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Zhu L, Cui X, Yan Z, Tao Y, Shi L, Zhang X, Yao Y, Shi L. Design and evaluation of a multi-epitope DNA vaccine against HPV16. Hum Vaccin Immunother 2024; 20:2352908. [PMID: 38780076 PMCID: PMC11123455 DOI: 10.1080/21645515.2024.2352908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
Cervical cancer, among the deadliest cancers affecting women globally, primarily arises from persistent infection with high-risk human papillomavirus (HPV). To effectively combat persistent infection and prevent the progression of precancerous lesions into malignancy, a therapeutic HPV vaccine is under development. This study utilized an immunoinformatics approach to predict epitopes of cytotoxic T lymphocytes (CTLs) and helper T lymphocytes (HTLs) using the E6 and E7 oncoproteins of the HPV16 strain as target antigens. Subsequently, through meticulous selection of T-cell epitopes and other necessary elements, a multi-epitope vaccine was constructed, exhibiting good immunogenic, physicochemical, and structural characteristics. Furthermore, in silico simulations showed that the vaccine not only interacted well with toll-like receptors (TLR2/TLR3/TLR4), but also induced a strong innate and adaptive immune response characterized by elevated Th1-type cytokines, such as interferon-gamma (IFN-γ) and interleukin-2 (IL2). Additionally, our study investigated the effects of different immunization intervals on immune responses, aiming to optimize a time-efficient immunization program. In animal model experiments, the vaccine exhibited robust immunogenic, therapeutic, and prophylactic effects. Administered thrice, it consistently induced the expansion of specific CD4 and CD8 T cells, resulting in substantial cytokines release and increased proliferation of memory T cell subsets in splenic cells. Overall, our findings support the potential of this multi-epitope vaccine in combating HPV16 infection and signify its candidacy for future HPV vaccine development.
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Affiliation(s)
- Lanfang Zhu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xiangjie Cui
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Zhiling Yan
- Department of Gynaecologic Oncology, The No. 3 Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yufen Tao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Lei Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xinwen Zhang
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Li Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
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2
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Quiros-Fernandez I, Libório-Ramos S, Leifert L, Schönfelder B, Vlodavsky I, Cid-Arregui A. Dual T cell receptor/chimeric antigen receptor engineered NK-92 cells targeting the HPV16 E6 oncoprotein and the tumor-associated antigen L1CAM exhibit enhanced cytotoxicity and specificity against tumor cells. J Med Virol 2024; 96:e29630. [PMID: 38659368 DOI: 10.1002/jmv.29630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/08/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
The human papillomavirus type 16 (HPV16) causes a large fraction of genital and oropharyngeal carcinomas. To maintain the transformed state, the tumor cells must continuously synthesize the E6 and E7 viral oncoproteins, which makes them tumor-specific antigens. Indeed, specific T cell responses against them have been well documented and CD8+ T cells engineered to express T cell receptors (TCRs) that recognize epitopes of E6 or E7 have been tested in clinical studies with promising results, yet with limited clinical success. Using CD8+ T cells from peripheral blood of healthy donors, we have identified two novel TCRs reactive to an unexplored E618-26 epitope. These TCRs showed limited standalone cytotoxicity against E618-26-HLA-A*02:01-presenting tumor cells. However, a single-signaling domain chimeric antigen receptor (ssdCAR) targeting L1CAM, a cell adhesion protein frequently overexpressed in HPV16-induced cancer, prompted a synergistic effect that significantly enhanced the cytotoxic capacity of NK-92/CD3/CD8 cells armored with both TCR and ssdCAR when both receptors simultaneously engaged their respective targets, as shown by live microscopy of 2-D and 3-D co-cultures. Thus, virus-specific TCRs from the CD8+ T cell repertoire of healthy donors can be combined with a suitable ssdCAR to enhance the cytotoxic capacity of the effector cells and, indirectly, their specificity.
