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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. Retraction Note: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:872. [PMID: 37938785 PMCID: PMC10665177 DOI: 10.1038/s41586-023-06731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Pereira M, Richetta C, Ghosh M, Rosoy E, Bertrand L, Ramirez C, Jeger-Madiot R, Faure M, Esclatine A, Stevanovic S, Graff-Dubois S, Manoury B, Moris A. Autophagy Receptors in the presentation of Viral antigens by MHC-II molecules. Mol Immunol 2022. [DOI: 10.1016/j.molimm.2022.05.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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Walter B, Canjuga D, Yuez SG, Ghosh M, Bozko P, Przystal J, Govindarajan P, Anderle N, Keller AL, Tatagiba M, Schenke-Layland K, Rammensee HG, Stevanovic S, Malek NP, Schmees C, Tabatabai G. EXTH-48. NOVEL COMBINATION THERAPY IN PRECLINICAL GLIOMA MODELS USING THE CELL CYCLE STABILIZING COMPOUND ARGYRIN F AND CHECKPOINT INHIBITION. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Glioblastoma are incurable aggressive tumors and remain a therapeutic challenge. Glioblastoma frequently harbor alterations in the retinoblastoma pathway with subsequent cell cycle abnormalities. Here, we aimed to investigate the anti-glioma activity of the cell cycle-stabilizing compound Argyrin F and its potential treatment-induced vulnerabilities to exploit possibilities for novel combination therapies. We investigated cell viability, clonogenic survival, cell cycle status and immunoblots of human and murine glioma cells treated with Argyrin F. Moreover, we established an ex vivo glioma model using residual freshly resected tissue from patients, i.e. patient-derived microtumors (PDMs). Additionally, we extracted autologous tumor infiltrating lymphocytes (TILs) to perform co-culturing experiments. We performed mass spectrometry-based immunopeptidomics and used the orthotopic syngeneic SMA560/VM/Dk glioma mouse model. Argyrin F displayed anti-glioma efficacy in glioma cell lines in vitro and in PDM models ex vivo. Moreover, Argyrin F treatment induced cell cycle arrest, reduced clonogenic survival in vitro and prolonged survival in vivo. Argyrin F-treated SMA560 glioma displayed 4.6-fold more glioma-infiltrating CD8+ T cells. We discovered a distinctive treatment-induced immunopeptidome. Combination of Argyrin F plus PD-1 antibody increased cellular toxicity in PDM/TILs co-cultures ex vivo and prolonged overall survival compared with monotherapies in vivo. We conclude that our experimental data suggest a novel combination of Argyrin F plus PD-1 blockade and its clinical translation.
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Affiliation(s)
- Bianca Walter
- Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Denis Canjuga
- Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Simge G Yuez
- Eberhard-Karls University Tübingen, Reutlingen, Germany
| | - Michael Ghosh
- Eberhard-Karls University Tübingen, Tübingen, Germany
| | | | | | | | - Nicole Anderle
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Anna-Lena Keller
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Marcos Tatagiba
- Eberhard-Karls University Tübingen, Department of Neurosurgery, Tübingen, Germany
| | | | | | | | - Nisar P Malek
- Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Christian Schmees
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ghazaleh Tabatabai
- Eberhard-Karls University Tübingen, Department of Neurology and Interdisciplinary Neuro-Oncology, Tübingen, Germany
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5
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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: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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Yarmarkovich M, Warrington JM, Marshall QF, Shen H, Li W, Beasley M, Marco MD, Stevanovic S, Sgourakis NG, Dimitrov D, Smith P, Maris JM. Abstract 1493: Discovery and CAR T targeting of lineage-restricted neuroblastoma oncoproteins. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The MHC presents a snapshot of the intracellular proteome for surveillance by T cells, including peptides from mutated proteins (neoantigens) and nonmutated but aberrantly expressed proteins. Though peptides derived from nonmutated oncoproteins may be presented on MHC, self-antigens are not normally immunogenic to native T cells. Neuroblastoma presents a unique combination of challenges in identifying and targeting tumor-specific antigens: low mutational burden and low MHC expression.
Methods and Results: Using an immunogenomic and immunopeptidomics approach in 16 human neuroblastoma samples, we identified 265 novel antigens presented on MHC and prioritized 6 (including the PHOX2B master regulator) as lead preclinical candidates based on: 1) binding affinity to common HLA alleles, 2) extent of differential gene expression, 3) lack of MHC presentation in healthy tissue, 4) biological relevance to neuroblastoma, and 5) recurrence across multiple tumors. We validated PHOX2B binding to the predicted HLA allele A24 using crystallography of the refolded peptide-MHC (pMHC) complex, and confirmed the peptide sequence using LC/MS/MS of the synthetic peptide. Upon antigen validation, we engineered CAR receptors to induce immunogenicity to self-antigens. Phage display libraries were used to pan for tumor-specific scFv's, using predicted cross-reactive pMHCs as decoys, generating candidate scFv's that were cloned into CAR constructs. We developed an algorithm to predict cross-reactivity against normal tissue pMHCs and screened CARs for cross-reactivity, prioritizing constructs with high tumor antigen affinity and low cross-reactivity. Lead CARs demonstrate complete elimination of tumor cells in less than 24 hours using 1:1 E:T ratios in neuroblastoma cells, and not in other cancer lines expressing HLA-A24 but not PHOX2B, demonstrating highly specific and potent killing. Robust CAR killing was induced by pulsing HLA-A24+/PHOX2B- melanoma cells with PHOX2B peptide but not with potential cross-reactive peptides. Finally, two lead CAR constructs induced complete regression of established neuroblastoma HLA-A24+ SKNAS xenografts, with additional murine trials ongoing.
Conclusion: Neuroblastomas present a unique ligandome, including a significant number of antigens derived from lineage-restricted oncoproteins. We demonstrate proof-of-concept using scFv-based CARs to target the previously undruggable PHOX2B transcription factor in in vitro and in vivo studies. These data provide a basis for targeting non-immunogenic lineage-restricted oncoproteins using CAR T cells in neuroblastoma and other human cancers.
Citation Format: Mark Yarmarkovich, John M. Warrington, Quinlen F. Marshall, Helena Shen, Wei Li, Matt Beasley, Moreno Di Marco, Stefan Stevanovic, Nikolaos G. Sgourakis, Dimiter Dimitrov, Peter Smith, John M. Maris. Discovery and CAR T targeting of lineage-restricted neuroblastoma oncoproteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1493.
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Affiliation(s)
| | | | | | - Helena Shen
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | - Wei Li
- 2University of Pittsburgh, Pittsburgh, PA
| | | | | | | | | | | | | | - John M. Maris
- 1Children's Hospital of Philadelphia, Philadelphia, PA
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7
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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. Adv Therap 2021. [DOI: 10.1002/adtp.202100078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Wang J, Jelcic I, Mühlenbruch L, Haunerdinger V, Toussaint NC, Zhao Y, Cruciani C, Faigle W, Naghavian R, Foege M, Binder TMC, Eiermann T, Opitz L, Fuentes-Font L, Reynolds R, Kwok WW, Nguyen JT, Lee JH, Lutterotti A, Münz C, Rammensee HG, Hauri-Hohl M, Sospedra M, Stevanovic S, Martin R. HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis. Cell 2020; 183:1264-1281.e20. [PMID: 33091337 PMCID: PMC7707104 DOI: 10.1016/j.cell.2020.09.054] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
The HLA-DR15 haplotype is the strongest genetic risk factor for multiple sclerosis (MS), but our understanding of how it contributes to MS is limited. Because autoreactive CD4+ T cells and B cells as antigen-presenting cells are involved in MS pathogenesis, we characterized the immunopeptidomes of the two HLA-DR15 allomorphs DR2a and DR2b of human primary B cells and monocytes, thymus, and MS brain tissue. Self-peptides from HLA-DR molecules, particularly from DR2a and DR2b themselves, are abundant on B cells and thymic antigen-presenting cells. Furthermore, we identified autoreactive CD4+ T cell clones that can cross-react with HLA-DR-derived self-peptides (HLA-DR-SPs), peptides from MS-associated foreign agents (Epstein-Barr virus and Akkermansia muciniphila), and autoantigens presented by DR2a and DR2b. Thus, both HLA-DR15 allomorphs jointly shape an autoreactive T cell repertoire by serving as antigen-presenting structures and epitope sources and by presenting the same foreign peptides and autoantigens to autoreactive CD4+ T cells in MS. HLA-DR15 present abundant HLA-DR-derived self-peptides on B cells Autoreactive T cells in MS recognize HLA-DR-derived self-peptides/DR15 complexes Foreign peptides/DR15 complexes trigger potential autoreactive T cells in MS HLA-DR15 shape an autoreactive T cell repertoire by cross-reactivity/restriction
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Affiliation(s)
- Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Ivan Jelcic
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Lena Mühlenbruch
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Veronika Haunerdinger
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich 8093, Switzerland; Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD 20850, USA
| | - Carolina Cruciani
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Reza Naghavian
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Magdalena Foege
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Thomas M C Binder
- HLA Laboratory of the Stefan Morsch Foundation (SMS), Birkenfeld 55765, Germany
| | - Thomas Eiermann
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich 8057, Switzerland
| | - Laura Fuentes-Font
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Richard Reynolds
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Julie T Nguyen
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Jar-How Lee
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Andreas Lutterotti
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Mireia Sospedra
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Stefan Stevanovic
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland.
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9
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Marcu A, Bichmann L, Kuchenbecker L, Backert L, Kowalewski DJ, Freudenmann LK, Löffler MW, Lübke M, Walz J, Velz J, Moch H, Regli L, Silginer M, Weller M, Schlosser A, Kohlbacher O, Stevanovic S, Rammensee HG, Neidert MC. The HLA Ligand Atlas: A novel immuno-oncology resource for T-cell antigen discovery. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3128 Background: The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system, which is the basis for T cell-dependent tumor rejection. Therefore, a comprehensive map of the entirety of both HLA class I- and class II-presented peptides from various benign tissues is a highly sought after resource, as it enables the definition of tumor-association on the immunologically pivotal level of the HLA ligandome. Methods: Human tissue samples were snap frozen post mortem during autopsy. The study was approved by the local IRB. HLA ligands were immunopurified and characterized using an Orbitrap Fusion Lumos mass spectrometer coupled to an Ultimate 3000 RSLC Nano UHPLC System. Data acquisition was performed as technical triplicates in data-dependent mode, and data were analyzed using the containerized, computational pipeline MHCquant. Results: In this work, we describe the HLA Ligand Atlas, a comprehensive collection of matched HLA class I and class II ligandomes from 29 non-malignant tissues and 13 human subjects (208 samples in total), covering 38 HLA class I, and 17 HLA*DRB alleles and comprising 48,381 HLA class I and 16,146 HLA class II peptides. Nearly 50% of HLA ligands have not been previously described. The HLA Ligand Atlas is publicly available as a raw data resource, but also in the form of a user-friendly web interface that allows users to quickly formulate complex queries against the data set. Both downloadable data and the query interface are available at www.hla-ligand-atlas.org. Conclusions: This data set provides a valuable tool for research in diverse fields such as systems biology, general immunology, autoimmune disease and organ transplantation. Most importantly, the HLA Ligand Atlas provides essential information for translational applications in immuno-oncology. The knowledge of HLA ligands from benign tissues strongly supports the informed design of proteogenomic HLA-dependent target discovery approaches.
