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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] [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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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] [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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Pandey K, Wang SS, Mifsud NA, Faridi P, Davenport AJ, Webb AI, Sandow JJ, Ayala R, Monje M, Cross RS, Ramarathinam SH, Jenkins MR, Purcell AW. A combined immunopeptidomics, proteomics, and cell surface proteomics approach to identify immunotherapy targets for diffuse intrinsic pontine glioma. Front Oncol 2023; 13:1192448. [PMID: 37637064 PMCID: PMC10455951 DOI: 10.3389/fonc.2023.1192448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Diffuse intrinsic pontine glioma (DIPG), recently reclassified as a subtype of diffuse midline glioma, is a highly aggressive brainstem tumor affecting children and young adults, with no cure and a median survival of only 9 months. Conventional treatments are ineffective, highlighting the need for alternative therapeutic strategies such as cellular immunotherapy. However, identifying unique and tumor-specific cell surface antigens to target with chimeric antigen receptor (CAR) or T-cell receptor (TCR) therapies is challenging. Methods In this study, a multi-omics approach was used to interrogate patient-derived DIPG cell lines and to identify potential targets for immunotherapy. Results Through immunopeptidomics, a range of targetable peptide antigens from cancer testis and tumor-associated antigens as well as peptides derived from human endogenous retroviral elements were identified. Proteomics analysis also revealed upregulation of potential drug targets and cell surface proteins such as Cluster of differentiation 27 (CD276) B7 homolog 3 protein (B7H3), Interleukin 13 alpha receptor 2 (IL-13Rα2), Human Epidermal Growth Factor Receptor 3 (HER2), Ephrin Type-A Receptor 2 (EphA2), and Ephrin Type-A Receptor 3 (EphA3). Discussion The results of this study provide a valuable resource for the scientific community to accelerate immunotherapeutic approaches for DIPG. Identifying potential targets for CAR and TCR therapies could open up new avenues for treating this devastating disease.
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Affiliation(s)
- Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stacie S. Wang
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Children’s Cancer Centre, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Nicole A. Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Clinical Sciences, Department of Medicine, Monash University, Clayton, VIC, Australia
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Alexander J. Davenport
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I. Webb
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jarrod J. Sandow
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michelle Monje
- Department of Neurology and Neurological Sciences and Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Ryan S. Cross
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- LaTrobe Institute for Molecular Science, LaTrobe University, Bundoora, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler AR, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. CELL REPORTS METHODS 2023; 3:100511. [PMID: 37426761 PMCID: PMC10326451 DOI: 10.1016/j.crmeth.2023.100511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.
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Affiliation(s)
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Zhaoguan Wu
- CHU Sainte Justine Research Center, Montreal, QC, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Department of Chemistry, University of Montreal, Montreal, QC, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Etienne Caron
- CHU Sainte Justine Research Center, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, QC, Canada
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5
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Damiani D, Tiribelli M. Checkpoint Inhibitors in Acute Myeloid Leukemia. Biomedicines 2023; 11:1724. [PMID: 37371818 DOI: 10.3390/biomedicines11061724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The prognosis of acute myeloid leukemia (AML) remains unsatisfactory. Among the reasons for the poor response to therapy and high incidence of relapse, there is tumor cell immune escape, as AML blasts can negatively influence various components of the immune system, mostly weakening T-cells. Since leukemic cells can dysregulate immune checkpoints (ICs), receptor-based signal transductors that lead to the negative regulation of T-cells and, eventually, to immune surveillance escape, the inhibition of ICs is a promising therapeutic strategy and has led to the development of so-called immune checkpoint inhibitors (ICIs). ICIs, in combination with conventional chemotherapy, hypomethylating agents or targeted therapies, are being increasingly tested in cases of AML, but the results reported are often conflicting. Here, we review the main issues concerning the immune system in AML, the main pathways leading to immune escape and the results obtained from clinical trials of ICIs, alone or in combination, in newly diagnosed or relapsed/refractory AML.
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Affiliation(s)
- Daniela Damiani
- Division of Hematology and Stem Cell Transplantation, Udine Hospital, 33100 Udine, Italy
- Department of Medicine, Udine University, 33100 Udine, Italy
| | - Mario Tiribelli
- Division of Hematology and Stem Cell Transplantation, Udine Hospital, 33100 Udine, Italy
- Department of Medicine, Udine University, 33100 Udine, Italy
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6
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Shi ZR, Duan YX, Cui F, Wu ZJ, Li MP, Song PP, Peng QL, Ye WT, Yin KL, Kang MQ, Yu YX, Yang J, Tang W, Liao R. Integrated proteogenomic characterization reveals an imbalanced hepatocellular carcinoma microenvironment after incomplete radiofrequency ablation. J Exp Clin Cancer Res 2023; 42:133. [PMID: 37231509 DOI: 10.1186/s13046-023-02716-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Efforts to precisely assess tumor-specific T-cell immune responses still face major challenges, and the potential molecular mechanisms mediating hepatocellular carcinoma (HCC) microenvironment imbalance after incomplete radiofrequency ablation (iRFA) are unclear. This study aimed to provide further insight into the integrated transcriptomic and proteogenomic landscape and identify a new target involved in HCC progression following iRFA. METHODS Peripheral blood and matched tissue samples were collected from 10 RFA-treated HCC patients. Multiplex immunostaining and flow cytometry were used to assess local and systemic immune responses. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were explored via transcriptomic and proteogenomic analyses. Proteinase-3 (PRTN3) was identified in these analyses. And then, the ability of PRTN3 to predict overall survival (OS) was assessed in 70 HCC patients with early recurrence after RFA. In vitro CCK-8, wound healing and transwell assays were conducted to observe interactions between Kupffer cells (KCs) and HCC cells induced by PRTN3. The protein levels of multiple oncogenic factors and signaling pathway components were detected by western blotting. A xenograft mouse model was built to observe the tumorigenic effect of PRTN3 overexpression on HCC. RESULTS Multiplex immunostaining revealed no immediate significant change in local immune cell counts in periablational tumor tissues after 30 min of iRFA. Flow cytometry showed significantly increased levels of CD4+ T cells, CD4+CD8+ T cells, and CD4+CD25+CD127- Tregs and significantly decreased the levels of CD16+CD56+ natural killer cells on day 5 after cRFA (p < 0.05). Transcriptomics and proteomics revealed 389 DEGs and 20 DEPs. Pathway analysis showed that the DEP-DEGs were mainly enriched in the immunoinflammatory response, cancer progression and metabolic processes. Among the DEP-DEGs, PRTN3 was persistently upregulated and closely associated with the OS of patients with early recurrent HCC following RFA. PRTN3 expressed in KCs may affect the migration and invasion of heat stress-treated HCC cells. PRTN3 promotes tumor growth via multiple oncogenic factors and the PI3K/AKT and P38/ERK signaling pathways. CONCLUSIONS This study provides a comprehensive overview of the immune response and transcriptomic and proteogenomic landscapes of the HCC milieu induced by iRFA, revealing that PRTN3 promotes HCC progression after iRFA. TRIAL REGISTRATION ChiCTR2200055606, http://www.chictr.org.cn/showproj.aspx?proj=32588 .
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Affiliation(s)
- Zheng-Rong Shi
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Yu-Xin Duan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Fang Cui
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhong-Jun Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Mao-Ping Li
- Department of Ultrasound, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pei-Pei Song
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Qi-Ling Peng
- Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Wen-Tao Ye
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Kun-Li Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Mei-Qing Kang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Yan-Xi Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Jian Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China
| | - Wei Tang
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Rui Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. Youyi Rd, Chongqing, 400016, China.
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7
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Shapiro IE, Bassani-Sternberg M. The impact of immunopeptidomics: From basic research to clinical implementation. Semin Immunol 2023; 66:101727. [PMID: 36764021 DOI: 10.1016/j.smim.2023.101727] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
The immunopeptidome is the set of peptides presented by the major histocompatibility complex (MHC) molecules, in humans also known as the human leukocyte antigen (HLA), on the surface of cells that mediate T-cell immunosurveillance. The immunopeptidome is a sampling of the cellular proteome and hence it contains information about the health state of cells. The peptide repertoire is influenced by intra- and extra-cellular perturbations - such as in the case of drug exposure, infection, or oncogenic transformation. Immunopeptidomics is the bioanalytical method by which the presented peptides are extracted from biological samples and analyzed by high-performance liquid chromatography coupled to tandem mass spectrometry (MS), resulting in a deep qualitative and quantitative snapshot of the immunopeptidome. In this review, we discuss published immunopeptidomics studies from recent years, grouped into three main domains: i) basic, ii) pre-clinical and iii) clinical research and applications. We review selected fundamental immunopeptidomics studies on the antigen processing and presentation machinery, on HLA restriction and studies that advanced our understanding of various diseases, and how exploration of the antigenic landscape allowed immune targeting at the pre-clinical stage, paving the way to pioneering exploratory clinical trials where immunopeptidomics is directly implemented in the conception of innovative treatments for cancer patients.
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Affiliation(s)
- Ilja E Shapiro
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland.
