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Hackenbruch C, Bauer J, Heitmann JS, Maringer Y, Nelde A, Denk M, Zieschang L, Kammer C, Federmann B, Jung S, Martus P, Malek NP, Nikolaou K, Salih HR, Bitzer M, Walz JS. FusionVAC22_01: a phase I clinical trial evaluating a DNAJB1-PRKACA fusion transcript-based peptide vaccine combined with immune checkpoint inhibition for fibrolamellar hepatocellular carcinoma and other tumor entities carrying the oncogenic driver fusion. Front Oncol 2024; 14:1367450. [PMID: 38606105 PMCID: PMC11007196 DOI: 10.3389/fonc.2024.1367450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
The DNAJB1-PRKACA fusion transcript was identified as the oncogenic driver of tumor pathogenesis in fibrolamellar hepatocellular carcinoma (FL-HCC), also known as fibrolamellar carcinoma (FLC), as well as in other tumor entities, thus representing a broad target for novel treatment in multiple cancer entities. FL-HCC is a rare primary liver tumor with a 5-year survival rate of only 45%, which typically affects young patients with no underlying primary liver disease. Surgical resection is the only curative treatment option if no metastases are present at diagnosis. There is no standard of care for systemic therapy. Peptide-based vaccines represent a low side-effect approach relying on specific immune recognition of tumor-associated human leucocyte antigen (HLA) presented peptides. The induction (priming) of tumor-specific T-cell responses against neoepitopes derived from gene fusion transcripts by peptide-vaccination combined with expansion of the immune response and optimization of immune function within the tumor microenvironment achieved by immune-checkpoint-inhibition (ICI) has the potential to improve response rates and durability of responses in malignant diseases. The phase I clinical trial FusionVAC22_01 will enroll patients with FL-HCC or other cancer entities carrying the DNAJB1-PRKACA fusion transcript that are locally advanced or metastatic. Two doses of the DNAJB1-PRKACA fusion-based neoepitope vaccine Fusion-VAC-XS15 will be applied subcutaneously (s.c.) with a 4-week interval in combination with the anti-programmed cell death-ligand 1 (PD-L1) antibody atezolizumab starting at day 15 after the first vaccination. Anti-PD-L1 will be applied every 4 weeks until end of the 54-week treatment phase or until disease progression or other reason for study termination. Thereafter, patients will enter a 6 months follow-up period. The clinical trial reported here was approved by the Ethics Committee II of the University of Heidelberg (Medical faculty of Mannheim) and the Paul-Ehrlich-Institute (P-00540). Clinical trial results will be published in peer-reviewed journals. Trial registration numbers EU CT Number: 2022-502869-17-01 and ClinicalTrials.gov Registry (NCT05937295).
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Affiliation(s)
- Christopher Hackenbruch
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Monika Denk
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Lisa Zieschang
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Christine Kammer
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Birgit Federmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Susanne Jung
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Peter Martus
- Institute for Medical Biometrics and Clinical Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Nisar P. Malek
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
- Center for Personalized Medicine, University of Tübingen, Tübingen, Germany
- The M3 Research Institute, University of Tübingen, Tübingen, Germany
| | - Konstantin Nikolaou
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R. Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Michael Bitzer
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
- Center for Personalized Medicine, University of Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
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Jung S, Schlenk RF, Hackenbruch C, Roldan Pinzon SSL, Bitzer M, Pflügler M, Walz JS, Jung G, Heitmann JS, Salih HR. Protocol of a first-in-human clinical trial to evaluate the safety, tolerability, and preliminary efficacy of the bispecific CD276xCD3 antibody CC-3 in patients with colorectal cancer (CoRe_CC-3). Front Oncol 2024; 14:1351901. [PMID: 38410109 PMCID: PMC10896605 DOI: 10.3389/fonc.2024.1351901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction Colorectal cancer (CRC) is the third most common cancer worldwide in men and women. In the metastasized stage, treatment options and prognosis are limited. To address the high medical need of this patient population, we generated a CD276xCD3 bispecific antibody termed CC-3. CD276 is expressed on CRC cells and on tumor vessels, thereby allowing for a "dual" anticancer effect. Methods and analysis This first-in-human clinical study is planned as a prospective multicenter trial, enrolling patients with metastatic CRC after three lines of therapy. During the dose-escalation part, initially, an accelerated titration design with single-patient cohorts is employed. Here, each patient will receive a fixed dose level (starting with 50 µg for the first patient); however, between patients, dose level may be increased by up to 100%, depending on the decision of a safety review committee. Upon occurrence of any adverse events (AEs) grade ≥2, dose-limiting toxicity (DLT), or reaching a dose level of ≥800 µg, the escalation will switch to a standard 3 + 3 dose design. After maximum tolerated dose (MTD) has been determined, defined as no more than one of the six patients experiencing DLT, an additional 14 patients receive CC-3 at the MTD level in the dose-expansion phase. Primary endpoints are incidence and severity of AEs, as well as the best objective response to the treatment according to response evaluation criteria in solid tumors (RECIST) 1.1. Secondary endpoints include overall safety, efficacy, survival, quality of life, and pharmacokinetic investigations. Ethics and dissemination The CD276xCD3 study was approved by the Ethics Committee of the Medical Faculty of the Heinrich Heine University Düsseldorf and the Paul-Ehrlich-Institut (P00702). Clinical trial results will be published in peer-reviewed journals. Trial registration numbers: ClinicalTrials.cov Registry (NCT05999396) and EU ClinicalTrials Registry (EU trial number 2022-503084-15-00).
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Affiliation(s)
- Susanne Jung
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
| | - Richard F Schlenk
- NCT Trial Center, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Christopher Hackenbruch
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
| | - Sandra S L Roldan Pinzon
- NCT Trial Center, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Bitzer
- Department of Gastroenterology, Gastrointestinal Oncology, Hepatology, Infectiology and Geriatrics, University Hospital Tübingen, Tübingen, Germany
| | - Martin Pflügler
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
| | - Gundram Jung
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
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Tandler C, Heitmann JS, Michel TM, Marconato M, Jaeger SU, Tegeler CM, Denk M, Richter M, Oezbek MT, Maringer Y, Schroeder SM, Schneiderhan-Marra N, Wiesmüller KH, Bitzer M, Ruetalo N, Schindler M, Meisner C, Fischer I, Rammensee HG, Salih HR, Walz JS. Long-term efficacy of the peptide-based COVID-19 T cell activator CoVac-1 in healthy adults. Int J Infect Dis 2024; 139:69-77. [PMID: 38016500 DOI: 10.1016/j.ijid.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
OBJECTIVES T cell immunity is key for the control of viral infections including SARS-CoV-2, in particular with regard to immune memory and protection against arising genetic variants. METHODS We recently evaluated a peptide-based SARS-CoV-2 T cell activator termed CoVac-1 in a first-in-human trial in healthy adults. Here, we report on long-term safety and efficacy data of CoVac-1 until month 12. RESULTS CoVac-1 is well tolerated without long-term immune-related side effects and induces long-lasting anti-viral T cell responses in 100% of study participants, with potent expandability of clusters of differentiation (CD4+) and CD8+ T cells targeting multiple different CoVac-1 T cell epitopes. T cell responses were associated with stronger injection site reaction. Beyond induction of T cell immunity, 89% of subjects developed CoVac-1-specific immunoglobulin G antibodies which associated with the intensity of the T cell response, indicating that CoVac-1-specific CD4+ T cells support the induction of B-cell responses. Vaccination with approved COVID-19 vaccines boosted CoVac-1-specific T cell responses. Overall, a low SARS-CoV-2 infection rate (8.3%) was observed. CONCLUSION Together, a single application of CoVac-1 elicits long-lived and broad SARS-CoV-2-specific T cell immunity, which further supports the current evaluation of our T cell activator in patients with congenital or acquired B-cell defects.
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Affiliation(s)
- Claudia Tandler
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Tanja M Michel
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Maddalena Marconato
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Simon U Jaeger
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany; Dr. Margarete Fischer-Bosch Institute for Clinical Pharmacology, Stuttgart, Germany; Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Christian M Tegeler
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany; Department of Obstetrics and Gynecology, University Hospital Tübingen, Tübingen, Germany
| | - Monika Denk
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Marion Richter
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Melek Tutku Oezbek
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Sarah M Schroeder
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Department of Otorhinolaryngology, Head and Neck Surgery, University of Hospital Tübingen, Tübingen, Germany
| | | | | | - Michael Bitzer
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Meisner
- Robert Bosch Hospital, Robert Bosch Society for Medical Research, Stuttgart, Germany
| | - Imma Fischer
- Institute for Clinical Epidemiology and Applied Biometry, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, Institute of Immunology, University and University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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4
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Hoenisch Gravel N, Nelde A, Bauer J, Mühlenbruch L, Schroeder SM, Neidert MC, Scheid J, Lemke S, Dubbelaar ML, Wacker M, Dengler A, Klein R, Mauz PS, Löwenheim H, Hauri-Hohl M, Martin R, Hennenlotter J, Stenzl A, Heitmann JS, Salih HR, Rammensee HG, Walz JS. TOF IMS mass spectrometry-based immunopeptidomics refines tumor antigen identification. Nat Commun 2023; 14:7472. [PMID: 37978195 PMCID: PMC10656517 DOI: 10.1038/s41467-023-42692-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for the direct identification and characterization of naturally presented tumor-associated peptides, a key prerequisite for the development of T cell-based immunotherapies. This study reports on the implementation of ion mobility separation-based time-of-flight (TOFIMS) MS for next-generation immunopeptidomics, enabling high-speed and sensitive detection of HLA-presented peptides. Applying TOFIMS-based immunopeptidomics, a novel extensive benignTOFIMS dataset was generated from 94 primary benign samples of solid tissue and hematological origin, which enabled the expansion of benign reference immunopeptidome databases with > 150,000 HLA-presented peptides, the refinement of previously described tumor antigens, as well as the identification of frequently presented self antigens and not yet described tumor antigens comprising low abundant mutation-derived neoepitopes that might serve as targets for future cancer immunotherapy development.
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Affiliation(s)
- Naomi Hoenisch Gravel
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Marian C Neidert
- Neuroscience Center Zürich (ZNZ), University of Zürich and ETH Zürich, Zürich, Switzerland
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zürich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Zürich, Switzerland
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Steffen Lemke
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Marissa L Dubbelaar
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBIC), University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Anna Dengler
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Paul-Stefan Mauz
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zürich, Zürich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University and University Hospital Zürich, Zürich, Switzerland
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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5
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Nelde A, Schuster H, Heitmann JS, Bauer J, Maringer Y, Zwick M, Volkmer JP, Chen JY, Stanger AMP, Lehmann A, Appiah B, Märklin M, Rücker-Braun E, Salih HR, Roerden M, Schroeder SM, Häring MF, Schlosser A, Schetelig J, Schmitz M, Boerries M, Köhler N, Lengerke C, Majeti R, Weissman IL, Rammensee HG, Walz JS. Immune Surveillance of Acute Myeloid Leukemia Is Mediated by HLA-Presented Antigens on Leukemia Progenitor Cells. Blood Cancer Discov 2023; 4:468-489. [PMID: 37847741 PMCID: PMC10618727 DOI: 10.1158/2643-3230.bcd-23-0020] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023] Open
Abstract
Therapy-resistant leukemia stem and progenitor cells (LSC) are a main cause of acute myeloid leukemia (AML) relapse. LSC-targeting therapies may thus improve outcome of patients with AML. Here we demonstrate that LSCs present HLA-restricted antigens that induce T-cell responses allowing for immune surveillance of AML. Using a mass spectrometry-based immunopeptidomics approach, we characterized the antigenic landscape of patient LSCs and identified AML- and AML/LSC-associated HLA-presented antigens absent from normal tissues comprising nonmutated peptides, cryptic neoepitopes, and neoepitopes of common AML driver mutations of NPM1 and IDH2. Functional relevance of shared AML/LSC antigens is illustrated by presence of their cognizant memory T cells in patients. Antigen-specific T-cell recognition and HLA class II immunopeptidome diversity correlated with clinical outcome. Together, these antigens shared among AML and LSCs represent prime targets for T cell-based therapies with potential of eliminating residual LSCs in patients with AML. SIGNIFICANCE The elimination of therapy-resistant leukemia stem and progenitor cells (LSC) remains a major challenge in the treatment of AML. This study identifies and functionally validates LSC-associated HLA class I and HLA class II-presented antigens, paving the way to the development of LSC-directed T cell-based immunotherapeutic approaches for patients with AML. See related commentary by Ritz, p. 430 . This article is featured in Selected Articles from This Issue, p. 419.
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Affiliation(s)
- Annika Nelde
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas S. Heitmann
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Melissa Zwick
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens-Peter Volkmer
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - James Y. Chen
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - Anna M. Paczulla Stanger
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Ariane Lehmann
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
| | - Bismark Appiah
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Elke Rücker-Braun
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Helmut R. Salih
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Sarah M. Schroeder
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Max-Felix Häring
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | | | - Johannes Schetelig
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
- German Bone Marrow Donor Center (DKMS), Clinical Trials Unit, Dresden, Germany
| | - Marc Schmitz
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), partner site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Medical Center, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site, Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Köhler
- Department of Medicine I, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Claudia Lengerke
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
- Clinic for Hematology, University of Basel and University Hospital Basel, Basel, Switzerland
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, California
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Germany
| | - Juliane S. Walz
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
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6
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Goyal A, Bauer J, Hey J, Papageorgiou DN, Stepanova E, Daskalakis M, Scheid J, Dubbelaar M, Klimovich B, Schwarz D, Märklin M, Roerden M, Lin YY, Ma T, Mücke O, Rammensee HG, Lübbert M, Loayza-Puch F, Krijgsveld J, Walz JS, Plass C. DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts. Nat Commun 2023; 14:6731. [PMID: 37872136 PMCID: PMC10593957 DOI: 10.1038/s41467-023-42417-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 10/04/2022] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies.
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Affiliation(s)
- Ashish Goyal
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Joschka Hey
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German-Israeli Helmholtz Research School in Cancer Biology, Heidelberg, Germany
- German Center for Lung Research, (DZL) partner site Heidelberg, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Ekaterina Stepanova
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Daskalakis
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern, University Hospital, University of Bern, Bern, Switzerland
| | - Jonas Scheid
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Marissa Dubbelaar
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Boris Klimovich
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Dominic Schwarz
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Yu-Yu Lin
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Ma
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Mücke
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University of Tübingen and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Center for Lung Research, (DZL) partner site Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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7
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Seller A, Hackenbruch C, Walz JS, Nelde A, Heitmann JS. Long-Term Follow-Up of COVID-19 Convalescents-Immune Response Associated with Reinfection Rate and Symptoms. Viruses 2023; 15:2100. [PMID: 37896879 PMCID: PMC10611319 DOI: 10.3390/v15102100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
SARS-CoV-2 has spread worldwide, causing millions of deaths and leaving a significant proportion of people with long-term sequelae of COVID-19 ("post-COVID syndrome"). Whereas the precise mechanism of post-COVID syndrome is still unknown, the immune response after the first infection may play a role. Here, we performed a long-term follow-up analysis of 110 COVID-19 convalescents, analyzing the first SARS-CoV-2-directed immune response, vaccination status, long-term symptoms (approximately 2.5 years after first infection), and reinfections. A total of 96% of convalescents were vaccinated at least once against SARS-CoV-2 after their first infection. A reinfection rate of 47% was observed, and lower levels of anti-spike IgG antibodies after the first infection were shown to associate with reinfection. While T-cell responses could not be clearly associated with persistent postinfectious symptoms, convalescents with long-term symptoms showed elevated SARS-CoV-2-specific antibody levels at the first infection. Evaluating the immune response after the first infection might be a useful tool for identifying individuals with increased risk for re-infections and long-term symptoms.
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Affiliation(s)
- Anna Seller
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Obstetrics and Gynecology, University Hospital Tuebingen, Calwerstraße 7, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Christopher Hackenbruch
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Juliane S. Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Röntgenweg 11, 72076 Tuebingen, Germany
| | - Annika Nelde
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Röntgenweg 11, 72076 Tuebingen, Germany
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Department of Peptide-Based Immunotherapy, Institute of Immunology, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Röntgenweg 11, 72076 Tuebingen, Germany
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8
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Heitmann JS, Tandler C, Marconato M, Nelde A, Habibzada T, Rittig SM, Tegeler CM, Maringer Y, Jaeger SU, Denk M, Richter M, Oezbek MT, Wiesmüller KH, Bauer J, Rieth J, Wacker M, Schroeder SM, Hoenisch Gravel N, Scheid J, Märklin M, Henrich A, Klimovich B, Clar KL, Lutz M, Holzmayer S, Hörber S, Peter A, Meisner C, Fischer I, Löffler MW, Peuker CA, Habringer S, Goetze TO, Jäger E, Rammensee HG, Salih HR, Walz JS. Phase I/II trial of a peptide-based COVID-19 T-cell activator in patients with B-cell deficiency. Nat Commun 2023; 14:5032. [PMID: 37596280 PMCID: PMC10439231 DOI: 10.1038/s41467-023-40758-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/14/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
T-cell immunity is central for control of COVID-19, particularly in patients incapable of mounting antibody responses. CoVac-1 is a peptide-based T-cell activator composed of SARS-CoV-2 epitopes with documented favorable safety profile and efficacy in terms of SARS-CoV-2-specific T-cell response. We here report a Phase I/II open-label trial (NCT04954469) in 54 patients with congenital or acquired B-cell deficiency receiving one subcutaneous CoVac-1 dose. Immunogenicity in terms of CoVac-1-induced T-cell responses and safety are the primary and secondary endpoints, respectively. No serious or grade 4 CoVac-1-related adverse events have been observed. Expected local granuloma formation has been observed in 94% of study subjects, whereas systemic reactogenicity has been mild or absent. SARS-CoV-2-specific T-cell responses have been induced in 86% of patients and are directed to multiple CoVac-1 peptides, not affected by any current Omicron variants and mediated by multifunctional T-helper 1 CD4+ T cells. CoVac-1-induced T-cell responses have exceeded those directed to the spike protein after mRNA-based vaccination of B-cell deficient patients and immunocompetent COVID-19 convalescents with and without seroconversion. Overall, our data show that CoVac-1 induces broad and potent T-cell responses in patients with B-cell/antibody deficiency with a favorable safety profile, which warrants advancement to pivotal Phase III safety and efficacy evaluation. ClinicalTrials.gov identifier NCT04954469.
