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Meynard-Piganeau B, Feinauer C, Weigt M, Walczak AM, Mora T. TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes. Proc Natl Acad Sci U S A 2024; 121:e2316401121. [PMID: 38838016 PMCID: PMC11181096 DOI: 10.1073/pnas.2316401121] [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: 09/20/2023] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
The accurate prediction of binding between T cell receptors (TCR) and their cognate epitopes is key to understanding the adaptive immune response and developing immunotherapies. Current methods face two significant limitations: the shortage of comprehensive high-quality data and the bias introduced by the selection of the negative training data commonly used in the supervised learning approaches. We propose a method, Transformer-based Unsupervised Language model for Interacting Peptides and T cell receptors (TULIP), that addresses both limitations by leveraging incomplete data and unsupervised learning and using the transformer architecture of language models. Our model is flexible and integrates all possible data sources, regardless of their quality or completeness. We demonstrate the existence of a bias introduced by the sampling procedure used in previous supervised approaches, emphasizing the need for an unsupervised approach. TULIP recognizes the specific TCRs binding an epitope, performing well on unseen epitopes. Our model outperforms state-of-the-art models and offers a promising direction for the development of more accurate TCR epitope recognition models.
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Affiliation(s)
- Barthelemy Meynard-Piganeau
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris Seine, CNRS, Sorbonne Université, Paris75005, France
- Department of Computing Sciences, Bocconi University, Milan20100, Italy
| | | | - Martin Weigt
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris Seine, CNRS, Sorbonne Université, Paris75005, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’Ecole Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université de Paris Cité, Paris75005, France
| | - Thierry Mora
- Laboratoire de Physique de l’Ecole Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université de Paris Cité, Paris75005, France
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2
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Alviano AM, Biondi M, Grassenis E, Biondi A, Serafini M, Tettamanti S. Fully equipped CARs to address tumor heterogeneity, enhance safety, and improve the functionality of cellular immunotherapies. Front Immunol 2024; 15:1407992. [PMID: 38887285 PMCID: PMC11180895 DOI: 10.3389/fimmu.2024.1407992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Although adoptive transfer of chimeric antigen receptor (CAR)-engineered T cells has achieved unprecedented response rates in patients with certain hematological malignancies, this therapeutic modality is still far from fulfilling its remarkable potential, especially in the context of solid cancers. Antigen escape variants, off-tumor destruction of healthy tissues expressing tumor-associated antigens (TAAs), poor CAR-T cell persistence, and the occurrence of functional exhaustion represent some of the most prominent hurdles that limit CAR-T cell ability to induce long-lasting remissions with a tolerable adverse effect profile. In this review, we summarize the main approaches that have been developed to face such bottlenecks, including the adapter CAR (AdCAR) system, Boolean-logic gating, epitope editing, the modulation of cell-intrinsic signaling pathways, and the incorporation of safety switches to precisely control CAR-T cell activation. We also discuss the most pressing issues pertaining to the selection of co-stimulatory domains, with a focus on strategies aimed at promoting CAR-T cell persistence and optimal antitumor functionality.
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Affiliation(s)
- Antonio Maria Alviano
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marta Biondi
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Erica Grassenis
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Andrea Biondi
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Marta Serafini
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Sarah Tettamanti
- Tettamanti Center and Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
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3
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Yang K, Lu R, Mei J, Cao K, Zeng T, Hua Y, Huang X, Li W, Yin Y. The war between the immune system and the tumor - using immune biomarkers as tracers. Biomark Res 2024; 12:51. [PMID: 38816871 PMCID: PMC11137916 DOI: 10.1186/s40364-024-00599-5] [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: 12/06/2023] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
Nowadays, immunotherapy is one of the most promising anti-tumor therapeutic strategy. Specifically, immune-related targets can be used to predict the efficacy and side effects of immunotherapy and monitor the tumor immune response. In the past few decades, increasing numbers of novel immune biomarkers have been found to participate in certain links of the tumor immunity to contribute to the formation of immunosuppression and have entered clinical trials. Here, we systematically reviewed the oncogenesis and progression of cancer in the view of anti-tumor immunity, particularly in terms of tumor antigen expression (related to tumor immunogenicity) and tumor innate immunity to complement the cancer-immune cycle. From the perspective of integrated management of chronic cancer, we also appraised emerging factors affecting tumor immunity (including metabolic, microbial, and exercise-related markers). We finally summarized the clinical studies and applications based on immune biomarkers. Overall, immune biomarkers participate in promoting the development of more precise and individualized immunotherapy by predicting, monitoring, and regulating tumor immune response. Therefore, targeting immune biomarkers may lead to the development of innovative clinical applications.