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Affiliation(s)
- Ana Marcu
- University of Tübingen, Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Leon Bichmann
- University of Tübingen, Applied Bioinformatics, Center for Bioinformatics, Tübingen, Germany., Tübingen, Germany
| | - Leon Kuchenbecker
- University of Tübingen, Applied Bioinformatics, Center for Bioinformatics, Tübingen, Germany., Tübingen, Germany
| | - Linus Backert
- University of Tübingen, Applied Bioinformatics, Center for Bioinformatics, Tübingen, Germany., Tübingen, Germany
| | - Daniel J Kowalewski
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | | | - Markus W. Löffler
- University Hospital Tübingen, Department of Clinical Pharmacology, Tübingen, Germany
| | - Maren Lübke
- University of Tübingen, Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Juliane Walz
- University of Tübingen, Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Julia Velz
- University Hospital and University of Zurich, Clinical Neuroscience Center and Department of Neurosurgery, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Luca Regli
- University Hospital and University of Zürich, Clinical Neuroscience Center and Department of Neurosurgery, Zürich, Switzerland
| | - Manuela Silginer
- University Hospital and University of Zurich, Clinical Neuroscience Center and Department of Neurology, Zurich, Switzerland
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, and Neuroscience Center Zürich, University Hospital and University of Zürich, Zürich, Switzerland
| | - Andreas Schlosser
- Julius-Maximilians-University Würzburg, Rudolf Virchow Center for Experimental Biomedicine, Würzburg, Germany
| | - Oliver Kohlbacher
- University of Tübingen, Cluster of Excellence Machine Learning in the Sciences (EXC 2064), Tübingen, Germany
| | - Stefan Stevanovic
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany., Tübingen, Germany
| | - Hans-Georg Rammensee
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany., Tübingen, Germany
| | - Marian Christoph Neidert
- University Hospital and University of Zurich, Clinical Neuroscience Center and Department of Neurosurgery, Zurich, Switzerland
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10
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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: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [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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11
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Laban S, Eziç J, Bichmann L, Mytilineos D, Fürstberger A, Kestler H, Schuler P, Hoffmann T, Rammensee HG, Stevanovic S, Mühlenbruch L. HLA-ligandome analysis reveals target antigens of oropharyngeal squamous cell carcinoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz252.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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12
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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: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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13
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Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E. The SysteMHC Atlas project. Nucleic Acids Res 2019; 46:D1237-D1247. [PMID: 28985418 PMCID: PMC5753376 DOI: 10.1093/nar/gkx664] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/21/2017] [Indexed: 11/25/2022] Open
Abstract
Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.
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Affiliation(s)
- Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Patrick G A Pedrioli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Witold Wolski
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | | | - Emanuel Schmid
- Scientific IT Services (SIS), ETH Zurich, Zurich 8093, Switzerland
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Daniel Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Fabio Marino
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne 1011, Switzerland.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, The Netherlands.,Netherlands Proteomics Centre, Utrecht, 3584 CH, The Netherlands
| | | | - Kerrie Vaughan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Krista E Meijgaarden
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Natalie Nieuwenhuizen
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - John C Castle
- Vaccine Research and Translational Medicine, Agenus Switzerland Inc., 4157 Basel, Switzerland
| | - Alexey I Nesvizhskii
- Department of Pathology, BRCF Metabolomics Core, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, 1650, Argentina.,Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | | | | | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Anders Jimmy Ytterberg
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-171 77, Sweden.,Rheumatology Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Anthony W Purcell
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia
| | - Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre, Madrid 28049, Spain
| | - Alberto Paradela
- Proteomics Unit, Spanish National Biotechnology Centre, Madrid 28049, Spain
| | - Qi Wang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, OX3 7FZ, UK
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Cécile A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3720 BA, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, The Netherlands.,Netherlands Proteomics Centre, Utrecht, 3584 CH, The Netherlands
| | - Gustavo A de Souza
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway.,The Brain Institute, Universidade Federal do Rio Grande do Norte, 59056-450, Natal-RN, Brazil
| | - Ludvig M Sollid
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo 0372, Norway
| | - Arie Admon
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, 72076, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, 72076, Germany
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, H3T 1J4, Canada
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne 1011, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.,Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Etienne Caron
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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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: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Murphy JP, Yu Q, Konda P, Paulo JA, Jedrychowski MP, Kowalewski DJ, Schuster H, Kim Y, Clements D, Jain A, Stevanovic S, Gygi SP, Mancias JD, Gujar S. Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin. Anal Chem 2019; 91:5106-5115. [PMID: 30779550 DOI: 10.1021/acs.analchem.8b05616] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MHC-I peptides are intracellular-cleaved peptides, usually 8-11 amino acids in length, which are presented on the cell surface and facilitate CD8+ T cell responses. Despite the appreciation of CD8+ T-cell antitumor immune responses toward improvement in patient outcomes, the MHC-I peptide ligands that facilitate the response are poorly described. Along these same lines, although many therapies have been recognized for their ability to reinvigorate antitumor CD8+ T-cell responses, whether these therapies alter the MHC-I peptide repertoire has not been fully assessed due to the lack of quantitative strategies. We develop a multiplexing platform for screening therapy-induced MHC-I ligands by employing tandem mass tags (TMTs). We applied this approach to measuring responses to doxorubicin, which is known to promote antitumor CD8+ T-cell responses during its therapeutic administration in cancer patients. Using both in vitro and in vivo systems, we show successful relative quantitation of MHC-I ligands using TMT-based multiplexing and demonstrate that doxorubicin induces MHC-I peptide ligands that are largely derived from mitotic progression and cell-cycle proteins. This high-throughput MHC-I ligand discovery approach may enable further explorations to understand how small molecules and other therapies alter MHC-I ligand presentation that may be harnessed for CD8+ T-cell-based immunotherapies.
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Affiliation(s)
- J Patrick Murphy
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Qijia Yu
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States
| | - Prathyusha Konda
- Department of Microbiology and Immunology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Mark P Jedrychowski
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States.,Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - 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
| | - Youra Kim
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Derek Clements
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Aditya Jain
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology , University of Tübingen , 72076 Tübingen , Germany
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joseph D Mancias
- Division of Genomic Stability and DNA Repair, Department of Radiation Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts 02215 , United States
| | - Shashi Gujar
- Department of Pathology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.,Department of Microbiology and Immunology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada.,Centre for Innovative and Collaborative Health Systems Research Quality and System Performance , IWK Health Centre , Halifax , Nova Scotia B3K 6R8 , Canada
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17
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Ulges A, Hilf N, Wick W, Platten M, Dietrich PY, Frenzel K, Admon A, Burg SSVD, Deimling AV, Straten PT, Gouttefangeas C, Kroep JR, Martínez-Ricarte F, Okada H, Ottensmeier CH, Ponsati B, Poulsen HS, Stevanovic S, Tabatabai G, Rammensee HG, Sahin U, Maurer D, Mendrzyk R. Abstract A020: Immunomonitoring for actively personalized peptide vaccines (APVACs) during immunotherapeutic treatment of glioblastoma. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer immunotherapy to gliomas has so far failed to show encouraging results, as gliomas are rarely mutated and show various mechanisms of immune escape. To improve therapy to these type of cancer, the Glioma Actively Personalized Vaccine Consortium (GAPVAC) integrated a highly personalized peptide vaccine approach into glioblastoma standard of care treatment combining neoepitope and nonmutated tumor antigens to exploit the full repertoire of tumor antigens. In this phase I clinical trial fifteen patients received two different types of personalized peptide vaccines (APVAC1 and APVAC2), that were selected based on transcriptome, immunopeptidome and mutational analysis of the patient’s individual tumors. While APVAC1 vaccines were composed of nonmutated tumor antigens selected in a warehouse-based approach, APVAC2 vaccines primarily targeted neoepitopes. Both vaccines were used in combination with poly-ICLC and GM-CSF as adjuvants and demonstrated expected safety profile and outstanding Immunogenicity. Immunomonitoring of APVAC1 peptides was carried out using a combinatorial ex vivo Class I 2D multimer (2DMM) and Class II intracellular cytokine staining (ICS) assay with an outstanding sensitivity to detect even one peptide-specific cell in one million of CD4 or CD8 T-cells. Nonmutated APVAC1 class I peptides showed induction of persistent CD8 T-cell responses, mainly consisting of a highly favorable central memory phenotype (CM). Furthermore, APVAC1 class II peptides demonstrated induction of polyfunctional CD4 T-cells predominantly of a type 1 T helper cell (TH1) phenotype. Notably, an APVAC1 class II specific T-cell response was detected in tumor-infiltrating lymphocyte (TIL) fraction obtained from resection of one patient. On the other side, immune responses to APVAC2 peptides were analyzed using a pan-ICS assay including a single in vitro sensitization step to analyze a broad array of cytokines produced by CD4 T helper (TH) cells and CD8 CTLs in parallel. APVAC2 peptides showed excellent immunogenicity and induced potent and multifunctional CD4 T-cell responses, mostly of a TH1 phenotype that often concurred with CTL responses. Furthermore, the induction of APVAC1-specific CD8 memory cells, as a marker for the potency of the vaccine-induced immune responses, reversely correlated with the baseline frequencies of regulatory T-cells (Treg). Taken together, actively personalized peptide vaccines (APVACs) were highly immunogenic and induced sustained responses of a highly favorable CD4 and CD8 T-cell phenotype. The vaccination showed the expected safety profile and the approach was feasible, even in this highly individualized setting. Therefore, the APVAC vaccination approach clearly represents a step forward on the path to bring the benefit of immunotherapy to glioblastoma patients.
Citation Format: Alexander Ulges, Norbert Hilf, Wolfgang Wick, Michael Platten, Pierre-Yves Dietrich, Katrin Frenzel, Arie Admon, Sjoerd S.H. van der Burg, Andreas von Deimling, Per thor Straten, Cecile Gouttefangeas, Judith R. Kroep, Francisco Martínez-Ricarte, Hideo Okada, Christian H. Ottensmeier, Berta Ponsati, Hans S. Poulsen, Stefan Stevanovic, Ghazaleh Tabatabai, Hans-Georg Rammensee, Ugur Sahin, Dominik Maurer, Regina Mendrzyk. Immunomonitoring for actively personalized peptide vaccines (APVACs) during immunotherapeutic treatment of glioblastoma [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A020.
