16. We employed Chou-Talalay analysis to identify the synergistic treatment sequence chemotherapy, virotherapy, and finally radiotherapy (CT-VT-RT). RNA sequencing and immunopeptidome analyses were used to delineate treatment-induced molecular and immunological profiles. CT-VT-RT displayed synergistic anti-glioma activity and initiated a type 1 interferon response, along with canonical Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling, and downstream interferon-stimulated genes were induced, resulting in apoptotic cascades. Furthermore, antigen presentation along with immunostimulatory chemokines was increased in CT-VT-RT-treated glioma cells, indicating a treatment-induced pro-inflammatory phenotype. We identified novel treatment-induced viral and tumor-associated peptides through HLA ligandome analysis. Our data delineate an actionable treatment-induced molecular and immunological signature of CT-VT-RT, and they could be exploited for the design of novel tailored treatment strategies involving virotherapy and immunotherapy.
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Affiliation(s)
- Srinath Rajaraman
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Denis Canjuga
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Michael Ghosh
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen 72076, Germany
| | - Marius Cosmin Codrea
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Raika Sieger
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Florian Wedekink
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Marcos Tatagiba
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Marilin Koch
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine VIII, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Michael D Mühlebach
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Ghazaleh Tabatabai
- Interdisciplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, Departments of Neurology and Neurosurgery, University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen 72076, Germany.,German Translational Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
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36
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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] [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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37
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Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJ, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani‐Sternberg M. Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). Proteomics 2018; 18:e1800110. [PMID: 29791771 PMCID: PMC6033177 DOI: 10.1002/pmic.201800110] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Indexed: 12/19/2022]
Abstract
Minimal information about an immuno-peptidomics experiment (MIAIPE) is an initiative of the members of the Human Immuno-Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement, and associated mass spectrometry (MS)-related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (minimal information about a proteomics experiment) guidelines.
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Affiliation(s)
- Jennie R. Lill
- Department of MicrochemistryProteomics and LipidomicsGenentech Inc.1 DNA WaySouth San FranciscoCA94080USA
| | - Peter A. van Veelen
- Center for Proteomics and MetabolomicsLeiden University Medical CenterAlbinusdreef 22333ZA LeidenThe Netherlands
| | - Stefan Tenzer
- Institute for ImmunologyUniversity Medical Center of the Johannes Gutenberg University MainzLangenbeckstr. 155131MainzGermany
| | - Arie Admon
- Faculty of BiologyTechnion‐Israel Institute of TechnologyHaifa3200003Israel
| | - Etienne Caron
- Department of BiologyInstitute of Molecular Systems BiologyETH Zurich8093, ZurichSwitzerland
| | - Joshua E. Elias
- Department of Chemical and Systems BiologyStanford UniversityStanfordCA94305USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesScience4LifeUtrecht UniversityPadualaan 83584CH UtrechtThe Netherlands
- Netherlands Proteomics CentrePadualaan 83584CH UtrechtThe Netherlands
| | - Miguel Marcilla
- Proteomics UnitSpanish National Biotechnology CentreMadrid28049Spain
| | - Fabio Marino
- Ludwig Institute for Cancer ResearchUniversity of Lausanne1066EpalingesSwitzerland
- Department of OncologyUniversity of Lausanne1015LausanneSwitzerland
| | - Markus Müller
- Vital ITSwiss Institute of Bioinformatics1015LausanneSwitzerland
| | - Bjoern Peters
- La Jolla Institute for Allergy and ImmunologyDivision of Vaccine DiscoveryLa JollaCA92037USA
| | - Anthony Purcell
- Infection and Immunity ProgramDepartment of Biochemistry and Molecular BiologyMonash Biomedicine Discovery InstituteMonash UniversityClayton3800Australia
| | - Alessandro Sette
- La Jolla Institute for Allergy and ImmunologyDivision of Vaccine DiscoveryLa JollaCA92037USA
- University of CaliforniaLa JollaCA92093USA