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Affiliation(s)
- Kai Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Rongrong Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Jie Mei
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Kai Cao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Tianyu Zeng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Yijia Hua
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
- Gusu School, Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
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4
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Sotirov S, Dimitrov I. Tumor-Derived Antigenic Peptides as Potential Cancer Vaccines. Int J Mol Sci 2024; 25:4934. [PMID: 38732150 PMCID: PMC11084719 DOI: 10.3390/ijms25094934] [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: 02/11/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Peptide antigens derived from tumors have been observed to elicit protective immune responses, categorized as either tumor-associated antigens (TAAs) or tumor-specific antigens (TSAs). Subunit cancer vaccines incorporating these antigens have shown promise in inducing protective immune responses, leading to cancer prevention or eradication. Over recent years, peptide-based cancer vaccines have gained popularity as a treatment modality and are often combined with other forms of cancer therapy. Several clinical trials have explored the safety and efficacy of peptide-based cancer vaccines, with promising outcomes. Advancements in techniques such as whole-exome sequencing, next-generation sequencing, and in silico methods have facilitated the identification of antigens, making it increasingly feasible. Furthermore, the development of novel delivery methods and a deeper understanding of tumor immune evasion mechanisms have heightened the interest in these vaccines among researchers. This article provides an overview of novel insights regarding advancements in the field of peptide-based vaccines as a promising therapeutic avenue for cancer treatment. It summarizes existing computational methods for tumor neoantigen prediction, ongoing clinical trials involving peptide-based cancer vaccines, and recent studies on human vaccination experiments.
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Affiliation(s)
| | - Ivan Dimitrov
- Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia, 2, Dunav Str., 1000 Sofia, Bulgaria;
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5
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Jeffreys N, Brockman JM, Zhai Y, Ingber DE, Mooney DJ. Mechanical forces amplify TCR mechanotransduction in T cell activation and function. APPLIED PHYSICS REVIEWS 2024; 11:011304. [PMID: 38434676 PMCID: PMC10848667 DOI: 10.1063/5.0166848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/08/2023] [Indexed: 03/05/2024]
Abstract
Adoptive T cell immunotherapies, including engineered T cell receptor (eTCR) and chimeric antigen receptor (CAR) T cell immunotherapies, have shown efficacy in treating a subset of hematologic malignancies, exhibit promise in solid tumors, and have many other potential applications, such as in fibrosis, autoimmunity, and regenerative medicine. While immunoengineering has focused on designing biomaterials to present biochemical cues to manipulate T cells ex vivo and in vivo, mechanical cues that regulate their biology have been largely underappreciated. This review highlights the contributions of mechanical force to several receptor-ligand interactions critical to T cell function, with central focus on the TCR-peptide-loaded major histocompatibility complex (pMHC). We then emphasize the role of mechanical forces in (i) allosteric strengthening of the TCR-pMHC interaction in amplifying ligand discrimination during T cell antigen recognition prior to activation and (ii) T cell interactions with the extracellular matrix. We then describe approaches to design eTCRs, CARs, and biomaterials to exploit TCR mechanosensitivity in order to potentiate T cell manufacturing and function in adoptive T cell immunotherapy.
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Affiliation(s)
| | | | - Yunhao Zhai
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, USA
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6
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Khodke P, Kumbhar BV. Engineered CAR-T cells: An immunotherapeutic approach for cancer treatment and beyond. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:157-198. [PMID: 38762269 DOI: 10.1016/bs.apcsb.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Chimeric Antigen Receptor (CAR) T cell therapy is a type of adoptive immunotherapy that offers a promising avenue for enhancing cancer treatment since traditional cancer treatments like chemotherapy, surgery, and radiation therapy have proven insufficient in completely eradicating tumors, despite the relatively positive outcomes. It has been observed that CAR-T cell therapy has shown promising results in treating the majority of hematological malignancies but also have a wide scope for other cancer types. CAR is an extra receptor on the T-cell that helps to increase and accelerate tumor destruction by efficiently activating the immune system. It is made up of three domains, the ectodomain, transmembrane, and the endodomain. The ectodomain is essential for antigen recognition and binding, whereas the co-stimulatory signal is transduced by the endodomain. To date, the Food and Drug Administration (FDA) has granted approval for six CAR-T cell therapies. However, despite its remarkable success, CAR-T therapy is associated with numerous adverse events and has certain limitations. This chapter focuses on the structure and function of the CAR domain, various generations of CAR, and the process of CAR-T cell development, adverse effects, and challenges in CAR-T therapy. CAR-T cell therapy also has scopes in other disease conditions which include systemic lupus erythematosus, multiple sclerosis, and myocardial fibrosis, etc.
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Affiliation(s)
- Purva Khodke
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-be University, Mumbai, India
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-be University, Mumbai, India.