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Affiliation(s)
- Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Claudia Tandler
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Maddalena Marconato
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Timorshah Habibzada
- Institute of Clinical Cancer Research, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt, Germany
| | - Susanne M Rittig
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Christian M Tegeler
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Simon U Jaeger
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute for Clinical Pharmacology, Stuttgart, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Monika Denk
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Marion Richter
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Melek T Oezbek
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | - Jens Bauer
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Naomi Hoenisch Gravel
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Scheid
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Annika Henrich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Boris Klimovich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Kim L Clar
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Martina Lutz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Samuel Holzmayer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Meisner
- Robert Bosch Hospital, Robert Bosch Society for Medical Research, Stuttgart, Germany
| | - Imma Fischer
- Institute for Clinical Epidemiology and Applied Biometry, University Hospital Tübingen, Tübingen, Germany
| | - Markus W Löffler
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Caroline Anna Peuker
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Stefan Habringer
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité -Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité (Junior) (Digital) Clinician Scientist Program, Berlin, Germany
| | - Thorsten O Goetze
- Institute of Clinical Cancer Research, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt, Germany
| | - Elke Jäger
- Department for Oncology and Hematology, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt, Germany
| | - Hans-Georg Rammensee
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.
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9
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Heitmann JS, Schlenk RF, Dörfel D, Kayser S, Döhner K, Heuser M, Thol F, Kapp-Schwoerer S, Labrenz J, Edelmann D, Märklin M, Vogel W, Bethge W, Walz JS, Große-Hovest L, Steiner M, Jung G, Salih HR. Phase I study evaluating the Fc-optimized FLT3 antibody FLYSYN in AML patients with measurable residual disease. J Hematol Oncol 2023; 16:96. [PMID: 37587502 PMCID: PMC10433561 DOI: 10.1186/s13045-023-01490-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND About half of AML patients achieving complete remission (CR) display measurable residual disease (MRD) and eventually relapse. FLYSYN is an Fc-optimized antibody for eradication of MRD directed to FLT3/CD135, which is abundantly expressed on AML cells. METHODS This first-in-human, open-label, single-arm, multicenter trial included AML patients in CR with persisting or increasing MRD and evaluated safety/tolerability, pharmacokinetics and preliminary efficacy of FLYSYN at different dose levels administered intravenously (cohort 1-5: single dose of 0.5 mg/m2, 1.5 mg/m2, 5 mg/m2, 15 mg/m2, 45 mg/m2; cohort 6: 15 mg/m2 on day 1, 15 and 29). Three patients were treated per cohort except for cohorts 4 and 6, which were expanded to nine and ten patients, respectively. Primary objective was safety, and secondary efficacy objective was ≥ 1 log MRD reduction or negativity in bone marrow. RESULTS Overall, 31 patients were treated, of whom seven patients (22.6%) experienced a transient decrease in neutrophil count (two grade 3, others ≤ grade 2). No infusion-related reaction or dose-limiting toxicity was observed. Adverse events (AEs) were mostly mild to moderate, with the most frequent AEs being hematologic events and laboratory abnormalities. Response per predefined criteria was documented in 35% of patients, and two patients maintained MRD negativity until end of study. Application of 45 mg/m2 FLYSYN as single or cumulative dose achieved objective responses in 46% of patients, whereas 28% responded at lower doses. CONCLUSIONS FLYSYN monotherapy is safe and well-tolerated in AML patients with MRD. Early efficacy data are promising and warrant further evaluation in an up-coming phase II trial. Trial registration This clinical is registered on clinicaltrials.gov (NCT02789254).
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Affiliation(s)
- Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Richard F Schlenk
- NCT Trial Center, National Center for Tumor Diseases, German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniela Dörfel
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
- Department of Hematology, Oncology and Immunology, KRH Klinikum Siloah, Hannover, Germany
| | - Sabine Kayser
- NCT Trial Center, National Center for Tumor Diseases, German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
- Medical Clinic and Policlinic 1, Hematology, Cellular Therapy and Hemostaseology, University of Leipzig Medical Center, Leipzig, Germany
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service Baden-Württemberg-Hessen, Mannheim, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Jannik Labrenz
- NCT Trial Center, National Center for Tumor Diseases, German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
| | - Dominic Edelmann
- NCT Trial Center, National Center for Tumor Diseases, German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg, Germany
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Wichard Vogel
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Wolfgang Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | | | | | - Gundram Jung
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
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10
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Medici G, Freudenmann LK, Velz J, Wang SSY, Kapolou K, Paramasivam N, Mühlenbruch L, Kowalewski DJ, Vasella F, Bilich T, Frey BM, Dubbelaar ML, Patterson AB, Zeitlberger AM, Silginer M, Roth P, Weiss T, Wirsching HG, Krayenbühl N, Bozinov O, Regli L, Rammensee HG, Rushing EJ, Sahm F, Walz JS, Weller M, Neidert MC. A T-cell antigen atlas for meningioma: novel options for immunotherapy. Acta Neuropathol 2023; 146:173-190. [PMID: 37368072 PMCID: PMC10329067 DOI: 10.1007/s00401-023-02605-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023]
Abstract
Meningiomas are the most common primary intracranial tumors. Although most symptomatic cases can be managed by surgery and/or radiotherapy, a relevant number of patients experience an unfavorable clinical course and additional treatment options are needed. As meningiomas are often perfused by dural branches of the external carotid artery, which is located outside the blood-brain barrier, they might be an accessible target for immunotherapy. However, the landscape of naturally presented tumor antigens in meningioma is unknown. We here provide a T-cell antigen atlas for meningioma by in-depth profiling of the naturally presented immunopeptidome using LC-MS/MS. Candidate target antigens were selected based on a comparative approach using an extensive immunopeptidome data set of normal tissues. Meningioma-exclusive antigens for HLA class I and II are described here for the first time. Top-ranking targets were further functionally characterized by showing their immunogenicity through in vitro T-cell priming assays. Thus, we provide an atlas of meningioma T-cell antigens which will be publicly available for further research. In addition, we have identified novel actionable targets that warrant further investigation as an immunotherapy option for meningioma.
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Affiliation(s)
- Gioele Medici
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland.
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland.
| | - Lena K Freudenmann
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Julia Velz
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Sophie Shih-Yüng Wang
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery and Neurotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Konstantina Kapolou
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Roche Diagnostics International Ltd, Rotkreuz, Switzerland
| | - Nagarajan Paramasivam
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Lena Mühlenbruch
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
| | - Daniel J Kowalewski
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Flavio Vasella
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Tatjana Bilich
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Beat M Frey
- Blood Transfusion Service, Swiss Red Cross, Schlieren, Switzerland
| | - Marissa L Dubbelaar
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, 72076, Tübingen, Baden-Württemberg, Germany
| | | | - Anna Maria Zeitlberger
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007, St. Gallen, Switzerland
| | - Manuela Silginer
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Patrick Roth
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Tobias Weiss
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Hans-Georg Wirsching
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Niklaus Krayenbühl
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Oliver Bozinov
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007, St. Gallen, Switzerland
| | - Luca Regli
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Elisabeth Jane Rushing
- Department of Neuropathology, University Hospital and University of Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane S Walz
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Marian C Neidert
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Frauenklinikstrasse 10, 8091, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007, St. Gallen, Switzerland
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11
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Wacker M, Bauer J, Wessling L, Dubbelaar M, Nelde A, Rammensee HG, Walz JS. Immunoprecipitation methods impact the peptide repertoire in immunopeptidomics. Front Immunol 2023; 14:1219720. [PMID: 37545538 PMCID: PMC10400765 DOI: 10.3389/fimmu.2023.1219720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Mass spectrometry-based immunopeptidomics is the only unbiased method to identify naturally presented HLA ligands, which is an indispensable prerequisite for characterizing novel tumor antigens for immunotherapeutic approaches. In recent years, improvements based on devices and methodology have been made to optimize sensitivity and throughput in immunopeptidomics. However, developments in ligand isolation, mass spectrometric analysis, and subsequent data processing can have a marked impact on the quality and quantity of immunopeptidomics data. Methods In this work, we compared the immunopeptidome composition in terms of peptide yields, spectra quality, hydrophobicity, retention time, and immunogenicity of two established immunoprecipitation methods (column-based and 96-well-based) using cell lines as well as primary solid and hematological tumor samples. Results Although, we identified comparable overall peptide yields, large proportions of method-exclusive peptides were detected with significantly higher hydrophobicity for the column-based method with potential implications for the identification of immunogenic tumor antigens. We showed that column preparation does not lose hydrophilic peptides in the hydrophilic washing step. In contrast, an additional 50% acetonitrile elution could partially regain lost hydrophobic peptides during 96-well preparation, suggesting a reduction of the bias towards the column-based method but not completely equalizing it. Discussion Together, this work showed how different immunoprecipitation methods and their adaptions can impact the peptide repertoire of immunopeptidomic analysis and therefore the identification of potential tumor-associated antigens.
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Affiliation(s)
- Marcel Wacker
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Laura Wessling
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marissa Dubbelaar
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
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12
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Naghavian R, Faigle W, Oldrati P, Wang J, Toussaint NC, Qiu Y, Medici G, Wacker M, Freudenmann LK, Bonté PE, Weller M, Regli L, Amigorena S, Rammensee HG, Walz JS, Brugger SD, Mohme M, Zhao Y, Sospedra M, Neidert MC, Martin R. Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma. Nature 2023; 617:807-817. [PMID: 37198490 PMCID: PMC10208956 DOI: 10.1038/s41586-023-06081-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Microbial organisms have key roles in numerous physiological processes in the human body and have recently been shown to modify the response to immune checkpoint inhibitors1,2. Here we aim to address the role of microbial organisms and their potential role in immune reactivity against glioblastoma. We demonstrate that HLA molecules of both glioblastoma tissues and tumour cell lines present bacteria-specific peptides. This finding prompted us to examine whether tumour-infiltrating lymphocytes (TILs) recognize tumour-derived bacterial peptides. Bacterial peptides eluted from HLA class II molecules are recognized by TILs, albeit very weakly. Using an unbiased antigen discovery approach to probe the specificity of a TIL CD4+ T cell clone, we show that it recognizes a broad spectrum of peptides from pathogenic bacteria, commensal gut microbiota and also glioblastoma-related tumour antigens. These peptides were also strongly stimulatory for bulk TILs and peripheral blood memory cells, which then respond to tumour-derived target peptides. Our data hint at how bacterial pathogens and bacterial gut microbiota can be involved in specific immune recognition of tumour antigens. The unbiased identification of microbial target antigens for TILs holds promise for future personalized tumour vaccination approaches.
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Affiliation(s)
- Reza Naghavian
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Cellerys AG, Schlieren, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Cellerys AG, Schlieren, Switzerland
- Immunity and Cancer, Institut Curie, PSL University, INSERM U932, Paris, France
| | - Pietro Oldrati
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Jian Wang
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Schlieren, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yuhan Qiu
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Gioele Medici
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marcel Wacker
- Department of Peptide-based Immunotherapy, University of Tübingen, University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Lena K Freudenmann
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | | | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology and Clinical Neuroscience, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luca Regli
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sebastian Amigorena
- Immunity and Cancer, Institut Curie, PSL University, INSERM U932, Paris, France
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University of Tübingen, University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Malte Mohme
- Department of Neurosurgery, University Hospital Hamburg Eppendorf, University of Hamburg, Hamburg, Germany
| | - Yingdong Zhao
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD, USA
| | - Mireia Sospedra
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland
- Cellerys AG, Schlieren, Switzerland
| | - Marian C Neidert
- Clinical Neuroscience Center, Department of Neurosurgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research Section (NIMS), Neurology Clinic, University of Zurich, University Hospital Zurich, Zurich, Switzerland.
- Cellerys AG, Schlieren, Switzerland.
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
- Therapeutic Immune Design Unit, Center for Molecular Medicine, Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden.
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13
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Hackenbruch C, Maringer Y, Tegeler CM, Walz JS, Nelde A, Heitmann JS. Elevated SARS-CoV-2-Specific Antibody Levels in Patients with Post-COVID Syndrome. Viruses 2023; 15:v15030701. [PMID: 36992410 PMCID: PMC10051370 DOI: 10.3390/v15030701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/31/2023] Open
Abstract
With the routine use of effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines, the number of life-threatening coronavirus disease 2019 (COVID-19) courses have largely been reduced. However, multiple COVID-19 convalescents, even after asymptomatic to moderate disease, suffer from post-COVID syndrome, with relevant limitations in daily life. The pathophysiologic mechanisms of post-COVID syndrome are still elusive, with dysregulation of the immune system suggested as a central mechanism. Here, we assessed COVID-19 post-infectious symptoms (5-6 months after PCR-confirmed acute infection) together with the humoral immune response against SARS-CoV-2 in non-hospitalized COVID-19 convalescents, early (5-6 weeks) and late (5-6 months) after their first positive SARS-CoV-2 PCR result. Convalescents reporting several post-infectious symptoms (>3) showed higher anti-spike and anti-nucleocapsid antibody levels 5-6 weeks after PCR-confirmed infection with the latter remained increased 5-6 months after positive PCR. Likewise, a higher post-infectious symptom score was associated with increased antibody levels. Of note, convalescents displaying neuro-psychiatric symptoms such as restlessness, palpitations, irritability, and headache, as well as general symptoms such as fatigue/reduced power had higher SARS-CoV-2-specific antibody levels compared with asymptomatic cases. The increased humoral immune response in convalescents with post-COVID syndrome might be useful for the detection of individuals with an increased risk for post-COVID syndrome.
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Affiliation(s)
- Christopher Hackenbruch
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Röntgenweg 11, 72076 Tübingen, Germany
| | - Yacine Maringer
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Röntgenweg 11, 72076 Tübingen, Germany
- Department for Peptide-Based Immunotherapy, University and University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Christian M Tegeler
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Röntgenweg 11, 72076 Tübingen, Germany
- Department for Peptide-Based Immunotherapy, University and University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Röntgenweg 11, 72076 Tübingen, Germany
- Department for Peptide-Based Immunotherapy, University and University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Röntgenweg 11, 72076 Tübingen, Germany
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14
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Schroeder SM, Nelde A, Walz JS. Viral T-cell epitopes - Identification, characterization and clinical application. Semin Immunol 2023; 66:101725. [PMID: 36706520 DOI: 10.1016/j.smim.2023.101725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
T-cell immunity, mediated by CD4+ and CD8+ T cells, represents a cornerstone in the control of viral infections. Virus-derived T-cell epitopes are represented by human leukocyte antigen (HLA)-presented viral peptides on the surface of virus-infected cells. They are the prerequisite for the recognition of infected cells by T cells. Knowledge of viral T-cell epitopes provides on the one hand a diagnostic tool to decipher protective T-cell immune responses in the human population and on the other hand various prophylactic and therapeutic options including vaccination approaches and the transfer of virus-specific T cells. Such approaches have already been proven to be effective against various viral infections, particularly in immunocompromised patients lacking sufficient humoral, antibody-based immune response. This review provides an overview on the state of the art as well as current studies regarding the identification and characterization of viral T-cell epitopes and approaches of clinical application. In the first chapter in silico prediction tools and direct, mass spectrometry-based identification of viral T-cell epitopes is compared. The second chapter provides an overview of commonly used assays for further characterization of T-cell responses and phenotypes. The final chapter presents an overview of clinical application of viral T-cell epitopes with a focus on human immunodeficiency virus (HIV), human cytomegalovirus (HCMV) and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), being representatives of relevant viruses.
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Affiliation(s)
- Sarah M Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Department for Otorhinolaryngology, Head, and Neck Surgery, University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany; Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany; Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.