| | - Theo Sturm
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesScience4LifeUtrecht UniversityPadualaan 83584CH UtrechtThe Netherlands
- Netherlands Proteomics CentrePadualaan 83584CH UtrechtThe Netherlands
| | - Nicola Ternette
- The Jenner InstituteTarget Discovery Institute Mass Spectrometry LaboratoryUniversity of OxfordOxfordOX3 7FZUK
| | - Juan Antonio Vizcaíno
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Trust Genome CampusHinxtonCambridgeCB10 1SDUK
| | - Michal Bassani‐Sternberg
- Ludwig Institute for Cancer ResearchUniversity of Lausanne1066EpalingesSwitzerland
- Department of OncologyUniversity of Lausanne1015LausanneSwitzerland
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38
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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] [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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39
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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] [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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40
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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] [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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41
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Erhard F, Halenius A, Zimmermann C, L’Hernault A, Kowalewski DJ, Weekes MP, Stevanovic S, Zimmer R, Dölken L. Improved Ribo-seq enables identification of cryptic translation events. Nat Methods 2018; 15:363-366. [PMID: 29529017 PMCID: PMC6152898 DOI: 10.1038/nmeth.4631] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023]
Abstract
Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation initiation. We experimentally validated translation using major histocompatibility complex class I (MHC I) peptidomics and observed that sORF-derived peptides efficiently enter the MHC I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.
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Affiliation(s)
- Florian Erhard
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333 München, Germany
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Anne Halenius
- Institute of Virology, Medical Center, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Cosima Zimmermann
- Institute of Virology, Medical Center, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Anne L’Hernault
- AstraZeneca UK Ltd, Innovative Medicines & Early Development, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Daniel J. Kowalewski
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen Auf der Morgenstelle 15, 72076 Tübingen, Germany
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB20XY Cambridge, United Kingdom
| | - Stefan Stevanovic
- Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Ralf Zimmer
- Institute for Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333 München, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
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42
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A meta-analysis of HLA peptidome composition in different hematological entities: entity-specific dividing lines and "pan-leukemia" antigens. Oncotarget 2018; 8:43915-43924. [PMID: 28159928 PMCID: PMC5546449 DOI: 10.18632/oncotarget.14918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/26/2016] [Indexed: 12/15/2022] Open
Abstract
Hematological malignancies (HM) are highly amenable targets for immunotherapeutic intervention and may be effectively treated by antigen-specific T-cell based treatment. Recent studies demonstrate that physiologically occurring anti-cancer T-cell responses in certain HM entities target broadly presented non-mutated epitopes. HLA ligands are thus implied as prime targets for broadly applicable and antigen-specific off-the-shelf compounds. With the aim of assessing the presence of common targets shared among different HM which may enable addressing a larger patient collective we conducted a meta-analysis of 83 mass spectrometry-based HLA peptidome datasets (comprising 40,361 unique peptide identifications) across four major HM (19 AML, 16 CML, 35 CLL, and 13 MM/MCL samples) and investigated similarities and differences within the HLA presented antigenic landscape. We found the cancer HLA peptidome datasets to cluster specifically along entity and lineage lines, suggesting that the immunopeptidome directly reflects the differences in the underlying (tumor-)biology. In line with these findings, we only detected a small set of entity-spanning antigens, which were predominantly characterized by low presentation frequencies within the different patient cohorts. These findings suggest that design of T-cell immunotherapies for the treatment of HM should ideally be conducted in an entity-specific fashion.