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7
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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8
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Okura Y, Ikawa-Teranishi Y, Mizoroki A, Takahashi N, Tsushima T, Irie M, Harfuddin Z, Miura-Okuda M, Ito S, Nakamura G, Takesue H, Ozono Y, Nishihara M, Yamada K, Gan SW, Hayasaka A, Ishii S, Wakabayashi T, Muraoka M, Nagaya N, Hino H, Nemoto T, Kuramochi T, Torizawa T, Shimada H, Kitazawa T, Okazaki M, Nezu J, Sollid LM, Igawa T. Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease. Nat Commun 2023; 14:8502. [PMID: 38135691 PMCID: PMC10746718 DOI: 10.1038/s41467-023-44083-4] [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: 10/02/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
In human celiac disease (CeD) HLA-DQ2.5 presents gluten peptides to antigen-specific CD4+ T cells, thereby instigating immune activation and enteropathy. Targeting HLA-DQ2.5 with neutralizing antibody for treating CeD may be plausible, yet using pan-HLA-DQ antibody risks affecting systemic immunity, while targeting selected gluten peptide:HLA-DQ2.5 complex (pHLA-DQ2.5) may be insufficient. Here we generate a TCR-like, neutralizing antibody (DONQ52) that broadly recognizes more than twenty-five distinct gluten pHLA-DQ2.5 through rabbit immunization with multi-epitope gluten pHLA-DQ2.5 and multidimensional optimization. Structural analyses show that the proline-rich and glutamine-rich motif of gluten epitopes critical for pathogenesis is flexibly recognized by multiple tyrosine residues present in the antibody paratope, implicating the mechanisms for the broad reactivity. In HLA-DQ2.5 transgenic mice, DONQ52 demonstrates favorable pharmacokinetics with high subcutaneous bioavailability, and blocks immunity to gluten while not affecting systemic immunity. Our results thus provide a rationale for clinical testing of DONQ52 in CeD.
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Affiliation(s)
- Yuu Okura
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | | | - Akihiko Mizoroki
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | | | - Machiko Irie
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | | | - Shunsuke Ito
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Genki Nakamura
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Hiroaki Takesue
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Yui Ozono
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | - Kenta Yamada
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Siok Wan Gan
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Akira Hayasaka
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Shinya Ishii
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | - Masaru Muraoka
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Nishiki Nagaya
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Hiroshi Hino
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Takayuki Nemoto
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Taichi Kuramochi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Takuya Torizawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | | | | | - Makoto Okazaki
- Chugai Pharmabody Research Pte. Ltd., Singapore, Singapore
| | - Junichi Nezu
- R&D Portfolio Management Department, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Ludvig M Sollid
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomoyuki Igawa
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan.
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9
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Jumaniyazova E, Lokhonina A, Dzhalilova D, Kosyreva A, Fatkhudinov T. Immune Cells in the Tumor Microenvironment of Soft Tissue Sarcomas. Cancers (Basel) 2023; 15:5760. [PMID: 38136307 PMCID: PMC10741982 DOI: 10.3390/cancers15245760] [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: 11/14/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Soft tissue sarcomas (STSs) are a rare heterogeneous group of malignant neoplasms characterized by their aggressive course and poor response to treatment. This determines the relevance of research aimed at studying the pathogenesis of STSs. By now, it is known that STSs is characterized by complex relationships between the tumor cells and immune cells of the microenvironment. Dynamic interactions between tumor cells and components of the microenvironment enhance adaptation to changing environmental conditions, which provides the high aggressive potential of STSs and resistance to antitumor therapy. Today, active research is being conducted to find effective antitumor drugs and to evaluate the possibility of using therapy with immune cells of STS. The difficulty in assessing the efficacy of new antitumor options is primarily due to the high heterogeneity of this group of malignant neoplasms. Studying the role of immune cells in the microenvironment in the progression STSs and resistance to antitumor therapies will provide the discovery of new biomarkers of the disease and the prediction of response to immunotherapy. In addition, it will help to initially divide patients into subgroups of good and poor response to immunotherapy, thus avoiding wasting precious time in selecting the appropriate antitumor agent.
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Affiliation(s)
- Enar Jumaniyazova
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia (T.F.)
| | - Anastasiya Lokhonina
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia (T.F.)
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, 4 Oparina Street, 117997 Moscow, Russia
| | - Dzhuliia Dzhalilova
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia (T.F.)
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
| | - Anna Kosyreva
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia (T.F.)
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
| | - Timur Fatkhudinov
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia (T.F.)
