1
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Srivastava PK. Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines. J Clin Invest 2024; 134:e176740. [PMID: 38426497 PMCID: PMC10904052 DOI: 10.1172/jci176740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A proportion of somatic mutations in tumors create neoepitopes that can prime T cell responses that target the MHC I-neoepitope complexes on tumor cells, mediating tumor control or rejection. Despite the compelling centrality of neoepitopes to cancer immunity, we know remarkably little about what constitutes a neoepitope that can mediate tumor control in vivo and what distinguishes such a neoepitope from the vast majority of similar candidate neoepitopes that are inefficacious in vivo. Studies in mice as well as clinical trials have begun to reveal the unexpected paradoxes in this area. Because cancer neoepitopes straddle that ambiguous ground between self and non-self, some rules that are fundamental to immunology of frankly non-self antigens, such as viral or model antigens, do not appear to apply to neoepitopes. Because neoepitopes are so similar to self-epitopes, with only small changes that render them non-self, immune response to them is regulated at least partially the way immune response to self is regulated. Therefore, neoepitopes are viewed and understood here through the clarifying lens of negative thymic selection. Here, the emergent questions in the biology and clinical applications of neoepitopes are discussed critically and a mechanistic and testable framework that explains the complexity and translational potential of these wonderful antigens is proposed.
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2
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Custodio JM, Ayres CM, Rosales TJ, Brambley CA, Arbuiso AG, Landau LM, Keller GLJ, Srivastava PK, Baker BM. Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc Natl Acad Sci U S A 2023; 120:e2312057120. [PMID: 38085776 PMCID: PMC10742377 DOI: 10.1073/pnas.2312057120] [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: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.
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Affiliation(s)
- Jean M. Custodio
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Tatiana J. Rosales
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Chad A. Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Alyssa G. Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Lauren M. Landau
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Grant L. J. Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Pramod K. Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT06030
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
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3
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Sidiropoulos DN, Ho WJ, Jaffee EM, Kagohara LT, Fertig EJ. Systems immunology spanning tumors, lymph nodes, and periphery. CELL REPORTS METHODS 2023; 3:100670. [PMID: 38086385 PMCID: PMC10753389 DOI: 10.1016/j.crmeth.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/20/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
The immune system defines a complex network of tissues and cell types that orchestrate responses across the body in a dynamic manner. The local and systemic interactions between immune and cancer cells contribute to disease progression. Lymphocytes are activated in lymph nodes, traffic through the periphery, and impact cancer progression through their interactions with tumor cells. As a result, therapeutic response and resistance are mediated across tissues, and a comprehensive understanding of lymphocyte dynamics requires a systems-level approach. In this review, we highlight experimental and computational methods that can leverage the study of leukocyte trafficking through an immunomics lens and reveal how adaptive immunity shapes cancer.
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Affiliation(s)
- Dimitrios N Sidiropoulos
- Johns Hopkins University School of Medicine, Baltimore, MD, USA; Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Won Jin Ho
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Elizabeth M Jaffee
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA
| | - Luciane T Kagohara
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA.