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Affiliation(s)
- Alexander Ulges
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Norbert Hilf
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Wolfgang Wick
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Michael Platten
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Pierre-Yves Dietrich
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Katrin Frenzel
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Arie Admon
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Sjoerd S.H. van der Burg
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Andreas von Deimling
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Per thor Straten
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Cecile Gouttefangeas
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Judith R. Kroep
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Francisco Martínez-Ricarte
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Hideo Okada
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Christian H. Ottensmeier
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Berta Ponsati
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Hans S. Poulsen
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Stefan Stevanovic
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Ghazaleh Tabatabai
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Ugur Sahin
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Dominik Maurer
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
| | - Regina Mendrzyk
- Immatics Biotechnologies GmbH, Tübingen, Germany; University Hospital Heidelberg, Heidelberg, Germany; Université de Genève, Genève, Switzerland; BioNTech AG, Mainz, Germany; Technion - Israel Institute of Technology, Haifa, Israel; Leiden University Medical Center, Rotterdam, The Netherlands; University Hospital Herlev, Herlev, Denmark; Leiden University Medical Center, Leiden, The Netherlands; Vall d’Hebron University Hospital, Barcelona, Spain; University of California San Francisco, San Francisco, CA; University of Southampton, Southampton, United Kingdom; BCN Peptides S.A., Barcelona, Spain; Ringhospitalet, Copenhagen, Denmark; University of Tübingen, Tübingen, Germany
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18
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Dolashki A, Dolashka P, Stenzl A, Stevanovic S, Aicher WK, Velkova L, Velikova R, Voelter W. Antitumour activity of Helix hemocyanin against bladder carcinoma permanent cell lines. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1507755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aleksandar Dolashki
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pavlina Dolashka
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Arnulf Stenzl
- Department of Urology, University of Tübingen Hospital, Tübingen, Germany
| | - Stefan Stevanovic
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Wilhelm K. Aicher
- Department of Urology, University of Tübingen Hospital, Tübingen, Germany
| | - Lyudmila Velkova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Radostina Velikova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Wolfgang Voelter
- Interfacultary Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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19
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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. Mol Ther 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Wick W, Dietrich PY, HIlf N, Platten M, Frenzel K, Admon A, van der Burg S, von Deimling A, Gouttefangeas C, Kroep J, Martinez-Ricarte F, Okada H, Ottensmeier C, Ponsati B, Poulsen H, Stevanovic S, Tabatabai G, Rammensee HG, Sahin U, Singh-Jasuja H. ATIM-20. GAPVAC-101 TRIAL OF A HIGHLY PERSONALIZED PEPTIDE VACCINATION FOR PATIENTS WITH NEWLY DIAGNOSED GLIOBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Baden-Wurttemberg, Germany
| | | | - Norbert HIlf
- Immatics biotechnologies GmbH, Tübingen, Baden-Wurttemberg, Germany
| | - Michael Platten
- University of Heidelberg, Mannheim, Mannheim, Baden-Wurttemberg, Germany
| | | | - Arie Admon
- Technion - Israel Institute of Technology, Haifa, Tel Aviv, Israel
| | | | | | - Cecile Gouttefangeas
- CIMT - Association for Cancer Immunotherapy, Mainz, Tübingen, Baden-Wurttemberg, Germany
| | - Judith Kroep
- Leiden University Medical Center, Liege, Belgium
| | | | - Hideho Okada
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Hans Poulsen
- Ringhospitalet, Copenhagen, Midtjylland, Denmark
| | | | - Ghazaleh Tabatabai
- Interdisciplinary Division of Neuro-Oncology, Departments of Neurology and Neurosurgery, University Hospital Tuebingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tuebingen, Tuebingen, Germany, Tuebingen, Baden-Wurttemberg, Germany
| | | | - Ugur Sahin
- BioNTech AG, Mainz, Rheinland-Pfalz, Germany
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21
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Braun S, Marcu A, Billich T, Engler T, Schuster H, Taran FA, Hartkopf AD, Wallwiener D, Brucker SY, Rammensee HG, Stevanovic S, Wagner P. Entwicklung einer Multipeptidvakzine zur Therapie des Ovarialkarzinoms. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- S Braun
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
| | - A Marcu
- Interfakultäres Institut für Zellbiologie, Universität Tübingen, Abteilung für Immunologie, Tübingen, Deutschland
| | - T Billich
- Interfakultäres Institut für Zellbiologie, Universität Tübingen, Abteilung für Immunologie, Tübingen, Deutschland
| | - T Engler
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
| | - H Schuster
- Interfakultäres Institut für Zellbiologie, Universität Tübingen, Abteilung für Immunologie, Tübingen, Deutschland
| | - FA Taran
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
| | - AD Hartkopf
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
| | - D Wallwiener
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
| | - SY Brucker
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
| | - HG Rammensee
- Interfakultäres Institut für Zellbiologie, Universität Tübingen, Abteilung für Immunologie, Tübingen, Deutschland
| | - S Stevanovic
- Interfakultäres Institut für Zellbiologie, Universität Tübingen, Abteilung für Immunologie, Tübingen, Deutschland
| | - P Wagner
- Universitätsfrauenklinik Tübingen, Tübingen, Deutschland
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22
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Dietrich P, Wick W, Hilf N, Frenzel K, Gouttefangeas C, Platten M, thor Straten P, Lassen U, Rodon J, Bukur V, Admon A, van der Burg SH, von Deimling A, Kroep JR, Martinez-Ricarte F, Okada H, Ottensmeier CH, Ponsati B, Poulsen HS, Stevanovic S, Tabatabai G, Rammensee H, Sahin U, Singh-Jasuja H. OS2.2 Highly personalized peptide vaccination for patients with newly diagnosed glioblastoma: the GAPVAC trial. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy139.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - W Wick
- University of Heidelberg, Heidelberg, Germany
| | - N Hilf
- Immatics biotechnologies GmbH, Geneva, Germany
| | | | | | - M Platten
- University of Heidelberg, Campus Mannheim, Mannheim, Germany
| | | | - U Lassen
- Ringhospitalet Copenhagen, Copenhagen, Denmark
| | - J Rodon
- Vall d`Hebron, Barcelona, Spain
| | | | | | | | | | - J R Kroep
- University of Leiden University, Leiden, Belgium
| | | | - H Okada
- University of San Francisco, San Francisco, CA, United States
| | | | | | - H S Poulsen
- University of Copenhagen, Copenhagen, Denmark
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23
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Reustle A, Marco MD, Büttner F, Winter S, Kandabarau S, Kowalewski D, Backert L, Rausch S, Hennenlotter J, Scharpf M, Fend F, Stenzl A, Bedke J, Stevanovic S, Schwab M, Schaeffeler E. Abstract 5687: Integrative -omics analysis to identify drug targets for ccRCC immunotherapy. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer and frequently diagnosed at advanced disease stages. Cure of advanced and metastatic ccRCC is achieved only in rare cases with currently available therapies, consisting of tyrosine kinase and mTOR inhibitors, due to intrinsic or acquired resistance mechanisms. We developed a workflow to identify potential drug targets involved in ccRCC pathogenesis for immunotherapeutic approaches and combinatorial treatment strategies.
Methods
We analyzed frequent ccRCC-specific peptides by HLA ligandomics of 55 ccRCC tumors, paired non-tumor tissues and 158 other benign tissues from various organs. To extract cellular pathways with enrichment in ccRCC compared to the S3 region of kidney proximal tubules, which represents the region of ccRCC origin, we performed transcriptome and gene set enrichment analyses in 51 of the 55 tumor tissues of our study cohort and in a microdissected sample of the S3 region (S3-transcriptome data taken from Cheval et al., PloS One 2012). ccRCC-specific pathway genes were intersected with the tumor-exclusive peptide source genes from the HLA ligandome analysis to retrieve a list of candidate target genes. By integrating gene expression data of an independent ccRCC cohort from the Cancer Genome Atlas (TCGA KIRC, n=452), the candidates were validated on the level of individual gene expression and pathway enrichment. Integration of DNA methylation (TCGA KIRC, n=273) and somatic mutation data (TCGA KIRC, n=392) was used to refine the candidate list.
Results
Of the frequent ccRCC-specific HLA class I and II peptide source genes, 203 were involved in ccRCC-enriched pathways in both cohorts. 136 of the genes passed the selection criteria of minimal expression in tumors (> 7.2 log2 FPKM-UQ) and induction compared to paired non-tumor tissues. 89 of the candidate targets were affected by somatic point mutations in one up to eight patients, potentially giving rise to patient-specific neo-epitopes. 110 of the candidate genes displayed altered DNA methylation patterns in tumors compared to non-tumor tissues, offering the possibility of epigenetic targeting.
Conclusion
The presented workflow, integrating HLA ligandomics, transcriptomics and genomics, yields a list of genes with frequent ccRCC-specific HLA-presented peptides that could be targeted in immunotherapeutic approaches, such as ccRCC-directed peptide vaccines. Moreover, the selected genes are involved in ccRCC-enriched cellular pathways and might therefore be important factors of ccRCC pathogenesis, potentially restraining rapid resistance development when they are used as drug targets. The list represents a pre-selection of potential drug targets for novel immunotherapeutic and combinatorial therapy approaches, which need to be further evaluated.
Citation Format: Anna Reustle, Moreno Di Marco, Florian Büttner, Stefan Winter, Siarhei Kandabarau, Daniel Kowalewski, Linus Backert, Steffen Rausch, Joerg Hennenlotter, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Jens Bedke, Stefan Stevanovic, Matthias Schwab, Elke Schaeffeler. Integrative -omics analysis to identify drug targets for ccRCC immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5687.
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Affiliation(s)
- Anna Reustle
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart and University of Tuebingen, Stuttgart, Germany
| | - Moreno Di Marco
- 2Department of Immunology, University of Tuebingen, Tuebingen, Germany
| | - Florian Büttner
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart and University of Tuebingen, Stuttgart, Germany
| | - Stefan Winter
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart and University of Tuebingen, Stuttgart, Germany
| | - Siarhei Kandabarau
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart and University of Tuebingen, Stuttgart, Germany
| | - Daniel Kowalewski
- 2Department of Immunology, University of Tuebingen, Tuebingen, Germany
| | - Linus Backert
- 2Department of Immunology, University of Tuebingen, Tuebingen, Germany
| | - Steffen Rausch
- 3Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Joerg Hennenlotter
- 3Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcus Scharpf
- 4Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Falko Fend
- 4Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- 3Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jens Bedke
- 3Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Stefan Stevanovic
- 2Department of Immunology, University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart and University of Tuebingen, Stuttgart, Germany
| | - Elke Schaeffeler
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Stuttgart and University of Tuebingen, Stuttgart, Germany
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24
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Haen S, Löffler MW, Kohlbacher O, Nahnsen S, Mohr C, Stieglbaueren M, Hrstic P, Buonaguro L, Martus P, Häntschel M, Gouttefangeas C, Beckert S, Königsrainer A, Stevanovic S, Kanz L, Rammensee HG. Abstract CT057: Phase I trial to evaluate the feasibility and safety of an individualized peptide vaccine of unmodified cancer antigens: PepIVAC-01. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-ct057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Current research has entered into an unprecedented territory of analytical possibilities represented by so called “omics” technologies, allowing the examination of patients and their individual diseases on a previously unimaginable level. This development represents a serious challenge considering established trial designs and research conduct, particularly in early phase clinical trials, since novel theranostics (biomarker based allocation therapies) in principle would allow for patient selection far beyond traditional stratification approaches; further, many different therapeutic combinatorial therapies cannot be easily evaluated in a traditional way within a reasonable timeframe. The summit of this paradigm is biomarker-based selection and manufacturing of a previously undefined drug product directly adapted to patient- and disease-specific features. In our view, such an approach is ideally suited for cancer immunotherapy, since both malignancies and the human immune system require a high level of individuality. Hence, defining naturally presented HLA-Ligands specific for individual malignancies and manufacturing respective T cell targets according to current Good Manufacturing Practice (GMP) standards formulated as a multi-peptide vaccine in a clinical trial is a completely new state of the art approach. On this background, we designed a pilot clinical trial and implemented the required environment, addressing patients with particularly high unmet medical need and exceedingly high relapse rates in an adjuvant setting. The trial follows a platform design including different disease entities, encompassing non-small cell lung cancer (NSCLC), advanced colorectal cancer (CRC), triple negative breast cancer, cholangiocarcinoma, hepatocellular carcinoma (HCC) and high-risk soft tissue sarcoma. Target selection follows a five-pronged approach and is based on analyzing patient autologous tumor material on different omics levels, including the whole exome and transcriptome as well as the HLA-ligandome (comprehensive analysis of the naturally presented HLA ligands on tumor (and benign) tissue by tandem mass spectrometry) to select ideal immunological targets. Further, this trial will endorse a three tier escalation protocol featuring an individual multi-peptide vaccine with Montanide ISA 51 VG and topical imiquimod in a first step, combined with the novel lipopeptide adjuvant XS-15 (TLR7 ligand) and finally introducing a checkpoint inhibitor as a third tier. This pilot trial will primarily focus on endpoints safety and feasibility but endorse various secondary objectives including detailed immunomonitoring of induced vaccine responses and other immune markers. The HCC trial part is supported by the European Commission's 7th Framework Program (www.hepavac.eu).