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
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10
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Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sci Immunol 2023; 8:eadj5792. [PMID: 38039376 PMCID: PMC10782944 DOI: 10.1126/sciimmunol.adj5792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Peptide-centric chimeric antigen receptors (PC-CARs) recognize oncoprotein epitopes displayed by cell-surface human leukocyte antigens (HLAs) and offer a promising strategy for targeted cancer therapy. We have previously developed a PC-CAR targeting a neuroblastoma-associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes. Here, we determine the 2.1-angstrom crystal structure of the PC-CAR-PHOX2B-HLA-A*24:02-β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). This PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactive group, covering a combined global population frequency of up to 46.7%. Biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation, and CAR T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
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Affiliation(s)
- Yi Sun
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tyler J. Florio
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sagar Gupta
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C. Young
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Quinlen F. Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samuel E. Garfinkle
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Georgia F. Papadaki
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hau V. Truong
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Mycek
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peiyao Li
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | | | - Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Leena Mallik
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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11
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Bailey SR, Berger TR, Graham C, Larson RC, Maus MV. Four challenges to CAR T cells breaking the glass ceiling. Eur J Immunol 2023; 53:e2250039. [PMID: 36585889 DOI: 10.1002/eji.202250039] [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: 10/08/2022] [Revised: 11/21/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
Cell-based therapies using chimeric antigen receptor T cells (CAR T) have had dramatic efficacy in the clinic and can even mediate curative responses in patients with hematologic malignancies. As living drugs, engineered cells can still be detected in some patients even years after the original infusion. The excitement around the cell therapy field continues to expand as recent reports have shown that CAR T cells can induce remission in patients with autoimmune disease. While these promising advances in the field garner hope for wide-spread utility of CAR T therapies across diseases, several roadblocks exist that currently limit the access and efficacy of this therapy in the clinic. Herein, we will discuss four major obstacles that the CAR T field faces, including toxicity, identifying tumor-specific antigens, improving function in solid tumors, and reducing manufacturing complexity and cost. CAR T cells have potential for a multitude of diseases, but these glass ceilings will need to be broken in order to improve clinical responses and make this potentially life-saving therapy accessible to a larger patient population.
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Affiliation(s)
- Stefanie R Bailey
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Trisha R Berger
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Charlotte Graham
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Rebecca C Larson
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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12
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Izadpanah A, Mohammadkhani N, Masoudnia M, Ghasemzad M, Saeedian A, Mehdizadeh H, Poorebrahim M, Ebrahimi M. Update on immune-based therapy strategies targeting cancer stem cells. Cancer Med 2023; 12:18960-18980. [PMID: 37698048 PMCID: PMC10557910 DOI: 10.1002/cam4.6520] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Accumulating data reveals that tumors possess a specialized subset of cancer cells named cancer stem cells (CSCs), responsible for metastasis and recurrence of malignancies, with various properties such as self-renewal, heterogenicity, and capacity for drug resistance. Some signaling pathways or processes like Notch, epithelial to mesenchymal transition (EMT), Hedgehog (Hh), and Wnt, as well as CSCs' surface markers such as CD44, CD123, CD133, and epithelial cell adhesion molecule (EpCAM) have pivotal roles in acquiring CSCs properties. Therefore, targeting CSC-related signaling pathways and surface markers might effectively eradicate tumors and pave the way for cancer survival. Since current treatments such as chemotherapy and radiation therapy cannot eradicate all of the CSCs and tumor relapse may happen following temporary recovery, improving novel and more efficient therapeutic options to combine with current treatments is required. Immunotherapy strategies are the new therapeutic modalities with promising results in targeting CSCs. Here, we review the targeting of CSCs by immunotherapy strategies such as dendritic cell (DC) vaccines, chimeric antigen receptors (CAR)-engineered immune cells, natural killer-cell (NK-cell) therapy, monoclonal antibodies (mAbs), checkpoint inhibitors, and the use of oncolytic viruses (OVs) in pre-clinical and clinical studies. This review will mainly focus on blood malignancies but also describe solid cancers.
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Affiliation(s)
- Amirhossein Izadpanah
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
| | - Niloufar Mohammadkhani
- Department of Clinical BiochemistrySchool of Medicine, Shahid Beheshti University of Medical SciencesTehranIran
| | - Mina Masoudnia
- Department of ImmunologySchool of Medicine, Shahid Beheshti University of Medical SciencesTehranIran
| | - Mahsa Ghasemzad
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Department of Molecular Cell Biology‐Genetics, Faculty of Basic Sciences and Advanced Technologies in BiologyUniversity of Science and CultureTehranIran
| | - Arefeh Saeedian
- Radiation Oncology Research CenterCancer Research Institute, Tehran University of Medical SciencesTehranIran
- Department of Radiation OncologyCancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical SciencesTehranIran
| | - Hamid Mehdizadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
| | - Mansour Poorebrahim
- Arnie Charbonneau Cancer Research Institute, University of CalgaryAlbertaCalgaryCanada
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research CenterRoyan Institute for Stem Cell Biology and Technology, ACECRTehranIran
- Department of regenerative medicineCell Science research Center, Royan Institute for stem cell biology and technology, ACECRTehranIran
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13
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Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [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: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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14
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Peri A, Salomon N, Wolf Y, Kreiter S, Diken M, Samuels Y. The landscape of T cell antigens for cancer immunotherapy. NATURE CANCER 2023:10.1038/s43018-023-00588-x. [PMID: 37415076 DOI: 10.1038/s43018-023-00588-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
Abstract
The remarkable capacity of immunotherapies to induce durable regression in some patients with metastatic cancer relies heavily on T cell recognition of tumor-presented antigens. As checkpoint-blockade therapy has limited efficacy, tumor antigens have the potential to be exploited for complementary treatments, many of which are already in clinical trials. The surge of interest in this topic has led to the expansion of the tumor antigen landscape with the emergence of new antigen categories. Nonetheless, how different antigens compare in their ability to elicit efficient and safe clinical responses remains largely unknown. Here, we review known cancer peptide antigens, their attributes and the relevant clinical data and discuss future directions.