| | - Elana J Fertig
- Johns Hopkins Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, MD, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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4
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Huff AL, Longway G, Mitchell JT, Andaloori L, Davis-Marcisak E, Chen F, Lyman MR, Wang R, Mathew J, Barrett B, Rahman S, Leatherman J, Yarchoan M, Azad NS, Yegnasubramanian S, Kagohara LT, Fertig EJ, Jaffee EM, Armstrong TD, Zaidi N. CD4 T cell-activating neoantigens enhance personalized cancer vaccine efficacy. JCI Insight 2023; 8:e174027. [PMID: 38063199 PMCID: PMC10795827 DOI: 10.1172/jci.insight.174027] [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: 07/18/2023] [Accepted: 10/17/2023] [Indexed: 12/18/2023] Open
Abstract
Personalized cancer vaccines aim to activate and expand cytotoxic antitumor CD8+ T cells to recognize and kill tumor cells. However, the role of CD4+ T cell activation in the clinical benefit of these vaccines is not well defined. We previously established a personalized neoantigen vaccine (PancVAX) for the pancreatic cancer cell line Panc02, which activates tumor-specific CD8+ T cells but required combinatorial checkpoint modulators to achieve therapeutic efficacy. To determine the effects of neoantigen-specific CD4+ T cell activation, we generated a vaccine (PancVAX2) targeting both major histocompatibility complex class I- (MHCI-) and MHCII-specific neoantigens. Tumor-bearing mice vaccinated with PancVAX2 had significantly improved control of tumor growth and long-term survival benefit without concurrent administration of checkpoint inhibitors. PancVAX2 significantly enhanced priming and recruitment of neoantigen-specific CD8+ T cells into the tumor with lower PD-1 expression after reactivation compared with the CD8+ vaccine alone. Vaccine-induced neoantigen-specific Th1 CD4+ T cells in the tumor were associated with decreased Tregs. Consistent with this, PancVAX2 was associated with more proimmune myeloid-derived suppressor cells and M1-like macrophages in the tumor, demonstrating a less immunosuppressive tumor microenvironment. This study demonstrates the biological importance of prioritizing and including CD4+ T cell-specific neoantigens for personalized cancer vaccine modalities.
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Affiliation(s)
- Amanda L. Huff
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gabriella Longway
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jacob T. Mitchell
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Lalitya Andaloori
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Emily Davis-Marcisak
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Fangluo Chen
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Melissa R. Lyman
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rulin Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jocelyn Mathew
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Benjamin Barrett
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sabahat Rahman
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - James Leatherman
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mark Yarchoan
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nilofer S. Azad
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Srinivasan Yegnasubramanian
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- inHealth Precision Medicine Program
| | - Luciane T. Kagohara
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, and
| | - Elana J. Fertig
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, and
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Todd D. Armstrong
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Neeha Zaidi
- Johns Hopkins Convergence Institute and
- Johns Hopkins Bloomberg Kimmel Institute for Immunotherapy, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
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5
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [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] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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6
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Haldar SD, Vilar E, Maitra A, Zaidi N. Worth a Pound of Cure? Emerging Strategies and Challenges in Cancer Immunoprevention. Cancer Prev Res (Phila) 2023; 16:483-495. [PMID: 37001882 PMCID: PMC10548442 DOI: 10.1158/1940-6207.capr-22-0478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/06/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Cancer immunoprevention applies immunologic approaches such as vaccines to prevent, rather than to treat or cure, cancer. Despite limited success in the treatment of advanced disease, the development of cancer vaccines to intercept premalignant states is a promising area of current research. These efforts are supported by the rationale that vaccination in the premalignant setting is less susceptible to mechanisms of immune evasion compared with established cancer. Prophylactic vaccines have already been developed for a minority of cancers mediated by oncogenic viruses (e.g., hepatitis B and human papillomavirus). Extending the use of preventive vaccines to non-virally driven malignancies remains an unmet need to address the rising global burden of cancer. This review provides a broad overview of clinical trials in cancer immunoprevention with an emphasis on emerging vaccine targets and delivery platforms, translational challenges, and future directions.