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15
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Mühlenbruch L, Abou-Kors T, Dubbelaar ML, Bichmann L, Kohlbacher O, Bens M, Thomas J, Ezić J, Kraus JM, Kestler HA, von Witzleben A, Mytilineos J, Fürst D, Engelhardt D, Doescher J, Greve J, Schuler PJ, Theodoraki MN, Brunner C, Hoffmann TK, Rammensee HG, Walz JS, Laban S. The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination. Br J Cancer 2023; 128:1777-1787. [PMID: 36823366 PMCID: PMC9949688 DOI: 10.1038/s41416-023-02197-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND The immune peptidome of OPSCC has not previously been studied. Cancer-antigen specific vaccination may improve clinical outcome and efficacy of immune checkpoint inhibitors such as PD1/PD-L1 antibodies. METHODS Mapping of the OPSCC HLA ligandome was performed by mass spectrometry (MS) based analysis of naturally presented HLA ligands isolated from tumour tissue samples (n = 40) using immunoaffinity purification. The cohort included 22 HPV-positive (primarily HPV-16) and 18 HPV-negative samples. A benign reference dataset comprised of the HLA ligandomes of benign haematological and tissue datasets was used to identify tumour-associated antigens. RESULTS MS analysis led to the identification of naturally HLA-presented peptides in OPSCC tumour tissue. In total, 22,769 peptides from 9485 source proteins were detected on HLA class I. For HLA class II, 15,203 peptides from 4634 source proteins were discovered. By comparative profiling against the benign HLA ligandomic datasets, 29 OPSCC-associated HLA class I ligands covering 11 different HLA allotypes and nine HLA class II ligands were selected to create a peptide warehouse. CONCLUSION Tumour-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi)personalised strategies.
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Affiliation(s)
- Lena Mühlenbruch
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,German Cancer Consortium (DKTK), Partner Site Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Tsima Abou-Kors
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marissa L. Dubbelaar
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Leon Bichmann
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Oliver Kohlbacher
- grid.10392.390000 0001 2190 1447Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence Machine Learning in the Sciences (EXC2064), Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.411544.10000 0001 0196 8249Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Institute for Bioinformatics and Medical Informatics, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Martin Bens
- grid.418245.e0000 0000 9999 5706Leibniz-Institute on Aging, Fritz-Lipmann-Institute, 07745 Jena, Thüringen Germany
| | - Jaya Thomas
- grid.5491.90000 0004 1936 9297CRUK and NIHR Experimental Cancer Medicine Center & School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
| | - Jasmin Ezić
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johann M. Kraus
- grid.6582.90000 0004 1936 9748Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Hans A. Kestler
- grid.6582.90000 0004 1936 9748Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Adrian von Witzleben
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Joannis Mytilineos
- grid.410712.10000 0004 0473 882XInstitute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden–Württemberg–Hessen, and University Hospital Ulm, Ulm, Germany ,grid.6582.90000 0004 1936 9748Institute of Transfusion Medicine, Ulm University, Ulm, Germany ,German Stem Cell Donor Registry, German Red Cross Blood Transfusion Service, Ulm, Germany
| | - Daniel Fürst
- grid.410712.10000 0004 0473 882XInstitute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden–Württemberg–Hessen, and University Hospital Ulm, Ulm, Germany ,grid.6582.90000 0004 1936 9748Institute of Transfusion Medicine, Ulm University, Ulm, Germany
| | - Daphne Engelhardt
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johannes Doescher
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Jens Greve
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Patrick J. Schuler
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marie-Nicole Theodoraki
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Cornelia Brunner
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Thomas K. Hoffmann
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Hans-Georg Rammensee
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,German Cancer Consortium (DKTK), Partner Site Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Juliane S. Walz
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.411544.10000 0001 0196 8249Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Baden-Württemberg 72076 Germany
| | - Simon Laban
- Department of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany.
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16
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Maringer Y, Nelde A, Schroeder SM, Schuhmacher J, Hörber S, Peter A, Karbach J, Jäger E, Walz JS. Durable spike-specific T cell responses after different COVID-19 vaccination regimens are not further enhanced by booster vaccination. Sci Immunol 2022; 7:eadd3899. [PMID: 36318037 PMCID: PMC9798886 DOI: 10.1126/sciimmunol.add3899] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Several COVID-19 vaccines are approved to prevent severe disease outcome after SARS-CoV-2 infection. Whereas induction and functionality of antiviral antibody response are largely studied, the induction of T cells upon vaccination with the different approved COVID-19 vaccines is less studied. Here, we report on T cell immunity 4 weeks and 6 months after different vaccination regimens and 4 weeks after an additional booster vaccination in comparison with SARS-CoV-2 T cell responses in convalescents and prepandemic donors using interferon-gamma ELISpot assays and flow cytometry. Increased T cell responses and cross-recognition of B.1.1.529 Omicron variant-specific mutations were observed ex vivo in mRNA- and heterologous-vaccinated donors compared with vector-vaccinated donors. Nevertheless, potent expandability of T cells targeting the spike protein was observed for all vaccination regimens, with frequency, diversity, and the ability to produce several cytokines of vaccine-induced T cell responses comparable with those in convalescent donors. T cell responses for all vaccinated donors significantly exceeded preexisting cross-reactive T cell responses in prepandemic donors. Booster vaccination led to a significant increase in anti-spike IgG responses, which showed a marked decline 6 months after complete vaccination. In contrast, T cell responses remained stable over time after complete vaccination with no significant effect of booster vaccination on T cell responses and cross-recognition of Omicron BA.1 and BA.2 mutations. This suggested that booster vaccination is of particular relevance for the amelioration of antibody response. Together, our work shows that different vaccination regimens induce broad and long-lasting spike-specific CD4+ and CD8+ T cell immunity to SARS-CoV-2.
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Affiliation(s)
- Yacine Maringer
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Sarah M. Schroeder
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Juliane Schuhmacher
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Julia Karbach
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Elke Jäger
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Juliane S. Walz
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Corresponding author.
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17
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Nelde A, Rieth J, Roerden M, Dubbelaar ML, Gravel NH, Bauer J, Klein R, Hoheisel T, Mahrhofer H, Göpel S, Bitzer M, Hörber S, Peter A, Heitmann JS, Walz JS. Increased soluble HLA in COVID-19 present a disease-related, diverse immunopeptidome associated with T cell immunity. iScience 2022; 25:105643. [PMID: 36439376 PMCID: PMC9675079 DOI: 10.1016/j.isci.2022.105643] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/20/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022] Open
Abstract
HLA-presented antigenic peptides are central components of T cell-based immunity in infectious disease. Beside HLA molecules on cell surfaces, soluble HLA molecules (sHLA) are released in the blood suggested to impact cellular immune responses. We demonstrated that sHLA levels were significantly increased in COVID-19 patients and convalescent individuals compared to a control cohort and positively correlated with SARS-CoV-2-directed cellular immunity. Of note, patients with severe courses of COVID-19 showed reduced sHLA levels. Mass spectrometry-based characterization of sHLA-bound antigenic peptides, the so-called soluble immunopeptidome, revealed a COVID-19-associated increased diversity of HLA-presented peptides and identified a naturally presented SARS-CoV-2-derived peptide from the viral nucleoprotein in the plasma of COVID-19 patients. Of interest, sHLA serum levels directly correlated with the diversity of the soluble immunopeptidome. Together, these findings suggest an inflammation-driven release of sHLA in COVID-19, directly influencing the diversity of the soluble immunopeptidome with implications for SARS-CoV-2-directed T cell-based immunity and disease outcome.
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18
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Bauer J, Köhler N, Maringer Y, Bucher P, Bilich T, Zwick M, Dicks S, Nelde A, Dubbelaar M, Scheid J, Wacker M, Heitmann JS, Schroeder S, Rieth J, Denk M, Richter M, Klein R, Bonzheim I, Luibrand J, Holzer U, Ebinger M, Brecht IB, Bitzer M, Boerries M, Feucht J, Salih HR, Rammensee HG, Hailfinger S, Walz JS. The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma. Nat Commun 2022; 13:6401. [PMID: 36302754 PMCID: PMC9613889 DOI: 10.1038/s41467-022-33746-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 07/29/2022] [Accepted: 09/30/2022] [Indexed: 02/01/2023] Open
Abstract
The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma, a lethal disease lacking specific therapies. This study reports on the identification, characterization, and immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in fibrolamellar hepatocellular carcinoma. DNAJB1-PRKACA-derived HLA class I and HLA class II ligands induce multifunctional cytotoxic CD8+ and T-helper 1 CD4+ T cells, and their cellular processing and presentation in DNAJB1-PRKACA expressing tumor cells is demonstrated by mass spectrometry-based immunopeptidome analysis. Single-cell RNA sequencing further identifies multiple T cell receptors from DNAJB1-PRKACA-specific T cells. Vaccination of a fibrolamellar hepatocellular carcinoma patient, suffering from recurrent short interval disease relapses, with DNAJB1-PRKACA-derived peptides under continued Poly (ADP-ribose) polymerase inhibitor therapy induces multifunctional CD4+ T cells, with an activated T-helper 1 phenotype and high T cell receptor clonality. Vaccine-induced DNAJB1-PRKACA-specific T cell responses persist over time and, in contrast to various previous treatments, are accompanied by durable relapse free survival of the patient for more than 21 months post vaccination. Our preclinical and clinical findings identify the DNAJB1-PRKACA protein as source for immunogenic neoepitopes and corresponding T cell receptors and provide efficacy in a single-patient study of T cell-based immunotherapy specifically targeting this oncogenic fusion.
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Affiliation(s)
- Jens Bauer
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Natalie Köhler
- grid.5963.9Department of Internal Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, Albert Ludwigs University, Freiburg, Germany ,grid.5963.9CIBSS – Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Yacine Maringer
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Philip Bucher
- grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Pediatric Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Tatjana Bilich
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Melissa Zwick
- grid.5963.9Department of Internal Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, Albert Ludwigs University, Freiburg, Germany ,grid.5963.9Faculty of Biology, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Severin Dicks
- grid.5963.9Faculty of Biology, Albert-Ludwigs-Universität, Freiburg, Germany ,grid.5963.9Institute of Medical Bioinformatics and Systems Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annika Nelde
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Marissa Dubbelaar
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Jonas Scheid
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Jonas S. Heitmann
- grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Sarah Schroeder
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Otorhinolaryngology, Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Monika Denk
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner site Tübingen, Tübingen, Germany
| | - Marion Richter
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner site Tübingen, Tübingen, Germany
| | - Reinhild Klein
- grid.411544.10000 0001 0196 8249Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Irina Bonzheim
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Julia Luibrand
- grid.411544.10000 0001 0196 8249Department of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ursula Holzer
- grid.10392.390000 0001 2190 1447Department of Pediatric Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Martin Ebinger
- grid.10392.390000 0001 2190 1447Department of Pediatric Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Ines B. Brecht
- grid.10392.390000 0001 2190 1447Department of Pediatric Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Michael Bitzer
- grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner site Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Melanie Boerries
- grid.5963.9Institute of Medical Bioinformatics and Systems Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site, Freiburg, Germany
| | - Judith Feucht
- grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Pediatric Hematology and Oncology, University Children’s Hospital, University of Tübingen, Tübingen, Germany
| | - Helmut R. Salih
- grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner site Tübingen, Tübingen, Germany
| | - Stephan Hailfinger
- grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.16149.3b0000 0004 0551 4246Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Juliane S. Walz
- grid.411544.10000 0001 0196 8249Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany ,grid.411544.10000 0001 0196 8249Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner site Tübingen, Tübingen, Germany
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19
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Marconato M, Maringer Y, Walz JS, Nelde A, Heitmann JS. Immunopeptidome Diversity in Chronic Lymphocytic Leukemia Identifies Patients with Favorable Disease Outcome. Cancers (Basel) 2022; 14:cancers14194659. [PMID: 36230581 PMCID: PMC9563800 DOI: 10.3390/cancers14194659] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Immunosurveillance of cancer is mediated by T cell-based recognition of tumor-associated antigens, i.e., short peptides that are presented on the surface of cells on human leukocyte antigen (HLA) molecules. This encourages the analysis of the entirety of HLA-presented peptides, the so-called immunopeptidome, of malignant and benign cells, in order to identify novel therapeutic targets presented exclusively on malignant cells. In the present study, we aim to investigate the role of previously described immunopeptidome-defined antigen presentation in chronic lymphocytic leukemia (CLL) patients for clinical characteristics and disease outcome. We observed that higher yields of presented total and CLL-exclusive peptides were associated with a more favorable disease course, suggesting efficient immunosurveillance in a subgroup of patients and the possibility of further investigating T cell-based therapeutic approaches for CLL. Abstract Chronic lymphocytic leukemia (CLL) is characterized by recurrent relapses and resistance to treatment, even with novel therapeutic approaches. Despite being considered as a disease with low mutational burden and thus poor immunogenic, CLL seems to retain the ability of eliciting specific T cell activation. Accordingly, we recently found non-mutated tumor-associated antigens to play a central role in CLL immunosurveillance. Here, we investigated the association of total and CLL-exclusive HLA class I and HLA class II peptide presentation in the mass spectrometry-defined immunopeptidome of leukemic cells with clinical features and disease outcome of 57 CLL patients. Patients whose CLL cells present a more diverse immunopeptidome experienced fewer relapses. During the follow-up phase of up to 10 years, patients with an HLA class I-restricted presentation of high numbers of total and CLL-exclusive peptides on their malignant cells showed a more favorable disease course with a prolonged progression-free survival (PFS). Overall, our results suggest the existence of an efficient T cell-based immunosurveillance mediated by CLL-associated tumor antigens, supporting ongoing efforts in developing T cell-based immunotherapeutic strategies for CLL.
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Affiliation(s)
- Maddalena Marconato
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Yacine Maringer
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Juliane S. Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
- Department of Peptide-Based Immunotherapy, University and University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-7071-2987305; Fax: +49-7071-294391
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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20
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Wabitsch S, McCallen JD, Kamenyeva O, Ruf B, McVey JC, Kabat J, Walz JS, Rotman Y, Bauer KC, Craig AJ, Pouzolles M, Phadke I, Catania V, Green BL, Fu C, Diggs LP, Heinrich B, Wang XW, Ma C, Greten TF. Metformin treatment rescues CD8 + T-cell response to immune checkpoint inhibitor therapy in mice with NAFLD. J Hepatol 2022; 77:748-760. [PMID: 35378172 PMCID: PMC9391315 DOI: 10.1016/j.jhep.2022.03.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/08/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Non-alcoholic steatohepatitis (NASH) represents the fastest growing underlying cause of hepatocellular carcinoma (HCC) and has been shown to impact immune effector cell function. The standard of care for the treatment of advanced HCC is immune checkpoint inhibitor (ICI) therapy, yet NASH may negatively affect the efficacy of ICI therapy in HCC. The immunologic mechanisms underlying the impact of NASH on ICI therapy remain unclear. METHODS Herein, using multiple murine NASH models, we analysed the influence of NASH on the CD8+ T-cell-dependent anti-PD-1 responses against liver cancer. We characterised CD8+ T cells' transcriptomic, functional, and motility changes in mice receiving a normal diet (ND) or a NASH diet. RESULTS NASH blunted the effect of anti-PD-1 therapy against liver cancers in multiple murine models. NASH caused a proinflammatory phenotypic change of hepatic CD8+ T cells. Transcriptomic analysis revealed changes related to NASH-dependent impairment of hepatic CD8+ T-cell metabolism. In vivo imaging analysis showed reduced motility of intratumoural CD8+ T cells. Metformin treatment rescued the efficacy of anti-PD-1 therapy against liver tumours in NASH. CONCLUSIONS We discovered that CD8+ T-cell metabolism is critically altered in the context of NASH-related liver cancer, impacting the effectiveness of ICI therapy - a finding which has therapeutic implications in patients with NASH-related liver cancer. LAY SUMMARY Non-alcoholic steatohepatitis represents the fastest growing cause of hepatocellular carcinoma. It is also associated with reduced efficacy of immunotherapy, which is the standard of care for advanced hepatocellular carcinoma. Herein, we show that non-alcoholic steatohepatitis is associated with impaired motility, metabolic function, and response to anti-PD-1 treatment in hepatic CD8+ T cells, which can be rescued by metformin treatment.
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Affiliation(s)
- Simon Wabitsch
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin D McCallen
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olena Kamenyeva
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Benjamin Ruf
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John C McVey
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Juliane S Walz
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yaron Rotman
- Liver and Energy Metabolism Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kylynda C Bauer
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amanda J Craig
- Laboratory of Human Carcinogenesis, Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marie Pouzolles
- Basic to Translation Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ira Phadke
- Basic to Translation Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vanessa Catania
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin L Green
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Claude Fu
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laurence P Diggs
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bernd Heinrich
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, MD, USA
| | - Chi Ma
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, MD, USA.