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Affiliation(s)
- Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nadja Salomon
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Yochai Wolf
- Ella Lemelbaum Institute for Immuno-oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Sebastian Kreiter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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15
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Chen Z, Lin C, Pei H, Yuan X, Xu J, Zou M, Zhang X, Fossier A, Liu M, Goo S, Lei L, Yang J, Novick C, Xu J, Ying G, Zhou Z, Wu J, Tang C, Zhang W, Wang Z, Wang Z, Zhang H, Guo W, Hu Q, Ji H, Chen R. Antibody-based binding domain fused to TCRγ chain facilitates T cell cytotoxicity for potent anti-tumor response. Oncogenesis 2023; 12:33. [PMID: 37349298 DOI: 10.1038/s41389-023-00480-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/12/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy has demonstrated potent clinical efficacy in the treatment of hematopoietic malignancies. However, the application of CAR-T in solid tumors has been limited due in part to the expression of inhibitory molecules in the tumor microenvironment, leading to T-cell exhaustion. To overcome this limitation, we have developed a synthetic T-cell receptor (TCR) that targets programmed death-ligand 1 (PD-L1), a molecule that is widely expressed in various solid tumors and plays a pivotal role in T-cell exhaustion. Our novel TCR platform is based on antibody-based binding domain, which is typically a single-chain variable fragment (scFv), fused to the γδ TCRs (TCRγδ). We have utilized the T-cell receptor alpha constant (TRAC) locus editing approach to express cell surface scFv of anti-PD-L1, which is fused to the constant region of the TCRγ or TCRδ chain in activated T cells derived from peripheral blood mononuclear cells (PBMCs). Our results indicate that these reconfigured receptors, both γ-TCRγδ and δ-TCRγδ, have the capability to transduce signals, produce inflammatory cytokines, degranulate and exert tumor killing activity upon engagement with PD-L1 antigen in vitro. Additionally, we have also shown that γ-TCRγδ exerted superior efficacy than δ-TCRγδ in in vivo xenograft model.
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Affiliation(s)
- Zhao Chen
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Changyou Lin
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Hong Pei
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Xiaomei Yuan
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Jia Xu
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Mingwei Zou
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Xinyuan Zhang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Amber Fossier
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Meizhu Liu
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Seungah Goo
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Lei Lei
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Jia Yang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Catherine Novick
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Jiqing Xu
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Ge Ying
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Zhihong Zhou
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Jianbo Wu
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Chunyi Tang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Wenying Zhang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Zhenping Wang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Zhihao Wang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Huitang Zhang
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Wenzhong Guo
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Qidong Hu
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Henry Ji
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA
| | - Runqiang Chen
- Sorrento Therapeutics Inc, 4955 Directors Place, San Diego, CA, USA.
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16
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Zhuang C, Gould JE, Enninful A, Shao S, Mak M. Biophysical and mechanobiological considerations for T-cell-based immunotherapy. Trends Pharmacol Sci 2023; 44:366-378. [PMID: 37172572 PMCID: PMC10188210 DOI: 10.1016/j.tips.2023.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 05/15/2023]
Abstract
Immunotherapies modulate the body's defense system to treat cancer. While these therapies have shown efficacy against multiple types of cancer, patient response rates are limited, and the off-target effects can be severe. Typical approaches in developing immunotherapies tend to focus on antigen targeting and molecular signaling, while overlooking biophysical and mechanobiological effects. Immune cells and tumor cells are both responsive to biophysical cues, which are prominent in the tumor microenvironment. Recent studies have shown that mechanosensing - including through Piezo1, adhesions, and Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) - influences tumor-immune interactions and immunotherapeutic efficacy. Furthermore, biophysical methods such as fluidic systems and mechanoactivation schemes can improve the controllability and manufacturing of engineered T cells, with potential for increasing therapeutic efficacy and specificity. This review focuses on leveraging advances in immune biophysics and mechanobiology toward improving chimeric antigen receptor (CAR) T-cell and anti-programmed cell death protein 1 (anti-PD-1) therapies.
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Affiliation(s)
- Chuzhi Zhuang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jared E Gould
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Stephanie Shao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Michael Mak
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA.