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MESH Headings
- Humans
- Oncogene Proteins, Viral/immunology
- Oncogene Proteins, Viral/genetics
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Repressor Proteins/immunology
- Repressor Proteins/genetics
- CD8-Positive T-Lymphocytes/immunology
- Killer Cells, Natural/immunology
- Human papillomavirus 16/immunology
- Human papillomavirus 16/genetics
- Cytotoxicity, Immunologic
- Cell Line, Tumor
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Affiliation(s)
- Isaac Quiros-Fernandez
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Research Center on Tropical Diseases (CIET)/Research Center on Surgery and Cancer (CICICA), Faculty of Microbiology, Universidad de Costa Rica, San Jose, Costa Rica
| | - Sofia Libório-Ramos
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Leifert
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bruno Schönfelder
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Angel Cid-Arregui
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
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3
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Guo N, Niu Z, Yan Z, Liu W, Shi L, Li C, Yao Y, Shi L. Immunoinformatics Design and In Vivo Immunogenicity Evaluation of a Conserved CTL Multi-Epitope Vaccine Targeting HPV16 E5, E6, and E7 Proteins. Vaccines (Basel) 2024; 12:392. [PMID: 38675774 PMCID: PMC11053576 DOI: 10.3390/vaccines12040392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/01/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Human papillomavirus type 16 (HPV16) infection is responsible for more than 50% of global cervical cancer cases. The development of a vaccine based on cytotoxic T-lymphocyte (CTL) epitopes is a promising strategy for eliminating pre-existing HPV infections and treating patients with cervical cancer. In this study, an immunoinformatics approach was used to predict HLA-I-restricted CTL epitopes in HPV16 E5, E6, and E7 proteins, and a set of conserved CTL epitopes co-restricted by human/murine MHCs was screened and characterized, with the set containing three E5, four E6, and four E7 epitopes. Subsequently, the immunogenicity of the epitope combination was assessed in mice, and the anti-tumor effects of the multi-epitope peptide vaccine E5E6E7pep11 and the recombinant protein vaccine CTB-Epi11E567 were evaluated in the TC-1 mouse tumor model. The results demonstrated that mixed epitope peptides could induce antigen-specific IFN-γ secretion in mice. Prophylactic immunization with E5E6E7pep11 and CTB-Epi11E567 was found to provide 100% protection against tumor growth in mice. Moreover, both types of the multi-epitope vaccine significantly inhibited tumor growth and prolonged mouse survival. In conclusion, in this study, a multi-epitope vaccine targeting HPV16 E5, E6, and E7 proteins was successfully designed and evaluated, demonstrating potential immunogenicity and anti-tumor effects and providing a promising strategy for immunotherapy against HPV-associated tumors.
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Affiliation(s)
- Ni Guo
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; (N.G.); (Z.N.); (W.L.); (C.L.)
| | - Zhixin Niu
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; (N.G.); (Z.N.); (W.L.); (C.L.)
| | - Zhiling Yan
- Department of Gynaecologic Oncology, Peking University Cancer Hospital Yunnan & Yunnan Cancer Hospital & The Third Affiliated Hospital of Kunming Medical University, Kunming 650118, China;
| | - Weipeng Liu
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; (N.G.); (Z.N.); (W.L.); (C.L.)
| | - Lei Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China;
| | - Chuanyin Li
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; (N.G.); (Z.N.); (W.L.); (C.L.)
| | - Yufeng Yao
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China; (N.G.); (Z.N.); (W.L.); (C.L.)
| | - Li Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, China;
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Xiang N, Zhang K, Zhao Y, Xu C, Zhang X, Meng S. Characterization of antigen presentation capability for neoantigen-based products using targeted LC-MS/MS method. J Pharm Biomed Anal 2024; 240:115886. [PMID: 38184916 DOI: 10.1016/j.jpba.2023.115886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 01/09/2024]
Abstract
The generation of an immune response in neoantigen-based products relies on antigen presentation, which is closely analyzed by bioassays for T-cell functions such as tetramer or cytokine release. Mass spectrometry (MS) has the potential to directly assess the antigen-presenting capability of antigen-presenting cells (APCs), offering advantages such as speed, multi-target analysis, robustness, and ease of transferability. However, it has not been used for quality control of these products due to challenges in sensitivity, including the number of cells and peptide diversity. In this study, we describe the development and validation of an improved targeted LC-MS/MS method with high sensitivity for characterizing antigen presentation, which could be applied in the quality control of neoantigen-based products. The parameters for the extraction were carefully optimized by different short peptides. Highly sensitive targeted triple quadrupole mass spectrometry combined with ultra-high performance liquid chromatography (UHPLC) was employed using a selective ion monitoring mode (Multiple Reaction Monitoring, MRM). Besides, we successfully implemented robust quality control peptides to ensure the reliability and consistency of this method, which proved invaluable for different APCs. With reference to the guidelines from ICH Q2 (R2), M10, as well as considering the specific attributes of the product itself, we validated the method for selectivity, specificity, sensitivity, limit of detection (LOD), recovery rate, matrix effect, repeatability, and application in dendritic cells (DCs) associated with neoantigen-based products. The validation process yields satisfactory results. Combining this approach with T cell assays will comprehensively assess cell product quality attributes from physicochemical and biological perspectives.
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Affiliation(s)
- Nan Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China
| | - Kehua Zhang
- The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China
| | - Yinghua Zhao
- SCIEX China, 5F, Building 1, No. 24 Jiuxianqiao Middle Road, Chaoyang District, Beijing, China
| | - Chongfeng Xu
- The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China
| | - Xiuqing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shufang Meng
- The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China.