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8
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Schossig P, Coskun E, Arsenic R, Horst D, Sehouli J, Bergmann E, Andresen N, Sigler C, Busse A, Keller U, Ochsenreither S. Target Selection for T-Cell Therapy in Epithelial Ovarian Cancer: Systematic Prioritization of Self-Antigens. Int J Mol Sci 2023; 24:ijms24032292. [PMID: 36768616 PMCID: PMC9916968 DOI: 10.3390/ijms24032292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Adoptive T cell-receptor therapy (ACT) could represent a promising approach in the targeted treatment of epithelial ovarian cancer (EOC). However, the identification of suitable tumor-associated antigens (TAAs) as targets is challenging. We identified and prioritized TAAs for ACT and other immunotherapeutic interventions in EOC. A comprehensive list of pre-described TAAs was created and candidates were prioritized, using predefined weighted criteria. Highly ranked TAAs were immunohistochemically stained in a tissue microarray of 58 EOC samples to identify associations of TAA expression with grade, stage, response to platinum, and prognosis. Preselection based on expression data resulted in 38 TAAs, which were prioritized. Along with already published Cyclin A1, the TAAs KIF20A, CT45, and LY6K emerged as most promising targets, with high expression in EOC samples and several identified peptides in ligandome analysis. Expression of these TAAs showed prognostic relevance independent of molecular subtypes. By using a systematic vetting algorithm, we identified KIF20A, CT45, and LY6K to be promising candidates for immunotherapy in EOC. Results are supported by IHC and HLA-ligandome data. The described method might be helpful for the prioritization of TAAs in other tumor entities.
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Affiliation(s)
- Paul Schossig
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Ebru Coskun
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ruza Arsenic
- Department of Pathology, Universitätsklinikum Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - David Horst
- Insitute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jalid Sehouli
- Department of Gynecology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Tumorbank Ovarian Cancer Network, 13353 Berlin, Germany
| | - Eva Bergmann
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Nadine Andresen
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christian Sigler
- Charité Comprehensive Cancer Center, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Antonia Busse
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Sebastian Ochsenreither
- Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Charité Comprehensive Cancer Center, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Correspondence:
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9
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Riether C. Regulation of hematopoietic and leukemia stem cells by regulatory T cells. Front Immunol 2022; 13:1049301. [PMID: 36405718 PMCID: PMC9666425 DOI: 10.3389/fimmu.2022.1049301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/20/2022] [Indexed: 01/25/2023] Open
Abstract
Adult bone marrow (BM) hematopoietic stem cells (HSCs) are maintained in a quiescent state and sustain the continuous production of all types of blood cells. HSCs reside in a specialized microenvironment the so-called HSC niche, which equally promotes HSC self-renewal and differentiation to ensure the integrity of the HSC pool throughout life and to replenish hematopoietic cells after acute injury, infection or anemia. The processes of HSC self-renewal and differentiation are tightly controlled and are in great part regulated through cellular interactions with classical (e.g. mesenchymal stromal cells) and non-classical niche cells (e.g. immune cells). In myeloid leukemia, some of these regulatory mechanisms that evolved to maintain HSCs, to protect them from exhaustion and immune destruction and to minimize the risk of malignant transformation are hijacked/disrupted by leukemia stem cells (LSCs), the malignant counterpart of HSCs, to promote disease progression as well as resistance to therapy and immune control. CD4+ regulatory T cells (Tregs) are substantially enriched in the BM compared to other secondary lymphoid organs and are crucially involved in the establishment of an immune privileged niche to maintain HSC quiescence and to protect HSC integrity. In leukemia, Tregs frequencies in the BM even increase. Studies in mice and humans identified the accumulation of Tregs as a major immune-regulatory mechanism. As cure of leukemia implies the elimination of LSCs, the understanding of these immune-regulatory processes may be of particular importance for the development of future treatments of leukemia as targeting major immune escape mechanisms which revolutionized the treatment of solid tumors such as the blockade of the inhibitory checkpoint receptor programmed cell death protein 1 (PD-1) seems less efficacious in the treatment of leukemia. This review will summarize recent findings on the mechanisms by which Tregs regulate stem cells and adaptive immune cells in the BM during homeostasis and in leukemia.
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Affiliation(s)
- Carsten Riether
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland,*Correspondence: Carsten Riether,
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10
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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: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [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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11
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Artzy-Schnirman A, Abu-Shah E, Chandrawati R, Altman E, Yusuf N, Wang ST, Ramos J, Hansel CS, Haus-Cohen M, Dahan R, Arif S, Dustin ML, Peakman M, Reiter Y, Stevens MM. Artificial Antigen Presenting Cells for Detection and Desensitization of Autoreactive T cells Associated with Type 1 Diabetes. NANO LETTERS 2022; 22:4376-4382. [PMID: 35616515 PMCID: PMC9185737 DOI: 10.1021/acs.nanolett.2c00819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Autoimmune diseases and in particular type 1 diabetes rely heavily on treatments that target the symptoms rather than prevent the underlying disease. One of the barriers to better therapeutic strategies is the inability to detect and efficiently target rare autoreactive T-cell populations that are major drivers of these conditions. Here, we develop a unique artificial antigen-presenting cell (aAPC) system from biocompatible polymer particles that allows specific encapsulation of bioactive ingredients. Using our aAPC, we demonstrate that we are able to detect rare autoreactive CD4 populations in human patients, and using mouse models, we demonstrate that our particles are able to induce desensitization in the autoreactive population. This system provides a promising tool that can be used in the prevention of autoimmunity before disease onset.
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Affiliation(s)
- Arbel Artzy-Schnirman
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, Prince Consort Road, London SW7 2AZ, U.K.
| | - Enas Abu-Shah
- Kennedy
Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology
and Musculoskeletal Sciences, University
of Oxford, Oxford OX3 7FY, U.K.
- Sir
William Dunn School of Pathology, University
of Oxford, Oxford OX1 3RE, U.K.
| | - Rona Chandrawati
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, Prince Consort Road, London SW7 2AZ, U.K.
| | - Efrat Altman
- Laboratory
of Molecular Immunology, Faculty of Biology and Technion Integrated
Cancer Center, Technion-Israel Institute
of Technology, Haifa 3200003, Israel
| | - Norkhairin Yusuf
- Department
of Immunobiology, Guy’s, King’s
& St Thomas’ School of Medicine, second Floor, New Guy’s
House, Guy’s Hospital, London SE1 9RT, U.K.
| | - Shih-Ting Wang
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, Prince Consort Road, London SW7 2AZ, U.K.
| | - Jose Ramos
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, Prince Consort Road, London SW7 2AZ, U.K.
| | - Catherine S. Hansel
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, Prince Consort Road, London SW7 2AZ, U.K.
| | - Maya Haus-Cohen
- Laboratory
of Molecular Immunology, Faculty of Biology and Technion Integrated
Cancer Center, Technion-Israel Institute
of Technology, Haifa 3200003, Israel
| | - Rony Dahan
- Department
of Systems Immunology, Weizmann Institute
of Science, Rehovot 761001, Israel
| | - Sefina Arif
- Department
of Immunobiology, Guy’s, King’s
& St Thomas’ School of Medicine, second Floor, New Guy’s
House, Guy’s Hospital, London SE1 9RT, U.K.
| | - Michael L. Dustin
- Kennedy
Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology
and Musculoskeletal Sciences, University
of Oxford, Oxford OX3 7FY, U.K.
| | - Mark Peakman
- Department
of Immunobiology, Guy’s, King’s
& St Thomas’ School of Medicine, second Floor, New Guy’s
House, Guy’s Hospital, London SE1 9RT, U.K.
| | - Yoram Reiter
- Laboratory
of Molecular Immunology, Faculty of Biology and Technion Integrated
Cancer Center, Technion-Israel Institute
of Technology, Haifa 3200003, Israel
| | - Molly M. Stevens
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, Prince Consort Road, London SW7 2AZ, U.K.
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12
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Unmasking the suppressed immunopeptidome of EZH2 mutated diffuse large B-cell lymphomas with combination drug treatment. Blood Adv 2022; 6:4107-4121. [PMID: 35561310 PMCID: PMC9327544 DOI: 10.1182/bloodadvances.2021006069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
Exploring the repertoire of peptides presented on major histocompatibility complexes (MHC) has been utilized to identify targets for immunotherapy in many hematological malignancies. However, there is a paucity of such data for diffuse large B-cell lymphomas (DLBCL), which might be explained by the profound downregulation of MHC expression in many DLBCLs, and in particular in the Enhancer of Zeste homolog 2 (EZH2) -mutated subgroup. Epigenetic drug treatment, especially in the context of interferon gamma (IFN-γ), restored MHC expression in DLBCL. DLBCL MHC-presented peptides were identified via mass spectrometry following tazemetostat or decitabine treatments alone, or in combination with IFN-γ. Such treatment synergistically increased MHC class I surface protein expression up to 50-fold and class II expression up to 3-fold. Peptides presented on MHC complexes increased to a similar extent for MHC class I and class II. Overall, these treatments restored the diversity of the immunopeptidome to levels described in healthy B cells for 2 out of 3 cell lines and allowed the systematic search for new targets for immunotherapy. Consequently, we identified multiple MHC ligands from regulator of G protein signaling 13 (RGS13) and E2F transcription factor 8 (E2F8) on different MHC alleles, none of which have been described in healthy tissues and therefore represent tumor-specific MHC ligands, which are unmasked only after drug treatment. Overall, our results show that EZH2 inhibition in combination with decitabine and IFN-γ can expand the repertoire of MHC ligands presented on DLBCLs by revealing suppressed epitopes, thus allowing the systematic analysis and identification of new potential immunotherapy targets.