Citation Format: Sebastian Haen, Markus W. Löffler, Oliver Kohlbacher, Sven Nahnsen, Christopher Mohr, Monika Stieglbaueren, Patricia Hrstic, Luigi Buonaguro, Peter Martus, Maik Häntschel, Cécile Gouttefangeas, Stefan Beckert, Alfred Königsrainer, Stefan Stevanovic, Lothar Kanz, Hans-Georg Rammensee. Phase I trial to evaluate the feasibility and safety of an individualized peptide vaccine of unmodified cancer antigens: PepIVAC-01 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT057.
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Affiliation(s)
- Sebastian Haen
- 1Eberhard-Karls-University of Tübingen, Tuebingen, Germany
| | | | - Oliver Kohlbacher
- 2German Cancer Consortium and German Cancer Research Center, Tuebingen, Germany
| | - Sven Nahnsen
- 1Eberhard-Karls-University of Tübingen, Tuebingen, Germany
| | | | | | | | | | - Peter Martus
- 1Eberhard-Karls-University of Tübingen, Tuebingen, Germany
| | - Maik Häntschel
- 1Eberhard-Karls-University of Tübingen, Tuebingen, Germany
| | | | - Stefan Beckert
- 1Eberhard-Karls-University of Tübingen, Tuebingen, Germany
| | - Alfred Königsrainer
- 2German Cancer Consortium and German Cancer Research Center, Tuebingen, Germany
| | | | - Lothar Kanz
- 1Eberhard-Karls-University of Tübingen, Tuebingen, Germany
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25
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Marcu A, Trautwein N, Stevanovic S, Johann P, Technau A, Lager J, Monoranu CM, Henkel L, Krauß J, Ebinger M, Schuhmann M, Thomale U, Pietsch T, Wölfl M, Schlegel PG, Frühwald M, Oyen F, Reisner Y, Rammensee HG, Eyrich M. IMMU-28. DECIPHERING THE AT/RT LIGANDOME. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ana Marcu
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Nico Trautwein
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | | | - Antje Technau
- Children’s Hospital, University Medical Center, Würzburg, Germany
| | - Johanna Lager
- Children’s Hospital, University Medical Center, Würzburg, Germany
| | | | - Lisa Henkel
- Children’s Hospital, University Medical Center, Würzburg, Germany
| | - Jürgen Krauß
- Department of Neurosurgery, University Medical Center, Würzburg, Germany
| | - Martin Ebinger
- Children’s Hospital, University Medical Center, Tübingen, Germany
| | - Martin Schuhmann
- Department of Neurosurgery, University Medical Center, Tübingen, Germany
| | | | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, Bonn, Germany
| | - Matthias Wölfl
- Children’s Hospital, University Medical Center, Würzburg, Germany
| | | | | | - Florian Oyen
- Children’s Hospital, University Medical Center, Hamburg, Germany
| | | | | | - Matthias Eyrich
- Children’s Hospital, University Medical Center, Würzburg, Germany
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26
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Wick W, Dietrich PY, Kuttruff S, Hilf N, Frenzel K, Admon A, van der Burg SH, von Deimling A, Gouttefangeas C, Kroep JR, Martinez-Ricarte F, Okada H, Ottensmeier CH, Ponsati B, Poulsen HS, Stevanovic S, Tabatabai G, Rammensee HG, Sahin U, Singh H. GAPVAC-101: First-in-human trial of a highly personalized peptide vaccination approach for patients with newly diagnosed glioblastoma. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.2000] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | - Norbert Hilf
- immatics biotechnologies GmbH, Tübingen, Germany
| | - Katrin Frenzel
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, DE
| | | | | | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Cecile Gouttefangeas
- Institute of Cell Biology, Dept. of Immunology, University of Tuebingen, Tuebingen, Germany
| | | | | | - Hideho Okada
- University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | | | | | | | - Stefan Stevanovic
- Institute of Cell Biology, Dept. of Immunology, University of Tuebingen, Tuebingen, Germany
| | | | - Hans-Georg Rammensee
- Institute of Cell Biology, Dept. of Immunology, University of Tuebingen, Tuebingen, Germany
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27
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Platten M, Schilling D, Bunse L, Wick A, Bunse T, Riehl D, Karapanagiotou-Schenkel I, Harting I, Sahm F, Schmitt A, Steinbach JP, Weyerbrock A, Hense J, Misch M, Krex D, Stevanovic S, Tabatabai G, von Deimling A, Schmitt M, Wick W. A mutation-specific peptide vaccine targeting IDH1R132H in patients with newly diagnosed malignant astrocytomas: A first-in-man multicenter phase I clinical trial of the German Neurooncology Working Group (NOA-16). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.2001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Michael Platten
- Mannheim University Hospital, German Cancer Research Center (DKFZ), Mannheim, Germany
| | | | - Lukas Bunse
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Antje Wick
- Neurology Clinic, University of Heidelberg, National Center for Tumor Diseases, Heidelberg, Germany
| | | | | | | | - Inga Harting
- Department of Neuroradiology, University of Heidelberg Medical Center, Heidelberg, Germany
| | - Felix Sahm
- Heidelberg University Hospital, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anita Schmitt
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Astrid Weyerbrock
- Department of Neurosurgery, University of Freiburg, Freiburg, Germany
| | - Jörg Hense
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Martin Misch
- University of Berlin Charite Medical Center, Berlin, Germany
| | - Dietmar Krex
- Carl Gustav Carus University Hospital Dresden - Department of Neurosurgery, Dresden, Germany
| | - Stefan Stevanovic
- Institute of Cell Biology, Dept. of Immunology, University of Tuebingen, Tuebingen, Germany
| | | | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
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28
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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: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Poetz O, Dieze T, Hammer H, Weiß F, Sommersdorf C, Templin MF, Esdar C, Zimmermann A, Stevanovic S, Bedke J, Stenzl A, Joos TO. Peptide-Based Sandwich Immunoassay for the Quantification of the Membrane Transporter Multidrug Resistance Protein 1. Anal Chem 2018; 90:5788-5794. [DOI: 10.1021/acs.analchem.8b00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Theresa Dieze
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Helen Hammer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Frederik Weiß
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Cornelia Sommersdorf
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Markus F. Templin
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Christina Esdar
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | - Stefan Stevanovic
- Eberhard Karls University, Department of Immunology, 72076 Tübingen, Germany
| | - Jens Bedke
- Eberhard Karls University, Department of Urology, 72076 Tübingen, Germany
| | - Arnulf Stenzl
- Eberhard Karls University, Department of Urology, 72076 Tübingen, Germany
| | - Thomas O. Joos
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
- SIGNATOPE GmbH Markwiesenstrasse 55, 72770 Reutlingen, Germany
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30
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Stevanovic S, Pervan B. A GPS Phase-Locked Loop Performance Metric Based on the Phase Discriminator Output. Sensors (Basel) 2018; 18:s18010296. [PMID: 29351250 PMCID: PMC5795916 DOI: 10.3390/s18010296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/13/2018] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
We propose a novel GPS phase-lock loop (PLL) performance metric based on the standard deviation of tracking error (defined as the discriminator's estimate of the true phase error), and explain its advantages over the popular phase jitter metric using theory, numerical simulation, and experimental results. We derive an augmented GPS phase-lock loop (PLL) linear model, which includes the effect of coherent averaging, to be used in conjunction with this proposed metric. The augmented linear model allows more accurate calculation of tracking error standard deviation in the presence of additive white Gaussian noise (AWGN) as compared to traditional linear models. The standard deviation of tracking error, with a threshold corresponding to half of the arctangent discriminator pull-in region, is shown to be a more reliable/robust measure of PLL performance under interference conditions than the phase jitter metric. In addition, the augmented linear model is shown to be valid up until this threshold, which facilitates efficient performance prediction, so that time-consuming direct simulations and costly experimental testing can be reserved for PLL designs that are much more likely to be successful. The effect of varying receiver reference oscillator quality on the tracking error metric is also considered.
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Affiliation(s)
| | - Boris Pervan
- Illinois Institute of Technology (IIT), Chicago, IL 60616, USA.
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31
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Heidenreich F, Rücker-Braun E, Walz JS, Eugster A, Kühn D, Dietz S, Nelde A, Tunger A, Wehner R, Link CS, Middeke JM, Stölzel F, Tonn T, Stevanovic S, Rammensee HG, Bonifacio E, Bachmann M, Zeis M, Ehninger G, Bornhäuser M, Schetelig J, Schmitz M. Mass spectrometry-based identification of a naturally presented receptor tyrosine kinase-like orphan receptor 1-derived epitope recognized by CD8 + cytotoxic T cells. Haematologica 2017; 102:e460-e464. [PMID: 28838995 DOI: 10.3324/haematol.2017.167312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Falk Heidenreich
- DKMS German Bone Marrow Donor Center, Clinical Trials Unit, Dresden, Germany .,Department of Medicine I, University Hospital of Dresden, Germany
| | - Elke Rücker-Braun
- Department of Medicine I, University Hospital of Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Germany
| | - Juliane S Walz
- Department of Hematology and Oncology, University of Tübingen, Germany
| | - Anne Eugster
- Center for Regenerative Therapies Dresden, TU Dresden, Germany
| | - Denise Kühn
- Center for Regenerative Therapies Dresden, TU Dresden, Germany
| | - Sevina Dietz
- Center for Regenerative Therapies Dresden, TU Dresden, Germany
| | - Annika Nelde
- Department of Hematology and Oncology, University of Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Germany
| | - Antje Tunger
- Institute of Immunology, Medical Faculty Carl Gustav Carus, TU Dresden, Germany.,National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Germany
| | - Rebekka Wehner
- Institute of Immunology, Medical Faculty Carl Gustav Carus, TU Dresden, Germany.,National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Germany
| | - Cornelia S Link
- Department of Medicine I, University Hospital of Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Germany
| | - Jan M Middeke
- Department of Medicine I, University Hospital of Dresden, Germany
| | | | - Torsten Tonn
- German Red Cross Blood Donation Service North-East, Dresden, Germany
| | - Stefan Stevanovic
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Germany.,German Cancer Consortium (DKTK), Tübingen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Germany.,German Cancer Consortium (DKTK), Tübingen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ezio Bonifacio
- Center for Regenerative Therapies Dresden, TU Dresden, Germany
| | - Michael Bachmann
- Center for Regenerative Therapies Dresden, TU Dresden, Germany.,National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,Department of Radioimmunology, Institute of Radiopharmaceutical Cancer Research, Helmholtz Center Dresden-Rossendorf, Dresden, Germany
| | | | - Gerhard Ehninger
- Department of Medicine I, University Hospital of Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Germany.,National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Martin Bornhäuser
- Department of Medicine I, University Hospital of Dresden, Germany.,Center for Regenerative Therapies Dresden, TU Dresden, Germany.,National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
| | - Johannes Schetelig
- DKMS German Bone Marrow Donor Center, Clinical Trials Unit, Dresden, Germany.,Department of Medicine I, University Hospital of Dresden, Germany
| | - Marc Schmitz
- Center for Regenerative Therapies Dresden, TU Dresden, Germany.,Institute of Immunology, Medical Faculty Carl Gustav Carus, TU Dresden, Germany.,National Center for Tumor Diseases, University Hospital Carl Gustav Carus, TU Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Dresden, Germany
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32
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Yarmarkovich M, Marco MD, Padovan O, Lobby J, Eisenlohr L, Monos D, Stevanovic S, Maris JM. Abstract 5824: MHC class I immunogenicity and novel tumor antigen discovery in neuroblastoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Neuroblastoma is a childhood tumor characterized by relatively few somatic mutations and low MHC expression, which has thus far largely precluded it from investigation using adoptive immunotherapy.