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5
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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6
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Ternette N, Adamopoulou E, Purcell AW. How mass spectrometric interrogation of MHC class I ligandomes has advanced our understanding of immune responses to viruses. Semin Immunol 2023; 68:101780. [PMID: 37276649 DOI: 10.1016/j.smim.2023.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Affiliation(s)
- Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK.
| | - Eleni Adamopoulou
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford OX37BN, UK
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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7
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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8
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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Peng X, Woodhouse I, Hancock G, Parker R, Marx K, Müller J, Salatino S, Partridge T, Nicastri A, Liao H, Kruppa G, Hellner K, Dorrell L, Ternette N. Novel canonical and non-canonical viral antigens extend current targets for immunotherapy of HPV-driven cervical cancer. iScience 2023; 26:106101. [PMID: 36876126 PMCID: PMC9978627 DOI: 10.1016/j.isci.2023.106101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Current immunotherapeutic approaches for human papillomavirus (HPV)-driven cervical cancer target the viral oncogenes E6 and E7. We report viral canonical and alternative reading frame (ARF)-derived sequences presented on cervical tumor cells, including antigens encoded by the conserved viral gene E1. We confirm immunogenicity of the identified viral peptides in HPV-positive women, and women with cervical intraepithelial neoplasia. We observe consistent transcription of the E1, E6, and E7 genes in 10 primary cervical tumor resections from the four most common high-risk HPV subtypes (HPV16, 18, 31, and 45), suggesting the suitability of E1 as therapeutic target. We finally confirm HLA presentation of canonical peptides derived from E6 and E7, and ARF-derived viral peptides from a reverse-strand transcript spanning the HPV E1 and E2 genes in primary human cervical tumor tissue. Our results extend currently known viral immunotherapeutic targets in cervical cancer and highlight E1 as an important cervical cancer antigen.
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Affiliation(s)
- Xu Peng
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Isaac Woodhouse
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
| | - Gemma Hancock
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Kristina Marx
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Julius Müller
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Silvia Salatino
- Wellcome Centre Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
| | - Annalisa Nicastri
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Hanqing Liao
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
| | - Gary Kruppa
- Bruker Daltonics, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Karin Hellner
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, John Radcliffe Hospital, OX3 9DU Oxford, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, OX3 7FZ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
- Immunocore Ltd., OX14 4RY Abingdon, UK
| | - Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, OX3 7DQ Oxford, UK
- The Jenner Institute, University of Oxford, OX3 7DQ Oxford, UK
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Schifflers C, Zottnick S, Förster JD, Kruse S, Yang R, Wiethoff H, Bozza M, Hoppe-Seyler K, Heikenwälder M, Harbottle RP, Michiels C, Riemer AB. Development of an Orthotopic HPV16-Dependent Base of Tongue Tumor Model in MHC-Humanized Mice. Pathogens 2023; 12:pathogens12020188. [PMID: 36839460 PMCID: PMC9958775 DOI: 10.3390/pathogens12020188] [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: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCC) caused by infections with high-risk human papillomaviruses (HPV) are responsible for an increasing number of head and neck cancers, particularly in the oropharynx. Despite the significant biological differences between HPV-driven and HPV-negative HNSCC, treatment strategies are similar and not HPV targeted. HPV-driven HNSCC are known to be more sensitive to treatment, particularly to radiotherapy, which is at least partially due to HPV-induced immunogenicity. The development of novel therapeutic strategies that are specific for HPV-driven cancers requires tumor models that reflect as closely as possible the characteristics and complexity of human tumors and their response to treatment. Current HPV-positive cancer models lack one or more hallmarks of their human counterpart. This study presents the development of a new HPV16 oncoprotein-dependent tumor model in MHC-humanized mice, modeling the major biologic features of HPV-driven tumors and presenting HLA-A2-restricted HPV16 epitopes. Furthermore, this model was developed to be orthotopic (base of tongue). Thus, it also reflects the correct tumor microenvironment of HPV-driven HNSCC. The cancer cells are implanted in a manner that allows the exact control of the anatomical location of the developing tumor, thereby homogenizing tumor growth. In conclusion, the new model is suited to study HPV16-specific therapeutic vaccinations and other immunotherapies, as well as tumor-targeted interventions, such as surgery or radiotherapy, or a combination of all these modalities.