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Kuželová K, Brodská B, Marková J, Petráčková M, Schetelig J, Ransdorfová Š, Gašová Z, Šálek C. NPM1 and DNMT3A mutations are associated with distinct blast immunophenotype in acute myeloid leukemia. Oncoimmunology 2022; 11:2073050. [PMID: 35558161 PMCID: PMC9090295 DOI: 10.1080/2162402x.2022.2073050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The immune system is important for elimination of residual leukemic cells during acute myeloid leukemia (AML) therapy. Anti-leukemia immune response can be inhibited by various mechanisms leading to immune evasion and disease relapse. Selected markers of immune escape were analyzed on AML cells from leukapheresis at diagnosis (N = 53). Hierarchical clustering of AML immunophenotypes yielded distinct genetic clusters. In the absence of DNMT3A mutation, NPM1 mutation was associated with decreased HLA expression and low levels of other markers (CLIP, PD-L1, TIM-3). Analysis of an independent cohort confirmed decreased levels of HLA transcripts in patients with NPM1 mutation. Samples with combined NPM1 and DNMT3A mutations had high CLIP surface amount suggesting reduced antigen presentation. TIM-3 transcript correlated not only with TIM-3 surface protein but also with CLIP and PD-L1. In our cohort, high levels of TIM-3/PD-L1/CLIP were associated with lower survival. Our results suggest that AML genotype is related to blast immunophenotype, and that high TIM-3 transcript levels in AML blasts could be a marker of immune escape. Cellular pathways regulating resistance to the immune system might contribute to the predicted response to standard therapy of patients in specific AML subgroups and should be targeted to improve AML treatment.
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Affiliation(s)
- Kateřina Kuželová
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic,CONTACT Kateřina Kuželová Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Barbora Brodská
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jana Marková
- Clinical Department, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Martina Petráčková
- Department of Gene Immunotherapy Research, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Johannes Schetelig
- Medical Clinic I, Division Hematology, Cell Therapy, and Medical Oncology, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Šárka Ransdorfová
- Department of Cytogenetics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Zdenka Gašová
- Department of Apheresis, Institute of Hematology and Blood Transfusion, Prague, Czech Republic,Institute of Clinical and Experimental Hematology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Cyril Šálek
- Clinical Department, Institute of Hematology and Blood Transfusion, Prague, Czech Republic,Institute of Clinical and Experimental Hematology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
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Hernández-Malmierca P, Vonficht D, Schnell A, Uckelmann HJ, Bollhagen A, Mahmoud MAA, Landua SL, van der Salm E, Trautmann CL, Raffel S, Grünschläger F, Lutz R, Ghosh M, Renders S, Correia N, Donato E, Dixon KO, Hirche C, Andresen C, Robens C, Werner PS, Boch T, Eisel D, Osen W, Pilz F, Przybylla A, Klein C, Buchholz F, Milsom MD, Essers MAG, Eichmüller SB, Hofmann WK, Nowak D, Hübschmann D, Hundemer M, Thiede C, Bullinger L, Müller-Tidow C, Armstrong SA, Trumpp A, Kuchroo VK, Haas S. Antigen presentation safeguards the integrity of the hematopoietic stem cell pool. Cell Stem Cell 2022; 29:760-775.e10. [PMID: 35523139 PMCID: PMC9202612 DOI: 10.1016/j.stem.2022.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/08/2021] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are responsible for the production of blood and immune cells. Throughout life, HSPCs acquire oncogenic aberrations that can cause hematological cancers. Although molecular programs maintaining stem cell integrity have been identified, safety mechanisms eliminating malignant HSPCs from the stem cell pool remain poorly characterized. Here, we show that HSPCs constitutively present antigens via major histocompatibility complex class II. The presentation of immunogenic antigens, as occurring during malignant transformation, triggers bidirectional interactions between HSPCs and antigen-specific CD4+ T cells, causing stem cell proliferation, differentiation, and specific exhaustion of aberrant HSPCs. This immunosurveillance mechanism effectively eliminates transformed HSPCs from the hematopoietic system, thereby preventing leukemia onset. Together, our data reveal a bidirectional interaction between HSPCs and CD4+ T cells, demonstrating that HSPCs are not only passive receivers of immunological signals but also actively engage in adaptive immune responses to safeguard the integrity of the stem cell pool.
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Affiliation(s)
- Pablo Hernández-Malmierca
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Dominik Vonficht
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexandra Schnell
- Evergrande Center for Immunologic Diseases, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hannah J Uckelmann
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA; Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alina Bollhagen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mohamed A A Mahmoud
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Sophie-Luise Landua
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Elise van der Salm
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christine L Trautmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Simon Raffel
- Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Florian Grünschläger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Raphael Lutz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Simon Renders
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Nádia Correia
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Elisa Donato
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Karin O Dixon
- Evergrande Center for Immunologic Diseases, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christoph Hirche
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Carolin Andresen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Claudia Robens
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Paula S Werner
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Tobias Boch
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany; Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Eisel
- Research Group GMP & T Cell Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Wolfram Osen
- Research Group GMP & T Cell Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Franziska Pilz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Adriana Przybylla
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Corinna Klein
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Frank Buchholz
- Medical Faculty, University Hospital Carl Gustav Carus, NCT/UCC Section Medical Systems Biology, TU Dresden, Dresden, Germany
| | - Michael D Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Experimental Hematology, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marieke A G Essers
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefan B Eichmüller
- Research Group GMP & T Cell Therapy, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Wolf-Karsten Hofmann
- Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany; Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, University Hospital Mannheim, Mannheim, Germany; Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Hundemer
- Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Christian Thiede
- German Cancer Consortium (DKTK), Heidelberg, Germany; Medical Department 1, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Lars Bullinger
- German Cancer Consortium (DKTK), Heidelberg, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Cancer Immunology, Berlin, Germany
| | - Carsten Müller-Tidow
- Department of Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston, MA, USA; Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School, and Brigham and Women's Hospital, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Department of Hematology, Oncology and Cancer Immunology, Berlin, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
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15
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HLA-DR Presentation of the Tumor Antigen MSLN Associates with Clinical Outcome of Ovarian Cancer Patients. Cancers (Basel) 2022; 14:cancers14092260. [PMID: 35565389 PMCID: PMC9101593 DOI: 10.3390/cancers14092260] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The immunopeptidome represents the entirety of peptides that are presented on the surface of cells on human leukocyte antigen (HLA) molecules and are recognized by the T-cell receptors of CD4+ and CD8+ T-cells. Malignant cells present tumor-associated antigens essential for tumor immune surveillance, which can be targeted by T-cell-based immunotherapy approaches. For ovarian carcinomas, various tumor-associated antigens, such as Mucin-16 and Mesothelin, have been described. The aim of our study is to analyze immunopeptidome-defined tumor antigen presentation in ovarian carcinoma patients in relation to clinical characteristics and disease outcomes to define potential biomarkers. Our work demonstrates the central role of HLA-DR-restricted peptide presentation of the tumor antigen Mesothelin and of CD4+ T-cell responses for tumor immune surveillance, and underlines Mesothelin as a prime target antigen for novel immunotherapeutic approaches for ovarian carcinoma patients. Abstract T-cell recognition of HLA-presented antigens is central for the immunological surveillance of malignant disease and key for the development of novel T-cell-based immunotherapy approaches. In recent years, large-scale immunopeptidome studies identified naturally presented tumor-associated antigens for several malignancies. Regarding ovarian carcinoma (OvCa), Mucin-16 (MUC16) and Mesothelin (MSLN) were recently described as the top HLA class I- and HLA class II-presented tumor antigens, respectively. Here, we investigate the role and impact of immunopeptidome-presented tumor antigens on the clinical outcomes of 39 OvCa patients with a follow-up time of up to 50 months after surgery. Patients with a HLA-restricted presentation of high numbers of different MSLN-derived peptides on their tumors exhibited significantly prolonged progression-free (PFS) and overall survival (OS), whereas the presentation of MUC16-derived HLA class I-restricted peptides had no impact. Furthermore, a high HLA-DRB gene expression was associated with increased PFS and OS. In line, in silico prediction revealed that MSLN-derived HLA class II-presented peptides are predominantly presented on HLA-DR allotypes. In conclusion, the correlation of MSLN tumor antigen presentation and HLA-DRB gene expression with prolonged survival indicates a central role of CD4+ T-cell responses for tumor immune surveillance in OvCa, and highlights the importance of immunopeptidome-guided tumor antigen discovery.