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21
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Junker D, Becker M, Wagner TR, Kaiser PD, Maier S, Grimm TM, Griesbaum J, Marsall P, Gruber J, Traenkle B, Heinzel C, Pinilla YT, Held J, Fendel R, Kreidenweiss A, Nelde A, Maringer Y, Schroeder S, Walz JS, Althaus K, Uzun G, Mikus M, Bakchoul T, Schenke-Layland K, Bunk S, Haeberle H, Göpel S, Bitzer M, Renk H, Remppis J, Engel C, Franz AR, Harries M, Kessel B, Lange B, Strengert M, Krause G, Zeck A, Rothbauer U, Dulovic A, Schneiderhan-Marra N. Antibody Binding and Angiotensin-Converting Enzyme 2 Binding Inhibition Is Significantly Reduced for Both the BA.1 and BA.2 Omicron Variants. Clin Infect Dis 2022; 76:e240-e249. [PMID: 35717657 PMCID: PMC9384292 DOI: 10.1093/cid/ciac498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/11/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The rapid emergence of the Omicron variant and its large number of mutations led to its classification as a variant of concern (VOC) by the World Health Organization. Subsequently, Omicron evolved into distinct sublineages (eg, BA.1 and BA.2), which currently represent the majority of global infections. Initial studies of the neutralizing response toward BA.1 in convalescent and vaccinated individuals showed a substantial reduction. METHODS We assessed antibody (immunoglobulin G [IgG]) binding, ACE2 (angiotensin-converting enzyme 2) binding inhibition, and IgG binding dynamics for the Omicron BA.1 and BA.2 variants compared to a panel of VOCs/variants of interest, in a large cohort (N = 352) of convalescent, vaccinated, and infected and subsequently vaccinated individuals. RESULTS While Omicron was capable of efficiently binding to ACE2, antibodies elicited by infection or immunization showed reduced binding capacities and ACE2 binding inhibition compared to wild type. Whereas BA.1 exhibited less IgG binding compared to BA.2, BA.2 showed reduced inhibition of ACE2 binding. Among vaccinated samples, antibody binding to Omicron only improved after administration of a third dose. CONCLUSIONS Omicron BA.1 and BA.2 can still efficiently bind to ACE2, while vaccine/infection-derived antibodies can bind to Omicron. The extent of the mutations within both variants prevents a strong inhibitory binding response. As a result, both Omicron variants are able to evade control by preexisting antibodies.
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Affiliation(s)
| | | | | | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Tanja M Grimm
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Johanna Griesbaum
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Patrick Marsall
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Jens Gruber
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Constanze Heinzel
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Yudi T Pinilla
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany,German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany,German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Annika Nelde
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Yacine Maringer
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Sarah Schroeder
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Department of Otorhinolaryngology, Head and Neck Surgery, University of Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Karina Althaus
- Center for Clinical Transfusion Medicine, Tuebingen, Germany,Institute of Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Gunalp Uzun
- Center for Clinical Transfusion Medicine, Tuebingen, Germany
| | - Marco Mikus
- Center for Clinical Transfusion Medicine, Tuebingen, Germany
| | - Tamam Bakchoul
- Center for Clinical Transfusion Medicine, Tuebingen, Germany,Institute of Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Katja Schenke-Layland
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tuebingen, Tuebingen, Germany,Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Stefanie Bunk
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Helene Haeberle
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Siri Göpel
- German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Bitzer
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany,Center for Personalized Medicine, University of Tuebingen, Tuebingen, Germany
| | - Hanna Renk
- University Children’s Hospital, Tuebingen, Germany
| | | | - Corinna Engel
- University Children’s Hospital, Tuebingen, Germany,Center for Pediatric Clinical Studies, University Hospital Tuebingen, Tuebingen, Germany
| | - Axel R Franz
- University Children’s Hospital, Tuebingen, Germany,Center for Pediatric Clinical Studies, University Hospital Tuebingen, Tuebingen, Germany
| | - Manuela Harries
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Barbora Kessel
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Berit Lange
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Helmholtz Centre for Infection Research, Braunschweig, Germany,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture of Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gerard Krause
- Helmholtz Centre for Infection Research, Braunschweig, Germany,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture of Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany,Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
| | - Alex Dulovic
- Correspondence: A. Dulovic, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, Reutlingen, 72770 Germany ()
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Dubbelaar ML, Freudenmann LK, Scheid J, Velz J, Medici G, Kapolou K, Mohme M, Bichmann L, Gauder M, Czemmel S, Mohr C, Kowalewski DJ, Westphal M, Lamszus K, Regli L, Weller M, Rammensee HG, Salih H, Neidert MC, Walz JS. Abstract 1991: Characterization of the exome, transcriptome, and immunopeptidome to map alterations in primary and recurrent glioblastoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1991] [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
Glioblastoma is known as the most aggressive and most common malignant primary tumor in the central nervous system. Current treatment options comprise maximal surgical resection followed by radiation and/or chemotherapy with temozolomide. However, these therapies are not able to eliminate all tumor cells, which in turn inevitably leads to disease recurrence and an alteration of identified targets in the context of clonal evolution and potential hypermutation. T cell-based immunotherapy holds great promise to target malignant cells with CAR T cell and vaccination strategies, showing first promising results in glioblastoma. These therapies rely on the rejection of cancer cells through recognition of tumor antigens and T cell-mediated cytotoxicity. In previous work, we have characterized such tumor antigens in primary glioblastoma (Neidert et al., Acta Neuropathol, 2018), nonetheless, alterations in relapsed disease have not been addressed thus far. This study investigated the whole exome, transcriptome, and mass-spectrometry-based immunopeptidome of 38 primary and 24 recurrent tumors, including 22 autologous glioblastoma pairs, to determine alterations that occur during glioblastoma progression on multiple comics levels. In concordance with Neftel et al., Cell, 2019, we identified mutations that can be allocated to astrocyte- and mesenchymal-like classified genes. In addition, an increase in the mutation rate in recurrent glioblastoma was observed which is attributed to radiation and chemotherapy pretreatment of tumors. These newly arising tumor-specific mutations give rise to HLA-presented neoepitopes in the primary cohort. Moreover, we identified transcripts that are differentially expressed between the two cohorts, showing a higher expression of transcripts related to immune system responses in the recurrent cohort. Immunopeptidome analysis of the two cohorts revealed high frequent glioblastoma-exclusive HLA class I and class II ligands presented in both the primary and recurrent cohort, serving as universally applicable tumor antigens. Class I and II HLA ligands of each sample were analyzed and revealed 2,146 HLA class I- and 2,753 HLA class II presented antigens that were uniquely identified on primary glioblastoma. A total of 610 and 1,886 source proteins represent recurrence-exclusive antigens presented on HLA class I or II molecules, respectively. Together this work addressed differences in tumor antigen expression and presentation between primary and recurrent glioblastoma using these omics layers to create an overview of the alterations that occur during disease progression. Besides providing a deep insight into the glioblastoma (immuno-)biology during progression, this study yields targets for innovative immunotherapeutic approaches to eliminate residual cells and improve survival in glioblastoma patients.
Citation Format: Marissa L. Dubbelaar, Lena K. Freudenmann, Jonas Scheid, Julia Velz, Gioele Medici, Konstantina Kapolou, Malte Mohme, Leon Bichmann, Marie Gauder, Stefan Czemmel, Christopher Mohr, Daniel J. Kowalewski, Manfred Westphal, Katrin Lamszus, Luca Regli, Michael Weller, Hans-Georg Rammensee, Helmut Salih, Marian C. Neidert, Juliane S. Walz. Characterization of the exome, transcriptome, and immunopeptidome to map alterations in primary and recurrent glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1991.
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Affiliation(s)
| | | | | | - Julia Velz
- 3Clinical Neuroscience Center, Zurich, Switzerland
| | | | | | - Malte Mohme
- 4University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Marie Gauder
- 6Quantitative Biology Center (QBiC), Tübingen, Germany
| | | | | | | | | | - Katrin Lamszus
- 7University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Luca Regli
- 3Clinical Neuroscience Center, Zurich, Switzerland
| | - Michael Weller
- 8Laboratory of Molecular Neuro-Oncology, Zurich, Switzerland
| | | | - Helmut Salih
- 1Clinical Cooperation Unit Translational Immunology, Tübingen, Germany
| | | | - Juliane S. Walz
- 1Clinical Cooperation Unit Translational Immunology, Tübingen, Germany
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23
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Nelde A, Schuster H, Bilich T, Bauer J, Roerden M, Schroeder S, Heitmann JS, Rücker-Braun E, Rammensee HG, Salih HR, Walz JS. Abstract 3168: Immunopeptidome-defined acute myeloid leukemia progenitor cell-associated antigens are targeted in vivo by AML patients’ T cells. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3168] [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
Despite recent advances and the approval of novel molecular therapies in acute myeloid leukemia (AML), the disease is still characterized by high relapse rates and poor overall survival due to the persistence of therapy-resistant residual leukemic progenitor cells (LPCs). T cell-based immunotherapy has been suggested as a novel therapeutic option to eliminate minimal residual disease and achieve long-lasting remissions. One main prerequisite for immunotherapy development is the selection of immunogenic targets that show natural, high-frequent, and tumor-exclusive presentation on the cell surface of malignant cells. In a previous study we characterized the antigenic landscape of AML by mass spectrometry to identify AML-specific T cell epitopes (Berlin et al. Leukemia 2015). Here, we aimed to analyze the immunopeptidome of primary AML progenitor cells (n = 10, purity >80% CD34+CD38-) to identify LPC-associated antigens that enable the specific targeting of AML LPCs. Additionally, we analyzed an extended set of AML patient samples (n = 47) to screen for naturally presented neoepitopes and to identify broadly applicable AML-associated target antigens that are presented on both AML blasts and LPCs.
We identified more than 16,000 HLA class I- and 17,000 HLA class II-presented peptides on LPCs and 72,000 HLA class I and 61,000 HLA class II peptides in the total AML cohort. Comparative profiling of LPCs, AML blasts, and a benign tissue database (n = 332) revealed HLA class I- and HLA class II-presented LPC-exclusive as well as frequently presented AML-associated antigens on both AML blasts and LPCs. Besides these tumor-exclusive self-peptides, we detected naturally presented neoepitopes derived from two frequent mutations (NPM1 and IDH2) in this low-mutational burden malignancy.
For immunogenicity analyses we selected 16 HLA class I- and 15 HLA class II-restricted peptides comprising unmutated as well as mutation-derived antigens. In vitro priming experiments showed the induction of peptide-specific, multi-functional, and cytotoxic CD8+ effector cells in samples of healthy volunteers and AML patients.
We were able to detect strong preexisting memory T cell responses targeting LPC-associated antigens in AML patients with detection frequencies of up to 20%. Retrospective analyses revealed that patients with preexisting peptide-specific T cell responses showed improved overall survival compared to patients without any memory responses against our targets.
Taken together, we identified novel, naturally presented, LPC-exclusive, and AML-associated self-antigens and neoepitopes presented on both AML blasts and LPCs. We could demonstrate the immunogenicity of 14/16 (88%) HLA class I and 13/15 (87%) HLA class II antigens highlighting their potential as promising targets for T cell-based immunotherapy approaches to eliminate minimal residual disease in AML patients.
Citation Format: Annika Nelde, Heiko Schuster, Tatjana Bilich, Jens Bauer, Malte Roerden, Sarah Schroeder, Jonas S. Heitmann, Elke Rücker-Braun, Hans-Georg Rammensee, Helmut R. Salih, Juliane S. Walz. Immunopeptidome-defined acute myeloid leukemia progenitor cell-associated antigens are targeted in vivo by AML patients’ T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3168.
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Affiliation(s)
- Annika Nelde
- 1University Hospital Tübingen, Tübingen, Germany
| | | | | | - Jens Bauer
- 1University Hospital Tübingen, Tübingen, Germany
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24
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Tandler C, Heitmann JS, Marconato M, Maringer Y, Denk M, Richter M, Nelde A, Fischer I, Löffler MW, Rammensee HG, Salih HR, Walz JS. Abstract CT258: Interim safety and immunogenicity results of a phase I trial evaluating the multi-peptide COVID-19 vaccine candidate CoVac-1 for induction of SARS-CoV-2 T cell immunity in cancer patients with disease- or treatment-related immunoglobulin deficiency. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-ct258] [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
Individuals with impaired ability to mount a humoral immune response, either during natural infection or upon prophylactic vaccination, are at high risk for a severe course of COVID-19. Besides humoral immunity mediated by B cells, T cell immunity is key for the control of viral infections. We developed the peptide-based vaccine candidate CoVac-1, which primarily aims for the induction of SARS-CoV-2-specific T cells. CoVac-1 comprises six promiscuous HLA-DR-binding SARS-CoV-2-derived T cell epitopes from various viral proteins proven (i) to be frequently and HLA-independently recognized by T cells in COVID-19 convalescents, (ii) to be of pathophysiological relevance for T cell immunity to combat COVID-19, and (iii) to mediate long-term immunity after infection (Nelde et al. Nat Immunol 2021, Bilich et al. Sci Transl Med 2021). CoVac-1 vaccine peptides are adjuvanted with the novel toll-like receptor 1/2 agonist XS15 emulsified in Montanide࣪ ISA51 VG. In a first-in-human clinical trial in healthy adults (NCT04546841), CoVac-1 showed a favorable safety profile and induced profound and long-lasting T cell immunity after single dose administration in 100% of the study subjects, mediated by multifunctional T-helper 1 CD4+ and CD8+ T cells. CoVac-1-induced T cell responses surpassed those after SARS-CoV-2 infection as well as those after vaccination with approved vaccines and were unaffected by current SARS-CoV-2 variants of concern (Heitmann et al. Nature 2021). Here we present the interim safety and immunogenicity results of our Phase I/II trial evaluating CoVac-1 in patients with congenital or acquired B cell deficiency, mainly comprising leukemia and lymphoma patients (NCT04954469). 64% of study subjects had previously been vaccinated with approved vaccines without developing any humoral immune response. Alike in the healthy adults, CoVac-1 showed a good safety and tolerability profile without relevant systemic adverse events. CoVac-1-specific T cell responses could be documented in 93% of study subjects on day 28 after CoVac-1 application, with earliest responses evidenced at day 14 (71%). Vaccine-induced T cell responses were mediated by multifunctional T-helper 1 CD4+ T cells. Of note, CoVac-1 induced T cell responses in this highly immune compromised study population were similar to those occurring in healthy volunteers after natural infection or induced by approved vaccines. These results identify CoVac-1 as promising vaccine candidate for cancer and other immunocompromised patients with immunoglobulin deficiency. Recruitment of the Phase II part of the trial is ongoing with results expected for March 2022.
Citation Format: Claudia Tandler, Jonas S. Heitmann, Maddalena Marconato, Yacine Maringer, Monika Denk, Marion Richter, Annika Nelde, Imma Fischer, Markus W. Löffler, Hans-Georg Rammensee, Helmut R. Salih, Juliane S. Walz. Interim safety and immunogenicity results of a phase I trial evaluating the multi-peptide COVID-19 vaccine candidate CoVac-1 for induction of SARS-CoV-2 T cell immunity in cancer patients with disease- or treatment-related immunoglobulin deficiency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT258.
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Affiliation(s)
- Claudia Tandler
- 1Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
| | - Jonas S. Heitmann
- 1Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
| | - Maddalena Marconato
- 2Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, Tübingen, Germany
| | - Yacine Maringer
- 1Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
| | - Monika Denk
- 3Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marion Richter
- 3Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- 1Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
| | - Imma Fischer
- 4Institute for Clinical Epidemiology and Applied Biometry, University Hospital Tübingen, Tübingen, Germany
| | - Markus W. Löffler
- 3Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- 5Institute for Cell Biology, Department of Immunology, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
| | - Helmut R. Salih
- 1Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- 1Clinical Collaboration Unit Translational Immunology, University Hospital Tübingen, and Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany
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25
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Tegeler CM, Heitmann JS, Salih HR, Walz JS, Nelde A. Abstract 1972: Clinical implications of HLA expression and immunopeptidome-presented tumor antigens in ovarian carcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1972] [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
Ovarian carcinoma (OvCa) is the seventh most common malignancy in women and the eighth leading cause of cancer-related deaths worldwide. In a previous study, we characterized the antigenic landscape of ovarian carcinoma by mass spectrometry-based immunopeptidomics and identified novel OvCa-associated tumor antigens, including Mucin-16 (MUC-16) and Mesothelin (MSLN) with the aim to develop novel T cell-based immunotherapies (Schuster et al. PNAS 2017). Here, we analyzed the immunopeptidomics data of this OvCa cohort in relation to clinical patient characteristics and disease outcome. Analysis included 43 OvCa patients with respective immunopeptidomics and RNA sequencing data, comprising immunopeptidome diversity, tumor antigen presentation and expression (MUC16, MSLN) as well as HLA mRNA expression.Analyzing HLA class I-restricted tumor antigen presentation in relation to clinical data, we could show that nodal-positive patients presented more frequently HLA-restricted peptides derived from the tumor antigen MUC16 (p = 0.0087) and showed significantly increased numbers of unique MUC16-derived HLA-presented peptides within the total immunopeptidome (p = 0.042) compared to nodal-negative patients. No significant difference in HLA class I immunopeptidome diversity, overall tumor antigen presentation, and expression was observed for histological subtypes, grading, or the prevalence of distant metastases. For HLA class II-restricted tumor antigen presentation and HLA expression in relation to clinical data, we observed a more diverse HLA class II immunopeptidome in terms of different HLA class II-presented peptides (p = 0.011) for patients with high tumor grading (G3) compared to low/intermediate (G1/G2) grading. In line, the tumors of these patients also presented an increased number of different MSLN-derived HLA class II-restricted peptides (p = 0.021). No significant difference in HLA class II immunopeptidome diversity, tumor antigen presentation and expression was seen for the prevalence of distant metastasis, histological subtypes, or nodal positivity.Of note, patients presenting MSLN-derived peptides in their immunopeptidome showed a significantly prolonged recurrence-free survival (RFS, p = 0.011). In addition, patients exhibiting a high expression of HLA-DR showed a significantly increased RFS (p = 0.018 for HLA-DRA, p = 0.0031 for HLA-DRB).In conclusion, this work provides first insights on the relation of immunopeptidomic characteristics, comprising HLA expression and tumor antigen presentation, with clinical characteristics and disease outcome of OvCa patients. The observed correlation of HLA-DR expression and HLA class II tumor antigen presentation with prolonged RFS indicates a central role of CD4+ T cell responses for anti-tumor immune surveillance in ovarian cancer.