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Affiliation(s)
- Saurav D. Haldar
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anirban Maitra
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
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7
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Kallingal A, Olszewski M, Maciejewska N, Brankiewicz W, Baginski M. Cancer immune escape: the role of antigen presentation machinery. J Cancer Res Clin Oncol 2023; 149:8131-8141. [PMID: 37031434 PMCID: PMC10374767 DOI: 10.1007/s00432-023-04737-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
The mechanisms of antigen processing and presentation play a crucial role in the recognition and targeting of cancer cells by the immune system. Cancer cells can evade the immune system by downregulating or losing the expression of the proteins recognized by the immune cells as antigens, creating an immunosuppressive microenvironment, and altering their ability to process and present antigens. This review focuses on the mechanisms of cancer immune evasion with a specific emphasis on the role of antigen presentation machinery. The study of the immunopeptidome, or peptidomics, has provided insights into the mechanisms of cancer immune evasion and has potential applications in cancer diagnosis and treatment. Additionally, manipulating the epigenetic landscape of cancer cells plays a critical role in suppressing the immune response against cancer. Targeting these mechanisms through the use of HDACis, DNMTis, and combination therapies has the potential to improve the efficacy of cancer immunotherapy. However, further research is needed to fully understand the mechanisms of action and optimal use of these therapies in the clinical setting.
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Affiliation(s)
- Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland.
| | - Mateusz Olszewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Natalia Maciejewska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Wioletta Brankiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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8
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Stein-O’Brien GL, Le DT, Jaffee EM, Fertig EJ, Zaidi N. Converging on a Cure: The Roads to Predictive Immunotherapy. Cancer Discov 2023; 13:1053-1057. [PMID: 37067199 PMCID: PMC10548443 DOI: 10.1158/2159-8290.cd-23-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
SUMMARY Convergence science teams integrating clinical, biological, engineering, and computational expertise are inventing new forecast systems to monitor and predict evolutionary changes in tumor and immune interactions during early cancer progression and therapeutic response. The resulting methods should inform a new predictive medicine paradigm to select adaptive immunotherapeutic regimens personalized to patients' tumors at a given time during their cancer progression for durable patient response.
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Affiliation(s)
- Genevieve L. Stein-O’Brien
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
- Kavli Neurodiscovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Dung T. Le
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
- Johns Hopkins Bloomberg-Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth M. Jaffee
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
- Johns Hopkins Bloomberg-Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elana J. Fertig
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Johns Hopkins Bloomberg-Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland
| | - Neeha Zaidi
- Johns Hopkins Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
- Johns Hopkins Bloomberg-Kimmel Institute for Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
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9
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Current Trends in Neoantigen-Based Cancer Vaccines. Pharmaceuticals (Basel) 2023; 16:ph16030392. [PMID: 36986491 PMCID: PMC10056833 DOI: 10.3390/ph16030392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Cancer immunotherapies are treatments that use drugs or cells to activate patients’ own immune systems against cancer cells. Among them, cancer vaccines have recently been rapidly developed. Based on tumor-specific antigens referred to as neoantigens, these vaccines can be in various forms such as messenger (m)RNA and synthetic peptides to activate cytotoxic T cells and act with or without dendritic cells. Growing evidence suggests that neoantigen-based cancer vaccines possess a very promising future, yet the processes of immune recognition and activation to relay identification of a neoantigen through the histocompatibility complex (MHC) and T-cell receptor (TCR) remain unclear. Here, we describe features of neoantigens and the biological process of validating neoantigens, along with a discussion of recent progress in the scientific development and clinical applications of neoantigen-based cancer vaccines.