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Impact of Micropolymorphism Outside the Peptide Binding Groove in the Clinically Relevant Allele HLA-C*14 on T Cell Responses in HIV-1 Infection. J Virol 2022; 96:e0043222. [PMID: 35475667 PMCID: PMC9131871 DOI: 10.1128/jvi.00432-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is increasing evidence for the importance of human leukocyte antigen C (HLA-C)-restricted CD8+ T cells in HIV-1 control, but these responses are relatively poorly investigated. The number of HLA-C-restricted HIV-1 epitopes identified is much smaller than those of HLA-A-restricted or HLA-B-restricted ones. Here, we utilized a mass spectrometry-based approach to identify HIV-1 peptides presented by HLA-C*14:03 protective and HLA-C*14:02 nonprotective alleles. We identified 25 8- to 11-mer HLA-I-bound HIV-1 peptides from HIV-1-infected HLA-C*14:02+/14:03+ cells. Analysis of T cell responses to these peptides identified novel 6 T cell epitopes targeted in HIV-1-infected HLA-C*14:02+/14:03+ subjects. Analyses using HLA stabilization assays demonstrated that all 6 epitope peptides exhibited higher binding to and greater cell surface stabilization of HLA-C*14:02 than HLA-C*14:03. T cell response magnitudes were typically higher in HLA-C*14:02+ than HLA-C*14:03+ individuals, with responses to the Pol KM9 and Nef epitopes being significantly higher. The results show that HLA-C*14:02 can elicit stronger T cell responses to HIV-1 than HLA-C*14:03 and suggest that the single amino acid difference between these HLA-C14 subtypes at position 21, outside the peptide-binding groove, indirectly influences the stability of peptide-HLA-C*14 complexes and induction/expansion of HIV-specific T cells. Taken together with a previous finding that KIR2DL2+ NK cells recognized HLA-C*14:03+ HIV-1-infected cells more than HLA-C*14:02+ ones, the present study indicates that these HLA-C*14 subtypes differentially impact HIV-1 control by T cells and NK cells. IMPORTANCE Some human leukocyte antigen (HLA) class I alleles are associated with good clinical outcomes in HIV-1 infection and are called protective HLA alleles. Identification of T cell epitopes restricted by protective HLA alleles can give important insight into virus-immune system interactions and inform design of immune-based prophylactic/therapeutic strategies. Although epitopes restricted by many protective HLA-A/B alleles have been identified, protective HLA-C alleles are relatively understudied. Here, we identified 6 novel T cell epitopes presented by both HLA-C*14:02 (no association with protection) and HLA-C*14:03 (protective) using a mass spectrometry-based immunopeptidome profiling approach. We found that these peptides bound to and stabilized HLA-C*14:02 better than HLA-C*14:03 and observed differences in induction/expansion of epitope-specific T cell responses in HIV-infected HLA-C*14:02+ versus HLA-C*14:03+ individuals. These results enhance understanding of how the microstructural difference at position 21 between these HLA-C*14 subtypes may influence cellular immune responses involved in viral control in HIV-1 infection.
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17
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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.
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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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18
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Abstract
Despite FDA approval of nine new drugs for patients with acute myeloid leukemia (AML) in the United States over the last 4 years, AML remains a major area of unmet medical need among hematologic malignancies. In this review, we discuss the development of promising new molecular targeted approaches for AML, including menin inhibition, novel IDH1/2 inhibitors, and preclinical means to target TET2, ASXL1, and RNA splicing factor mutations. In addition, we review progress in immune targeting of AML through anti-CD47, anti-SIRPα, and anti-TIM-3 antibodies; bispecific and trispecific antibodies; and new cellular therapies in development for AML.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Omar Abdel-Wahab
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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19
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Caprioli C, Nazari I, Milovanovic S, Pelicci PG. Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities. Front Oncol 2022; 11:796477. [PMID: 35186713 PMCID: PMC8847379 DOI: 10.3389/fonc.2021.796477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
Myeloid neoplasms (MN) are heterogeneous clonal disorders arising from the expansion of hematopoietic stem and progenitor cells. In parallel with genetic and epigenetic dynamics, the immune system plays a critical role in modulating tumorigenesis, evolution and therapeutic resistance at the various stages of disease progression. Single-cell technologies represent powerful tools to assess the cellular composition of the complex tumor ecosystem and its immune environment, to dissect interactions between neoplastic and non-neoplastic components, and to decipher their functional heterogeneity and plasticity. In addition, recent progress in multi-omics approaches provide an unprecedented opportunity to study multiple molecular layers (DNA, RNA, proteins) at the level of single-cell or single cellular clones during disease evolution or in response to therapy. Applying single-cell technologies to MN holds the promise to uncover novel cell subsets or phenotypic states and highlight the connections between clonal evolution and immune escape, which is crucial to fully understand disease progression and therapeutic resistance. This review provides a perspective on the various opportunities and challenges in the field, focusing on key questions in MN research and discussing their translational value, particularly for the development of more efficient immunotherapies.
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Affiliation(s)
- Chiara Caprioli
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy.,Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy.,Hematology and Bone Marrow Transplant Unit, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Iman Nazari
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy.,Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
| | - Sara Milovanovic
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy.,Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy.,Scuola Europea di Medicina Molecolare (SEMM) European School of Molecular Medicine, Milan, Italy
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20
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Lahman MC, Schmitt TM, Paulson KG, Vigneron N, Buenrostro D, Wagener FD, Voillet V, Martin L, Gottardo R, Bielas J, McElrath JM, Stirewalt DL, Pogosova-Agadjanyan EL, Yeung CC, Pierce RH, Egan DN, Bar M, Hendrie PC, Kinsella S, Vakil A, Butler J, Chaffee M, Linton J, McAfee MS, Hunter DS, Bleakley M, Rongvaux A, Van den Eynde BJ, Chapuis AG, Greenberg PD. Targeting an alternate Wilms' tumor antigen 1 peptide bypasses immunoproteasome dependency. Sci Transl Med 2022; 14:eabg8070. [PMID: 35138909 DOI: 10.1126/scitranslmed.abg8070] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Designing effective antileukemic immunotherapy will require understanding mechanisms underlying tumor control or resistance. Here, we report a mechanism of escape from immunologic targeting in an acute myeloid leukemia (AML) patient, who relapsed 1 year after immunotherapy with engineered T cells expressing a human leukocyte antigen A*02 (HLA-A2)-restricted T cell receptor (TCR) specific for a Wilms' tumor antigen 1 epitope, WT1126-134 (TTCR-C4). Resistance occurred despite persistence of functional therapeutic T cells and continuous expression of WT1 and HLA-A2 by the patient's AML cells. Analysis of the recurrent AML revealed expression of the standard proteasome, but limited expression of the immunoproteasome, specifically the beta subunit 1i (β1i), which is required for presentation of WT1126-134. An analysis of a second patient treated with TTCR-C4 demonstrated specific loss of AML cells coexpressing β1i and WT1. To determine whether the WT1 protein continued to be processed and presented in the absence of immunoproteasome processing, we identified and tested a TCR targeting an alternative, HLA-A2-restricted WT137-45 epitope that was generated by immunoproteasome-deficient cells, including WT1-expressing solid tumor lines. T cells expressing this TCR (TTCR37-45) killed the first patients' relapsed AML resistant to WT1126-134 targeting, as well as other primary AML, in vitro. TTCR37-45 controlled solid tumor lines lacking immunoproteasome subunits both in vitro and in an NSG mouse model. As proteasome composition can vary in AML, defining and preferentially targeting these proteasome-independent epitopes may maximize therapeutic efficacy and potentially circumvent AML immune evasion by proteasome-related immunoediting.
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Affiliation(s)
- Miranda C Lahman
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Thomas M Schmitt
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kelly G Paulson
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Nathalie Vigneron
- Ludwig Institute for Cancer Research, 1200 Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Denise Buenrostro
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Felecia D Wagener
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Hutchinson Centre Research Institute of South Africa, Cape Town 8001, South Africa
| | - Lauren Martin
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jason Bielas
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98115, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Julie M McElrath
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Derek L Stirewalt
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA
| | | | - Cecilia C Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98115, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Robert H Pierce
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Daniel N Egan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Merav Bar
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Paul C Hendrie
- University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Sinéad Kinsella
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Aesha Vakil
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jonah Butler
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Chaffee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jonathan Linton
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Megan S McAfee
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel S Hunter
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Marie Bleakley
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Anthony Rongvaux
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Immunology, University of Washington, Seattle, WA 98115, USA
| | - Benoit J Van den Eynde
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium.,Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK.,Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
| | - Aude G Chapuis
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98115, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Philip D Greenberg
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington School of Medicine, Seattle, WA 98115, USA.,Department of Immunology, University of Washington, Seattle, WA 98115, USA
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21
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Yao F, Zhao C, Zhong F, Qin T, Li S, Liu J, Huang B, Wang X. Bioinformatics analysis and identification of hub genes and immune-related molecular mechanisms in chronic myeloid leukemia. PeerJ 2022; 10:e12616. [PMID: 35111390 PMCID: PMC8781323 DOI: 10.7717/peerj.12616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/18/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Chronic myeloid leukemia (CML) is a malignant hyperplastic tumor of the bone marrow originating from pluripotent hematopoietic stem cells. The advent of tyrosine kinase inhibitors (TKIs) has greatly improved the survival rate of patients with CML. However, TKI-resistance leads to the disease recurrence and progression. This study aimed to identify immune-related genes (IRGs) associated with CML progression. METHODS We extracted the gene's expression profiles from the Gene Expression Omnibus (GEO). Bioinformatics analysis was used to determine the differentially expressed IRGs of CML and normal peripheral blood mononuclear cells (PBMCs). Functional enrichment and gene set enrichment analysis (GSEA) were used to explore its potential mechanism. Hub genes were identified using Molecular Complex Detection (MCODE) and the CytoHubba plugin. The hub genes' diagnostic value was evaluated using the receiver operating characteristic (ROC). The relative proportions of infiltrating immune cells in each CML sample were evaluated using CIBERSORT. Quantitative real-time PCR (RT-qPCR) was used to validate the hub gene expression in clinical samples. RESULTS A total of 31 differentially expressed IRGs were identified. GO analyses revealed that the modules were typically enriched in the receptor ligand activity, cytokine activity, and endopeptidase activity. KEGG enrichment analysis of IRGs revealed that CML involved Th17 cell differentiation, the NF-kappa B signaling pathway, and cytokine-cytokine receptor interaction. A total of 10 hub genes were selected using the PPI network. GSEA showed that these hub genes were related to the gamma-interferon immune response, inflammatory response, and allograft rejection. ROC curve analysis suggested that six hub genes may be potential biomarkers for CML diagnosis. Further analysis indicated that immune cells were associated with the pathogenesis of CML. The RT-qPCR results showed that proteinase 3 (PRTN3), cathepsin G (CTSG), matrix metalloproteinase 9 (MMP9), resistin (RETN), eosinophil derived neurotoxin (RNase2), eosinophil cationic protein (ECP, RNase3) were significantly elevated in CML patients' PBMCs compared with healthy controls. CONCLUSION These results improved our understanding of the functional characteristics and immune-related molecular mechanisms involved in CML progression and provided potential diagnostic biomarkers and therapeutic targets.