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43
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Zeiner PS, Zinke J, Kowalewski DJ, Bernatz S, Tichy J, Ronellenfitsch MW, Thorsen F, Berger A, Forster MT, Muller A, Steinbach JP, Beschorner R, Wischhusen J, Kvasnicka HM, Plate KH, Stefanović S, Weide B, Mittelbronn M, Harter PN. CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival. Acta Neuropathol Commun 2018; 6:18. [PMID: 29490700 PMCID: PMC5831742 DOI: 10.1186/s40478-018-0521-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 02/18/2018] [Indexed: 12/30/2022] Open
Abstract
Despite multidisciplinary local and systemic therapeutic approaches, the prognosis for most patients with brain metastases is still dismal. The role of adaptive and innate anti-tumor response including the Human Leukocyte Antigen (HLA) machinery of antigen presentation is still unclear. We present data on the HLA class II-chaperone molecule CD74 in brain metastases and its impact on the HLA peptidome complexity.We analyzed CD74 and HLA class II expression on tumor cells in a subset of 236 human brain metastases, primary tumors and peripheral metastases of different entities in association with clinical data including overall survival. Additionally, we assessed whole DNA methylome profiles including CD74 promoter methylation and differential methylation in 21 brain metastases. We analyzed the effects of a siRNA mediated CD74 knockdown on HLA-expression and HLA peptidome composition in a brain metastatic melanoma cell line.We observed that CD74 expression on tumor cells is a strong positive prognostic marker in brain metastasis patients and positively associated with tumor-infiltrating T-lymphocytes (TILs). Whole DNA methylome analysis suggested that CD74 tumor cell expression might be regulated epigenetically via CD74 promoter methylation. CD74high and TILhigh tumors displayed a differential DNA methylation pattern with highest enrichment scores for antigen processing and presentation. Furthermore, CD74 knockdown in vitro lead to a reduction of HLA class II peptidome complexity, while HLA class I peptidome remained unaffected.In summary, our results demonstrate that a functional HLA class II processing machinery in brain metastatic tumor cells, reflected by a high expression of CD74 and a complex tumor cell HLA peptidome, seems to be crucial for better patient prognosis.
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Affiliation(s)
- P S Zeiner
- Edinger Institute (Institute of Neurology), Goethe-University, Heinrich-Hoffmann-Str. 7, D-60528, Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Neurooncology, Goethe-University, Frankfurt am Main, Germany
| | - J Zinke
- Edinger Institute (Institute of Neurology), Goethe-University, Heinrich-Hoffmann-Str. 7, D-60528, Frankfurt am Main, Germany
| | - D J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | - S Bernatz
- Edinger Institute (Institute of Neurology), Goethe-University, Heinrich-Hoffmann-Str. 7, D-60528, Frankfurt am Main, Germany
| | - J Tichy
- Dr. Senckenberg Institute of Neurooncology, Goethe-University, Frankfurt am Main, Germany
| | - M W Ronellenfitsch
- Dr. Senckenberg Institute of Neurooncology, Goethe-University, Frankfurt am Main, Germany
| | - F Thorsen
- Department of Biomedicine, The Kristian Gerhard Jebsen Brain Tumour Research Center and The Molecular Imaging Center, University of Bergen, Bergen, Norway
| | - A Berger
- Institute for Virology, Goethe-University, Frankfurt am Main, Germany
| | - M T Forster
- Department of Neurosurgery, Goethe-University, Frankfurt am Main, Germany
| | - A Muller
- Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - J P Steinbach
- Dr. Senckenberg Institute of Neurooncology, Goethe-University, Frankfurt am Main, Germany
- German Cancer Research Center DKFZ Heidelberg, Germany and German Cancer Consortium DKTK partner site, Frankfurt/Mainz, Germany
| | - R Beschorner
- Department of Pathology and Neuropathology, University of Tuebingen, Tuebingen, Germany
| | - J Wischhusen
- Department of Gynecology, University of Wuerzburg, Wuerzburg, Germany
| | - H M Kvasnicka
- Goethe-University, Dr. Senckenberg Institute for Pathology, Frankfurt am Main, Germany
| | - K H Plate
- Edinger Institute (Institute of Neurology), Goethe-University, Heinrich-Hoffmann-Str. 7, D-60528, Frankfurt am Main, Germany
- German Cancer Research Center DKFZ Heidelberg, Germany and German Cancer Consortium DKTK partner site, Frankfurt/Mainz, Germany
| | - S Stefanović
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - B Weide
- Department of Dermatology, University of Tuebingen, Tuebingen, Germany
| | - M Mittelbronn
- Edinger Institute (Institute of Neurology), Goethe-University, Heinrich-Hoffmann-Str. 7, D-60528, Frankfurt am Main, Germany
- German Cancer Research Center DKFZ Heidelberg, Germany and German Cancer Consortium DKTK partner site, Frankfurt/Mainz, Germany
- Luxembourg Centre of Neuropathology (LCNP), 3555, Dudelange, Luxembourg
- Laboratoire National de Santé, Department of Pathology, 3555, Dudelange, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4361, Esch-sur-Alzette, Luxembourg
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), 1526, Luxembourg, Luxembourg
| | - P N Harter
- Edinger Institute (Institute of Neurology), Goethe-University, Heinrich-Hoffmann-Str. 7, D-60528, Frankfurt am Main, Germany.