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10
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Lahiri A, Maji A, Potdar PD, Singh N, Parikh P, Bisht B, Mukherjee A, Paul MK. Lung cancer immunotherapy: progress, pitfalls, and promises. Mol Cancer 2023; 22:40. [PMID: 36810079 PMCID: PMC9942077 DOI: 10.1186/s12943-023-01740-y] [Citation(s) in RCA: 170] [Impact Index Per Article: 170.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/22/2022] [Indexed: 02/23/2023] Open
Abstract
Lung cancer is the primary cause of mortality in the United States and around the globe. Therapeutic options for lung cancer treatment include surgery, radiation therapy, chemotherapy, and targeted drug therapy. Medical management is often associated with the development of treatment resistance leading to relapse. Immunotherapy is profoundly altering the approach to cancer treatment owing to its tolerable safety profile, sustained therapeutic response due to immunological memory generation, and effectiveness across a broad patient population. Different tumor-specific vaccination strategies are gaining ground in the treatment of lung cancer. Recent advances in adoptive cell therapy (CAR T, TCR, TIL), the associated clinical trials on lung cancer, and associated hurdles are discussed in this review. Recent trials on lung cancer patients (without a targetable oncogenic driver alteration) reveal significant and sustained responses when treated with programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) checkpoint blockade immunotherapies. Accumulating evidence indicates that a loss of effective anti-tumor immunity is associated with lung tumor evolution. Therapeutic cancer vaccines combined with immune checkpoint inhibitors (ICI) can achieve better therapeutic effects. To this end, the present article encompasses a detailed overview of the recent developments in the immunotherapeutic landscape in targeting small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). Additionally, the review also explores the implication of nanomedicine in lung cancer immunotherapy as well as the combinatorial application of traditional therapy along with immunotherapy regimens. Finally, ongoing clinical trials, significant obstacles, and the future outlook of this treatment strategy are also highlighted to boost further research in the field.
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Affiliation(s)
- Aritraa Lahiri
- grid.417960.d0000 0004 0614 7855Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246 India
| | - Avik Maji
- grid.416241.4Department of Radiation Oncology, N. R. S. Medical College & Hospital, 138 A.J.C. Bose Road, Kolkata, 700014 India
| | - Pravin D. Potdar
- grid.414939.20000 0004 1766 8488Department of Molecular Medicine and Stem Cell Biology, Jaslok Hospital and Research Centre, Mumbai, 400026 India
| | - Navneet Singh
- grid.415131.30000 0004 1767 2903Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Purvish Parikh
- Department of Clinical Hematology, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan 302022 India ,grid.410871.b0000 0004 1769 5793Department of Medical Oncology, Tata Memorial Hospital, Mumbai, Maharashtra 400012 India
| | - Bharti Bisht
- grid.19006.3e0000 0000 9632 6718Division of Thoracic Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Anubhab Mukherjee
- Esperer Onco Nutrition Pvt Ltd, 4BA, 4Th Floor, B Wing, Gundecha Onclave, Khairani Road, Sakinaka, Andheri East, Mumbai, Maharashtra, 400072, India.
| | - Manash K. Paul
- grid.19006.3e0000 0000 9632 6718Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA ,grid.411639.80000 0001 0571 5193Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
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11
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Tumor antigens and vaccines in colorectal cancer. MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Zhu Y, Huang CX, Zhang L, Wang ZF, Zhao DL, Ding F, Zhang SY, Li YQ, Chen LZ. Promoting the formation of Pi-stacking interaction to improve CTL cells activation between modified peptide and HLA. Am J Transl Res 2022; 14:5164-5177. [PMID: 35958484 PMCID: PMC9360904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE This study aims to investigate the use of single residue substitution to promote the formation of pi-stacking interactions between peptides and Human leukocyte antigen (HLA)-A*2402 molecules to improve the affinity of peptides and HLA molecules, as well as the level of cytotoxic T lymphocyte (CTL) cells activated by peptides-HLA (p-HLA) complex. METHODS Molecular docking and molecular dynamics simulation were used to simulate and analyze the interactions and binding free energies between HLA-A*2402-restricted antigen peptides and HLA molecules, before and after the single residue substitution. HLA-A*2402 restricted antigen peptides before and after the single residue replacement were loaded into dendritic cells (DCs) in vitro, and further Enzyme-Linked ImmunoSpot (ELispot) test was carried out to evaluate the effect of modified antigen peptides on the immune activation of CTL cells. RESULT After replacing the antigen peptides with a single residue, some of them could promote the formation of pi-stacking interaction. The binding free energy between the modified antigen peptides and HLA-A*2402, as well as the level of immune activation of CTL cells were mostly higher than before, especially after the replacement of the 9th residue of the polypeptide, such as C9F and C9W. There was a significant negative correlation between the level of activated CTL cells by modified antigen peptides and the total interaction amount of hydrogen bonds and salt bridges. CONCLUSION Promoting the formation of pi-stacking interaction between antigen peptides and HLA-A*2402 molecules could increase the total binding free energy of p-HLA complex and the level of CTL cells activation. In addition, the amount of hydrogen bonds and salt bridges between peptides and HLA could reduce the level of immune activation. All the characteristics above can improve the immunogenicities of the weak antigens.