Citation Format: Christian M. Tegeler, Jonas S. Heitmann, Helmut R. Salih, Juliane S. Walz, Annika Nelde. Clinical implications of HLA expression and immunopeptidome-presented tumor antigens in ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1972.
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Affiliation(s)
| | | | | | | | - Annika Nelde
- 1University Hospital of Tübingen, Tübingen, Germany
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26
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Schroeder S, Gross T, Nelde A, Wacker M, Bauer J, Rieth J, Dubbelaar M, Muehlenbruch L, Maringer Y, Mauz PS, Sailer M, Philipp J, Becker S, Breuer T, Salih HR, Rammensee HG, Löwenheim H, Walz JS. Abstract 3555: Immunopeptidomics-guided tumor antigen warehouse design for peptide-based immunotherapy in head and neck squamous cell carcinomas. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3555] [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
Head and neck squamous cell carcinomas (HNSCC) are the sixth most common malignancies worldwide. 45% of patients are diagnosed at a late tumor stage associated with poor survival. For metastatic, unresectable or recurrent (m/uR) HNSCC, immune checkpoint inhibition (ICI) was recently approved as a novel therapeutic option showing significant survival benefits compared to standard chemotherapy-based treatment. However, response to ICI is still limited to a small number of patients calling for further improvement of T cell-based immunotherapies. Peptide-based approaches, which rely on the specific immune recognition of tumor-associated human leukocyte antigen (HLA) presented peptides, represent promising and low side effect treatment options. Peptide vaccination has been shown to enhance and induce long-term anti-tumoral immune responses and even clinical responses in HNSCC patients. However, current vaccines are either monovalent, based on patient-individual tumor-specific mutations or restricted to a single HLA allotype and therefore neither widely applicable nor suitable for reliable studies and large-scale production. In this study, using mass spectrometry (MS) -based immunopeptidome analysis of a large cohort of HNSCC patient (n = 30) tumor and adjacent benign samples, we established a tumor-associated off-the-shelf peptide warehouse for broadly applicable personalized therapies. The malignant dataset, comprising 91651 HLA ligands, was compared to adjacent benign and various benign tissues (www.hla-ligand-atlas.org) to identify tumor-exclusive antigens. Further antigen selection was based on allotype-specific high frequent presentation. In total, 23 frequently presented and tumor-exclusive HNSCC-associated peptides were selected for six of the most common HLA class I allotypes (A*01, A*02, A*24, B*15, B*35, B*40) covering >75% of the world population, as well as five HLA class II presented peptides binding various different HLA class II allotypes. Immunogenicity was validated by IFN-γ ELISPOT screening for spontaneous preexisting T cell responses targeting the respective peptides as well as by in vitro priming experiments of naïve T cells in HNSCC patients and healthy volunteers. Furthermore, immunopeptidome analyses identified these antigens in patient plasma samples providing first evidence for “liquid biopsy” immunopeptidome analysis without the need of primary tumor tissue. A phase I study evaluating safety, immunogenicity as well as first efficacy of this warehouse-based vaccine in combination with ICI in HNSCC patients is currently being set up, with personalized peptide selection based on individual HLA-allotype and MS analysis of patient tumor/plasma sample. In conclusion, we here designed a peptide warehouse that enables a polyvalent and widely applicable but still personalized peptide vaccination in HNSCC patients.
Citation Format: Sarah Schroeder, Thorben Gross, Annika Nelde, Marcel Wacker, Jens Bauer, Jonas Rieth, Marissa Dubbelaar, Lena Muehlenbruch, Yacine Maringer, Paul-Stefan Mauz, Martin Sailer, Julia Philipp, Sven Becker, Thomas Breuer, Helmut R. Salih, Hans-Georg Rammensee, Hubert Löwenheim, Juliane S. Walz. Immunopeptidomics-guided tumor antigen warehouse design for peptide-based immunotherapy in head and neck squamous cell carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3555.
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Affiliation(s)
| | | | - Annika Nelde
- 2Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Marcel Wacker
- 2Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Jens Bauer
- 2Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Jonas Rieth
- 2Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | | | - Lena Muehlenbruch
- 2Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Yacine Maringer
- 2Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | | | | | | | - Sven Becker
- 1University Hospital Tuebingen, Tuebingen, Germany
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Wacker M, Medici G, Dubbelaar M, Bauer J, Nelde A, Regli L, Weller M, Salih HR, Rammensee HG, Neidert MC, Walz JS. Abstract 1375: The intra-tumoral spatial heterogeneity of T-cell antigens in glioblastoma: An integrated multi-omics approach. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1375] [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
Glioblastoma is the most common primary malignant neoplasm of the central nervous system in adults. Current treatment options comprise maximal surgical resection followed by radiation and/or chemotherapy with temozolomide. However, these procedures are unable to eliminate all tumor cells, which in turn lead to disease recurrence accounting for the poor prognosis. Glioblastoma is a highly infiltrative tumor in which recurrence originates from the unresectable peritumoral infiltration zone. Thus, novel treatment options specifically targeting the tumor cells in the infiltration zone are needed to prevent relapse and enable long-lasting remission. In this work, we performed multi-omics spatial analysis of the necrotic center (NEC), the gadolinium contrast-enhanced region (T1), and the infiltration zone (INF) to assess immunological relevant aspects of tumor heterogeneity. By integrating mass spectrometry-based immunopeptidome analysis with next generation sequencing methods (whole exome and RNA sequencing, DNA methylation), we aimed to identify the intra-tumoral regional heterogeneity of T cell antigens with a special focus on the peritumoral infiltration zone. For multi-omics analysis, HLA peptides and genetic material from 15 glioblastoma patients were extracted and analyzed from the three zones NEC, T1, INF and for four patients additionally from adjacent benign (BEN) brain tissue. A total of 24,699 unique HLA class I and 17,394 HLA class II peptides were identified. Comparative profiling of peptides from our study and a benign tissue database (in-house (n=429) combined with HLA ligand atlas (https://hla-ligand-atlas.org)) revealed that 6% (970/15,579), 5% (829/16,442) and 5% (725/13,891) of HLA class I peptides were exclusively presented in the INF, T1 and NEC zone, respectively. 6% (394/7,150), 7% (589/8,736) and 13% (1,725/12,908) of HLA class II peptides showed exclusive representation in the INF, T1 and NEC zone, respectively. Importantly, due to the spatial analysis of the immunopeptidome, we revealed 970 HLA class I and 394 HLA class II peptides exclusively presented in the INF zone. Interestingly, one INF-associated HLA class I peptide, which showed frequent presentation in 36% of glioblastoma immunopeptidomes, is derived from the brain and acute leukemia cytoplasmic protein (BAALC), a highly expressed cell cycle inducer (via MEK kinase-1) in several cancers, including glioblastoma. Integrated RNA/DNA sequencing enabled a greater understanding of spatial tumor antigen presentation and lead to the identification of INF-specific neoepitopes derived from tumor-specific mutations. In summary, we identified the intra-tumoral regional heterogeneity of tumor antigens, which could be used in the future for specific immunotherapy approaches targeting the infiltration zone of glioblastoma.
Citation Format: Marcel Wacker, Gioele Medici, Marissa Dubbelaar, Jens Bauer, Annika Nelde, Luca Regli, Michael Weller, Helmut R. Salih, Hans-Georg Rammensee, Marian C. Neidert, Juliane S. Walz. The intra-tumoral spatial heterogeneity of T-cell antigens in glioblastoma: An integrated multi-omics approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1375.
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Affiliation(s)
| | | | | | - Jens Bauer
- 1University Hospital Tübingen, Tübingen, Germany
| | - Annika Nelde
- 1University Hospital Tübingen, Tübingen, Germany
| | - Luca Regli
- 2University Hospital Zürich, Zürich, Switzerland
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Bauer J, Köhler N, Maringer Y, Bucher P, Bilich T, Zwick M, Dicks S, Nelde A, Dubbelaar M, Scheid J, Wacker M, Heitmann JJ, Schroeder S, Rieth J, Denk M, Richter M, Klein R, Bonzheim I, Luibrand J, Holzer U, Ebinger M, Brecht IB, Bitzer M, Boerries M, Salih HR, Rammensee HG, Hailfinger S, Walz JS. Abstract 2008: The oncogenic fusion protein DNAJB1-PRKACA can be actively targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2008] [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
Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare tumor disease, which affects children and adolescents without history of primary liver disease. Beside surgical resection established treatment options are lacking for FL-HCC. Recently, the DNAJB1-PRKACA fusion transcript was identified as the oncogenic driver of tumor pathogenesis in 100% of FL-HCC patients. Here, we investigated the role of the DNAJB1-PRKACA fusion protein as a source for immunogenic neoepitopes and showed first immunotherapeutic application of these antigens in a FL-HCC patient.HLA class I- and class II-presented neoantigens derived from the DNAJB1-PRKACA fusion protein were predicted in silico using NetMHCpan 4.1 and SYFPEITHI 1.0, or NetMHCIIpan 4.0, respectively. With this workflow nine binding cores of nine amino acid length for a total of 1290 different HLA class II alleles, as well as 13 HLA class I ligands for the 20 most frequent HLA class I allotypes (European population, iedb.org) were identified. Cellular processing and HLA presentation of DNAJB1-PRKACA-derived peptides was proven by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) of DNAJB1-PRKACA-transduced HCC cell lines. Immunogenicity of DNAJB1-PRKACA-derived peptides was assessed for the HLA class II peptide (PII-1) and the HLA-A*24 peptide (PA*24) by in vitro priming experiments which showed an induction of multifunctional peptide-specific CD4+ and CD8+ T cells, respectively, with expression of CD107a, IFNγ, and TNF upon peptide-pulsing. Furthermore, PA*24-specific T cells showed antigen-specific lysis of autologous peptide-loaded target cells and single-cell next-generation sequencing (10x Genomics) of PA*24-specific CD8+ T cells further enabled the identification of DNAJB1-PRKACA-reactive T cell receptors. Based on these preclinical data we applied a peptide vaccine, consisting of three HLA class I ligands (PA*02, PB*44, and PC*05) and PII-1 spanning the DNAJB1-PRKACA fusion region, to a 15-year old patient with histologically confirmed FL-HCC, who experienced multiple tumor relapses after early liver transplant due to unresectable FL-HCC not responsive to chemotherapy. After two vaccinations in vivo induction of multifunctional CD4+ T cells targeting PII-1 and PB*44 was observed by IFNγ ELISPOT. Single-cell RNA sequencing of vaccine-induced CD4+ T cells revealed distinct gene expression clusters of T cell activation and high TCR clonality. DNAJB1-PRKACA-specific T cells persisted in peripheral blood and were accompanied by relapse free survival of the patient until now, more than one year post vaccination. These findings identified the DNAJB1-PRKACA fusion transcript as novel prime source for broadly applicable neoepitopes and corresponding TCRs and provide first evidence for their application in cancer immunotherapy of FL-HCC.
Citation Format: Jens Bauer, Natalie Köhler, Yacine Maringer, Philip Bucher, Tatjana Bilich, Melissa Zwick, Severin Dicks, Annika Nelde, Marissa Dubbelaar, Jonas Scheid, Marcel Wacker, Jonas J. Heitmann, Sarah Schroeder, Jonas Rieth, Monika Denk, Marion Richter, Reinhild Klein, Irina Bonzheim, Julia Luibrand, Ursula Holzer, Martin Ebinger, Ines B. Brecht, Michael Bitzer, Melanie Boerries, Helmut R. Salih, Hans-Georg Rammensee, Stephan Hailfinger, Juliane S. Walz. The oncogenic fusion protein DNAJB1-PRKACA can be actively targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2008.
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Affiliation(s)
- Jens Bauer
- 1University Hospital Tübingen, Tübingen, Germany
| | | | | | | | | | | | | | - Annika Nelde
- 1University Hospital Tübingen, Tübingen, Germany
| | | | - Jonas Scheid
- 1University Hospital Tübingen, Tübingen, Germany
| | | | | | | | - Jonas Rieth
- 1University Hospital Tübingen, Tübingen, Germany
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Junker D, Dulovic A, Becker M, Wagner TR, Kaiser PD, Traenkle B, Kienzle K, Bunk S, Struemper C, Haeberle H, Schmauder K, Ruetalo N, Malek N, Althaus K, Koeppen M, Rothbauer U, Walz JS, Schindler M, Bitzer M, Göpel S, Schneiderhan-Marra N. COVID-19 patient serum less potently inhibits ACE2-RBD binding for various SARS-CoV-2 RBD mutants. Sci Rep 2022; 12:7168. [PMID: 35505068 PMCID: PMC9062870 DOI: 10.1038/s41598-022-10987-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 12/06/2021] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
As global vaccination campaigns against SARS-CoV-2 proceed, there is particular interest in the longevity of immune protection, especially with regard to increasingly infectious virus variants. Neutralizing antibodies (Nabs) targeting the receptor binding domain (RBD) of SARS-CoV-2 are promising correlates of protective immunity and have been successfully used for prevention and therapy. As SARS-CoV-2 variants of concern (VOCs) are known to affect binding to the ACE2 receptor and by extension neutralizing activity, we developed a bead-based multiplex ACE2-RBD inhibition assay (RBDCoV-ACE2) as a highly scalable, time-, cost-, and material-saving alternative to infectious live-virus neutralization tests. By mimicking the interaction between ACE2 and the RBD, this serological multiplex assay allows the simultaneous analysis of ACE2 binding inhibition to the RBDs of all SARS-CoV-2 VOCs and variants of interest (VOIs) in a single well. Following validation against a classical virus neutralization test and comparison of performance against a commercially available assay, we analyzed 266 serum samples from 168 COVID-19 patients of varying severity. ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma. ACE2 binding inhibition, while highly individualistic, positively correlated with IgG levels. ACE2 binding inhibition also correlated with disease severity up to WHO grade 7, after which it reduced.
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Affiliation(s)
- Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Katharina Kienzle
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Stefanie Bunk
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Carlotta Struemper
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Helene Haeberle
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Kristina Schmauder
- Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Nisar Malek
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany.,Center for Personalized Medicine, Eberhard Karls University, Tübingen, Germany
| | - Karina Althaus
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael Koeppen
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany
| | - Juliane S Walz
- Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Bitzer
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany.,Center for Personalized Medicine, Eberhard Karls University, Tübingen, Germany
| | - Siri Göpel
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany. .,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
| | - Nicole Schneiderhan-Marra
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.
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Tegeler CM, Bilich T, Maringer Y, Salih HR, Walz JS, Nelde A, Heitmann JS. Prevalence of COVID-19-associated symptoms during acute infection in relation to SARS-CoV-2-directed humoral and cellular immune responses in a mild-diseased convalescent cohort. Int J Infect Dis 2022; 120:187-195. [PMID: 35429640 PMCID: PMC9007751 DOI: 10.1016/j.ijid.2022.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Objectives Besides SARS-CoV-2-directed humoral immune responses, T cell responses are indispensable for effective antiviral immunity. Recent data have shown a correlation between COVID-19 symptoms and humoral immune response, but so far, little is known about the association of SARS-CoV-2-directed T cell responses and disease severity. Herein, we evaluated the prevalence of different clinical COVID-19 symptoms in relation to SARS-CoV-2-directed humoral and cellular immune responses. Methods The severity of eight different symptoms during acute infection were assessed using questionnaires from 193 convalescent individuals and were evaluated in relation to SARS-CoV-2 antibody levels and intensity of SARS-CoV-2-specific T cell responses 2–8 weeks after positive polymerase chain reaction. Results Although increased IgG serum levels could be associated with severity of most symptoms, no difference in T cell response intensity between different symptom severities was observed for the majority of COVID-19 symptoms. However, when analyzing loss of smell or taste and cough, awareness of more severe symptoms was associated with reduced T cell response intensities. Conclusions These data suggest that rapid virus clearance mediated by SARS-CoV-2-specific T cells prevents severe symptoms of COVID-19.