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22
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Acute myeloid leukemia cell membrane-coated nanoparticles for cancer vaccination immunotherapy. Leukemia 2022; 36:994-1005. [PMID: 34845316 PMCID: PMC8979812 DOI: 10.1038/s41375-021-01432-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022]
Abstract
Cancer vaccines are promising treatments to prevent relapse after chemotherapy in acute myeloid leukemia (AML) patients, particularly for those who cannot tolerate intensive consolidation therapies. Here, we report the development of an AML cell membrane-coated nanoparticle (AMCNP) vaccine platform, in which immune-stimulatory adjuvant-loaded nanoparticles are coated with leukemic cell membrane material. This AMCNP vaccination strategy stimulates leukemia-specific immune responses by co-delivering membrane-associated antigens along with adjuvants to antigen-presenting cells. To demonstrate that this AMCNP vaccine enhances leukemia-specific antigen presentation and T cell responses, we modified a murine AML cell line to express membrane-bound chicken ovalbumin as a model antigen. AMCNPs were efficiently acquired by antigen-presenting cells in vitro and in vivo and stimulated antigen cross-presentation. Vaccination with AMCNPs significantly enhanced antigen-specific T cell expansion and effector function compared with control vaccines. Prophylactic vaccination with AMCNPs enhanced cellular immunity and protected against AML challenge. Moreover, in an AML post-remission vaccination model, AMCNP vaccination significantly enhanced survival in comparison to vaccination with whole leukemia cell lysates. Collectively, AMCNPs retained AML-specific antigens, elicited enhanced antigen-specific immune responses, and provided therapeutic benefit against AML challenge.
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23
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Barbosa CRR, Barton J, Shepherd AJ, Mishto M. Mechanistic diversity in MHC class I antigen recognition. Biochem J 2021; 478:4187-4202. [PMID: 34940832 PMCID: PMC8786304 DOI: 10.1042/bcj20200910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.
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Affiliation(s)
- Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| | - Justin Barton
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Adrian J. Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
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24
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Zitvogel L, Perreault C, Finn OJ, Kroemer G. Beneficial autoimmunity improves cancer prognosis. Nat Rev Clin Oncol 2021; 18:591-602. [PMID: 33976418 DOI: 10.1038/s41571-021-00508-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2021] [Indexed: 02/06/2023]
Abstract
Many tumour antigens that do not arise from cancer cell-specific mutations are targets of humoral and cellular immunity despite their expression on non-malignant cells. Thus, in addition to the expected ability to detect mutations and stress-associated shifts in the immunoproteome and immunopeptidome (the sum of MHC class I-bound peptides) unique to malignant cells, the immune system also recognizes antigens expressed in non-malignant cells, which can result in autoimmune reactions against non-malignant cells from the tissue of origin. These autoimmune manifestations include, among others, vitiligo, thyroiditis and paraneoplastic syndromes, concurrent with melanoma, thyroid cancer and non-small-cell lung cancer, respectively. Importantly, despite the undesirable effects of these symptoms, such events can have prognostic value and correlate with favourable disease outcomes, suggesting 'beneficial autoimmunity'. Similarly, the occurrence of dermal and endocrine autoimmune adverse events in patients receiving immune-checkpoint inhibitors can have a positive predictive value for therapeutic outcomes. Neoplasias derived from stem cells deemed 'not essential' for survival (such as melanocytes, thyroid cells and most cells in sex-specific organs) have a particularly good prognosis, perhaps because the host can tolerate autoimmune reactions that destroy tumour cells at some cost to non-malignant tissues. In this Perspective, we discuss examples of spontaneous as well as therapy-induced autoimmunity that correlate with favourable disease outcomes and make a strong case in favour of this 'beneficial autoimmunity' being important not only in patients with advanced-stage disease but also in cancer immunosurveillance.
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Affiliation(s)
- Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France. .,Université Paris Saclay, Faculty of Medicine, Le Kremlin-Bicêtre, France. .,INSERM U1015, Gustave Roussy, Villejuif, France. .,Equipe labellisée par la Ligue contre le cancer, Villejuif, France. .,Center of Clinical Investigations in Biotherapies of Cancer (CICBT) BIOTHERIS, Villejuif, France. .,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Guido Kroemer
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France. .,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China. .,Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Institut Universitaire de France, Paris, France. .,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France. .,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France. .,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
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25
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Targeting intracellular WT1 in AML with a novel RMF-peptide-MHC specific T-cell bispecific antibody. Blood 2021; 138:2655-2669. [PMID: 34280257 DOI: 10.1182/blood.2020010477] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 11/20/2022] Open
Abstract
Antibody-based immunotherapy is a promising strategy for targeting chemo-resistant leukemic cells. However, classical antibody-based approaches are restricted to targeting lineage-specific cell-surface antigens. By targeting intracellular antigens, a large number of other leukemia-associated targets would become accessible. In this study, we evaluated a novel T-cell bispecific (TCB) antibody, generated using CrossMab and knob-into-holes technology, containing a bivalent T-cell receptor-like binding domain that recognizes the RMFPNAPYL peptide derived from the intracellular tumor antigen Wilms' tumor 1 (WT1) in the context of human leukocyte antigen (HLA) A*02. Binding to CD3ε recruits T cells irrespective of their T-cell receptor specificity. WT1-TCB elicited antibody-mediated T-cell cytotoxicity against AML cell lines in a WT1- and HLA-restricted manner. Specific lysis of primary AML cells was mediated in ex vivo long-term co-cultures utilizing allogenic (mean specific lysis: 67±6% after 13-14 days; ±SEM; n=18) or autologous, patient-derived T cells (mean specific lysis: 54±12% after 11-14 days; ±SEM; n=8). WT1-TCB-treated T cells exhibited higher cytotoxicity against primary AML cells than an HLA-A*02 RMF-specific T-cell clone. Combining WT1-TCB with the immunomodulatory drug lenalidomide further enhanced antibody-mediated T-cell cytotoxicity against primary AML cells (mean specific lysis on day 3-4: 45.4±9.0% vs 70.8±8.3%; p=0.015; ±SEM; n=9-10). In vivo, WT1-TCB-treated humanized mice bearing SKM-1 tumors showed a significant and dose-dependent reduction in tumor growth. In summary, we show that WT1-TCB facilitates potent in vitro, ex vivo and in vivo killing of AML cell lines and primary AML cells; these results led to the initiation of a phase I trial in patients with r/r AML (NCT04580121).
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26
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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: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [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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27
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The immunopeptidome guides permissive HLA mismatch. Blood 2021; 137:864-865. [PMID: 33599759 DOI: 10.1182/blood.2020009266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Ehx G, Larouche JD, Durette C, Laverdure JP, Hesnard L, Vincent K, Hardy MP, Thériault C, Rulleau C, Lanoix J, Bonneil E, Feghaly A, Apavaloaei A, Noronha N, Laumont CM, Delisle JS, Vago L, Hébert J, Sauvageau G, Lemieux S, Thibault P, Perreault C. Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes. Immunity 2021; 54:737-752.e10. [PMID: 33740418 DOI: 10.1016/j.immuni.2021.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/24/2020] [Accepted: 02/26/2021] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) has not benefited from innovative immunotherapies, mainly because of the lack of actionable immune targets. Using an original proteogenomic approach, we analyzed the major histocompatibility complex class I (MHC class I)-associated immunopeptidome of 19 primary AML samples and identified 58 tumor-specific antigens (TSAs). These TSAs bore no mutations and derived mainly (86%) from supposedly non-coding genomic regions. Two AML-specific aberrations were instrumental in the biogenesis of TSAs, intron retention, and epigenetic changes. Indeed, 48% of TSAs resulted from intron retention and translation, and their RNA expression correlated with mutations of epigenetic modifiers (e.g., DNMT3A). AML TSA-coding transcripts were highly shared among patients and were expressed in both blasts and leukemic stem cells. In AML patients, the predicted number of TSAs correlated with spontaneous expansion of cognate T cell receptor clonotypes, accumulation of activated cytotoxic T cells, immunoediting, and improved survival. These TSAs represent attractive targets for AML immunotherapy.