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Affiliation(s)
- Christoph Schifflers
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Cell Biology Research Unit (URBC)–Namur Research Institute for Life Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Samantha Zottnick
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Jonas D. Förster
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Sebastian Kruse
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Ruwen Yang
- Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hendrik Wiethoff
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Helmholtz-University Group Cell Plasticity and Epigenetic Remodeling, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Matthias Bozza
- DNA Vector Laboratory, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Karin Hoppe-Seyler
- Molecular Therapy of Virus-Associated Cancers, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mathias Heikenwälder
- Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard P. Harbottle
- DNA Vector Laboratory, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Carine Michiels
- Cell Biology Research Unit (URBC)–Namur Research Institute for Life Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Angelika B. Riemer
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Molecular Vaccine Design, German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-3820
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11
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Mohan N, Wellach K, Özerdem C, Veits N, Förster JD, Foehr S, Bonsack M, Riemer AB. Effects of hypoxia on antigen presentation and T cell-based immune recognition of HPV16-transformed cells. Front Immunol 2022; 13:918528. [DOI: 10.3389/fimmu.2022.918528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Attempts to develop a therapeutic vaccine against human papillomavirus (HPV)-induced malignancies have mostly not been clinically successful to date. One reason may be the hypoxic microenvironment present in most tumors, including cervical cancer. Hypoxia dysregulates the levels of human leukocyte antigen (HLA) class I molecules in different tumor entities, impacts the function of cytotoxic T cells, and leads to decreased protein levels of the oncoproteins E6 and E7 in HPV-transformed cells. Therefore, we investigated the effect of hypoxia on the presentation of HPV16 E6- and E7-derived epitopes in cervical cancer cells and its effect on epitope-specific T cell cytotoxicity. Hypoxia induced downregulation of E7 protein levels in all analyzed cell lines, as assessed by Western blotting. However, contrary to previous reports, no perturbation of antigen processing and presentation machinery (APM) components and HLA-A2 surface expression upon hypoxia treatment was detected by mass spectrometry and flow cytometry, respectively. Cytotoxicity assays performed in hypoxic conditions showed differential effects on the specific killing of HPV16-positive cervical cancer cells by epitope-specific CD8+ T cell lines in a donor- and peptide-specific manner. Effects of hypoxia on the expression of PD-L1 were ruled out by flow cytometry analysis. Altogether, our results under hypoxia show a decreased expression of E6 and E7, but an intact APM, and epitope- and donor-dependent effects on T cell cytotoxicity towards HPV16-positive target cells. This suggests that successful immunotherapies can be developed for hypoxic HPV-induced cervical cancer, with careful choice of target epitopes, and ideally in combination with hypoxia-alleviating measures.
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12
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Becker JP, Riemer AB. The Importance of Being Presented: Target Validation by Immunopeptidomics for Epitope-Specific Immunotherapies. Front Immunol 2022; 13:883989. [PMID: 35464395 PMCID: PMC9018990 DOI: 10.3389/fimmu.2022.883989] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Presentation of tumor-specific or tumor-associated peptides by HLA class I molecules to CD8+ T cells is the foundation of epitope-centric cancer immunotherapies. While often in silico HLA binding predictions or in vitro immunogenicity assays are utilized to select candidates, mass spectrometry-based immunopeptidomics is currently the only method providing a direct proof of actual cell surface presentation. Despite much progress in the last decade, identification of such HLA-presented peptides remains challenging. Here we review typical workflows and current developments in the field of immunopeptidomics, highlight the challenges which remain to be solved and emphasize the importance of direct target validation for clinical immunotherapy development.
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Affiliation(s)
- Jonas P Becker
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy and Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
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13
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A TCR mimic monoclonal antibody for the HPV-16 E7-epitope p11-19/HLA-A*02:01 complex. PLoS One 2022; 17:e0265534. [PMID: 35298559 PMCID: PMC8929633 DOI: 10.1371/journal.pone.0265534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
More effective treatments are needed for human papilloma virus (HPV)-induced cancers despite HPV virus vaccination. The oncogenic HPV protein targets are currently undruggable and intracellular and therefore there are no antibodies to these targets. Here we report the discovery of TCR mimic monoclonal antibodies (TCRm mAb) specific for the HPV E7 protein p11-19, YMLDLQPET, when presented on the cell surface in the context of HLA-A*02:01 by use of human phage display libraries. One of the mAbs, 3F8, was able to specifically mediate T cell- redirected cytotoxicity, in a bispecific T cell engager (BiTE) form. While further studies are required to assess the therapeutic potential of this approach, the study provided the proof of concept that TCRm mAb could be a therapeutic strategy for HPV-induced human cancers.