Methods: We characterized MHC-presented antigens in 8 patient derived xenograft (PDX) tumors using LC/MS/MS immunopeptidomics. We developed a method to identify antigens derived from differentially expressed proteins by combining RNA-seq data from 153 neuroblastoma and 1641 healthy tissues, and ligandomic data from 190 healthy tissues. We also performed functional characterization on the ability HLA-A2 neuroblastoma lines to elicit a T-cell response using CEF1 antigen-specific T-cell hyrbidoma when challenged with flu virus, and performed bioinformatic analysis of the TME.
Results: From 8 PDX tumors, we identified a total of 14119 MHC-presented antigens. Interestingly, we observed antigens from all tumors which stained negative for MHC by IHC, suggesting that antigens can be identified from tumors below the detection limits of the standard staining protocols. We first searched the ligandome dataset for all possible neoantigens of 8-14aa arising from known mutations. Not having found any mutated neoantigens, we developed a method to search for tumor antigens derived neuroblastoma-specific proteins. We discovered 83 MHC ligands that derive from neuroblastoma-specific proteins, which we expect to be promising targets for adoptive T-cell therapy. We also found a number of recurrent antigens across tumor samples, suggesting that the proteins from which these antigens derive could be used in HLA-agnostic tumors vaccines.
To test whether the MHC expression in neuroblastoma is sufficient to induce a T-cell response, we characterized the ability of neuroblastoma cells to elicit a CD8 response to CEF1 antigen. We demonstrate that despite low MHC expression in all lines tested, 4/7 lines are able to induce a robust T-cell response to flu antigen greater than HLA-A2 melanoma cells (>20pg/mL IL-2 release in all responsive lines).
We also characterized immune activity in patient tumors using Granzyme A (GZMA) and Perforin (PRF1) as surrogates for T-cell activity. We observed a strong correlation between known T-cell-recruiting cytokines (particularly CXCL5/9/10) and GZMA/PRF1 (p=2.51x10-35), providing further evidence that T-cells are active in the tumor microenvironment despite low MHC expression on tumor cells.
Conclusions: We identify neuroblastoma-specific MHC class I antigens in each of the 8 PDX tumors we tested, yielding a total of 83 novel antigens. We conclude that neuroblastoma tumors harbor promising tumor-specific targets for immunotherapy despite low rates of somatic mutation and low MHC expression, and that at least a subset of these tumors are able to induce a robust response using antigen-specific T-cell hybridomas. We also describe methods of identifying tumor-specific MHC antigens in other tumors with low mutational burden.
Note: This abstract was not presented at the meeting.
Citation Format: Mark Yarmarkovich, Moreno Di Marco, Olivia Padovan, Jenna Lobby, Laurence Eisenlohr, Dimitrios Monos, Stefan Stevanovic, John M. Maris. MHC class I immunogenicity and novel tumor antigen discovery in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5824. doi:10.1158/1538-7445.AM2017-5824
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Affiliation(s)
| | | | | | - Jenna Lobby
- 3Children's Hospital of Pennsylvania, Philadelphia, PA
| | | | | | | | - John M. Maris
- 3Children's Hospital of Pennsylvania, Philadelphia, PA
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Neidert MC, Kowalewski DJ, Wolpert F, Stevanovic S, Rammensee H, Lamszus K, Westphal M, Regli L, Weller M, Eisele G. P06.05 The natural HLA ligandome of glioblastoma stem-like cells: Antigen discovery for T-cell based immunotherapy. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Kind L, Stevanovic S, Wuttig S, Wimberger S, Hofer J, Müller B, Pieles U. Biomimetic Remineralization of Carious Lesions by Self-Assembling Peptide. J Dent Res 2017; 96:790-797. [PMID: 28346861 DOI: 10.1177/0022034517698419] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Caries is the most common disease in the world. Great efforts have been undertaken for prevention and to identify a regenerative treatment solution for dental caries. Self-assembling β-sheet forming peptides have previously shown to form 3-dimensional fiber networks supporting tissue regeneration. In particular, the self-assembling peptide P11-4 has shown potential in the treatment and prevention of dental caries. It has previously been shown that application of monomeric P11-4 solution to early carious lesions can increase net mineral gain by forming de novo hydroxyapatite crystals. The hypothesis for the mode of action was that monomeric self-assembling peptide P11-4 diffuses into the subsurface lesion body and assembles therein into higher order fibrils, facilitating mineralization of the subsurface volume by mimicking the natural biomineralization of the tooth enamel, and it remains within the lesion body as a scaffold built-in by the newly formed hydroxyapatite. The aim of the present study was to investigate the mechanism of action of the self-assembling peptide P11-4 supporting mineralization of carious enamel. By various analytical methods, it could be shown that the self-assembling peptide P11-4 diffuses into the subsurface lesion, assembles into higher formed aggregates throughout the whole volume of the lesion, and supports nucleation of de novo hydroxyapatite nanocrystals and consequently results in increased mineral density within the subsurface carious lesion. The results showed that the application of self-assembling peptide P11-4 can facilitate the subsurface regeneration of the enamel lesion by supporting de novo mineralization in a similar mode of action as has been shown for the natural formation of dental enamel.
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Affiliation(s)
- L Kind
- 1 School of Life Sciences, Department of Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland (FHNW), Muttenz, Switzerland
| | - S Stevanovic
- 1 School of Life Sciences, Department of Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland (FHNW), Muttenz, Switzerland
| | - S Wuttig
- 1 School of Life Sciences, Department of Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland (FHNW), Muttenz, Switzerland
| | - S Wimberger
- 1 School of Life Sciences, Department of Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland (FHNW), Muttenz, Switzerland
| | - J Hofer
- 1 School of Life Sciences, Department of Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland (FHNW), Muttenz, Switzerland
| | - B Müller
- 2 Department of Biomedical Engineering, University of Basel, Biomaterials Science Center (BMC), Allschwil, Switzerland
| | - U Pieles
- 1 School of Life Sciences, Department of Chemistry and Bioanalytics, University of Applied Sciences and Arts Northwestern Switzerland (FHNW), Muttenz, Switzerland
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35
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wallwiener M, Simoes E, Hartkopf AD, Taran FA, Keilmann L, Sickenberger N, Stevanovic S, Belleville E, Ladra C, Schneeweiss A, Wallwiener D, Brucker SY, Graf J. Abstract P3-11-05: Reliability and acceptance of e-based survey instruments for measuring patient reported outcomes (PRO) in breast cancer patients: First results of the ePROCOM study. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p3-11-05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction
Especially in oncology patients, Patient Reported Outcomes (PRO) play an increasingly important role to measure subjectively perceived health status and treatment effects. At the moment, paper-based surveys of PRO still predominate (pPRO); in recent years, data on patient-relevant endpoints is being increasingly collected electronically (ePRO). The aim of the study was to analyze the acceptance of an ePRO-survey tool in breast cancer patients within the PRAEGNANT multicenter trial. Furthermore, it should be considered, whether differences in response behavior between pPRO and ePRO can be identified (reliability check).
Materials and Methods
ePROCOM (Patient Reported Outcomes and Compliance Anaysis) was conceptualized as a monocenter, randomized, parallel-group, cross-over study. Female patients with diagnosis breast cancer aged more than 18 years were included.We randomized the patients into one of two study arms. In study arm A the patients are first asked to use the electronic, web-based tool to document the patient questionnaire (EORTC QLQ C-30 and FACT-B). Afterwards the patients were asked to fill and evaluate the paper-based questionnaires accordingly, followed by evaluation of usability, acceptance and capability. In study arm B the course varies by meaning that paper-based evaluation will be followed by the assessment of electronic data capture.
Results
N=110 patients with breast cancer in adjuvant or neoadjuvant situation completing the study during an outpatient visit at the University Hospitals in Tuebingen and the National Cancer Centre Heidelberg (average age: 52.4). In most patients, there were no differences in terms of acceptance between pPRO and ePRO. Only in some older patients with a lower quality of life hurdles for ePRO could be identified, because of lower acceptance rates. We could not find significant differences in response behavior between pPRO and ePRO.
Discussion
Because no differences in response behavior could be identified, the tool can be define as reliable possibility to measure patient reported outcomes. E-PRO surveys appear to be suitable for use in breast cancer patients. However, there is a need of support in older and more ill patients, to participate form the technical capabilities of ePRO.
Citation Format: Wallwiener M, Simoes E, Hartkopf AD, Taran F-A, Keilmann L, Sickenberger N, Stevanovic S, Belleville E, Ladra C, Schneeweiss A, Wallwiener D, Brucker SY, Graf J. Reliability and acceptance of e-based survey instruments for measuring patient reported outcomes (PRO) in breast cancer patients: First results of the ePROCOM study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-11-05.