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17
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Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. Structural principles of peptide-centric Chimeric Antigen Receptor recognition guide therapeutic expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542108. [PMID: 37292750 PMCID: PMC10245919 DOI: 10.1101/2023.05.24.542108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Peptide-Centric Chimeric Antigen Receptors (PC-CARs), which recognize oncoprotein epitopes displayed by human leukocyte antigens (HLAs) on the cell surface, offer a promising strategy for targeted cancer therapy 1 . We have previously developed a PC-CAR targeting a neuroblastoma- associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes 2 . Here, we determine the 2.1 Å structure of the PC-CAR:PHOX2B/HLA-A*24:02/β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). The PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactivity group, covering a combined American population frequency of up to 25.2%. Comprehensive characterization using biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation and CAR-T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
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18
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Atilla E, Benabdellah K. The Black Hole: CAR T Cell Therapy in AML. Cancers (Basel) 2023; 15:2713. [PMID: 37345050 DOI: 10.3390/cancers15102713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Despite exhaustive studies, researchers have made little progress in the field of adoptive cellular therapies for relapsed/refractory acute myeloid leukemia (AML), unlike the notable uptake for B cell malignancies. Various single antigen-targeting chimeric antigen receptor (CAR) T cell Phase I trials have been established worldwide and have recruited approximately 100 patients. The high heterogeneity at the genetic and molecular levels within and between AML patients resembles a black hole: a great gravitational field that sucks in everything. One must consider the fact that only around 30% of patients show a response; there are, however, consequential off-tumor effects. It is obvious that a new point of view is needed to achieve more promising results. This review first introduces the unique therapeutic challenges of not only CAR T cells but also other adoptive cellular therapies in AML. Next, recent single-cell sequencing data for AML to assess somatically acquired alterations at the DNA, epigenetic, RNA, and protein levels are discussed to give a perspective on cellular heterogeneity, intercellular hierarchies, and the cellular ecosystem. Finally, promising novel strategies are summarized, including more sophisticated next-generation CAR T, TCR-T, and CAR NK therapies; the approaches with which to tailor the microenvironment and target neoantigens; and allogeneic approaches.
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Affiliation(s)
- Erden Atilla
- Fred Hutchinson Cancer Research Center, Clinical Research Division, 1100 Fairview Ave N, Seattle, WA 98109, USA
- GENYO Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer/University of Granada/Andalusian Regional Government, Health Sciences Technology Park, 18016 Granada, Spain
| | - Karim Benabdellah
- GENYO Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer/University of Granada/Andalusian Regional Government, Health Sciences Technology Park, 18016 Granada, Spain
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19
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Mercogliano MF, Bruni S, Mauro FL, Schillaci R. Emerging Targeted Therapies for HER2-Positive Breast Cancer. Cancers (Basel) 2023; 15:cancers15071987. [PMID: 37046648 PMCID: PMC10093019 DOI: 10.3390/cancers15071987] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Breast cancer is the most common cancer in women and the leading cause of death. HER2 overexpression is found in approximately 20% of breast cancers and is associated with a poor prognosis and a shorter overall survival. Tratuzumab, a monoclonal antibody directed against the HER2 receptor, is the standard of care treatment. However, a third of the patients do not respond to therapy. Given the high rate of resistance, other HER2-targeted strategies have been developed, including monoclonal antibodies such as pertuzumab and margetuximab, trastuzumab-based antibody drug conjugates such as trastuzumab-emtansine (T-DM1) and trastuzumab-deruxtecan (T-DXd), and tyrosine kinase inhibitors like lapatinib and tucatinib, among others. Moreover, T-DXd has proven to be of use in the HER2-low subtype, which suggests that other HER2-targeted therapies could be successful in this recently defined new breast cancer subclassification. When patients progress to multiple strategies, there are several HER2-targeted therapies available; however, treatment options are limited, and the potential combination with other drugs, immune checkpoint inhibitors, CAR-T cells, CAR-NK, CAR-M, and vaccines is an interesting and appealing field that is still in development. In this review, we will discuss the highlights and pitfalls of the different HER2-targeted therapies and potential combinations to overcome metastatic disease and resistance to therapy.
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20
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Seong G, D’Angelo SP. New therapeutics for soft tissue sarcomas: Overview of current immunotherapy and future directions of soft tissue sarcomas. Front Oncol 2023; 13:1150765. [PMID: 37007160 PMCID: PMC10052453 DOI: 10.3389/fonc.2023.1150765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
Soft tissue sarcoma is a rare and aggressive disease with a 40 to 50% metastasis rate. The limited efficacy of traditional approaches with surgery, radiation, and chemotherapy has prompted research in novel immunotherapy for soft tissue sarcoma. Immune checkpoint inhibitors such as anti-CTLA-4 and PD-1 therapies in STS have demonstrated histologic-specific responses. Some combinations of immunotherapy with chemotherapy, TKI, and radiation were effective. STS is considered a ‘cold’, non-inflamed tumor. Adoptive cell therapies are actively investigated in STS to enhance immune response. Genetically modified T-cell receptor therapy targeting cancer testis antigens such as NY-ESO-1 and MAGE-A4 demonstrated durable responses, especially in synovial sarcoma. Two early HER2-CAR T-cell trials have achieved stable disease in some patients. In the future, CAR-T cell therapies will find more specific targets in STS with a reliable response. Early recognition of T-cell induced cytokine release syndrome is crucial, which can be alleviated by immunosuppression such as steroids. Further understanding of the immune subtypes and biomarkers will promote the advancement of soft tissue sarcoma treatment.