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Affiliation(s)
- Ying Zhu
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou 310000, Zhejiang, China
| | - Chang-Xin Huang
- Department of Oncology, The Affiliated Hospital of Hangzhou Normal UniversityHangzhou 310000, Zhejiang, China
| | - Le Zhang
- Master Class, Zhejiang Chinese Medical University, The Fourth School of Clinical MedicineHangzhou 310000, Zhejiang, China
| | - Ze-Fang Wang
- Master Class, Hangzhou Normal University, The School of MedicineHangzhou 3100000, Zhejiang, China
| | - Dong-Li Zhao
- Master Class, Zhejiang Chinese Medical University, The Fourth School of Clinical MedicineHangzhou 310000, Zhejiang, China
| | - Fei Ding
- Department of Oncology, The Affiliated Hospital of Hangzhou Normal UniversityHangzhou 310000, Zhejiang, China
| | - Si-Yu Zhang
- Department of Oncology, The Affiliated Hospital of Hangzhou Normal UniversityHangzhou 310000, Zhejiang, China
| | - Yong-Qiang Li
- Department of Oncology, The Affiliated Hospital of Hangzhou Normal UniversityHangzhou 310000, Zhejiang, China
| | - Ling-Zhi Chen
- Department of Blood Transfusion, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing UniversityJiaxing 314000, Zhejiang, China
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13
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Ochoa R, Lunardelli VAS, Rosa DS, Laio A, Cossio P. Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Front Immunol 2022; 13:862851. [PMID: 35572587 PMCID: PMC9094701 DOI: 10.3389/fimmu.2022.862851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Epitopes that bind simultaneously to all human alleles of Major Histocompatibility Complex class II (MHC II) are considered one of the key factors for the development of improved vaccines and cancer immunotherapies. To engineer MHC II multiple-allele binders, we developed a protocol called PanMHC-PARCE, based on the unsupervised optimization of the epitope sequence by single-point mutations, parallel explicit-solvent molecular dynamics simulations and scoring of the MHC II-epitope complexes. The key idea is accepting mutations that not only improve the affinity but also reduce the affinity gap between the alleles. We applied this methodology to enhance a Plasmodium vivax epitope for multiple-allele binding. In vitro rate-binding assays showed that four engineered peptides were able to bind with improved affinity toward multiple human MHC II alleles. Moreover, we demonstrated that mice immunized with the peptides exhibited interferon-gamma cellular immune response. Overall, the method enables the engineering of peptides with improved binding properties that can be used for the generation of new immunotherapies.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | | | - Daniela Santoro Rosa
- Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo, Sao Paulo, Brazil.,Institute for Investigation in Immunology (iii), Instituto Nacional de Ciência e Tecnologia (INCT), Sao Paulo, Brazil
| | - Alessandro Laio
- Physics Area, International School for Advanced Studies (SISSA), Trieste, Italy.,Condensed Matter and Statistical Physics Section, International Centre for Theoretical Physics (ICTP), Trieste, Italy
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Center for Computational Mathematics, Flatiron Institute, New York, NY, United States.,Center for Computational Biology, Flatiron Institute, New York, NY, United States
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14
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Huff AL, Jaffee EM, Zaidi N. Messenger RNA vaccines for cancer immunotherapy: progress promotes promise. J Clin Invest 2022; 132:e156211. [PMID: 35289317 PMCID: PMC8920340 DOI: 10.1172/jci156211] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic has elevated mRNA vaccines to global recognition due to their unprecedented success rate in protecting against a deadly virus. This international success is underscored by the remarkable versatility, favorable immunogenicity, and overall safety of the mRNA platform in diverse populations. Although mRNA vaccines have been studied in preclinical models and patients with cancer for almost three decades, development has been slow. The recent technological advances responsible for the COVID-19 vaccines have potential implications for successfully adapting this vaccine platform for cancer therapeutics. Here we discuss the lessons learned along with the chemical, biologic, and immunologic adaptations needed to optimize mRNA technology to successfully treat cancers.