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Nelde A, Flötotto L, Jürgens L, Szymik L, Hubert E, Bauer J, Schliemann C, Kessler T, Lenz G, Rammensee HG, Walz JS, Wethmar K. Upstream open reading frames regulate translation of cancer-associated transcripts and encode HLA-presented immunogenic tumor antigens. Cell Mol Life Sci 2022; 79:171. [PMID: 35239002 PMCID: PMC8894207 DOI: 10.1007/s00018-022-04145-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/21/2021] [Accepted: 01/10/2022] [Indexed: 02/04/2023]
Abstract
Background Upstream open reading frames (uORFs) represent translational control elements within eukaryotic transcript leader sequences. Recent data showed that uORFs can encode for biologically active proteins and human leukocyte antigen (HLA)-presented peptides in malignant and benign cells suggesting their potential role in cancer cell development and survival. However, the role of uORFs in translational regulation of cancer-associated transcripts as well as in cancer immune surveillance is still incompletely understood. Methods We examined the translational regulatory effect of 29 uORFs in 13 cancer-associated genes by dual-luciferase assays. Cellular expression and localization of uORF-encoded peptides (uPeptides) were investigated by immunoblotting and immunofluorescence-based microscopy. Furthermore, we utilized mass spectrometry-based immunopeptidome analyses in an extensive dataset of primary malignant and benign tissue samples for the identification of naturally presented uORF-derived HLA-presented peptides screening for more than 2000 uORFs. Results We provide experimental evidence for similarly effective translational regulation of cancer-associated transcripts through uORFs initiated by either canonical AUG codons or by alternative translation initiation sites (aTISs). We further demonstrate frequent cellular expression and reveal occasional specific cellular localization of uORF-derived peptides, suggesting uPeptide-specific biological implications. Immunopeptidome analyses delineated a set of 125 naturally presented uORF-derived HLA-presented peptides. Comparative immunopeptidome profiling of malignant and benign tissue-derived immunopeptidomes identified several tumor-associated uORF-derived HLA ligands capable to induce multifunctional T cell responses. Conclusion Our data provide direct evidence for the frequent expression of uPeptides in benign and malignant human tissues, suggesting a potentially widespread function of uPeptides in cancer biology. These findings may inspire novel approaches in direct molecular as well as immunotherapeutic targeting of cancer-associated uORFs and uPeptides. Supplementary Information The online version contains supplementary material available at 10.1007/s00018-022-04145-0.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, German Cancer Consortium (DKTK), University Hospital Tübingen, Otfried-Müller-Str. 10, 72076, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076, Tübingen, Germany
| | - Lea Flötotto
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Lara Jürgens
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Laura Szymik
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Elvira Hubert
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, German Cancer Consortium (DKTK), University Hospital Tübingen, Otfried-Müller-Str. 10, 72076, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076, Tübingen, Germany
| | - Christoph Schliemann
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Torsten Kessler
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, Department of Internal Medicine, German Cancer Consortium (DKTK), University Hospital Tübingen, Otfried-Müller-Str. 10, 72076, Tübingen, Germany. .,Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076, Tübingen, Germany. .,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076, Tübingen, Germany. .,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Robert Bosch Center for Tumor Diseases (RBCT), 70376, Stuttgart, Germany.
| | - Klaus Wethmar
- Department of Medicine A, Hematology, Oncology, Hemostaseology and Pneumology, University Hospital Münster, Albert-Schweitzer-Campus 1A, 48149, Münster, Germany.
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Marcu A, Schlosser A, Keupp A, Trautwein N, Johann P, Wölfl M, Lager J, Monoranu CM, Walz JS, Henkel LM, Krauß J, Ebinger M, Schuhmann M, Thomale UW, Pietsch T, Klinker E, Schlegel PG, Oyen F, Reisner Y, Rammensee HG, Eyrich M. Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors. J Immunother Cancer 2021; 9:jitc-2021-003404. [PMID: 34599019 PMCID: PMC8488729 DOI: 10.1136/jitc-2021-003404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 12/30/2022] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS tumors of infancy and early childhood. Hallmark is the surprisingly simple genome with inactivating mutations or deletions in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expanded T cells. However, it is unclear which epitopes T cells might recognize on AT/RT cells. Methods Here, we report a comprehensive mass spectrometry (MS)-based analysis of naturally presented human leukocyte antigen (HLA) class I and class II ligands on 23 AT/RTs. MS data were validated by matching with a human proteome dataset and exclusion of peptides that are part of the human benignome. Cryptic peptide ligands were identified using Peptide-PRISM. Results Comparative HLA ligandome analysis of the HLA ligandome revealed 55 class I and 139 class II tumor-exclusive peptides. No peptide originated from the SMARCB1 region. In addition, 61 HLA class I tumor-exclusive peptide sequences derived from non-canonically translated proteins. Combination of peptides from natural and cryptic class I and class II origin gave optimal representation of tumor cell compartments. Substantial overlap existed with the cryptic immunopeptidome of glioblastomas, but no concordance was found with extracranial tumors. More than 80% of AT/RT exclusive peptides were able to successfully prime CD8+ T cells, whereas naturally occurring memory responses in AT/RT patients could only be detected for class II epitopes. Interestingly, >50% of AT/RT exclusive class II ligands were also recognized by T cells from glioblastoma patients but not from healthy donors. Conclusions These findings highlight that AT/RTs, potentially paradigmatic for other pediatric tumors with a low mutational load, present a variety of highly immunogenic HLA class I and class II peptides from canonical as well as non-canonical protein sources. Inclusion of such cryptic peptides into therapeutic vaccines would enable an optimized mapping of the tumor cell surface, thereby reducing the likelihood of immune evasion.
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Affiliation(s)
- Ana Marcu
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany
| | | | - Anne Keupp
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Nico Trautwein
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Pascal Johann
- Swabian Children's Cancer Center, Augsburg, Germany.,DKFZ Heidelberg, Heidelberg, Germany
| | - Matthias Wölfl
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Johanna Lager
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Camelia Maria Monoranu
- Department of Neuropathology, Institute for Pathology, University of Würzburg, Würzburg, Germany
| | - Juliane S Walz
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany.,Cluster of Excellence iFIT (EXC2180), University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital of Tübingen, Tübingen, Germany
| | - Lisa M Henkel
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Jürgen Krauß
- Department of Neurosurgery, University Medical Center Würzburg, Würzburg, Germany
| | - Martin Ebinger
- University Children's Hospital, University Medical Center Tübingen, Tübingen, Germany
| | - Martin Schuhmann
- Department of Neurosurgery, University Medical Center Tübingen, Tübingen, Germany
| | | | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Erdwine Klinker
- Institute for Transfusion Medicine, University Medical Center Würzburg, Würzburg, Germany
| | - Paul G Schlegel
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
| | - Florian Oyen
- University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yair Reisner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Matthias Eyrich
- University Children's Hospital, University Medical Center Würzburg, Würzburg, Germany
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33
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Simnica D, Schultheiß C, Mohme M, Paschold L, Willscher E, Fitzek A, Püschel K, Matschke J, Ciesek S, Sedding DG, Zhao Y, Gagliani N, Maringer Y, Walz JS, Heide J, Schulze-Zur-Wiesch J, Binder M. Landscape of T-cell repertoires with public COVID-19-associated T-cell receptors in pre-pandemic risk cohorts. Clin Transl Immunology 2021; 10:e1340. [PMID: 34484739 PMCID: PMC8401425 DOI: 10.1002/cti2.1340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/27/2021] [Accepted: 08/15/2021] [Indexed: 01/19/2023] Open
Abstract
Objectives T cells have an essential role in the antiviral defence. Public T-cell receptor (TCR) clonotypes are expanded in a substantial proportion of COVID-19 patients. We set out to exploit their potential use as read-out for COVID-19 T-cell immune responses. Methods We searched for COVID-19-associated T-cell clones with public TCRs, as defined by identical complementarity-determining region 3 (CDR3) beta chain amino acid sequence that can be reproducibly detected in the blood of COVID-19 patients. Of the different clonotype identification algorithms used in this study, deep sequencing of brain tissue of five patients with fatal COVID-19 delivered 68 TCR clonotypes with superior representation across 140 immune repertoires of unrelated COVID-19 patients. Results Mining of immune repertoires from subjects not previously exposed to the virus showed that these clonotypes can be found in almost 20% of pre-pandemic immune repertoires of healthy subjects, with lower representation in repertoires from risk groups like individuals above the age of 60 years or patients with cancer. Conclusion Together, our data show that at least a proportion of the SARS-CoV-2 T-cell response is mediated by public TCRs that are present in repertoires of unexposed individuals. The lower representation of these clones in repertoires of risk groups or failure to expand such clones may contribute to more unfavorable clinical COVID-19 courses.
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Affiliation(s)
- Donjete Simnica
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Christoph Schultheiß
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Malte Mohme
- Department of Neurosurgery University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Lisa Paschold
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Edith Willscher
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Antonia Fitzek
- Institute of Legal Medicine University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Klaus Püschel
- Institute of Legal Medicine University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Jakob Matschke
- Department of Neuropathology University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Sandra Ciesek
- Institute of Medical Virology University Hospital Frankfurt Frankfurt am Main Germany
| | - Daniel G Sedding
- Mid-German Heart Center Department of Cardiology and Intensive Care Medicine University Hospital Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Yu Zhao
- III. Department of Medicine Division of Translational Immunology University Medical Center Hamburg-Eppendorf Hamburg Germany.,Institute of Medical Systems Biology University Medical Center Hamburg-Eppendorf Hamburg Germany.,Hamburg Center for Translational Immunology (HCTI) University Medical Center Hamburg-Eppendorf Hamburg Germany.,Center for Biomedical AI University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Nicola Gagliani
- Hamburg Center for Translational Immunology (HCTI) University Medical Center Hamburg-Eppendorf Hamburg Germany.,I. Department of Medicine and Department for General Visceral and Thoracic Surgery Hamburg Germany.,Immunology and Allergy Unit Department of Medicine Solna Karolinska Institute and University Hospital Stockholm Sweden
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology German Cancer Consortium (DKTK) Department of Internal Medicine University Hospital Tübingen Tübingen Germany.,Institute for Cell Biology Department of Immunology University of Tübingen Tübingen Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies" University of Tübingen Tübingen Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology German Cancer Consortium (DKTK) Department of Internal Medicine University Hospital Tübingen Tübingen Germany.,Institute for Cell Biology Department of Immunology University of Tübingen Tübingen Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies" University of Tübingen Tübingen Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT) Stuttgart Germany
| | - Janna Heide
- I. Department of Medicine (with section Gastroenterology and Infectious Diseases) University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Julian Schulze-Zur-Wiesch
- I. Department of Medicine (with section Gastroenterology and Infectious Diseases) University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Mascha Binder
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
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34
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Nelde A, Maringer Y, Bilich T, Salih HR, Roerden M, Heitmann JS, Marcu A, Bauer J, Neidert MC, Denzlinger C, Illerhaus G, Aulitzky WE, Rammensee HG, Walz JS. Immunopeptidomics-Guided Warehouse Design for Peptide-Based Immunotherapy in Chronic Lymphocytic Leukemia. Front Immunol 2021; 12:705974. [PMID: 34305947 PMCID: PMC8297687 DOI: 10.3389/fimmu.2021.705974] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/24/2021] [Indexed: 12/30/2022] Open
Abstract
Antigen-specific immunotherapies, in particular peptide vaccines, depend on the recognition of naturally presented antigens derived from mutated and unmutated gene products on human leukocyte antigens, and represent a promising low-side-effect concept for cancer treatment. So far, the broad application of peptide vaccines in cancer patients is hampered by challenges of time- and cost-intensive personalized vaccine design, and the lack of neoepitopes from tumor-specific mutations, especially in low-mutational burden malignancies. In this study, we developed an immunopeptidome-guided workflow for the design of tumor-associated off-the-shelf peptide warehouses for broadly applicable personalized therapeutics. Comparative mass spectrometry-based immunopeptidome analyses of primary chronic lymphocytic leukemia (CLL) samples, as representative example of low-mutational burden tumor entities, and a dataset of benign tissue samples enabled the identification of high-frequent non-mutated CLL-associated antigens. These antigens were further shown to be recognized by pre-existing and de novo induced T cells in CLL patients and healthy volunteers, and were evaluated as pre-manufactured warehouse for the construction of personalized multi-peptide vaccines in a first clinical trial for CLL (NCT04688385). This workflow for the design of peptide warehouses is easily transferable to other tumor entities and can provide the foundation for the development of broad personalized T cell-based immunotherapy approaches.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Marian C Neidert
- Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | | | - Gerald Illerhaus
- Clinic for Hematology and Oncology, Klinikum Stuttgart, Stuttgart, Germany
| | - Walter Erich Aulitzky
- Department of Hematology, Oncology and Palliative Medicine, Robert-Bosch-Krankenhaus Stuttgart, Stuttgart, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
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35
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Roerden M, Wirths S, Sökler M, Bethge WA, Vogel W, Walz JS. Impact of Mantle Cell Lymphoma Contamination of Autologous Stem Cell Grafts on Outcome after High-Dose Chemotherapy. Cancers (Basel) 2021; 13:cancers13112558. [PMID: 34071000 PMCID: PMC8197101 DOI: 10.3390/cancers13112558] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 11/19/2022] Open
Abstract
Simple Summary High-dose chemotherapy followed by autologous hematopoietic stem cell transplantation (Auto-HSCT) is a standard frontline treatment for fit mantle cell lymphoma (MCL) patients. As there is a need for predictive factors to identify patients unlikely to benefit from this therapy, we investigated the prognostic impact of lymphoma cell contamination of autologous stem cell grafts. Analyzing a cohort of 36 MCL patients, we show that lymphoma cell contamination of stem cell grafts is associated with poor outcomes after Auto-HSCT. Its analysis might thus improve risk assessment and enable risk-stratified treatment strategies for MCL patients. Abstract Novel predictive factors are needed to identify mantle cell lymphoma (MCL) patients at increased risk for relapse after high-dose chemotherapy and autologous hematopoietic stem cell transplantation (HDCT/Auto-HSCT). Although bone marrow and peripheral blood involvement is commonly observed in MCL and lymphoma cell contamination of autologous stem cell grafts might facilitate relapse after Auto-HSCT, prevalence and prognostic significance of residual MCL cells in autologous grafts are unknown. We therefore performed a multiparameter flow cytometry (MFC)-based measurable residual disease (MRD) assessment in autologous stem cell grafts and analyzed its association with clinical outcome in an unselected retrospective cohort of 36 MCL patients. MRD was detectable in four (11%) autologous grafts, with MRD levels ranging from 0.002% to 0.2%. Positive graft-MRD was associated with a significantly shorter progression-free and overall survival when compared to graft-MRD negative patients (median 9 vs. 56 months and 25 vs. 132 months, respectively) and predicted early relapse after Auto-HSCT (median time to relapse 9 vs. 44 months). As a predictor of outcome after HDCT/Auto-HSCT, MFC-based assessment of graft-MRD might improve risk stratification and support clinical decision making for risk-oriented treatment strategies in MCL.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (S.W.); (M.S.); (W.A.B.); (W.V.); (J.S.W.)
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Correspondence:
| | - Stefan Wirths
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (S.W.); (M.S.); (W.A.B.); (W.V.); (J.S.W.)
| | - Martin Sökler
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (S.W.); (M.S.); (W.A.B.); (W.V.); (J.S.W.)
| | - Wolfgang A. Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (S.W.); (M.S.); (W.A.B.); (W.V.); (J.S.W.)
| | - Wichard Vogel
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (S.W.); (M.S.); (W.A.B.); (W.V.); (J.S.W.)
| | - Juliane S. Walz
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (S.W.); (M.S.); (W.A.B.); (W.V.); (J.S.W.)