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Affiliation(s)
- Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Caroline Rulleau
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Albert Feghaly
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Céline M Laumont
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Jean-Sébastien Delisle
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Luca Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Josée Hébert
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 2M4, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montreal, QC H3C 3J7, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3C 3J7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada.
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29
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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: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [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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30
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Chen R, Fulton KM, Twine SM, Li J. IDENTIFICATION OF MHC PEPTIDES USING MASS SPECTROMETRY FOR NEOANTIGEN DISCOVERY AND CANCER VACCINE DEVELOPMENT. MASS SPECTROMETRY REVIEWS 2021; 40:110-125. [PMID: 31875992 DOI: 10.1002/mas.21616] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunotherapy with neoantigens presented by major histocompatibility complex (MHC) is one of the most promising approaches in cancer treatment. Using this approach, cancer vaccines can be designed to target tumor-specific mutations that are not found in normal tissues. Clinical trials have demonstrated an increased immune response and eradication of tumors after injecting synthetic peptides selected from the immunopeptidome. Although the sequence of MHC binding peptides can be predicted from genome sequencing and prediction algorithms, this approach results in large numbers of predicted peptides, requiring the confirmation by mass spectrometry (MS) analysis. Identification of MHC peptides by direct MS analysis of immunopeptidome is accurate and sensitive, with tens of thousands of unique peptides potentially identified from either cancer cell line or tumor tissue. Peptides with mutations can also be identified with patient-specific protein databases constructed from genome or transcriptome sequencing data. MS analysis also enables the characterization of the post-translational modifications (PTMs) of those antigens that cannot be predicted. Moreover, PTMs were found to be more efficient in triggering an immune response. In addition to reviewing recent advances in the identification of neoantigens using MS, the techniques for cancer vaccine candidate selection and formulation, vaccine delivery systems, and the potential for use in combination with other therapeutics are also discussed. It is anticipated that MS-based techniques will play an important role in future cancer vaccine development. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:110-125, 2021.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
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31
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Kuznetsov A, Voronina A, Govorun V, Arapidi G. Critical Review of Existing MHC I Immunopeptidome Isolation Methods. Molecules 2020; 25:E5409. [PMID: 33228004 PMCID: PMC7699222 DOI: 10.3390/molecules25225409] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
Major histocompatibility complex class I (MHC I) plays a crucial role in the development of adaptive immune response in vertebrates. MHC molecules are cell surface protein complexes loaded with short peptides and recognized by the T-cell receptors (TCR). Peptides associated with MHC are named immunopeptidome. The MHC I immunopeptidome is produced by the proteasome degradation of intracellular proteins. The knowledge of the immunopeptidome repertoire facilitates the creation of personalized antitumor or antiviral vaccines. A huge number of publications on the immunopeptidome diversity of different human and mouse biological samples-plasma, peripheral blood mononuclear cells (PBMCs), and solid tissues, including tumors-appeared in the scientific journals in the last decade. Significant immunopeptidome identification efficiency was achieved by advances in technology: the immunoprecipitation of MHC and mass spectrometry-based approaches. Researchers optimized common strategies to isolate MHC-associated peptides for individual tasks. They published many protocols with differences in the amount and type of biological sample, amount of antibodies, type and amount of insoluble support, methods of post-fractionation and purification, and approaches to LC-MS/MS identification of immunopeptidome. These parameters have a large impact on the final repertoire of isolated immunopeptidome. In this review, we summarize and compare immunopeptidome isolation techniques with an emphasis on the results obtained.
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Affiliation(s)
- Alexandr Kuznetsov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
| | - Alice Voronina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (A.K.); (A.V.); (V.G.)
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Georgij Arapidi
- Department of Molecular and Translational Medicine, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
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32
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Sachs A, Moore E, Kosaloglu-Yalcin Z, Peters B, Sidney J, Rosenberg SA, Robbins PF, Sette A. Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:539-549. [PMID: 32571843 PMCID: PMC7413297 DOI: 10.4049/jimmunol.1901173] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
The availability of MHC-binding prediction tools has been useful in guiding studies aimed at identifying candidate target Ags to generate reactive T cells and to characterize viral and tumor-reactive T cells. Nevertheless, prediction algorithms appear to function poorly for epitopes containing cysteine (Cys) residues, which can oxidize and form disulfide bonds with other Cys residues under oxidizing conditions, thus potentially interfering with their ability to bind to MHC molecules. Analysis of the results of HLA-A*02:01 class I binding assays carried out in the presence and absence of the reducing agent 2-ME indicated that the predicted affinity for 25% of Cys-containing epitopes was underestimated by a factor of 3 or more. Additional analyses were undertaken to evaluate the responses of human CD8+ tumor-reactive T cells against 10 Cys-containing HLA class I-restricted minimal determinants containing substitutions of α-aminobutyric acid (AABA), a cysteine analogue containing a methyl group in place of the sulfhydryl group present in Cys, for the native Cys residues. Substitutions of AABA for Cys at putative MHC anchor positions often significantly enhanced T cell recognition, whereas substitutions at non-MHC anchor positions were neutral, except for one epitope where this modification abolished T cell recognition. These findings demonstrate the need to evaluate MHC binding and T cell recognition of Cys-containing peptides under conditions that prevent Cys oxidation, and to adjust current prediction binding algorithms for HLA-A*02:01 and potentially additional class I alleles to more accurately rank peptides containing Cys anchor residues.
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Affiliation(s)
- Abraham Sachs
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1201
| | - Eugene Moore
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
| | - John Sidney
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1201
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1201;
| | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
- Department of Medicine, University of California, San Diego, San Diego, CA 92122
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33
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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: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [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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34
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Abstract
Adoptive immunotherapy with engineered T cells is at the forefront of cancer treatment. T cells can be engineered to express T-cell receptors (TCRs) specific for tumor-associated antigens (TAAs) derived from intracellular or cell surface proteins. T cells engineered with TCRs (TCR-T) allow for targeting diverse types of TAAs, including proteins overexpressed in malignant cells, those with lineage-restricted expression, cancer-testis antigens, and neoantigens created from abnormal, malignancy-restricted proteins. Minor histocompatibility antigens can also serve as TAAs for TCR-T to treat relapsed hematologic malignancies after allogeneic hematopoietic cell transplantation. Moreover, TCR constructs can be modified to improve safety and enhance function and persistence of TCR-T. Transgenic T-cell receptor therapies targeting 3 different TAAs are in early-phase clinical trials for treatment of hematologic malignancies. Preclinical studies of TCR-T specific for many other TAAs are underway and offer great promise as safe and effective therapies for a wide range of cancers.
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Affiliation(s)
- Melinda A Biernacki
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
| | - Michelle Brault
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Marie Bleakley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
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35
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Penter L, Wu CJ. Personal tumor antigens in blood malignancies: genomics-directed identification and targeting. J Clin Invest 2020; 130:1595-1607. [PMID: 31985488 PMCID: PMC7108890 DOI: 10.1172/jci129209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hematological malignancies have long been at the forefront of the development of novel immune-based treatment strategies. The earliest successful efforts originated from the extensive body of work in the field of allogeneic hematopoietic stem cell transplantation. These efforts laid the foundation for the recent exciting era of cancer immunotherapy, which includes immune checkpoint blockade, personal neoantigen vaccines, and adoptive T cell transfer. At the heart of the specificity of these novel strategies is the recognition of target antigens presented by malignant cells to T cells. Here, we review the advances in systematic identification of minor histocompatibility antigens and neoantigens arising from personal somatic alterations or recurrent driver mutations. These exciting efforts pave the path for the implementation of personalized combinatorial cancer therapy.