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Affiliation(s)
- Amanda L. Huff
- Department of Oncology
- The Sidney Kimmel Comprehensive Cancer Center
- The Skip Viragh Center for Pancreatic Cancer Research and Clinical Care
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and
- The Cancer Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Department of Oncology
- The Sidney Kimmel Comprehensive Cancer Center
- The Skip Viragh Center for Pancreatic Cancer Research and Clinical Care
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and
- The Cancer Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Neeha Zaidi
- Department of Oncology
- The Sidney Kimmel Comprehensive Cancer Center
- The Skip Viragh Center for Pancreatic Cancer Research and Clinical Care
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, and
- The Cancer Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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15
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Neoantigen Cancer Vaccines: Generation, Optimization, and Therapeutic Targeting Strategies. Vaccines (Basel) 2022; 10:vaccines10020196. [PMID: 35214655 PMCID: PMC8877108 DOI: 10.3390/vaccines10020196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 12/30/2022] Open
Abstract
Alternatives to conventional cancer treatments are highly sought after for high-risk malignancies that have a poor response to established treatment modalities. With research advancing rapidly in the past decade, neoantigen-based immunotherapeutic approaches represent an effective and highly tolerable therapeutic option. Neoantigens are tumor-specific antigens that are not expressed in normal cells and possess significant immunogenic potential. Several recent studies have described the conceptual framework and methodologies to generate neoantigen-based vaccines as well as the formulation of appropriate clinical trials to advance this approach for patient care. This review aims to describe some of the key studies in the recent literature in this rapidly evolving field and summarize the current advances in neoantigen identification and selection, vaccine generation and delivery, and the optimization of neoantigen-based therapeutic strategies, including the early data from pivotal clinical studies.
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16
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Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK. Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope. Nat Commun 2021; 12:6423. [PMID: 34741035 PMCID: PMC8571378 DOI: 10.1038/s41467-021-26646-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported to elicit CD8 T cell dependent tumor rejection in immunization-challenge studies. Here we show in a mouse model that a neo-epitope that poorly binds to MHC I is able to enhance the immunogenicity of a tumor in the absence of immunization. Fibrosarcoma cells with a naturally occurring mutation are edited to their wild type counterpart; the mutation is then re-introduced in order to obtain a cell line that is genetically identical to the wild type except for the neo-epitope-encoding mutation. Upon transplantation into syngeneic mice, all three cell lines form tumors that are infiltrated with activated T cells. However, lymphocytes from the two tumors that harbor the mutation show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement, and induce greater breadth of TCR reactivity than those of the wild type tumors. Structural modeling of the neo-epitope peptide/MHC I pairs suggests increased hydrophobicity of the neo-epitope surface, consistent with higher TCR reactivity. These results confirm the in vivo immunogenicity of low affinity or ‘non-binding’ epitopes that do not follow the canonical concept of MHC I-peptide recognition. The immunogenicity of peptides is believed to be determined by their high-affinity binding to MHC I. Here authors show that low-affinity MHC I-peptide interactions are also able to trigger robust T cell response and anti-tumour immunity in vivo.