- German Cancer Research Center DKFZ Heidelberg, Germany and German Cancer Consortium DKTK partner site, Frankfurt/Mainz, Germany.
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44
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Chong C, Marino F, Pak H, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M. High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics 2018; 17:533-548. [PMID: 29242379 PMCID: PMC5836376 DOI: 10.1074/mcp.tir117.000383] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues. Our methodology drastically reduces sample-handling and can be completed within five hours. We challenged our methodology by extracting HLA peptides from multiple replicates of tissues (n = 7) and cell lines (n = 21, 108 cells per replicate), which resulted in unprecedented depth, sensitivity and high reproducibility (Pearson correlations up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved sensitivity, even single measurements of peptides purified from 107 B-cells resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma (IFNγ). Our analysis revealed an augmented presentation of chymotryptic-like and longer ligands associated with IFNγ induced changes of the antigen processing and presentation machinery. This straightforward method is applicable for basic and clinical applications.
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Affiliation(s)
- Chloe Chong
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Fabio Marino
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - HuiSong Pak
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Julien Racle
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Roy T Daniel
- ¶Service of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Markus Müller
- ‖Vital IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Gfeller
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - George Coukos
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland;
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
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45
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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: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [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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46
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Miyamoto S, Kochin V, Kanaseki T, Hongo A, Tokita S, Kikuchi Y, Takaya A, Hirohashi Y, Tsukahara T, Terui T, Ishitani K, Hata F, Takemasa I, Miyazaki A, Hiratsuka H, Sato N, Torigoe T. The Antigen ASB4 on Cancer Stem Cells Serves as a Target for CTL Immunotherapy of Colorectal Cancer. Cancer Immunol Res 2018; 6:358-369. [PMID: 29371260 DOI: 10.1158/2326-6066.cir-17-0518] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/09/2017] [Accepted: 01/12/2018] [Indexed: 01/13/2023]
Abstract
Colorectal cancer consists of a small number of cancer stem cells (CSC) and many non-CSCs. Although rare in number, CSCs are a target for cancer therapy, because they survive conventional chemo- and radiotherapies and perpetuate tumor formation in vivo In this study, we conducted an HLA ligandome analysis to survey HLA-A24 peptides displayed by CSCs and non-CSCs of colorectal cancer. The analysis identified an antigen, ASB4, which was processed and presented by a CSC subset but not by non-CSCs. The ASB4 gene was expressed in CSCs of colorectal cancer, but not in cells that had differentiated into non-CSCs. Because ASB4 was not expressed by normal tissues, its peptide epitope elicited CD8+ cytotoxic T-cell (CTL) responses, which lysed CSCs of colorectal cancer and left non-CSCs intact. Therefore, ASB4 is a tumor-associated antigen that can elicit CTL responses specific to CSCs and can discriminate between two cellular subsets of colorectal cancer. Adoptively transferred CTLs specific for the CSC antigen ASB4 could infiltrate implanted colorectal cancer cell tumors and effectively prevented tumor growth in a mouse model. As the cancer cells implanted in these mice contained very few CSCs, the elimination of a CSC subset could be the condition necessary and sufficient to control tumor formation in vivo These results suggest that CTL-based immunotherapies against colorectal CSCs might be useful for preventing relapses. Cancer Immunol Res; 6(3); 358-69. ©2018 AACR.