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Affiliation(s)
- Livius Penter
- Department of Hematology, Oncology, and Tumor Immunology, Charité – Universitätsmedizin Berlin (CVK), Berlin, Germany
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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36
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Teck AT, Urban S, Quass P, Nelde A, Schuster H, Letsch A, Busse A, Walz JS, Keilholz U, Ochsenreither S. Cancer testis antigen Cyclin A1 harbors several HLA-A*02:01-restricted T cell epitopes, which are presented and recognized in vivo. Cancer Immunol Immunother 2020; 69:1217-1227. [PMID: 32157447 PMCID: PMC8222032 DOI: 10.1007/s00262-020-02519-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/12/2020] [Indexed: 01/22/2023]
Abstract
Cyclin A1 is a promising antigen for T cell therapy being selectively expressed in high-grade ovarian cancer (OC) and acute myeloid leukemia (AML) stem cells. For adoptive T cell therapy, a single epitope has to be selected, with high affinity to MHC class I and adequate processing and presentation by malignant cells to trigger full activation of specific T cells. In silico prediction with three algorithms indicated 13 peptides of Cyclin A1 9 to 11 amino acids of length to have high affinity to HLA-A*02:01. Ten of them proved to be affine in an HLA stabilization assay using TAP-deficient T2 cells. Their immunogenicity was assessed by repetitive stimulation of CD8+ T cells from two healthy donors with single-peptide-pulsed dendritic cells or monocytes. Intracellular cytokine staining quantified the enrichment of peptide-specific functional T cells. Seven peptides were immunogenic, three of them against both donors. Specific cell lines were cloned and used in killing assays to demonstrate recognition of endogenous Cyclin A1 in the HLA-A*02:01-positive AML cell line THP-1. Immunopeptidome analysis based on direct isolation of HLA-presented peptides by mass spectrometry of primary AML and OC samples identified four naturally presented epitopes of Cyclin A1. The immunopeptidome of HeLa cells transfected with Cyclin A1 and HLA-A*02:01 revealed six Cyclin A1-derived HLA ligands. Epitope p410–420 showed high affinity to HLA-A*02:01 and immunogenicity in both donors. It proved to be naturally presented on primary AML blast and provoked spontaneous functional response of T cells from treatment naïve OC and, therefore, warrants further development for clinical application.
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Affiliation(s)
- Anja Tatjana Teck
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany
| | - Sabrina Urban
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany
| | - Petra Quass
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany.,Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika Nelde
- Department of Immunology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Anne Letsch
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Antonia Busse
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Juliane Sarah Walz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Ochsenreither
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité Berlin, Berlin, Germany. .,Charité Comprehensive Cancer Center, Charitéplatz 1, 10117, Berlin, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany.
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37
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Ghosh M, Gauger M, Marcu A, Nelde A, Denk M, Schuster H, Rammensee HG, Stevanović S. Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies. Mol Cell Proteomics 2020; 19:432-443. [PMID: 31937595 PMCID: PMC7050110 DOI: 10.1074/mcp.c119.001652] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/09/2020] [Indexed: 12/30/2022] Open
Abstract
For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. To support clinical trials based on HLA-presented tumor-associated antigens, in this study the sensitive LC-MS/MS HLA class I antigen identification pipeline was fully validated for our technical equipment according to the current US Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines.The immunopeptidomes of JY cells with or without spiked-in, isotope labeled peptides, of peripheral blood mononuclear cells of healthy volunteers as well as a chronic lymphocytic leukemia and a bladder cancer sample were reliably identified using a data-dependent acquisition method. As the LC-MS/MS pipeline is used for identification purposes, the validation parameters include accuracy, precision, specificity, limit of detection and robustness.
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Affiliation(s)
- Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; Natural and Medical Science Institute at the University of Tübingen (NMI), Reutlingen, Germany
| | - Marion Gauger
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Monika Denk
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; German Cancer Research Center (DKFZ) partner site and German Cancer Consortium (DKTK) Tübingen, Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; German Cancer Research Center (DKFZ) partner site and German Cancer Consortium (DKTK) Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany; German Cancer Research Center (DKFZ) partner site and German Cancer Consortium (DKTK) Tübingen, Tübingen, Germany.
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38
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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] [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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39
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Biernacki MA, Bleakley M. Neoantigens in Hematologic Malignancies. Front Immunol 2020; 11:121. [PMID: 32117272 PMCID: PMC7033457 DOI: 10.3389/fimmu.2020.00121] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/16/2020] [Indexed: 12/18/2022] Open
Abstract
T cell cancer neoantigens are created from peptides derived from cancer-specific aberrant proteins, such as mutated and fusion proteins, presented in complex with human leukocyte antigens on the cancer cell surface. Because expression of the aberrant target protein is exclusive to malignant cells, immunotherapy directed against neoantigens should avoid “on-target, off-tumor” toxicity. The efficacy of neoantigen vaccines in melanoma and glioblastoma and of adoptive transfer of neoantigen-specific T cells in epithelial tumors indicates that neoantigens are valid therapeutic targets. Improvements in sequencing technology and innovations in antigen discovery approaches have facilitated the identification of neoantigens. In comparison to many solid tumors, hematologic malignancies have few mutations and thus fewer potential neoantigens. Despite this, neoantigens have been identified in a wide variety of hematologic malignancies. These include mutated nucleophosmin1 and PML-RARA in acute myeloid leukemia, ETV6-RUNX1 fusions and other mutated proteins in acute lymphoblastic leukemia, BCR-ABL1 fusions in chronic myeloid leukemia, driver mutations in myeloproliferative neoplasms, immunoglobulins in lymphomas, and proteins derived from patient-specific mutations in chronic lymphoid leukemias. We will review advances in the field of neoantigen discovery, describe the spectrum of identified neoantigens in hematologic malignancies, and discuss the potential of these neoantigens for clinical translation.
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Affiliation(s)
- Melinda A Biernacki
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington, Seattle, WA, United States
| | - Marie Bleakley
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
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40
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Croft NP. Peptide Presentation to T Cells: Solving the Immunogenic Puzzle: Systems Immunology Profiling of Antigen Presentation for Prediction of CD8 + T Cell Immunogenicity. Bioessays 2020; 42:e1900200. [PMID: 31958157 DOI: 10.1002/bies.201900200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Indexed: 02/02/2023]
Abstract
The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real-time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic-to elicit a T cell response-has remained both enigmatic and a long sought-after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.
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Affiliation(s)
- Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
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41
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Hardy MP, Vincent K, Perreault C. The Genomic Landscape of Antigenic Targets for T Cell-Based Leukemia Immunotherapy. Front Immunol 2019; 10:2934. [PMID: 31921187 PMCID: PMC6933603 DOI: 10.3389/fimmu.2019.02934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
Intensive fundamental and clinical research in cancer immunotherapy has led to the emergence and evolution of two parallel universes with surprisingly little interactions: the realm of hematologic malignancies and that of solid tumors. Treatment of hematologic cancers using allogeneic hematopoietic cell transplantation (AHCT) serendipitously led to the discovery that T cells specific for minor histocompatibility antigens (MiHAs) could cure hematopoietic cancers. Besides, studies based on treatment of solid tumor with ex vivo-expanded tumor infiltrating lymphocytes or immune checkpoint therapy demonstrated that anti-tumor responses could be achieved by targeting tumor-specific antigens (TSAs). It is our contention that much insight can be gained by sharing the tremendous amount of data generated in the two-abovementioned universes. Our perspective article has two specific goals. First, to discuss the value of methods currently used for MiHA and TSA discovery and to explain the key role of mass spectrometry analyses in this process. Second, to demonstrate the importance of broadening the scope of TSA discovery efforts beyond classic annotated protein-coding genomic sequences.
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Affiliation(s)
- Marie-Pierre Hardy
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Krystel Vincent
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Claude Perreault
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
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42
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Roerden M, Nelde A, Walz JS. Neoantigens in Hematological Malignancies-Ultimate Targets for Immunotherapy? Front Immunol 2019; 10:3004. [PMID: 31921218 PMCID: PMC6934135 DOI: 10.3389/fimmu.2019.03004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
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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43
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Perez MAS, Bassani-Sternberg M, Coukos G, Gfeller D, Zoete V. Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands. Front Immunol 2019; 10:2731. [PMID: 31824508 PMCID: PMC6883762 DOI: 10.3389/fimmu.2019.02731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/07/2019] [Indexed: 12/31/2022] Open
Abstract
Recent clinical developments in antitumor immunotherapy involving T-cell related therapeutics have led to a renewed interest for human leukocyte antigen class I (HLA-I) binding peptides, given their potential use as peptide vaccines. Databases of HLA-I binding peptides hold therefore information on therapeutic targets essential for understanding immunity. In this work, we use in depth and accurate HLA-I peptidomics datasets determined by mass-spectrometry (MS) and analyze properties of the HLA-I binding peptides with structure-based computational approaches. HLA-I binding peptides are studied grouping all alleles together or in allotype-specific contexts. We capitalize on the increasing number of structurally determined proteins to (1) map the 3D structure of HLA-I binding peptides into the source proteins for analyzing their secondary structure and solvent accessibility in the protein context, and (2) search for potential differences between these properties in HLA-I binding peptides and in a reference dataset of HLA-I motif-like peptides. This is performed by an in-house developed heuristic search that considers peptides across all the human proteome and converges to a collection of peptides that exhibit exactly the same motif as the HLA-I peptides. Our results, based on 9-mers matched to protein 3D structures, clearly show enriched sampling for HLA-I presentation of helical fragments in the source proteins. This enrichment is significant, as compared to 9-mer HLA-I motif-like peptides, and is not entirely explained by the helical propensity of the preferred residues in the HLA-I motifs. We give possible hypothesis for the secondary structure biases observed in HLA-I peptides. This contribution is of potential interest for researchers working in the field of antigen presentation and proteolysis. This knowledge refines the understanding of the rules governing antigen presentation and could be added to the parameters of the current peptide-MHC class I binding predictors to increase their antigen predictive ability.