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Affiliation(s)
- Gyuhee Seong
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, United States
| | - Sandra P. D’Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
- *Correspondence: Sandra P. D’Angelo,
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21
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 164] [Impact Index Per Article: 164.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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22
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Bluestone JA, McKenzie BS, Beilke J, Ramsdell F. Opportunities for Treg cell therapy for the treatment of human disease. Front Immunol 2023; 14:1166135. [PMID: 37153574 PMCID: PMC10154599 DOI: 10.3389/fimmu.2023.1166135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
Regulatory T (Treg) cells are essential for maintaining peripheral tolerance, preventing autoimmunity, and limiting chronic inflammatory diseases. This small CD4+ T cell population can develop in the thymus and in the peripheral tissues of the immune system through the expression of an epigenetically stabilized transcription factor, FOXP3. Treg cells mediate their tolerogenic effects using multiple modes of action, including the production of inhibitory cytokines, cytokine starvation of T effector (e.g., IL-2), Teff suppression by metabolic disruption, and modulation of antigen-presenting cell maturation or function. These activities together result in the broad control of various immune cell subsets, leading to the suppression of cell activation/expansion and effector functions. Moreover, these cells can facilitate tissue repair to complement their suppressive effects. In recent years, there has been an effort to harness Treg cells as a new therapeutic approach to treat autoimmune and other immunological diseases and, importantly, to re-establish tolerance. Recent synthetic biological advances have enabled the cells to be genetically engineered to achieve tolerance and antigen-specific immune suppression by increasing their specific activity, stability, and efficacy. These cells are now being tested in clinical trials. In this review, we highlight both the advances and the challenges in this arena, focusing on the efforts to develop this new pillar of medicine to treat and cure a variety of diseases.
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23
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Blazeska N, Kosaloglu-Yalcin Z, Vita R, Peters B, Sette A. IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community. Methods Mol Biol 2023; 2673:133-149. [PMID: 37258911 PMCID: PMC11008223 DOI: 10.1007/978-1-0716-3239-0_9] [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] [Indexed: 06/02/2023]
Abstract
Various methodologies have been utilized to analyze epitope-specific responses in the context of non-self-antigens, such as those associated with infectious diseases and allergies, and in the context of self-antigens, such as those associated with transplantation, autoimmunity, and cancer. Further to this, epitope-specific data, and its associated immunological context, are crucial to training and developing predictive algorithms and pipelines for the development of specific vaccines and diagnostics. In this chapter, we describe the methodology utilized to derive two sibling resources, the Immune Epitope Database (IEDB) and Cancer Epitope Database and Analysis Resource (CEDAR), to specifically host this data, and make them freely available to the scientific community.
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Affiliation(s)
- Nina Blazeska
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zeynep Kosaloglu-Yalcin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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Arman I, Haus-Cohen M, Reiter Y. The Intracellular Proteome as a Source for Novel Targets in CAR-T and T-Cell Engagers-Based Immunotherapy. Cells 2022; 12:cells12010027. [PMID: 36611821 PMCID: PMC9818436 DOI: 10.3390/cells12010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
The impressive clinical success of cancer immunotherapy has motivated the continued search for new targets that may serve to guide potent effector functions in an attempt to efficiently kill malignant cells. The intracellular proteome is an interesting source for such new targets, such as neo-antigens and others, with growing interest in their application for cell-based immunotherapies. These intracellular-derived targets are peptides presented by MHC class I molecules on the cell surface of malignant cells. These disease-specific class I HLA-peptide complexes can be targeted by specific TCRs or by antibodies that mimic TCR-specificity, termed TCR-like (TCRL) antibodies. Adoptive cell transfer of TCR engineered T cells and T-cell-receptor-like based CAR-T cells, targeted against a peptide-MHC of interest, are currently tested as cancer therapeutic agents in pre-clinical and clinical trials, along with soluble TCR- and TCRL-based agents, such as immunotoxins and bi-specific T cell engagers. Targeting the intracellular proteome using TCRL- and TCR-based molecules shows promising results in cancer immunotherapy, as exemplified by the success of the anti-gp100/HLA-A2 TCR-based T cell engager, recently approved by the FDA for the treatment of unresectable or metastatic uveal melanoma. This review is focused on the selection and isolation processes of TCR- and TCRL-based targeting moieties, with a spotlight on pre-clinical and clinical studies, examining peptide-MHC targeting agents in cancer immunotherapy.