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14
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Watts E, Potts GK, Ready DB, George Thompson AM, Lee J, Escobar EE, Patterson MJ, Brodbelt JS. Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2021; 93:13134-13142. [PMID: 34553926 DOI: 10.1021/acs.analchem.1c01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying major histocompatibility complex (MHC) class I immunopeptide antigens represents a key step in the development of immune-based targeted therapeutics and vaccines. However, the complete characterization of these antigens by tandem mass spectrometry remains challenging due to their short sequence length, high degree of hydrophobicity, and/or lack of sufficiently basic amino acids. This study seeks to address the potential for 193 nm ultraviolet photodissociation (UVPD) to improve the analysis of MHC class I immunopeptides by offering enhanced characterization of these sequences in lower charge states and differentiation of prominent isomeric leucine and isoleucine residues in the HLA-A*02:01 motif. Although electron transfer dissociation-higher energy collisional dissociation (EThcD) offered some success in the differentiation of leucine and isoleucine, 193 nm UVPD was able to confirm the identity of nearly 60% of leucine and isoleucine residues in a synthetic peptide mixture. Furthermore, 193 nm UVPD led to significantly more peptide identifications and higher scoring metrics than EThcD for peptides obtained from immunoprecipitation of MHC class I immunopeptides from in vitro cell culture. Additionally, 193 nm UVPD represents a promising complementary technique to higher-energy collisional dissociation (HCD), in which 424 of the 2593 peptides identified by 193 nm UVPD were not identified by HCD in HLA-A*02:01-specific immunoprecipitation and 804 of the 3300 peptides identified by 193 nm UVPD were not identified by HCD for pan HLA-A, -B, and -C immunoprecipitation. These results highlight that 193 nm UVPD offers an option for the characterization of immunopeptides, including differentiation of leucine and isoleucine residues.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | - Gregory K Potts
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Damien B Ready
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | | | - Janice Lee
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
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15
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Wang X, Sandberg ML, Martin AD, Negri KR, Gabrelow GB, Nampe DP, Wu ML, McElvain ME, Toledo Warshaviak D, Lee WH, Oh J, Daris ME, Chai F, Yao C, Furney J, Pigott C, Kamb A, Xu H. Potent, Selective CARs as Potential T-Cell Therapeutics for HPV-positive Cancers. J Immunother 2021; 44:292-306. [PMID: 34432728 PMCID: PMC8415731 DOI: 10.1097/cji.0000000000000386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Abstract
Next-generation T-cell therapies will likely continue to utilize T-cell receptors (TCRs) and chimeric antigen receptors (CARs) because each receptor type has advantages. TCRs often possess exceptional properties even when tested unmodified from patients' T cells. CARs are generally less sensitive, possibly because their ligand-binding domains are grafted from antibodies selected for binding affinity or avidity and not broadly optimized for a functional response. Because of the disconnect between binding and function among these receptor types, the ultimate potential of CARs optimized for sensitivity and selectivity is not clear. Here, we focus on a thoroughly studied immuno-oncology target, the HLA-A*02/HPV-E629-38 complex, and show that CARs can be optimized by a combination of high-throughput binding screens and low-throughput functional assays to have comparable activity to clinical TCRs in acute assays in vitro. These results provide a case study for the challenges and opportunities of optimizing high-performing CARs, especially in the context of targets utilized naturally by TCRs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Julyun Oh
- A2 Biotherapeutics, Agoura Hills, CA
| | | | - Falene Chai
- Innovative Targeting Solutions, Vancouver, BC, Canada
| | - Christine Yao
- Innovative Targeting Solutions, Vancouver, BC, Canada
| | - James Furney
- Innovative Targeting Solutions, Vancouver, BC, Canada
| | - Craig Pigott
- Innovative Targeting Solutions, Vancouver, BC, Canada
| | | | - Han Xu
- A2 Biotherapeutics, Agoura Hills, CA
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16
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Wang X, Martin AD, Negri KR, McElvain ME, Oh J, Wu ML, Lee WH, Ando Y, Gabrelow GB, Toledo Warshaviak D, Sandberg ML, Xu H, Kamb A. Extensive functional comparisons between chimeric antigen receptors and T cell receptors highlight fundamental similarities. Mol Immunol 2021; 138:137-149. [PMID: 34419823 DOI: 10.1016/j.molimm.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022]
Abstract
Though TCRs have been subject to limited engineering in the context of therapeutic design and optimization, they are used largely as found in nature. On the other hand, CARs are artificial, composed of different segments of proteins that function in the immune system. This characteristic raises the possibility of altered response to immune regulatory stimuli. Here we describe a large-scale, systematic comparison of CARs and TCRs across 5 different pMHC targets, with a total of 19 constructs examined in vitro. These functional measurements include CAR- and TCR-mediated activation, proliferation, and cytotoxicity in both acute and chronic settings. Surprisingly, we find no consistent difference between CARs and TCRs as receptor classes with respect to their relative sensitivity to major regulators of T cell activation: PD-L1, CD80/86 and IL-2. Though TCRs often emerge from human blood directly as potent, selective receptors, CARs must be heavily optimized to attain these properties for pMHC targets. Nonetheless, when iteratively improved and compared head to head in functional tests, CARs appear remarkably similar to TCRs with respect to immune modulation.