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Affiliation(s)
- M Wallwiener
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - E Simoes
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - AD Hartkopf
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - F-A Taran
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - L Keilmann
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - N Sickenberger
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - S Stevanovic
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - E Belleville
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - C Ladra
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - A Schneeweiss
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - D Wallwiener
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - SY Brucker
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
| | - J Graf
- University Hospital Tuebingen, Tuebingen, Germany; University Hospital Heidelberg, Hospital for General Obstetrics and Gynecology, Heidelberg
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Bunse T, Bunse L, Sahm F, Omokoko T, Stevanovic S, Deimling A, Sahin U, Schmitt M, Wick W, Platten M. OS2.1 Immune responses to a mutation-specific peptide vaccine targeting IDH1R132H in patients with IDH1R132H-mutated gliomas. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now188.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Dolashka P, Dolashki A, Van Beeumen J, Floetenmeyer M, Velkova L, Stevanovic S, Voelter W. Antimicrobial Activity of Molluscan Hemocyanins from Helix and Rapana Snails. Curr Pharm Biotechnol 2016; 17:263-70. [PMID: 26343131 DOI: 10.2174/1389201016666150907113435] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/18/2014] [Accepted: 12/11/2014] [Indexed: 11/22/2022]
Abstract
For the first time the antimicrobial activities of hemocyanins from the molluscs Rapana venosa (RvH) and Helix aspersa (HaH) have been tested. From the hemolymph of the garden snail H. aspersa one structural subunit (βc-HaH ) and eight functional units (FUs, βc-HaH-a to βc-HaH-h) were isolated, and their N-terminal sequences and molecular weights, ranging between 45 and 65 kDa, determined. The antimicrobial test of the hemocyanins against different bacteria showed that only two FUs from Rapana, RvH1-b and RvH1-e, exhibit a low inhibition effect against Staphylococcus aureus. In contrast and surprisingly, the structural subunit βc-HaH of H. aspersa not only shows strong antimicrobial activities against S. aureus and the likewise Gram-positive Streptococcus epidermidis, but also against the Gram-negative bacterium Escherichia coli. We suggest that this subunit therefore has the potential to become a substitute for the commonly used antibiotics against which bacterial resistance has gradually been developed.
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Affiliation(s)
- Pavlina Dolashka
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, G. Bonchev 9, 1113 Sofia, Bulgaria.
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Hanzelmann D, Joo HS, Franz-Wachtel M, Hertlein T, Stevanovic S, Macek B, Wolz C, Götz F, Otto M, Kretschmer D, Peschel A. Toll-like receptor 2 activation depends on lipopeptide shedding by bacterial surfactants. Nat Commun 2016; 7:12304. [PMID: 27470911 PMCID: PMC4974576 DOI: 10.1038/ncomms12304] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/21/2016] [Indexed: 12/18/2022] Open
Abstract
Sepsis caused by Gram-positive bacterial pathogens is a major fatal disease but its molecular basis remains elusive. Toll-like receptor 2 (TLR2) has been implicated in the orchestration of inflammation and sepsis but its role appears to vary for different pathogen species and clones. Accordingly, Staphylococcus aureus clinical isolates differ substantially in their capacity to activate TLR2. Here we show that strong TLR2 stimulation depends on high-level production of phenol-soluble modulin (PSM) peptides in response to the global virulence activator Agr. PSMs are required for mobilizing lipoproteins, the TLR2 agonists, from the staphylococcal cytoplasmic membrane. Notably, the course of sepsis caused by PSM-deficient S. aureus is similar in wild-type and TLR2-deficient mice, but TLR2 is required for protection of mice against PSM-producing S. aureus. Thus, a crucial role of TLR2 depends on agonist release by bacterial surfactants. Modulation of this process may lead to new therapeutic strategies against Gram-positive infections. The role played by human protein TLR2 in inflammation and sepsis varies for different bacterial pathogens. Here, Hanzelmann et al. show that the differential abilities of Staphylococcus aureus strains to activate TLR2 depend on their production of peptides that release lipoproteins known to act as TLR2 agonists.
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Affiliation(s)
- Dennis Hanzelmann
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Hwang-Soo Joo
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, Interfaculty Institute of Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Tobias Hertlein
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, Würzburg 97080, Germany
| | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, Interfaculty Institute of Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Christiane Wolz
- Department of Medical Microbiology and Hygiene, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Elfriede-Aulhorn-Straße 5, 72076 Tübingen, Germany
| | - Friedrich Götz
- Department of Microbial Genetics, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dorothee Kretschmer
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Hilf N, Frenzel K, Kuttruff-Coqui S, Heesch S, Kreiter S, Admon A, Bukur V, van der Burg S, Gouttefangeas C, Kroep JR, Schoenmaekers-Welters M, Piro J, Ponsati B, Poulsen HS, Lassen U, Martinez-Ricarte F, Rodon J, Sahuquillo J, Stieglbauer M, Stevanovic S, thor Straten P, Skardelly M, Tabatabai G, Platten M, Capper D, von Deimling A, Dutoit V, Okada H, Ottensmeier C, Feist RK, Fritsche J, Laske K, Lewandrowski P, Löwer M, Mendryzk R, Meyer M, Reinhardt C, Rössler B, Paruzynski A, Pawlowski N, Song C, Lea S, Weinschenk T, Huber C, Rammensee HG, Dietrich PY, Wolfgang W, Sahin U, Singh-Jasuja H. Abstract 2654: GAPVAC-101 phase I trial: First data of an innovative actively personalized peptide vaccination trial in patients with newly diagnosed glioblastoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Glioma Actively Personalized Vaccine Consortium (GAPVAC; funded by the European Union Framework 7 Program) aims at treating newly diagnosed glioblastoma (GB) patients with two distinct actively personalized vaccines (APVACs).
Resected tumor material is analyzed for multiple biomarkers to characterize the tumor in depth and to enable the design of APVACs tailored to each individual patient: Tumor-specific mutations, the HLA peptidome and gene expression profile are assessed by next-generation sequencing, mass spectrometry and RNA microarray analysis, respectively. Further, the patient-individual immune status is investigated by assessment of leukapheresis samples utilizing an in vitro immunogenicity platform. Data are integrated to define two distinct APVACs for each patient: APVAC1 is composed of up to ten peptides selected from a pre-manufactured “warehouse”. The warehouse contains 59 HLA class I-binding and three class II-binding tumor-associated peptides frequently over-presented in GB. APVAC2 is composed of one or two peptides that are de novo synthesized for a given patient and preferentially represent mutation-bearing neo-epitopes.
After a preparation phase in which the warehouse was generated and setup of APVAC selection and manufacturing processes took place, the GAPVAC-101 phase I clinical trial was initiated. Primary endpoints of the study are assessment of safety, feasibility of APVAC manufacturing and biological activity.
The trial is conducted at six European centers and recruits HLA-A*02:01 or A*24:02-positive patients with newly diagnosed GB after gross total resection. Patients receive APVAC1 and APVAC2 vaccinations plus immunomodulators (poly-ICLC and GM-CSF) three and six months post study enrolment, respectively, and concurrent to maintenance temozolomide (TMZ).
As of November 2015, 11 patients have been enrolled, of whom six already received APVAC vaccines. Composition and manufacturing are ongoing for four patients. All APVACs were generated in time without ultimate failures. APVAC1 vaccines differ substantially with 31 out of 59 warehouse peptides have been selected at least once, indicating the need for personalization due to tumor heterogeneity even for non-mutated epitopes. In patients’ tumor samples an average of 40 non-synonymous mutations (including known driver mutations) were identified. Injection site reactions were the most frequent toxicities so far. One brain edema (Grade 3) and one allergic reaction (Grade 4)were observed, both potentially related to the vaccinations. First data on biological activity of APVACs and updated clinical data will be presented at the Annual Meeting.
In conclusion, the GAPVAC concept has been successfully translated into the clinics and so far demonstrated to be safe and feasible with its level of personalization matching the observed tumor heterogeneity.
Citation Format: Norbert Hilf, Katrin Frenzel, Sabrina Kuttruff-Coqui, Sandra Heesch, Sebastian Kreiter, Arie Admon, Valesca Bukur, Sjoerd van der Burg, Cecile Gouttefangeas, Judith R. Kroep, Marij Schoenmaekers-Welters, Jordi Piro, Berta Ponsati, Hans Skovgaard Poulsen, Ulrik Lassen, Francisco Martinez-Ricarte, Jordi Rodon, Juan Sahuquillo, Monika Stieglbauer, Stefan Stevanovic, Per thor Straten, Marco Skardelly, Ghazaleh Tabatabai, Michael Platten, David Capper, Andreas von Deimling, Valérie Dutoit, Hideho Okada, Christian Ottensmeier, Randi Kristina Feist, Jens Fritsche, Karoline Laske, Peter Lewandrowski, Martin Löwer, Regina Mendryzk, Miriam Meyer, Carsten Reinhardt, Bernhard Rössler, Anna Paruzynski, Nina Pawlowski, Colette Song, Stevermann Lea, Toni Weinschenk, Christoph Huber, Hans-Georg Rammensee, Pierre-Yves Dietrich, Wick Wolfgang, Ugur Sahin, Harpreet Singh-Jasuja. GAPVAC-101 phase I trial: First data of an innovative actively personalized peptide vaccination trial in patients with newly diagnosed glioblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2654.
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Affiliation(s)
- Norbert Hilf
- 1Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | | | | | | | - Arie Admon
- 4TECHNION - Israel Institute of Technology, Haifa, Israel
| | | | | | | | | | | | | | | | | | - Ulrik Lassen
- 8Center for Cancer Immune Therapy, Copenhagen, Denmark
| | | | - Jordi Rodon
- 9Vall d’Hebron University Hospital, Barcelona, Spain
| | | | | | | | | | | | | | | | - David Capper
- 10University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Hideho Okada
- 12University of California San Francisco, San Francisco, CA
| | | | | | | | | | | | - Martin Löwer
- 14TRON -Translational Oncology at the University Medical Center Mainz, Mainz, Germany
| | | | - Miriam Meyer
- 1Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | | | | | | | - Colette Song
- 1Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | | | - Christoph Huber
- 3CIMT - Association for Cancer Immunotherapy, Mainz, Germany
| | | | | | - Wick Wolfgang
- 10University Hospital Heidelberg, Heidelberg, Germany
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Velthuis J, Klar R, Bönig H, Rovers J, Roy D, Prokop L, Stevanovic S, Ruediger M, Krackhardt A. Leukemia-associated Antigen Reactive T-cells in ATIR101, a Recipient-specific Allodepleted T-cell Product to Reduce Relapse Rates and GVHD after Haplo-HSCT. Cytotherapy 2016. [DOI: 10.1016/j.jcyt.2016.03.218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Platten M, Schilling D, Bunse T, Sahm F, Hueckelhoven A, Schenkel I, Stevanovic S, Schmitt A, Laumann M, Steinbach JP, Misch M, Tabatabai G, Weyerbrock A, Schnell O, Krex D, Hense J, Bendszus M, von Deimling A, Schmitt M, Wick W. A mutation-specific peptide vaccine targeting IDH1R132H in patients with newly diagnosed malignant astrocytomas: A first-in-man multicenter phase I clinical trial of the German Neurooncology Working Group (NOA-16). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.tps2082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Michael Platten
- Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Felix Sahm
- Heidelberg University Hospital, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Stefan Stevanovic
- Institute of Cell Biology, Dept. of Immunology, University of Tuebingen, Tuebingen, Germany
| | - Anita Schmitt
- University of Heidelberg Medical Center, Heidelberg, Germany
| | - Marion Laumann
- University of Heidelberg Medical Center, Heidelberg, Germany
| | | | - Martin Misch
- University of Berlin Charite Medical Center, Berlin, Germany
| | | | - Astrid Weyerbrock
- Department of Neurosurgery, University of Freiburg, Freiburg, Germany
| | - Oliver Schnell
- Department of Neurosurgery, University Hospital Munich LMU, Munich, Germany
| | - Dietmar Krex
- Carl Gustav Carus University Hospital Dresden - Department of Neurosurgery, Dresden, Germany
| | | | | | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
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Palesch D, Wagner J, Meid A, Molenda N, Sienczyk M, Burkhardt J, Münch J, Prokop L, Stevanovic S, Westhoff MA, Halatsch ME, Wirtz CR, Zimecki M, Burster T. Cathepsin G-mediated proteolytic degradation of MHC class I molecules to facilitate immune detection of human glioblastoma cells. Cancer Immunol Immunother 2016; 65:283-91. [PMID: 26837514 PMCID: PMC11028727 DOI: 10.1007/s00262-016-1798-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/16/2016] [Indexed: 10/22/2022]
Abstract
To mount an adaptive immune response, MHC I molecules present antigenic peptides to CTLs. Transcriptional reduction of MHC I molecules is a strategy of immune evasion, which impairs the detection of infected or tumorous cells by CTLs. Natural killer (NK) cells, on the other hand, eliminate target cells specifically in the absence of MHC I. Consequently, infected or tumorous cells partly retain their MHC I at the cell surface to avoid NK recognition. However, it remains unclear which protease degrades MHC I molecules and how these cells maintain a limited set of MHC I at the cell surface. Here, we demonstrate that cathepsin G (CatG), a serine protease, found in the endocytic compartment of APCs and, to a lesser extent, CatD and CatS proteolytically degrade MHC I molecules. Inhibition of CatG boosted MHC I expression at the cell surface of primary human immune cells. In contrast, human glioblastoma cells do not harbor active CatG and might have lost the ability to proteolytically degrade MHC I during tumorigenesis to avoid NK-mediated killing. Overexpression of CatG in glioblastoma cells resulted in a rapid and efficient MHC I degradation. In conclusion, CatG is an essential protease for regulating MHC I molecules and thus modulation of CatG activity might present a new avenue for therapeutic intervention.