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology (IKP) and Robert Bosch Center for Tumor Diseases (RBCT), Auerbachstr. 112, 70376 Stuttgart, Germany
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36
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Bilich T, Roerden M, Maringer Y, Nelde A, Heitmann JS, Dubbelaar ML, Peter A, Hörber S, Bauer J, Rieth J, Wacker M, Berner F, Flatz L, Held S, Brossart P, Märklin M, Wagner P, Erne E, Klein R, Rammensee HG, Salih HR, Walz JS. Preexisting and Post-COVID-19 Immune Responses to SARS-CoV-2 in Patients with Cancer. Cancer Discov 2021; 11:1982-1995. [PMID: 34011563 DOI: 10.1158/2159-8290.cd-21-0191] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/15/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Patients with cancer, in particular patients with hematologic malignancies, are at increased risk for critical illness upon COVID-19. We here assessed antibody as well as CD4+ and CD8+ T-cell responses in unexposed and SARS-CoV-2-infected patients with cancer to characterize SARS-CoV-2 immunity and to identify immunologic parameters contributing to COVID-19 outcome. Unexposed patients with hematologic malignancies presented with reduced prevalence of preexisting SARS-CoV-2 cross-reactive CD4+ T-cell responses and signs of T-cell exhaustion compared with patients with solid tumors and healthy volunteers. Whereas SARS-CoV-2 antibody responses did not differ between patients with COVID-19 and cancer and healthy volunteers, intensity, expandability, and diversity of SARS-CoV-2 T-cell responses were profoundly reduced in patients with cancer, and the latter associated with a severe course of COVID-19. This identifies impaired SARS-CoV-2 T-cell immunity as a potential determinant for dismal outcome of COVID-19 in patients with cancer. SIGNIFICANCE: This first comprehensive analysis of SARS-CoV-2 immune responses in patients with cancer reports on the potential implications of impaired SARS-CoV-2 T-cell responses for understanding pathophysiology and predicting severity of COVID-19, which in turn might allow for the development of therapeutic measures and vaccines for this vulnerable patient population.See related commentary by Salomé and Horowitz, p. 1877.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
- Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Marissa L Dubbelaar
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany.,Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Fiamma Berner
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Stefanie Held
- Department for Hematology and Oncology, University Hospital Bonn, Bonn, Germany
| | - Peter Brossart
- Department for Hematology and Oncology, University Hospital Bonn, Bonn, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Philipp Wagner
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Eva Erne
- Department of Urology, Medical Faculty and University Hospital, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany. .,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
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37
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Wagner TR, Ostertag E, Kaiser PD, Gramlich M, Ruetalo N, Junker D, Haering J, Traenkle B, Becker M, Dulovic A, Schweizer H, Nueske S, Scholz A, Zeck A, Schenke‐Layland K, Nelde A, Strengert M, Walz JS, Zocher G, Stehle T, Schindler M, Schneiderhan‐Marra N, Rothbauer U. NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies. EMBO Rep 2021; 22:e52325. [PMID: 33904225 PMCID: PMC8097376 DOI: 10.15252/embr.202052325] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 12/21/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
In light of the COVID-19 pandemic, there is an ongoing need for diagnostic tools to monitor the immune status of large patient cohorts and the effectiveness of vaccination campaigns. Here, we present 11 unique nanobodies (Nbs) specific for the SARS-CoV-2 spike receptor-binding domain (RBD), of which 8 Nbs potently inhibit the interaction of RBD with angiotensin-converting enzyme 2 (ACE2) as the major viral docking site. Following detailed epitope mapping and structural analysis, we select two inhibitory Nbs, one of which binds an epitope inside and one of which binds an epitope outside the RBD:ACE2 interface. Based on these, we generate a biparatopic nanobody (bipNb) with viral neutralization efficacy in the picomolar range. Using bipNb as a surrogate, we establish a competitive multiplex binding assay ("NeutrobodyPlex") for detailed analysis of the presence and performance of neutralizing RBD-binding antibodies in serum of convalescent or vaccinated patients. We demonstrate that NeutrobodyPlex enables high-throughput screening and detailed analysis of neutralizing immune responses in infected or vaccinated individuals, to monitor immune status or to guide vaccine design.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical BiotechnologyEberhard Karls UniversityTuebingenGermany
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Elena Ostertag
- Interfaculty Institute of BiochemistryEberhard Karls UniversityTuebingenGermany
| | - Philipp D Kaiser
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Marius Gramlich
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TuebingenTuebingenGermany
| | - Daniel Junker
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Julia Haering
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Bjoern Traenkle
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Matthias Becker
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Alex Dulovic
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Helen Schweizer
- Livestock Center of the Faculty of Veterinary MedicineLudwig Maximilians UniversityOberschleissheimGermany
| | - Stefan Nueske
- Livestock Center of the Faculty of Veterinary MedicineLudwig Maximilians UniversityOberschleissheimGermany
| | - Armin Scholz
- Livestock Center of the Faculty of Veterinary MedicineLudwig Maximilians UniversityOberschleissheimGermany
| | - Anne Zeck
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Katja Schenke‐Layland
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
- Department of Women’s HealthResearch Institute for Women’s HealthEberhard Karls UniversityTuebingenGermany
- Department of Medicine/CardiologyCardiovascular Research LaboratoriesDavid Geffen School of Medicine at UCLALos AngelesCAUSA
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TuebingenTuebingenGermany
- Institute for Cell BiologyDepartment of ImmunologyEberhard Karls UniversityTuebingenGermany
| | - Monika Strengert
- Department of EpidemiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- TWINCORE GmbHCentre for Experimental and Clinical Infection ResearchA Joint venture of the Hannover Medical School and the Helmholtz Centre for Infection ResearchHannoverGermany
| | - Juliane S Walz
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TuebingenTuebingenGermany
- Institute for Cell BiologyDepartment of ImmunologyEberhard Karls UniversityTuebingenGermany
- Dr. Margarete Fischer‐Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor DiseaseRBCTStuttgartGermany
| | - Georg Zocher
- Interfaculty Institute of BiochemistryEberhard Karls UniversityTuebingenGermany
| | - Thilo Stehle
- Interfaculty Institute of BiochemistryEberhard Karls UniversityTuebingenGermany
- Vanderbilt University School of MedicineNashvilleTNUSA
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TuebingenTuebingenGermany
| | | | - Ulrich Rothbauer
- Pharmaceutical BiotechnologyEberhard Karls UniversityTuebingenGermany
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
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38
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Bilich T, Nelde A, Heitmann JS, Maringer Y, Roerden M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Rachfalski D, Märklin M, Stevanović S, Rammensee HG, Salih HR, Walz JS. T cell and antibody kinetics delineate SARS-CoV-2 peptides mediating long-term immune responses in COVID-19 convalescent individuals. Sci Transl Med 2021; 13:eabf7517. [PMID: 33723016 PMCID: PMC8128286 DOI: 10.1126/scitranslmed.abf7517] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/14/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Long-term immunological memory to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for the development of population-level immunity, which is the aim of vaccination approaches. Reports on rapidly decreasing antibody titers have led to questions regarding the efficacy of humoral immunity alone. The relevance of T cell memory after coronavirus disease 2019 (COVID-19) remains unclear. Here, we investigated SARS-CoV-2 antibody and T cell responses in matched samples of COVID-19 convalescent individuals up to 6 months after infection. Longitudinal analysis revealed decreasing and stable spike- and nucleocapsid-specific antibody responses, respectively. In contrast, functional T cell responses remained robust, and even increased, in both frequency and intensity. Single peptide mapping of T cell diversity over time identified open reading frame-independent, dominant T cell epitopes mediating long-term SARS-CoV-2 T cell responses. Identification of these epitopes may be fundamental for COVID-19 vaccine design.
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Affiliation(s)
- Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - David Rachfalski
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), 70376 Stuttgart, Germany
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39
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Huergo LF, Selim KA, Conzentino MS, Gerhardt ECM, Santos ARS, Wagner B, Alford JT, Deobald N, Pedrosa FO, de Souza EM, Nogueira MB, Raboni SM, Souto D, Rego FGM, Zanette DL, Aoki MN, Nardin JM, Fornazari B, Morales HMP, Borges VA, Nelde A, Walz JS, Becker M, Schneiderhan-Marra N, Rothbauer U, Reis RA, Forchhammer K. Magnetic Bead-Based Immunoassay Allows Rapid, Inexpensive, and Quantitative Detection of Human SARS-CoV-2 Antibodies. ACS Sens 2021; 6:703-708. [PMID: 33496577 PMCID: PMC7860136 DOI: 10.1021/acssensors.0c02544] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
Immunological methods to detect SARS-CoV-2 seroconversion in humans are important to track COVID-19 cases and the humoral response to SARS-CoV-2 infections and immunization to future vaccines. The aim of this work was to develop a simple chromogenic magnetic bead-based immunoassay which allows rapid, inexpensive, and quantitative detection of human antibodies against SARS-CoV-2 in serum, plasma, or blood. Recombinant 6xHis-tagged SARS-CoV-2 Nucleocapsid protein was mobilized on the surface of Ni2+ magnetic beads and challenged with serum or blood samples obtained from controls or COVID-19 cases. The beads were washed, incubated with anti-human IgG-HPR conjugate, and immersed into a solution containing a chromogenic HPR substrate. Bead transfer and homogenization between solutions was aided by a simple low-cost device. The method was validated by two independent laboratories, and the performance to detect SARS-CoV-2 seroconversion in humans was in the same range as obtained using the gold standard immunoassays ELISA and Luminex, though requiring only a fraction of consumables, instrumentation, time to deliver results, and volume of sample. Furthermore, the results obtained with the method described can be visually interpreted without compromising accuracy as demonstrated by validation at a point-of-care unit. The magnetic bead immunoassay throughput can be customized on demand and is readily adapted to be used with any other 6xHis tagged protein or peptide as antigen to track other diseases.
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Affiliation(s)
- Luciano F. Huergo
- Setor Litoral, Federal University of
Paraná (UFPR) Matinhos, PR 83260-000,
Brazil
| | - Khaled A. Selim
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | | | - Edileusa C. M. Gerhardt
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Adrian R. S. Santos
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Berenike Wagner
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | - Janette T. Alford
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | - Nelli Deobald
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | - Fabio O. Pedrosa
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Emanuel M. de Souza
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Meri B. Nogueira
- Complexo Hospital das Clínicas,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Sônia M. Raboni
- Complexo Hospital das Clínicas,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Dênio Souto
- Chemistry Departament, Federal University
of Paraná (UFPR), Curitiba, PR 80060-000,
Brazil
| | - Fabiane G. M. Rego
- Post-Graduation Program in Pharmaceutical Sciences,
Federal University of Paraná (UFPR), Curitiba, PR
80060-000, Brazil
| | | | - Mateus N. Aoki
- Instituto Carlos Chagas -
FioCruz, Curitiba, PR 81310-020, Brazil
| | | | | | | | - Vânia A. Borges
- Secretaria Municipal de Saúde de
Guaratuba, Guaratuba, PR 83280-000, Brazil
| | - Annika Nelde
- Clinical Collaboration Unit Translational Immunology,
German Cancer Consortium (DKTK), Department of Internal Medicine, University
Hospital Tübingen, 72076 Tübingen,
Germany
- Department of Immunology, Institute for Cell Biology,
Tübingen University, 72076 Tübingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor Therapies”,
Tübingen University, 72076 Tübingen,
Germany
| | - Juliane S. Walz
- Clinical Collaboration Unit Translational Immunology,
German Cancer Consortium (DKTK), Department of Internal Medicine, University
Hospital Tübingen, 72076 Tübingen,
Germany
- Department of Immunology, Institute for Cell Biology,
Tübingen University, 72076 Tübingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor Therapies”,
Tübingen University, 72076 Tübingen,
Germany
- Department of Hematology, Oncology, Clinical
Immunology and Rheumatology, University Hospital
Tübingen, 72076 Tübingen, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences
Institute at the University of Tübingen, 72770 Tübingen,
Germany
| | | | - Ulrich Rothbauer
- NMI Natural and Medical Sciences
Institute at the University of Tübingen, 72770 Tübingen,
Germany
- Pharmaceutical Biotechnology,
Tübingen University, 72076 Tübingen,
Germany
| | - Rodrigo A. Reis
- Setor Litoral, Federal University of
Paraná (UFPR) Matinhos, PR 83260-000,
Brazil
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
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40
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Roerden M, Märklin M, Salih HR, Bethge WA, Klein R, Rammensee HG, Nelde A, Walz JS. Expression levels of HLA-DR in acute myeloid leukemia: implications for antigenicity and clinical outcome. Leuk Lymphoma 2021; 62:1907-1919. [PMID: 33648413 DOI: 10.1080/10428194.2021.1885659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Low human leukocyte antigen (HLA)-DR expression might compromise CD4+ T-cell-mediated anti-tumor immunity. Its immunological and clinical significance however remain undefined in non-promyelocytic acute myeloid leukemia (AML). Taking advantage of mass spectrometry-based immunopeptidome analysis of primary AML samples (n = 31), we studied the implications of low HLA-DR expression for antigen presentation and analyzed its association with disease characteristics and survival within a cohort of 399 AML patients. Remarkably, overall HLA-DR/DQ immunopeptidome diversity was preserved in AML with low HLA-DR expression (HLA-DRlow AML) and was associated with a shift in HLA-DR/DQ allotype abundances (HLA-DQ to HLA-DR/DQ ligand ratio 0.36 vs 0.19 in HLA-DRlow and HLA-DRhigh patients, respectively). Consistent with unimpaired antigenicity, survival was similar in HLA-DRlow and HLA-DRhigh patients. Demonstrating for the first time that overall HLA-DR/DQ antigen presentation is preserved in HLA-DRlow AML, our findings provide a rationale for the non-inferior outcome observed in HLA-DRlow AML patients.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Wolfgang A Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Annika Nelde
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
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41
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Abstract
The approach of peptide-based anticancer vaccination has proven the ability to induce cancer-specific immune responses in multiple studies for various cancer entities. However, clinical responses remain so far limited to single patients and broad clinical applicability was not achieved. Therefore, further efforts are required to improve peptide vaccination in order to integrate this low-side-effect therapy into the clinical routine of cancer therapy. To design clinically effective peptide vaccines in the future, different issues have to be addressed and optimized comprising antigen target selection as well as choice of optimal adjuvants and vaccination schedules. Furthermore, the combination of peptide-based vaccines with other immuno- and molecular targeted therapies as well as the development of predictive biomarkers could further improve efficacy. In this review, current approaches in the development of peptide-based vaccines and critical implications for optimal vaccine design are discussed.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany; Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
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42
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Heinrich B, Brown ZJ, Diggs LP, Vormehr M, Ma C, Subramanyam V, Rosato U, Ruf B, Walz JS, McVey JC, Wabitsch SF, Fu Q, Yu SJ, Zhang Q, Lai CW, Sahin U, Greten TF. Steatohepatitis Impairs T-cell-Directed Immunotherapies Against Liver Tumors in Mice. Gastroenterology 2021; 160:331-345.e6. [PMID: 33010248 PMCID: PMC7755834 DOI: 10.1053/j.gastro.2020.09.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/23/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Nonalcoholic steatohepatitis causes loss of hepatic CD4+ T cells and promotes tumor growth. The liver is the most common site of distant metastases from a variety of malignancies, many of which respond to immunotherapy. We investigated the effects of steatohepatitis on the efficacy of immunotherapeutic agents against liver tumors in mice. METHODS Steatohepatitis was induced by feeding C57BL/6NCrl or BALB/c AnNCr mice a methionine and choline-deficient diet or a choline-deficient l-amino acid-defined diet. Mice were given intrahepatic or subcutaneous injections of B16 melanoma and CT26 colon cancer cells, followed by intravenous injections of M30-RNA vaccine (M30) or intraperitoneal injections of an antibody against OX40 (aOX40) on days 3, 7, and 10 after injection of the tumor cells. We measured tumor growth and analyzed immune cells in tumor tissues by flow cytometry. Mice were given N-acetylcysteine to prevent loss of CD4+ T cells from liver. RESULTS Administration of M30 and aOX40 inhibited growth of tumors from intrahepatic injections of B16 or CT26 cells in mice on regular diet. However, M30 and/or aOX40 did not slow growth of liver tumors from B16 or CT26 cells in mice with diet-induced steatohepatitis (methionine and choline-deficient diet or choline-deficient l-amino acid-defined diet). Steatohepatitis did not affect the ability of M30 to slow growth of subcutaneous B16 tumors. In mice with steatohepatitis given N-acetylcysteine, which prevents loss of CD4+ T cells, M30 and aOX40 were able slow growth of hepatic tumors. Flow cytometry analysis of liver tumors revealed reduced CD4+ T cells and effector memory cells in mice with vs without steatohepatitis. CONCLUSIONS Steatohepatitis reduces the abilities of immunotherapeutic agents, such as M30 and aOX40, to inhibit tumor liver growth by reducing tumor infiltration by CD4+ T cells and effector memory cells. N-acetylcysteine restores T-cell numbers in tumors and increases the ability of M30 and aOX40 to slow tumor growth in mice.
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Affiliation(s)
- Bernd Heinrich
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zachary J. Brown
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Rutgers Robert Wood Johnson Medical School, Department of Surgery, New Brunswick, NJ
| | - Laurence P. Diggs
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mathias Vormehr
- Biopharmaceutical New Technologies (BioNTech) Corporation, An der Goldgrube 12, 55131 Mainz, Germany.,University Medical Center of the Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Chi Ma
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Varun Subramanyam
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Umberto Rosato
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Ruf
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juliane S. Walz
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Germany
| | - John C. McVey
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon F. Wabitsch
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qiong Fu
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Su Jong Yu
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Qianfei Zhang
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chunwei W. Lai
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ugur Sahin
- Biopharmaceutical New Technologies (BioNTech) Corporation, An der Goldgrube 12, 55131 Mainz, Germany.,University Medical Center of the Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany.,TRON – Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Freiligrathstraße 12, 55131 Mainz, Germany
| | - Tim F. Greten
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,NCI CCR Liver Cancer Program.,Correspondence: Tim F. Greten, MD, Thoracic and GI Malignancy Section, TGMB NIH/NCI/CCR, Building 10, Rm 2B28B, 9000 Rockville Pike, Bethesda MD 20892, USA, Telephone: +1 (240) 760 6114,
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Heitmann JS, Walz JS, Pflügler M, Kauer J, Schlenk RF, Jung G, Salih HR. Protocol of a prospective, multicentre phase I study to evaluate the safety, tolerability and preliminary efficacy of the bispecific PSMAxCD3 antibody CC-1 in patients with castration-resistant prostate carcinoma. BMJ Open 2020; 10:e039639. [PMID: 33067297 PMCID: PMC7569941 DOI: 10.1136/bmjopen-2020-039639] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Prostate cancer is the second most common cancer in men worldwide. When the disease becomes resistant to androgen-deprivation therapy, treatment options are sparse. To address the high medical need in castration-resistant prostate cancer (CRPC), we generated a novel PSMAxCD3 bispecific antibody termed CC-1. CC-1 binds to prostate-specific membrane antigen that is expressed on prostate cancer cells and tumour vessels, thereby allowing a dual anticancer effect. METHODS AND ANALYSIS This first in human clinical study is a prospective and multicentre trial which enrols patients with metastatic CRPC after failure of established third-line therapy. CC-1 is applied after prophylactic interleukin-6 receptor blockade with tocilizumab (once 8 mg/kg body weight). Each patient receives at least one cycle of CC-1 over a time course of 7 days in an inpatient setting. If clinical benefit is observed, up to five additional cycles of CC-1 can be applied. The study is divided in two parts: (1) a dose escalation phase with intraindividual dose increase from 28 µg to the target dose of 1156 µg based on a modified fast titration design by Simon et al to determine safety, tolerability and the maximum tolerated dose (MTD) as primary endpoints and (2) a dose expansion phase with additional 14 patients on the MTD level of part (1) to identify first signs of efficacy. Secondary endpoints compromise overall safety, tumour response, survival and a translational research programme with, among others, the analysis of CC-1 half-life, the induced immune response, as well as the molecular profiling in liquid biopsies. ETHICS AND DISSEMINATION The PSMAxCD3 study was approved by the Ethics Committee of The University Hospital Tübingen (100/2019AMG1) and the Paul-Ehrlich-Institut (3684/02). Clinical trial results will be published in peer-reviewed journals. TRIAL REGISTRATION NUMBERS ClinicalTrials.gov Registry (NCT04104607) and ClinicalTrials.eu Registry (EudraCT2019-000238-20).