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Affiliation(s)
- Marta A S Perez
- Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Human Integrated Tumor Immunology Discovery Engine, Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Human Integrated Tumor Immunology Discovery Engine, Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Computational Cancer Biology, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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44
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Zhang X, Qi Y, Zhang Q, Liu W. Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy. Biomed Pharmacother 2019; 120:109542. [PMID: 31629254 DOI: 10.1016/j.biopha.2019.109542] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
One of the challenges for cancer vaccine and adoptive T-cell-based immunotherapy is to identify the major histocompatibility complex (MHC)-associated non-self neoantigens recognized by T cells. T cell epitope in silico prediction algorithms have been widely used for neoantigen prediction; nonetheless, this platform lacks the experimental evidence of directly identification of the presented epitopes on cell surface. Currently, mass spectrometry (MS)-based proteomics is an advanced analytical technology for large-scale peptide sequencing, which has become a powerful tool for directly profiling the immunopeptidome presented by MHC molecules. Integrating with next-generation sequencing, proteogenomic analysis provides the "gold standard" for neoantigen identification at protein level. This method discovers the tumor-specific neoantigens derived from somatic mutations, proteasome splicing, noncoding RNA, and post-translational modified antigens. Herein, we review basis of antigen processing and presentation, tumor antigen classification, existing approaches for neoantigen discovery, quantitative proteomics, epitope prediction programs, and advantages and drawbacks of proteomics workflow for MHC immunopeptidome profiling. Furthermore, we summarize 40 recently published reports addressing the fundamental theory, breakthrough and most advanced updates for the mass spectrometry-based neoantigen discovery for cancer immunotherapy.
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Affiliation(s)
- Xiaomei Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Yue Qi
- Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA
| | - Qi Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA.
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45
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Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O. MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. J Proteome Res 2019; 18:3876-3884. [DOI: 10.1021/acs.jproteome.9b00313] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Stefan Stevanović
- German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen 72076, Germany
| | | | - Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
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46
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Identification of Immunodominant HIV-1 Epitopes Presented by HLA-C*12:02, a Protective Allele, Using an Immunopeptidomics Approach. J Virol 2019; 93:JVI.00634-19. [PMID: 31217245 PMCID: PMC6694829 DOI: 10.1128/jvi.00634-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023] Open
Abstract
Despite the fact that the cell surface expression level of HLA-C on both uninfected and HIV-infected cells is lower than those of HLA-A and -B, increasing evidence suggests an important role for HLA-C and HLA-C-restricted CD8+ T cell responses in determining the efficiency of viral control in HIV-1-infected individuals. Nonetheless, HLA-C-restricted T cell responses are much less well studied than HLA-A/B-restricted ones, and relatively few optimal HIV-1 CD8+ T cell epitopes restricted by HLA-C alleles have been defined. Recent improvements in the sensitivity of mass spectrometry (MS)-based approaches for profiling the immunopeptidome present an opportunity for epitope discovery on a large scale. Here, we employed an MS-based immunopeptidomic strategy to characterize HIV-1 peptides presented by a protective allele, HLA-C*12:02. We identified a total of 10,799 unique 8- to 12-mer peptides, including 15 HIV-1 peptides. The latter included 2 previously reported immunodominant HIV-1 epitopes, and analysis of T cell responses to the other HIV-1 peptides detected revealed an additional immunodominant epitope. These findings illustrate the utility of MS-based approaches for epitope definition and emphasize the capacity of HLA-C to present immunodominant T cell epitopes in HIV-infected individuals, indicating the importance of further evaluation of HLA-C-restricted responses to identify novel targets for HIV-1 prophylactic and therapeutic strategies.IMPORTANCE Mass spectrometry (MS)-based approaches are increasingly being employed for large-scale identification of HLA-bound peptides derived from pathogens, but only very limited profiling of the HIV-1 immunopeptidome has been conducted to date. Notably, a growing body of evidence has recently begun to indicate a protective role for HLA-C in HIV-1 infection, which may suggest that despite the fact that levels of HLA-C expression on both uninfected and HIV-1-infected cells are lower than those of HLA-A/B, HLA-C still presents epitopes to CD8+ T cells effectively. To explore this, we analyzed HLA-C*12:02-restricted HIV-1 peptides presented on HIV-1-infected cells expressing only HLA-C*12:02 (a protective allele) using liquid chromatography-tandem MS (LC-MS/MS). We identified a number of novel HLA-C*12:02-bound HIV-1 peptides and showed that although the majority of them did not elicit T cell responses during natural infection in a Japanese cohort, they included three immunodominant epitopes, emphasizing the contribution of HLA-C to epitope presentation on HIV-infected cells.
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Narayan R, Olsson N, Wagar LE, Medeiros BC, Meyer E, Czerwinski D, Khodadoust MS, Zhang L, Schultz L, Davis MM, Elias JE, Levy R. Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin. PLoS One 2019; 14:e0219547. [PMID: 31291378 PMCID: PMC6619824 DOI: 10.1371/journal.pone.0219547] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/20/2019] [Indexed: 12/31/2022] Open
Abstract
Somatic mutations in cancer are a potential source of cancer specific neoantigens. Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals. We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapeutic approaches. Here we sought to study the HLA Class I and II immunopeptidome of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry to evaluate for endogenous mutation-bearing HLA ligands from common shared AML mutations. We identified two endogenous, mutation-bearing HLA Class I ligands from nucleophosmin (NPM1). The ligands, AVEEVSLRK from two patient samples and C(cys)LAVEEVSL from OCI-AML3, are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively. Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous HLA ligands from mutated NPM1 supports future studies evaluating immunotherapeutic approaches against this shared target, for this subset of patients with AML.
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Affiliation(s)
- Rupa Narayan
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, United States of America
- * E-mail:
| | - Niclas Olsson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States of America
| | - Lisa E. Wagar
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States of America
| | - Bruno C. Medeiros
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, United States of America
| | - Everett Meyer
- Department of Medicine, Division of Blood and Marrow Transplantation, Stanford University, Stanford, CA, United States of America
| | - Debra Czerwinski
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, United States of America
| | - Michael S. Khodadoust
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, United States of America
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States of America
| | - Liora Schultz
- Department of Pediatrics, Division of Hematology/Oncology, Stanford University, Stanford, CA, United States of America
| | - Mark M. Davis
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States of America
| | - Joshua E. Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States of America
| | - Ron Levy
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, United States of America
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Bauer J, Nelde A, Bilich T, Walz JS. Antigen Targets for the Development of Immunotherapies in Leukemia. Int J Mol Sci 2019; 20:ijms20061397. [PMID: 30897713 PMCID: PMC6471800 DOI: 10.3390/ijms20061397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
Abstract
Immunotherapeutic approaches, including allogeneic stem cell transplantation and donor lymphocyte infusion, have significantly improved the prognosis of leukemia patients. Further efforts are now focusing on the development of immunotherapies that are able to target leukemic cells more specifically, comprising monoclonal antibodies, chimeric antigen receptor (CAR) T cells, and dendritic cell- or peptide-based vaccination strategies. One main prerequisite for such antigen-specific approaches is the selection of suitable target structures on leukemic cells. In general, the targets for anti-cancer immunotherapies can be divided into two groups: (1) T-cell epitopes relying on the presentation of peptides via human leukocyte antigen (HLA) molecules and (2) surface structures, which are HLA-independently expressed on cancer cells. This review discusses the most promising tumor antigens as well as the underlying discovery and selection strategies for the development of anti-leukemia immunotherapies.
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Affiliation(s)
- Jens Bauer
- Department of Hematology and Oncology, University Hospital Tübingen, 72076 Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany.
| | - Annika Nelde
- Department of Hematology and Oncology, University Hospital Tübingen, 72076 Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany.
| | - Tatjana Bilich
- Department of Hematology and Oncology, University Hospital Tübingen, 72076 Tübingen, Germany.
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany.
| | - Juliane S Walz
- Department of Hematology and Oncology, University Hospital Tübingen, 72076 Tübingen, Germany.
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The HLA ligandome landscape of chronic myeloid leukemia delineates novel T-cell epitopes for immunotherapy. Blood 2019; 133:550-565. [DOI: 10.1182/blood-2018-07-866830] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/01/2018] [Indexed: 12/30/2022] Open
Abstract
Abstract
Antileukemia immunity plays an important role in disease control and maintenance of tyrosine kinase inhibitor (TKI)-free remission in chronic myeloid leukemia (CML). Thus, antigen-specific immunotherapy holds promise for strengthening immune control in CML but requires the identification of CML-associated targets. In this study, we used a mass spectrometry–based approach to identify naturally presented HLA class I– and class II–restricted peptides in primary CML samples. Comparative HLA ligandome profiling using a comprehensive dataset of different hematological benign specimens and samples from CML patients in deep molecular remission delineated a panel of novel frequently presented CML-exclusive peptides. These nonmutated target antigens are of particular relevance because our extensive data-mining approach suggests the absence of naturally presented BCR-ABL– and ABL-BCR–derived HLA-restricted peptides and the lack of frequent tumor-exclusive presentation of known cancer/testis and leukemia-associated antigens. Functional characterization revealed spontaneous T-cell responses against the newly identified CML-associated peptides in CML patient samples and their ability to induce multifunctional and cytotoxic antigen-specific T cells de novo in samples from healthy volunteers and CML patients. Thus, these antigens are prime candidates for T-cell–based immunotherapeutic approaches that may prolong TKI-free survival and even mediate cure of CML patients.
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