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Affiliation(s)
- Xueyin Wang
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Aaron D Martin
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Kathleen R Negri
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Michele E McElvain
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Julyun Oh
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Ming-Lun Wu
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Wen-Hua Lee
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Yuta Ando
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Grant B Gabrelow
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | | | - Mark L Sandberg
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States
| | - Han Xu
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States.
| | - Alexander Kamb
- A2 Biotherapeutics, 30301 Agoura Rd., Agoura Hills, CA, 91301, United States.
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17
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Admon A. Are There Indeed Spliced Peptides in the Immunopeptidome? Mol Cell Proteomics 2021; 20:100099. [PMID: 34022431 PMCID: PMC8724635 DOI: 10.1016/j.mcpro.2021.100099] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
The claims that a large fraction of the immunopeptidome is composed of spliced major histocompatibility complex (MHC) peptides have stirred significant excitement and raised controversy. Here, I suggest that there are likely no spliced peptides in the immunopeptidome, and if they exist at all, they are extremely rare. I base this claim on both biochemical and bioinformatics considerations. First, as a reactant in normal proteolytic reactions, water will compete with transpeptidation, which has been suggested as the mechanism of peptide splicing. The high mobility and abundance of water in aqueous solutions renders transpeptidation very inefficient and therefore unlikely to occur. Second, new studies have refuted the bioinformatics assignments to spliced peptides of most of the immunopeptidome MS data, suggesting that the correct assignments are likely other canonical, noncanonical, and post-translationally modified peptides. Therefore, I call for rigorous experimental methodology using heavy stable isotope peptides spiking into the immunoaffinity-purified mixtures of natural MHC peptides and analysis by the highly reliable targeted MS, to claim that MHC peptides are indeed spliced. Peptide splicing was suggested to contribute to the immunopeptidome. I suggest that this idea should be reconsidered based on new evidences. Both biochemical and bioinformatics considerations argue against peptide splicing.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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18
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Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K, Gebert J, Kloor M, Neu-Yilik G, von Knebel Doeberitz M, Hentze MW, Kulozik AE. NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes. iScience 2021; 24:102389. [PMID: 33981976 PMCID: PMC8082087 DOI: 10.1016/j.isci.2021.102389] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 12/22/2022] Open
Abstract
Frameshifted protein sequences elicit tumor-specific T cell-mediated immune responses in microsatellite-unstable (MSI) cancers if presented by HLA class I molecules. However, their expression and presentation are limited by nonsense-mediated RNA decay (NMD). We employed an unbiased immunopeptidomics workflow to analyze MSI HCT-116 cells and identified >10,000 HLA class I-presented peptides including five frameshift-derived InDel neoepitopes. Notably, pharmacological NMD inhibition with 5-azacytidine stabilizes frameshift-bearing transcripts and increases the HLA class I-mediated presentation of InDel neoepitopes. The frameshift mutation underlying one of the identified InDel neoepitopes is highly recurrent in MSI colorectal cancer cell lines and primary patient samples, and immunization with the corresponding neoepitope induces strong CD8+ T cell responses in an HLA-A∗02:01 transgenic mouse model. Our data show directly that pharmacological NMD inhibition augments HLA class I-mediated presentation of immunogenic frameshift-derived InDel neoepitopes thus highlighting the clinical potential of NMD inhibition in anti-cancer immunotherapy strategies.
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Affiliation(s)
- Jonas P. Becker
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Dominic Helm
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Alejandro Hernandez-Sanchez
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Katharina Urban
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Johannes Gebert
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Matthias Kloor
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University, 69120 Heidelberg, Germany
- Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Matthias W. Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Andreas E. Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University, 69120 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University, 69120 Heidelberg, Germany
- Hopp Children's Cancer Center, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
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19
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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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20
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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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21
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HPV16-E7 Protein T Cell Epitope Prediction and Global Therapeutic Peptide Vaccine Design Based on Human Leukocyte Antigen Frequency: An In-Silico Study. Int J Pept Res Ther 2020; 27:365-378. [PMID: 32837456 PMCID: PMC7320846 DOI: 10.1007/s10989-020-10089-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2020] [Indexed: 02/08/2023]
Abstract
Cervical cancer is the second most common leading cause of women's death due to cancer worldwide, about 528,000 patients’ cases and 266,000 deaths per year, related to human papillomavirus (HPV). Peptide-based vaccines being safe, stable, and easy to produce have demonstrated great potential to develop therapeutic HPV vaccine. In this study, the major histocompatibility complex (MHC) class I, class II T cell epitopes of HPV16-E7 were predicted. Therefore, we designed a plan to find the most effective peptides to prompt appropriate immune responses. For this purpose, retrieving protein sequences, conserved region identification, phylogenic tree construction, T cell epitope prediction, epitope-predicted population coverage calculation, and molecular docking were performed consecutively and most effective immune response prompting peptides were selected. Based on different tools index, six CD8+ T cells and six CD4+ epitopes were chosen. This combination of 12 epitopes created a putative global vaccine with a 95.06% population coverage. These identified peptides can be employed further for peptide analysis and can be used as a peptide or poly-epitope candidates for therapeutic vaccine studies to treat HPV-associated cancers.