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Affiliation(s)
- Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Martin Pflügler
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Joseph Kauer
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Richard F Schlenk
- National Center of Tumor Diseases-Trial Center, National Center of Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
- Department of Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Gundram Jung
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
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Nelde A, Bilich T, Heitmann JS, Maringer Y, Salih HR, Roerden M, Lübke M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Traenkle B, Kaiser PD, Rothbauer U, Becker M, Junker D, Krause G, Strengert M, Schneiderhan-Marra N, Templin MF, Joos TO, Kowalewski DJ, Stos-Zweifel V, Fehr M, Rabsteyn A, Mirakaj V, Karbach J, Jäger E, Graf M, Gruber LC, Rachfalski D, Preuß B, Hagelstein I, Märklin M, Bakchoul T, Gouttefangeas C, Kohlbacher O, Klein R, Stevanović S, Rammensee HG, Walz JS. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nat Immunol 2020; 22:74-85. [PMID: 32999467 DOI: 10.1038/s41590-020-00808-x] [Citation(s) in RCA: 385] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022]
Abstract
T cell immunity is central for the control of viral infections. To characterize T cell immunity, but also for the development of vaccines, identification of exact viral T cell epitopes is fundamental. Here we identify and characterize multiple dominant and subdominant SARS-CoV-2 HLA class I and HLA-DR peptides as potential T cell epitopes in COVID-19 convalescent and unexposed individuals. SARS-CoV-2-specific peptides enabled detection of post-infectious T cell immunity, even in seronegative convalescent individuals. Cross-reactive SARS-CoV-2 peptides revealed pre-existing T cell responses in 81% of unexposed individuals and validated similarity with common cold coronaviruses, providing a functional basis for heterologous immunity in SARS-CoV-2 infection. Diversity of SARS-CoV-2 T cell responses was associated with mild symptoms of COVID-19, providing evidence that immunity requires recognition of multiple epitopes. Together, the proposed SARS-CoV-2 T cell epitopes enable identification of heterologous and post-infectious T cell immunity and facilitate development of diagnostic, preventive and therapeutic measures for COVID-19.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Maren Lübke
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Bjoern Traenkle
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Philipp D Kaiser
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.,Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Matthias Becker
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | | | - Markus F Templin
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Thomas O Joos
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | | | - Michael Fehr
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Armin Rabsteyn
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,Department of General Pediatrics, Oncology/Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Valbona Mirakaj
- Department of Anesthesia and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Julia Karbach
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Elke Jäger
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Michael Graf
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena-Christin Gruber
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - David Rachfalski
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Beate Preuß
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Ilona Hagelstein
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Tamam Bakchoul
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Cécile Gouttefangeas
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max-Planck-Institute for Developmental Biology, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany. .,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.
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Roerden M, Nelde A, Heitmann JS, Klein R, Rammensee HG, Bethge WA, Walz JS. HLA Evolutionary Divergence as a Prognostic Marker for AML Patients Undergoing Allogeneic Stem Cell Transplantation. Cancers (Basel) 2020; 12:cancers12071835. [PMID: 32650450 PMCID: PMC7408841 DOI: 10.3390/cancers12071835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
The diversity of human leukocyte antigens (HLAs) enables the presentation of immense repertoires of peptides, including tumor-associated antigens (TAAs). As a surrogate for immunopeptidome diversity, the HLA evolutionary divergence (HED) between individual HLA alleles might directly define the ability to present TAAs, a prerequisite for graft-versus-leukemia effects. We therefore analyzed the impact of HED on survival within a cohort of 171 acute myeloid leukemia (AML) patients after matched donor allogeneic hematopoietic stem cell transplantation (HSCT). Low HED (<25th percentile) of HLA class I (HEDclass I) or HLA-DR antigens (HEDDR) was a strong determinant for adverse overall survival after allogeneic HSCT (OS), with a hazard ratio for death of 1.9 (95% CI 1.2–3.2) and 2.1 (95% CI 1.3–3.4), respectively. Defining a cutoff value for the combined HEDtotal (HEDclass I and HEDDR), the respective 5 year OS was 29.7% and 64.9% in patients with low and high HEDtotal (p < 0.001), respectively. Furthermore, the risk of relapse was significantly higher in patients with low HEDtotal (hazard ratio (HR) 2.2, 95% CI 1.3–3.6) and event-free survival (EFS) was significantly reduced (5 year EFS 25.7% versus 54.4%, p < 0.001). We here introduce HED, a fundamental metric of immunopeptidome diversity, as a novel prognostic factor for AML patients undergoing allogeneic HSCT.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Correspondence: (M.R.); (J.S.W.)
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany;
| | - Jonas S. Heitmann
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany;
- German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, 72076 Tübingen, Germany
| | - Wolfgang A. Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
| | - Juliane S. Walz
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Correspondence: (M.R.); (J.S.W.)
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Abstract
Tumor cells always exhibit differences to normal cells. These differences can be recognized by the immune system, enabling the destruction of tumor cells by T cells, as was impressively demonstrated by the success of immune checkpoint inhibition, e.g., in malignant melanoma. Many cancers, however, do not respond to this kind of therapy. In these cases, vaccination against tumor antigens could be very helpful. Nevertheless, all of the efforts made in this respect during the past 30 years have been virtually futile. With current knowledge and technology there is new hope.
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Affiliation(s)
- H-G Rammensee
- Interfakultäres Institut für Zellbiologie (IFIZ), Abteilung Immunologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Deutschland. .,Deutsches Konsortium für Translationale Krebsforschung (DKTK) am Deutschen Krebsforschungszentrum (DKFZ), Partnerstandort Tübingen, Tübingen, Deutschland. .,Exzellenzcluster iFIT (EXC2180) "Individualisierung von Tumortherapien durch molekulare Bildgebung und funktionelle Identifizierung therapeutischer Zielstrukturen", Tübingen, Deutschland.
| | - M W Löffler
- Interfakultäres Institut für Zellbiologie (IFIZ), Abteilung Immunologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Deutschland.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) am Deutschen Krebsforschungszentrum (DKFZ), Partnerstandort Tübingen, Tübingen, Deutschland.,Exzellenzcluster iFIT (EXC2180) "Individualisierung von Tumortherapien durch molekulare Bildgebung und funktionelle Identifizierung therapeutischer Zielstrukturen", Tübingen, Deutschland.,Abteilung für Allgemeine, Viszeral- und Transplantationschirurgie, Universitätsklinikum Tübingen, Tübingen, Deutschland.,Abteilung Klinische Pharmakologie, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - J S Walz
- Interfakultäres Institut für Zellbiologie (IFIZ), Abteilung Immunologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Deutschland.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) am Deutschen Krebsforschungszentrum (DKFZ), Partnerstandort Tübingen, Tübingen, Deutschland.,Exzellenzcluster iFIT (EXC2180) "Individualisierung von Tumortherapien durch molekulare Bildgebung und funktionelle Identifizierung therapeutischer Zielstrukturen", Tübingen, Deutschland.,Medizinische Klinik II für Hämatologie, Onkologie, Immunologie und Rheumatologie, Universitätsklinikum Tübingen, Tübingen, Deutschland.,Klinische Kooperationseinheit (KKE) für Translationale Immunologie, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - C Bokemeyer
- Zentrum für Onkologie, II. Medizinische Klinik (Onkologie, Hämatologie, Knochenmarktransplantation mit Abteilung für Pneumologie), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - S P Haen
- Interfakultäres Institut für Zellbiologie (IFIZ), Abteilung Immunologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Deutschland.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) am Deutschen Krebsforschungszentrum (DKFZ), Partnerstandort Tübingen, Tübingen, Deutschland.,Zentrum für Onkologie, II. Medizinische Klinik (Onkologie, Hämatologie, Knochenmarktransplantation mit Abteilung für Pneumologie), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - C Gouttefangeas
- Interfakultäres Institut für Zellbiologie (IFIZ), Abteilung Immunologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Deutschland.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) am Deutschen Krebsforschungszentrum (DKFZ), Partnerstandort Tübingen, Tübingen, Deutschland.,Exzellenzcluster iFIT (EXC2180) "Individualisierung von Tumortherapien durch molekulare Bildgebung und funktionelle Identifizierung therapeutischer Zielstrukturen", Tübingen, Deutschland
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Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E. Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy. Genome Med 2020; 12:32. [PMID: 32228647 PMCID: PMC7106651 DOI: 10.1186/s13073-020-00731-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. Methods We analyzed HLA-presented peptides by MS-based ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues, and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate targets with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from The Cancer Genome Atlas (TCGA KIRC, n = 452). DNA methylation (TCGA KIRC, n = 273), somatic mutations (TCGA KIRC, n = 392), and gene ontology (GO) and correlations with tumor metabolites (cohort 1, n = 30) and immune-oncological markers (cohort 1, n = 37) were analyzed to characterize regulatory and functional involvements. CD8+ T cell priming assays were used to identify immunogenic peptides. The candidate gene EGLN3 was functionally investigated in cell culture. Results A total of 34,226 HLA class I- and 19,325 class II-presented peptides were identified in ccRCC tissue, of which 443 class I and 203 class II peptides were ccRCC-specific and presented in ≥ 3 tumors. One hundred eighty-five of the 499 corresponding source genes were involved in pathways activated by ccRCC tumors. After validation in the independent cohort from TCGA, 113 final candidate genes remained. Candidates were involved in extracellular matrix organization, hypoxic signaling, immune processes, and others. Nine of the 12 peptides assessed by immunogenicity analysis were able to activate naïve CD8+ T cells, including peptides derived from EGLN3. Functional analysis of EGLN3 revealed possible tumor-promoting functions. Conclusions Integration of HLA ligandomics, transcriptomics, genetic, and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is recommended to expand the treatment landscape of ccRCC.
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Affiliation(s)
- Anna Reustle
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Carolin Meyerhoff
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Siahei Kandabarau
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Florian Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Steffen Rausch
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Viktoria Stühler
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcus Scharpf
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany. .,University of Tuebingen, Tuebingen, Germany. .,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany. .,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany. .,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany.
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
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48
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Lübke M, Spalt S, Kowalewski DJ, Zimmermann C, Bauersfeld L, Nelde A, Bichmann L, Marcu A, Peper JK, Kohlbacher O, Walz JS, Le-Trilling VTK, Hengel H, Rammensee HG, Stevanović S, Halenius A. Identification of HCMV-derived T cell epitopes in seropositive individuals through viral deletion models. J Exp Med 2020; 217:e20191164. [PMID: 31869419 PMCID: PMC7062530 DOI: 10.1084/jem.20191164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/24/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022] Open
Abstract
In healthy individuals, immune control of persistent human cytomegalovirus (HCMV) infection is effectively mediated by virus-specific CD4+ and CD8+ T cells. However, identifying the repertoire of T cell specificities for HCMV is hampered by the immense protein coding capacity of this betaherpesvirus. Here, we present a novel approach that employs HCMV deletion mutant viruses lacking HLA class I immunoevasins and allows direct identification of naturally presented HCMV-derived HLA ligands by mass spectrometry. We identified 368 unique HCMV-derived HLA class I ligands representing an unexpectedly broad panel of 123 HCMV antigens. Functional characterization revealed memory T cell responses in seropositive individuals for a substantial proportion (28%) of these novel peptides. Multiple HCMV-directed specificities in the memory T cell pool of single individuals indicate that physiologic anti-HCMV T cell responses are directed against a broad range of antigens. Thus, the unbiased identification of naturally presented viral epitopes enabled a comprehensive and systematic assessment of the physiological repertoire of anti-HCMV T cell specificities in seropositive individuals.
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Affiliation(s)
- Maren Lübke
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Stefanie Spalt
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium, Partner Site Tübingen, Tübingen, Germany
| | - Daniel J. Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Cosima Zimmermann
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annika Nelde
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Janet Kerstin Peper
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Department of Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | | | - Hartmut Hengel
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium, Partner Site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- German Cancer Consortium, Partner Site Tübingen, Tübingen, Germany
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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49
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Bilich T, Nelde A, Bauer J, Walz S, Roerden M, Salih HR, Weisel K, Besemer B, Marcu A, Lübke M, Schuhmacher J, Neidert MC, Rammensee HG, Stevanović S, Walz JS. Mass spectrometry-based identification of a B-cell maturation antigen-derived T-cell epitope for antigen-specific immunotherapy of multiple myeloma. Blood Cancer J 2020; 10:24. [PMID: 32111817 PMCID: PMC7048774 DOI: 10.1038/s41408-020-0288-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023] Open
Abstract
The B-cell maturation antigen (BCMA) is currently being evaluated as promising tumor-associated surface antigen for T-cell-based immunotherapy approaches, such as CAR T cells and bispecific antibodies, in multiple myeloma (MM). Cytotoxic T cells bearing BCMA-specific T-cell receptors might further allow targeting HLA-presented antigens derived from the intracellular domain of BCMA. By analyzing a mass spectrometry-acquired immunopeptidome dataset of primary MM samples and MM cell lines for BCMA-derived HLA ligands, we identified the naturally presented HLA-B*18-restricted ligand P(BCMA)B*18. Additionally, P(BCMA)B*18 was identified on primary CLL samples, thereby expanding the range for possible applications. P(BCMA)B*18 induced multifunctional BCMA-specific cells de novo from naïve CD8+ T cells of healthy volunteers. These T cells exhibited antigen-specific lysis of autologous peptide-loaded cells. Even in the immunosuppressive context of MM, we detected spontaneous memory T-cell responses against P(BCMA)B*18 in patients. By applying CTLA-4 and PD-1 inhibition in vitro we induced multifunctional P(BCMA)B*18-specific CD8+ T cells in MM patients lacking preexisting BCMA-directed immune responses. Finally, we could show antigen-specific lysis of autologous peptide-loaded target cells and even MM.1S cells naturally presenting P(BCMA)B*18 using patient-derived P(BCMA)B*18-specific T cells. Hence, this BCMA-derived T-cell epitope represents a promising target for T-cell-based immunotherapy and monitoring following immunotherapy in B-cell malignancy patients.
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Affiliation(s)
- Tatjana Bilich
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Annika Nelde
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Jens Bauer
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Simon Walz
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
- University Hospital Tübingen, Department of Urology, Tübingen, Germany
| | - Malte Roerden
- University Hospital Tübingen, Department of Hematology and Oncology, Tübingen, Germany
| | - Helmut R Salih
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Katja Weisel
- University Hospital Tübingen, Department of Hematology and Oncology, Tübingen, Germany
- University Hospital Hamburg-Eppendorf, Department of Oncology, Hamburg-Eppendorf, Germany
| | - Britta Besemer
- University Hospital Tübingen, Department of Hematology and Oncology, Tübingen, Germany
| | - Ana Marcu
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Maren Lübke
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Juliane Schuhmacher
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | - Marian C Neidert
- University Hospital Zurich and University of Zurich, Department of Neurosurgery, Clinical Neuroscience Center, Zurich, Switzerland
| | - Hans-Georg Rammensee
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Institute for Cell Biology, Department of Immunology, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- University Hospital Tübingen, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Tübingen, Germany.
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50
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Abstract
Neoantigens derive from non-synonymous somatic mutations in malignant cells. Recognition of neoantigens presented via human leukocyte antigen (HLA) molecules on the tumor cell surface by T cells holds promise to enable highly specific and effective anti-cancer immune responses and thus neoantigens provide an exceptionally attractive target for immunotherapy. While genome sequencing approaches already enable the reliable identification of somatic mutations in tumor samples, the identification of mutation-derived, naturally HLA-presented neoepitopes as targets for immunotherapy remains challenging, particularly in low mutational burden cancer entities, including hematological malignancies. Several approaches have been utilized to identify neoepitopes from primary tumor samples. Besides whole genome sequencing with subsequent in silico prediction of potential mutation-derived HLA ligands, mass spectrometry (MS) allows for the only unbiased identification of naturally presented mutation-derived HLA ligands. The feasibility of characterizing and targeting these novel antigens has recently been demonstrated in acute myeloid leukemia (AML). Several immunogenic, HLA-presented peptides derived from mutated Nucleophosmin 1 (NPM1) were identified, allowing for the generation of T-cell receptor-transduced NPM1mut-specific T cells with anti-leukemic activity in a xenograft mouse model. Neoantigen-specific T-cell responses have also been identified for peptides derived from mutated isocitrate dehydrogenase (IDHmut), and specific T-cell responses could be induced by IDHmut peptide vaccination. In this review, we give a comprehensive overview on known neoantigens in hematological malignancies, present possible prediction and discovery tools and discuss their role as targets for immunotherapy approaches.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Rheumatology and Clinical Immunology, University Hospital Tübingen, Tübingen, Germany
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Department of Hematology, Oncology, Rheumatology and Clinical Immunology, University Hospital Tübingen, Tübingen, Germany
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany
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