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Affiliation(s)
- David Palesch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Johanna Wagner
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Annika Meid
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Nicole Molenda
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Marcin Sienczyk
- Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Jutta Burkhardt
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lea Prokop
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | - Mike-Andrew Westhoff
- Department Pediatrics and Adolescent Medicine, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Marc-Eric Halatsch
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Christian Rainer Wirtz
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Michal Zimecki
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Timo Burster
- Department of Neurosurgery, Ulm University Medical Center, Albert-Einstein-Allee 23, 89081, Ulm, Germany.
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland.
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Hedayat F, Stevanovic S, Milic A, Miljevic B, Nabi MN, Zare A, Bottle SE, Brown RJ, Ristovski ZD. Influence of oxygen content of the certain types of biodiesels on particulate oxidative potential. Sci Total Environ 2016; 545-546:381-388. [PMID: 26748002 DOI: 10.1016/j.scitotenv.2015.12.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
Oxidative potential (OP) is related to the organic phase, specifically to its oxygenated organic fraction (OOA). Furthermore, the oxygen content of fuel molecules has significant influence on particulate OP. Thus, this study aimed to explore the actual dependency of the OOA and ROS to the oxygen content of the fuel. In order to reach the goal, different biodiesels blends, with various ranges of oxygen content; have been employed. The compact time of flight aerosol mass spectrometer (c-ToF AMS) enabled better identification of OOA. ROS monitored by using two assays: DTT and BPEA-nit. Despite emitting lower mass, both assays agreed that oxygen content of a biodiesel is directly correlated with its OOA, and highly related to its OP. Hence, the more oxygen included in the considered biodiesels, the higher the OP of PM emissions. This highlights the importance of taking oxygen content into account while assessing emissions from new fuel types, which is relevant from a health effects standpoint.
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Affiliation(s)
- F Hedayat
- ILAQH (International Laboratory of Air Quality and Health), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - S Stevanovic
- ILAQH (International Laboratory of Air Quality and Health), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia; ARC (Centre of Excellence for Free Radical Chemistry and Biotechnology), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia.
| | - A Milic
- ILAQH (International Laboratory of Air Quality and Health), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - B Miljevic
- ILAQH (International Laboratory of Air Quality and Health), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - M N Nabi
- ILAQH (International Laboratory of Air Quality and Health), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia; BERF (Biofuel Engine Research Facility), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - A Zare
- BERF (Biofuel Engine Research Facility), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - S E Bottle
- ARC (Centre of Excellence for Free Radical Chemistry and Biotechnology), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - R J Brown
- BERF (Biofuel Engine Research Facility), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
| | - Z D Ristovski
- ILAQH (International Laboratory of Air Quality and Health), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia; BERF (Biofuel Engine Research Facility), Queensland University of Technology, 2 George St, Brisbane, 4000 QLD, Australia
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Peper JK, Röhle K, Schuster H, Wagner P, Rammensee HG, Stevanovic S. Abstract B104: Characterization and specificity analysis of tumor infiltrating lymphocytes in ovarian carcinoma. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-b104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The great majority of patients suffering from ovarian cancer (OvCa) relapse after initial therapy, making OvCa the most lethal gynecological malignancy. The immunogenic nature of OvCa is highlighted by frequent infiltration with immune cells, which represent an independent prognostic factor in OvCa patients and argues in favor for the development of immunotherapies, including peptide-based cancer vaccines. The phenotype of OvCa infiltrating T cells as well as their specificity and expression of inhibitory receptors is so far unknown. This information is however critically important for the design of novel immunotherapies including the application of checkpoint inhibitor therapy.
Materials and Methods: Tumor infiltrating lymphocytes (TILs) were isolated from fresh tumor tissue of OvCa patients obtained during tumor debulking surgery. The phenotype and expression of inhibitory molecules LAG3, CTLA4, PD1 and TIM3 was assessed by flow cytometry. Peptide specificity of infiltrating T cells was analyzed by screening for reactivity against naturally presented HLA ligands employing IFNγ ELISPOT and flow cytometry. These natural presented HLA ligands have been originally identified by mass spectrometry in an extensive HLA ligandome analysis of OvCa samples.
Results: TILs from each analyzed OvCa sample demonstrated expression of at least one of the investigated inhibitory receptors. While LAG3 and PD1 were most prominent during this analysis, CTLA4 expression was only weak or absent. Furthermore, high amounts of effector memory, but few naive or central memory T cells were present. Notably, OvCa infiltrating CD4+ T cells and CD8+ T cells shared a similar expression pattern of inhibitory surface markers within each single patient. We further obtained first results in peptide-specificity of OvCa-derived T cells by screening them for reactivity against naturally presented HLA ligands identified on OvCa samples.
Conclusion: In summary, we provide first insight into the expression of various inhibitory receptors on OvCa infiltrating T cells and their peptide specificities.
Citation Format: Janet Kerstin Peper, Kevin Röhle, Heiko Schuster, Philipp Wagner, Hans-Georg Rammensee, Stefan Stevanovic. Characterization and specificity analysis of tumor infiltrating lymphocytes in ovarian carcinoma. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B104.
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Affiliation(s)
| | - Kevin Röhle
- 1University of Tübingen, Department of Immunology, Tübingen, Germany,
| | - Heiko Schuster
- 1University of Tübingen, Department of Immunology, Tübingen, Germany,
| | - Philipp Wagner
- 2University Hospital Tübingen, Department of Obstetrics and Gynecology, Tübingen, Germany
| | | | - Stefan Stevanovic
- 1University of Tübingen, Department of Immunology, Tübingen, Germany,
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Kowalewski DJ, Walz S, Backert L, Schuster H, Kohlbacher O, Kanz L, Salih HR, Rammensee HG, Stevanovic S, Stickel JS. Abstract A112: Mapping the impact of proteasome inhibitor therapy on the antigenic landscape of multiple myeloma: Identifying robust targets for T cell immunotherapy. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-a112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent studies underscore that multiple myeloma is an immunogenic disease and suggest that it can be effectively treated by T cell based immunotherapy via immunomodulation. Unspecific immune checkpoint inhibition might be synergistically complemented by therapeutic vaccination, which may help induce and guide specific anti-cancer T cell responses. We have recently conducted a study which directly characterized the antigenic landscape of myeloma by mass spectrometric analysis of naturally presented HLA ligands and identified a panel of T cell epitopes characterized by exquisite myeloma-specificity. As novel immunotherapeutic interventions will have to be implemented as 2nd line treatments, it is of great importance to thoroughly characterize and take into account the effects of previous therapies on the antigenic landscape of target cells.
Here we present a longitudinal study of the HLA-presented immunopeptidome of myeloma cells under treatment with the 2nd generation proteasome inhibitor carfilzomib. We characterize and quantify the plasticity of the antigenic landscape and identify targets characterized by robust presentation.
We quantified HLA surface expression on 4 human myeloma cell lines (MM.1s, U266, RPMI8226 & JJN3) at t0, t24h and t48h after incubation with carfilzomib. Strikingly, we detected elevated levels of HLA class I post treatment for 3/4 cell lines, with absolute molecule counts ranging from 50,000-400,000 molecules/cell. Out of the >5,000 different HLA ligands we could identify on MM.1s and U266 by mass spectrometry, we were able to detect and longitudinally quantify 38 and 54 myeloma-associated epitopes described in previous studies, respectively. Importantly, the vast majority of these antigens (88.2%) showed robust presentation on myeloma cells under therapy. Around 12% of HLA ligands showed significant changes in abundance after carfilzomib treatment. Strikingly, we observed a significant reduction in aromatic residues at the C-terminal anchor position, which directly reflects the mechanism of action of carfilzomib on the HLA ligand level.
Our study provides direct insights into the plasticity of T cell antigen presentation on myeloma cells in a model of proteasome inhibitor therapy. We were able to characterize general changes in the immunopeptidome composition and identify robustly presented myeloma-associated epitopes. Our findings may help guide future clinical trials for 2nd line T cell immunotherapy of multiple myeloma.
Citation Format: Daniel J. Kowalewski, Simon Walz, Linus Backert, Heiko Schuster, Oliver Kohlbacher, Lothar Kanz, Helmut R. Salih, Hans-Georg Rammensee, Stefan Stevanovic, Juliane S. Stickel. Mapping the impact of proteasome inhibitor therapy on the antigenic landscape of multiple myeloma: Identifying robust targets for T cell immunotherapy. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A112.
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Affiliation(s)
- Daniel J. Kowalewski
- 1Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany,
| | - Simon Walz
- 2Department of Hematology and Oncology, University of Tuebingen, Tuebingen, Germany,
| | - Linus Backert
- 3Center for Bioinformatics and Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Heiko Schuster
- 1Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany,
| | - Oliver Kohlbacher
- 3Center for Bioinformatics and Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Lothar Kanz
- 2Department of Hematology and Oncology, University of Tuebingen, Tuebingen, Germany,
| | - Helmut R. Salih
- 2Department of Hematology and Oncology, University of Tuebingen, Tuebingen, Germany,
| | - Hans-Georg Rammensee
- 1Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany,
| | - Stefan Stevanovic
- 1Institute for Cell Biology, Department of Immunology, University of Tuebingen, Tuebingen, Germany,
| | - Juliane S. Stickel
- 2Department of Hematology and Oncology, University of Tuebingen, Tuebingen, Germany,
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Rabsteyn A, Kyzirakos C, Schröder C, Sturm M, Mohr C, Walzer M, Pflückhahn U, Walter M, Feldhahn M, Laske K, Bonin M, Ebinger M, Stevanovic S, Bauer P, Kohlbacher O, Gouttefangeas C, Rammensee HG, Handgretinger R, Lang P. Abstract A113: iVacALL: A personalized peptide-vaccination design platform for pediatric acute lymphoblastic leukemia patients based on patient-individual tumor-specific variants. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6074.cricimteatiaacr15-a113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We established a platform for the design of patient-individual peptide vaccination cocktails by combination of whole exome sequencing of tumor and normal tissue with in silico epitope prediction algorithms for individual patient HLA types.
Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy. Standard chemotherapy is a successful treatment in 80% of patients, only about 20% develop a relapse, however these patients have a dismal prognosis. Prevention of relapse after first-line chemotherapy or stem cell transplantation (SCT) is therefore mandatory. Accumulation of somatic mutations is one characteristic feature of malignant cells. These single nucleotide variants (SNVs) can lead to altered amino acid sequences of the translated proteins, which in turn can be presented as antigenic peptides on HLA molecules of the malignant cells. Mutated peptides represent ideal T cell targets as they are true neoantigens, specific for the tumor, and should not have been subject to central tolerance selection mechanisms. A peptide vaccination composed of mutated T cell epitopes specific for individual patient tumors is therefore a promising approach to prevent relapse in high-risk patients. For this purpose we detect nonsynonymous mutations by whole exome and transcriptome sequencing of patient leukemic blasts and normal reference tissue. HLA binding peptides harboring the altered amino acids are subsequently predicted in silico by algorithms SYFPEITHI, NetMHC and NetMHCpan for the patients' individual HLA type.
Whole exome sequencing was performed for 17 c-ALL, 2 cortical T-ALL and 1 pro-B-ALL sample pairs. ALL-specific SNVs, as well as insertions and deletions (InDels) were identified using a comparative bioinformatics pipeline. The determined variants were further validated by deep sequencing in 9/20 patients so far, with an average of 12 (+/- 8) validated mutations per patient. For all patients with validated variants, MHC class I and MHC class II epitopes could be predicted successfully.
We applied the platform for 3 patients based on compassionate need and designed individual peptide vaccines. One patient underwent haploidentical SCT with relapsed c-ALL, a second patient received autologous SCT with ependymoma and the third patient got allogeneic SCT with pro-B ALL. In all cases validated mutations could be identified and epitope prediction was performed for MHC I & II binders. The predicted peptides were synthesized and vaccination cocktails were formulated. The vaccination schedule provides 16 vaccinations over 33 weeks using GM-CSF and Imiquimod as adjuvant. The vaccination was generally well tolerated. Response to the vaccination was monitored by detection of T cells recognizing the vaccinated peptides occurring over time in peripheral blood of the patients. Monitoring was performed for each vaccination time point by prestimulation with the peptides and subsequent intracellular cytokine staining (ICS) of T cells and FACS analysis. In all 3 patients we could detect a developing CD4+ T cell response against the vaccinated mutated MHC II binding peptides.
Whole exome sequencing of pediatric ALL patients is feasible and yields a small amount of validated mutations per patients. However, these few mutations seem sufficient to predict HLA-binding peptides that are immunogenic when vaccinated and elicit specific T cell responses in patients. Moreover, the platform is not limited to ALL/leukemia but can also be applied for solid tumor patients.
Citation Format: Armin Rabsteyn, Christina Kyzirakos, Christopher Schröder, Marc Sturm, Christopher Mohr, Mathias Walzer, Ulrike Pflückhahn, Michael Walter, Magdalena Feldhahn, Karoline Laske, Michael Bonin, Martin Ebinger, Stefan Stevanovic, Peter Bauer, Oliver Kohlbacher, Cecile Gouttefangeas, Hans-Georg Rammensee, Rupert Handgretinger, Peter Lang. iVacALL: A personalized peptide-vaccination design platform for pediatric acute lymphoblastic leukemia patients based on patient-individual tumor-specific variants. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A113.
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Affiliation(s)
- Armin Rabsteyn
- 1University Children's Hospital Tübingen, Department of General Paediatrics, Oncology/Haematology, Tübingen, Germany,
| | - Christina Kyzirakos
- 1University Children's Hospital Tübingen, Department of General Paediatrics, Oncology/Haematology, Tübingen, Germany,
| | | | - Marc Sturm
- 2Institute for Human Genetics, University of Tübingen, Tübingen, Germany,
| | - Christopher Mohr
- 3Institute for Applied Bioinformatics, University of Tübingen, Tübingen, Germany,
| | - Mathias Walzer
- 3Institute for Applied Bioinformatics, University of Tübingen, Tübingen, Germany,
| | - Ulrike Pflückhahn
- 1University Children's Hospital Tübingen, Department of General Paediatrics, Oncology/Haematology, Tübingen, Germany,
| | - Michael Walter
- 2Institute for Human Genetics, University of Tübingen, Tübingen, Germany,
| | - Magdalena Feldhahn
- 3Institute for Applied Bioinformatics, University of Tübingen, Tübingen, Germany,
| | - Karoline Laske
- 4Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany,
| | - Michael Bonin
- 2Institute for Human Genetics, University of Tübingen, Tübingen, Germany,
| | - Martin Ebinger
- 1University Children's Hospital Tübingen, Department of General Paediatrics, Oncology/Haematology, Tübingen, Germany,
| | - Stefan Stevanovic
- 4Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany,
- 5German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Peter Bauer
- 2Institute for Human Genetics, University of Tübingen, Tübingen, Germany,
| | - Oliver Kohlbacher
- 3Institute for Applied Bioinformatics, University of Tübingen, Tübingen, Germany,
| | - Cecile Gouttefangeas
- 4Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany,
- 5German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- 4Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany,
- 5German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Rupert Handgretinger
- 1University Children's Hospital Tübingen, Department of General Paediatrics, Oncology/Haematology, Tübingen, Germany,
- 5German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Peter Lang
- 1University Children's Hospital Tübingen, Department of General Paediatrics, Oncology/Haematology, Tübingen, Germany,
- 5German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
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Dolashki A, Radkova M, Todorovska E, Ivanov M, Stevanovic S, Molin L, Traldi P, Voelter W, Dolashka P. Structure and Characterization of Eriphia verrucosa Hemocyanin. Mar Biotechnol (NY) 2015; 17:743-752. [PMID: 26256301 DOI: 10.1007/s10126-015-9653-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/25/2015] [Indexed: 06/04/2023]
Abstract
Arthropod hemocyanins (Hcs) are a family of large extracellular oxygen-transporting proteins with high molecular mass and hexameric or multi-hexameric molecular assembly. This study reports for the first time the isolation and characterization of the structure of an arthropod hemocyanin from crab Eriphia verrucosa (EvH) living in the Black Sea. Its oligomeric quaternary structure is based on different arrangements of a basic 6 × 75 kDa hexameric unit, and four of them (EvH1, EvH2, EvH3, and EvH4) were identified using ion-exchange chromatography. Subunit 3 (EvH3) shows high similarity scores (75.0, 87.5, 91.7, and 75.0 %, respectively) by comparison of the N-terminal sequence of subunit 1 from Cancer pagurus of the North Sea (Cp1), subunits 3 and 6 of Cancer magister (Cm3 and Cm6), and subunit 2 of Carcinus aestuarii (CaSS2), respectively. Moreover, a partial cDNA sequence (1309 bp) of E. verrucosa hemocyanin encoding a protein of 435 amino acids was isolated. The deduced amino acid sequence shows a high degree of similarity with subunits 3, 4, 5, and 6 of C. magister (81-84 %). Most of the hemocyanins are glycosylated, and three putative O-linkage sites were identified in the partial amino acid sequence of EvH at positions 444-446, 478-480, and 547-549, respectively. The higher stability of native Hc in comparison to its subunit EvH4 as determined by circular dichroism (CD) could be explained with the formation of a stabilizing quaternary structure.
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Affiliation(s)
- A Dolashki
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, G. Bonchev str. 9, Sofia, 1113, Bulgaria
| | - M Radkova
- AgroBioInstitute, 8 Dragan Tsankov, Str., 1164, Sofia, Bulgaria
| | - E Todorovska
- AgroBioInstitute, 8 Dragan Tsankov, Str., 1164, Sofia, Bulgaria
| | - M Ivanov
- AgroBioInstitute, 8 Dragan Tsankov, Str., 1164, Sofia, Bulgaria
| | - S Stevanovic
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, D-72076, Tϋbingen, Germany
| | - L Molin
- CNR-ISTM, Corso Stati Uniti 4, 35129, Padova, Italy
| | - P Traldi
- CNR-ISTM, Corso Stati Uniti 4, 35129, Padova, Italy
| | - W Voelter
- Interfacultary Institute of Biochemistry, University of Tϋbingen, Hoppe-Seyler-Str. 4, D-72076, Tϋbingen, Germany
| | - P Dolashka
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, G. Bonchev str. 9, Sofia, 1113, Bulgaria.
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Stevanovic S. II. Eine Kupferglanzpseudom orphose. Z KRIST-CRYST MATER 2015. [DOI: 10.1524/zkri.1908.45.1.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rahman MM, Stevanovic S, Islam MA, Heimann K, Nabi MN, Thomas G, Feng B, Brown RJ, Ristovski ZD. Particle emissions from microalgae biodiesel combustion and their relative oxidative potential. Environ Sci Process Impacts 2015; 17:1601-1610. [PMID: 26238214 DOI: 10.1039/c5em00125k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Microalgae are considered to be one of the most viable biodiesel feedstocks for the future due to their potential for providing economical, sustainable and cleaner alternatives to petroleum diesel. This study investigated the particle emissions from a commercially cultured microalgae and higher plant biodiesels at different blending ratios. With a high amount of long carbon chain lengths fatty acid methyl esters (C20 to C22), the microalgal biodiesel used had a vastly different average carbon chain length and level of unsaturation to conventional biodiesel, which significantly influenced particle emissions. Smaller blend percentages showed a larger reduction in particle emission than blend percentages of over 20%. This was due to the formation of a significant nucleation mode for the higher blends. In addition measurements of reactive oxygen species (ROS), showed that the oxidative potential of particles emitted from the microalgal biodiesel combustion were lower than that of regular diesel. Biodiesel oxygen content was less effective in suppressing particle emissions for biodiesels containing a high amount of polyunsaturated C20-C22 fatty acid methyl esters and generated significantly increased nucleation mode particle emissions. The observed increase in nucleation mode particle emission is postulated to be caused by very low volatility, high boiling point and high density, viscosity and surface tension of the microalgal biodiesel tested here. Therefore, in order to achieve similar PM (particulate matter) emission benefits for microalgal biodiesel likewise to conventional biodiesel, fatty acid methyl esters (FAMEs) with high amounts of polyunsaturated long-chain fatty acids (≥C20) may not be desirable in microalgal biodiesel composition.
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Affiliation(s)
- M M Rahman
- International Laboratory of Air Quality and Health (ILAQH), Biofuel Engine Research Facilities (BERF), Queensland University of Technology (QUT), Brisbane, QLD, Australia 4001.
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