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22
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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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23
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Ternette N, Purcell AW. Immunopeptidomics Special Issue. Proteomics 2019; 18:e1800145. [PMID: 29949244 DOI: 10.1002/pmic.201800145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, OX3, 7FZ, UK
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
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24
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Bonsack M, Hoppe S, Winter J, Tichy D, Zeller C, Küpper MD, Schitter EC, Blatnik R, Riemer AB. Performance Evaluation of MHC Class-I Binding Prediction Tools Based on an Experimentally Validated MHC–Peptide Binding Data Set. Cancer Immunol Res 2019; 7:719-736. [DOI: 10.1158/2326-6066.cir-18-0584] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 11/16/2022]
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25
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Vormehr M, Reinhard K, Blatnik R, Josef K, Beck JD, Salomon N, Suchan M, Selmi A, Vascotto F, Zerweck J, Wenschuh H, Diken M, Kreiter S, Türeci Ö, Riemer AB, Sahin U. A non-functional neoepitope specific CD8 + T-cell response induced by tumor derived antigen exposure in vivo. Oncoimmunology 2018; 8:1553478. [PMID: 30723585 DOI: 10.1080/2162402x.2018.1553478] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/09/2018] [Accepted: 11/18/2018] [Indexed: 12/21/2022] Open
Abstract
Cancer-associated mutations, mostly single nucleotide variations, can act as neoepitopes and prime targets for effective anti-cancer T-cell immunity. T cells recognizing cancer mutations are critical for the clinical activity of immune checkpoint blockade (ICB) and they are potent vaccine antigens. High frequencies of mutation-specific T cells are rarely spontaneously induced. Hence, therapies that broaden the tumor specific T-cell response are of interest. Here, we analyzed neoepitope-specific CD8+ T-cell responses mounted either spontaneously or after immunotherapy regimens, which induce local tumor inflammation and cell death, in mice bearing tumors of the widely used colon carcinoma cell line CT26. A comprehensive immune reactivity screening of 2474 peptides covering 628 transcribed CT26 point mutations was conducted. All tested treatment regimens were found to induce a single significant CD8+ T-cell response against a non-synonymous D733A point mutation in the Smc3 gene. Surprisingly, even though Smc3 D733A turned out to be the immune-dominant neoepitope in CT26 tumor bearing mice, neither T cells specific for this neoepitope nor their T cell receptors (TCRs) were able to recognize or lyse tumor cells. Moreover, vaccination with the D733A neoepitope did not result in anti-tumoral activity despite induction of specific T cells. This is to our knowledge the first report that neoepitope specific CD8+ T cells primed by tumor-released antigen exposure in vivo can be functionally irrelevant.