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Affiliation(s)
- Sho Miyamoto
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Department of Oral Surgery, Sapporo Medical University, Sapporo, Japan
| | - Vitaly Kochin
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.
| | - Ayumi Hongo
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Yasuhiro Kikuchi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Akari Takaya
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | | | | | | | | | | | - Ichiro Takemasa
- Department of Surgery, Sapporo Medical University, Sapporo, Japan
| | - Akihiro Miyazaki
- Department of Oral Surgery, Sapporo Medical University, Sapporo, Japan
| | | | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
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47
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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. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 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] [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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48
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Abstract
The interrogation of cell surface-presented immunogenic epitopes is of great importance to differentiate diseased cells in consequence to malignant transformation or viral infections. On the basis of this knowledge, next-generation immunotherapies against cancers, autoimmunity, or infectious diseases can be developed. The identification of altered peptide repertoires of transformed cells renders mass spectrometry-based analysis indispensable. This is evident considering the low correlation of gene or protein expression alterations, respectively, with changes in the peptide repertoire rendering those analyses less informative. Nevertheless, immunogenicity of peptides appearing to be exclusively found on diseased cells has to be finally proven in T cell-based assays. This review highlights the capabilities and limitations of mass spectrometry in the identification of entire immunopeptidomes, as well as individual potential immunogenic epitopes with a strong focus on cancer. Furthermore, an overview of state-of-the-art immunogenicity screens is presented.
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49
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Murphy JP, Konda P, Kowalewski DJ, Schuster H, Clements D, Kim Y, Cohen AM, Sharif T, Nielsen M, Stevanovic S, Lee PW, Gujar S. MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies. J Proteome Res 2017; 16:1806-1816. [PMID: 28244318 DOI: 10.1021/acs.jproteome.6b00971] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Class I major histocompatibility complex (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8+ T cells and thus are important for devising T-cell immunotherapies. In recent times, advances in mass spectrometry (MS) have enabled the precise identification of these MHC-I peptides, wherein MS spectra are compared against a reference proteome. Unfortunately, matching these spectra to reference proteome databases is hindered by inflated search spaces attributed to a lack of enzyme restriction in the searches, limiting the efficiency with which MHC ligands are discovered. Here we offer a solution to this problem whereby we developed a targeted database search approach and accompanying tool SpectMHC, that is based on a priori-predicted MHC-I peptides. We first validated the approach using MS data from two different allotype-specific immunoprecipitates for the C57BL/6 mouse background. We then developed allotype-specific HLA databases to search previously published MS data sets of human peripheral blood mononuclear cells (PBMCs). This targeted search strategy improved peptide identifications for both mouse and human ligandomes by greater than 2-fold and is superior to traditional "no enzyme" searches of reference proteomes. Our targeted database search promises to uncover otherwise missed novel T-cell epitopes of therapeutic potential.
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Affiliation(s)
- J Patrick Murphy
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Prathyusha Konda
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Daniel J Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , 72076 Tübingen, Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , 72076 Tübingen, Germany.,Immatics Biotechnologies GmbH , 72076 Tübingen, Germany
| | - Derek Clements
- Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Youra Kim
- Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Alejandro M Cohen
- Proteomics Core Facility, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Tanveer Sharif
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark , 2800 Kongens Lyngby, Denmark
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen , 72076 Tübingen, Germany
| | - Patrick W Lee
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.,Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
| | - Shashi Gujar
- Department of Microbiology and Immunology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.,Department of Pathology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.,Centre for Innovative and Collaborative Health Services Research, IWK Health Centre , Halifax, Nova Scotia B3K 6R8, Canada
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50
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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] [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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