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Affiliation(s)
- Hakimeh Ebrahimi-Nik
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Broad Institute of MIT and Harvard, 105 Broadway, Cambridge, MA, USA
| | - Marmar Moussa
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ryan P Englander
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Summit Singhaviranon
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Hiroko Miyadera
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - William L Corwin
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Arvinas, 5 science park, 395 Winchester Ave, New Haven, CT, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Adam T Hagymasi
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Tatiana V Shcheglova
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Ion I Mandoiu
- Department of Computer Sciences, University of Connecticut School of Engineering, Storrs, CT, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.
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17
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Bräunlein E, Lupoli G, Füchsl F, Abualrous ET, de Andrade Krätzig N, Gosmann D, Wietbrock L, Lange S, Engleitner T, Lan H, Audehm S, Effenberger M, Boxberg M, Steiger K, Chang Y, Yu K, Atay C, Bassermann F, Weichert W, Busch DH, Rad R, Freund C, Antes I, Krackhardt AM. Functional analysis of peripheral and intratumoral neoantigen-specific TCRs identified in a patient with melanoma. J Immunother Cancer 2021; 9:jitc-2021-002754. [PMID: 34518289 PMCID: PMC8438848 DOI: 10.1136/jitc-2021-002754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 12/11/2022] Open
Abstract
Background Neoantigens derived from somatic mutations correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of therapeutic approaches in personalized medicine, although many aspects of their quality and associated immune responses are not yet well understood. In a case study of metastatic malignant melanoma, we aimed to perform an in-depth characterization of neoantigens and respective T-cell responses in the context of immune checkpoint modulation. Methods Three neoantigens, which we identified either by immunopeptidomics or in silico prediction, were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient’s immune repertoire recognizing these antigens. TCRs were compared in vitro by multiparametric analyses including functional avidity, multicytokine secretion, and cross-reactivity screenings. A xenograft mouse model served to study in vivo functionality of selected TCRs. We investigated the patient’s TCR repertoire in blood and different tumor-related tissues over 3 years using TCR beta deep sequencing. Results Selected mutated peptide ligands with proven immunogenicity showed similar binding affinities to the human leukocyte antigen complex and comparable disparity to their wild-type counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs recognizing these antigens demonstrated distinct patterns in functionality and frequency. TCRs with lower functional avidity showed at least equal antitumor immune responses in vivo. Moreover, they occurred at high frequencies and particularly demonstrated long-term persistence within tumor tissues, lymph nodes and various blood samples associated with a reduced activation pattern on primary in vitro stimulation. Conclusions We performed a so far unique fine characterization of neoantigen-specific T-cell responses revealing defined reactivity patterns of neoantigen-specific TCRs. Our data highlight qualitative differences of these TCRs associated with function and longevity of respective T cells. Such features need to be considered for further optimization of neoantigen targeting including adoptive T-cell therapies using TCR-transgenic T cells.
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Affiliation(s)
- Eva Bräunlein
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Gaia Lupoli
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Franziska Füchsl
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Dario Gosmann
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Lukas Wietbrock
- TUM School of Life Sciences and Center for Integrated Protein Science Munich, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Sebastian Lange
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Huan Lan
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Stefan Audehm
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Manuel Effenberger
- Institute for Medical Microbiology Immunology and Hygiene, Technische Universität München, München, Germany
| | - Melanie Boxberg
- Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,MRI-TUM-Biobank at the Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Core Facility Experimental Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Yinshui Chang
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Kai Yu
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Cigdem Atay
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Florian Bassermann
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,MRI-TUM-Biobank at the Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Core Facility Experimental Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology Immunology and Hygiene, Technische Universität München, München, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Iris Antes
- TUM School of Life Sciences and Center for Integrated Protein Science Munich, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Angela M Krackhardt
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany .,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
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18
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Abstract
Ott et al. report the results of a phase 1B study in which a personalized neoantigen vaccine was combined with programmed death receptor-1 blockade in patients with advanced cancers. The study provides a framework for combinatorial vaccine therapies that could mount robust T cell responses, enhance tumor killing, and provide clinical benefit.
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Affiliation(s)
- Neeha Zaidi
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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