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Affiliation(s)
- Mathias Vormehr
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany.,Experimental and Translational Oncology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Katharina Reinhard
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany
| | - Renata Blatnik
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), and Molecular Vaccine Design, German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Kathrin Josef
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), and Molecular Vaccine Design, German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Jan David Beck
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Nadja Salomon
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Martin Suchan
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Abderraouf Selmi
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Fulvia Vascotto
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | | | | | - Mustafa Diken
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany.,TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Sebastian Kreiter
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany.,TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Özlem Türeci
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany
| | - Angelika B Riemer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), and Molecular Vaccine Design, German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Ugur Sahin
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany.,Experimental and Translational Oncology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany.,TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
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26
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Kruse S, Büchler M, Uhl P, Sauter M, Scherer P, Lan TCT, Zottnick S, Klevenz A, Yang R, Rösl F, Mier W, Riemer AB. Therapeutic vaccination using minimal HPV16 epitopes in a novel MHC-humanized murine HPV tumor model. Oncoimmunology 2018; 8:e1524694. [PMID: 30546964 DOI: 10.1080/2162402x.2018.1524694] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/21/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022] Open
Abstract
Therapeutic vaccination as a treatment option for HPV-induced cancers is actively pursued because the two HPV proteins E6 and E7 represent ideal targets for immunotherapy, as they are non-self and expressed in all tumor stages. MHC-humanized mice are valuable tools for the study of therapeutic cancer vaccines - given the availability of a suitable tumor model. Here, we present for the first time an HPV16 tumor model suitable for fully MHC-humanized A2.DR1 mice, PAP-A2 cells, which in contrast to existing HPV16 tumor models allows the exclusive study of HLA-A2- and DR1-mediated immune responses, without any interfering murine MHC-presented epitopes. We used several HPV16 epitopes that were shown to be presented on human cervical cancer cells by mass spectrometry for therapeutic anti-tumor vaccination in the new tumor model. All epitopes were immunogenic when rendered amphiphilic by incorporation into a molecule containing stearic acids. Prophylactic and therapeutic vaccination experiments with the epitope E7/11-19 demonstrated that effective immune responses could be induced with these vaccination approaches in A2.DR1 mice. Interestingly, the combination of E7/11-19 with other immunogenic HPV16 E6/E7 epitopes caused a reduction of vaccine efficacy, although all tested combinations resulted in a survival benefit. In summary, we present the first HPV16 tumor model for exclusive studies of HLA-A2-mediated anti-HPV tumor immune responses and show anti-tumor efficacy of minimal epitope vaccines.
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Affiliation(s)
- Sebastian Kruse
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marleen Büchler
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Philipp Uhl
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Max Sauter
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Scherer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tammy C T Lan
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Samantha Zottnick
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexandra Klevenz
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ruwen Yang
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Rösl
- Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
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27
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RNA editing derived epitopes function as cancer antigens to elicit immune responses. Nat Commun 2018; 9:3919. [PMID: 30254248 PMCID: PMC6156571 DOI: 10.1038/s41467-018-06405-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/30/2018] [Indexed: 02/08/2023] Open
Abstract
In addition to genomic mutations, RNA editing is another major mechanism creating sequence variations in proteins by introducing nucleotide changes in mRNA sequences. Deregulated RNA editing contributes to different types of human diseases, including cancers. Here we report that peptides generated as a consequence of RNA editing are indeed naturally presented by human leukocyte antigen (HLA) molecules. We provide evidence that effector CD8+ T cells specific for edited peptides derived from cyclin I are present in human tumours and attack tumour cells that are presenting these epitopes. We show that subpopulations of cancer patients have increased peptide levels and that levels of edited RNA correlate with peptide copy numbers. These findings demonstrate that RNA editing extends the classes of HLA presented self-antigens and that these antigens can be recognised by the immune system. RNA editing is a biological process that creates sequence variation. Here the authors show that peptides generated as a consequence of RNA editing are naturally presented by human leukocyte antigen (HLA) and serve as antigens to elicit anti-tumour immune responses.
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28
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The role of proteomics in the age of immunotherapies. Mamm Genome 2018; 29:757-769. [PMID: 30046851 DOI: 10.1007/s00335-018-9763-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
Abstract
The antigenic landscape of the adaptive immune response is determined by the peptides presented by immune cells. In recent years, a number of immune-based cancer therapies have been shown to induce remarkable clinical responses through the activation of the patient's immune system. As a result, there is a need to identify immune biomarkers capable of predicting clinical response. Recent advances in proteomics have led to considerable developments in the more comprehensive profiling of the immune response. "Immunoproteomics" utilises a rapidly increasing collection of technologies in order to identify and quantify antigenic peptides or proteins. This includes gel-based, array-based, mass spectrometry (MS), DNA-based, or computer-based (in silico) approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers to a depth not before understood. This review gives an overview of the emerging role of proteomics in improving personalisation of immunotherapy treatment.
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29
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Blatnik R, Mohan N, Bonsack M, Falkenby LG, Hoppe S, Josef K, Steinbach A, Becker S, Nadler WM, Rucevic M, Larsen MR, Salek M, Riemer AB. A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. Proteomics 2018; 18:e1700390. [PMID: 29603667 PMCID: PMC6033010 DOI: 10.1002/pmic.201700390] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/16/2018] [Indexed: 12/12/2022]
Abstract
For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3 -based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711-19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.
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Affiliation(s)
- Renata Blatnik
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Nitya Mohan
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Maria Bonsack
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Lasse G. Falkenby
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Stephanie Hoppe
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Kathrin Josef
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Alina Steinbach
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Sara Becker
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Wiebke M. Nadler
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM)HeidelbergGermany
| | - Marijana Rucevic
- Massachusetts General HospitalCenter for Cancer ResearchCharlestownMAUSA
| | - Martin R. Larsen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Mogjiborahman Salek
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Angelika B. Riemer
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
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