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Nanobody-based CAR T cells targeting intracellular tumor antigens. Biomed Pharmacother 2022; 156:113919. [DOI: 10.1016/j.biopha.2022.113919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/30/2022] Open
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Okumura S, Ishihara M, Kiyota N, Yakushijin K, Takada K, Kobayashi S, Ikeda H, Endo M, Kato K, Kitano S, Matsumine A, Nagata Y, Kageyama S, Shiraishi T, Yamada T, Horibe K, Takesako K, Miwa H, Watanabe T, Miyahara Y, Shiku H. Chimeric antigen receptor T-cell therapy targeting a MAGE A4 peptide and HLA-A*02:01 complex for unresectable advanced or recurrent solid cancer: protocol for a multi-institutional phase 1 clinical trial. BMJ Open 2022; 12:e065109. [PMID: 36375974 PMCID: PMC9664294 DOI: 10.1136/bmjopen-2022-065109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Adoptive cell transfer of genetically engineered T cells is a promising treatment for malignancies; however, there are few ideal cancer antigens expressed on the cell surface, and the development of chimeric antigen receptor T cells (CAR-T cells) for solid tumour treatment has been slow. CAR-T cells, which recognise major histocompatibility complex and peptide complexes presented on the cell surface, can be used to target not only cell surface antigens but also intracellular antigens. We have developed a CAR-T-cell product that recognises the complex of HLA-A*02:01 and an epitope of the MAGE-A4 antigen equipped with a novel signalling domain of human GITR (investigational product code: MU-MA402C) based on preclinical studies. METHODS AND ANALYSIS This is a dose-escalation, multi-institutional, phase 1 study to evaluate the tolerability and safety of MU-MA402C for patients with MAGE A4-positive and HLA-A*02:01-positive unresectable advanced or recurrent solid cancer. Two dose cohorts are planned: cohort 1, MU-MA402C 2×108/person; cohort 2, MU-MA402C 2×109/person. Prior to CAR-T-cell infusion, cyclophosphamide (CPA) and fludarabine (FLU) will be administered as preconditioning chemotherapy. Three evaluable subjects per cohort, for a total of 6 subjects (maximum of 12 subjects), will be recruited for this clinical trial. The primary endpoints are safety and tolerability. The severity of each adverse event will be evaluated in accordance with Common Terminology Criteria for Adverse Events V.5.0. The secondary endpoint is efficacy. Antitumour response will be evaluated according to Response Evaluation Criteria in Solid Tumours V.1.1. ETHICS AND DISSEMINATION This clinical trial will be conducted in accordance with the current version of Good Clinical Practice. The protocol was approved by the Clinical Research Ethics Review Committee of Mie University Hospital (approval number F-2021-017). The trial results will be published in peer-reviewed journals and/or disseminated through international conferences. TRIAL REGISTRATION NUMBER jRCT2043210077.
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Affiliation(s)
- Satoshi Okumura
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | | | - Naomi Kiyota
- Cancer Center, Kobe University Hospital, Kobe, Hyogo, Japan
- Department of Medical Oncology and Haematology, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Kimikazu Yakushijin
- Department of Medical Oncology and Haematology, Kobe University Hospital, Kobe, Hyogo, Japan
| | - Kohichi Takada
- Department of Medical Oncology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | | | - Hiroaki Ikeda
- Department of Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Makoto Endo
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shigehisa Kitano
- Department of Advanced Medical Development, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akihiko Matsumine
- Department of Orthopaedics and Rehabilitation Medicine, Unit of Surgery, Division of Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Yasuhiro Nagata
- Department of Community Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinichi Kageyama
- Department of Medical Oncology/Chemotherapy Center, Suzuka Kaisei Hospital, Suzuka, Mie, Japan
| | - Taizo Shiraishi
- Department of Pathology, Kuwana City Medical Center, Kuwana, Mie, Japan
| | - Tomomi Yamada
- Department of Medical Innovation, Osaka University Hospital, Osaka, Japan
| | - Keizo Horibe
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Kazuto Takesako
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Hiroshi Miwa
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Takashi Watanabe
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Yoshihiro Miyahara
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Hiroshi Shiku
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
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Zhou Z, Tao C, Li J, Tang JCO, Chan ASC, Zhou Y. Chimeric antigen receptor T cells applied to solid tumors. Front Immunol 2022; 13:984864. [PMID: 36389701 PMCID: PMC9659902 DOI: 10.3389/fimmu.2022.984864] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022] Open
Abstract
Chimeric antigen receptor T cell (CAR-T) therapy is novel tumor immunotherapy that enables autologous T to express synthetic receptors to specifically recognize the surface tumor-associated antigens for exerting subsequent antitumor effects, and eliminating the resistance, metastases and recurrence of cancer. Although CAR T cells have exhibited success in eradicating hematologic malignancies, their applications to solid tumors has not yet been achieved due to obstacles such as the immune-suppressor tumor microenvironment and lack of tumor specific target antigens. In this review, we presented advancements in the development of CAR T cell therapy in solid tumors, and offered a brief summary of the challenges, as well as novel engineering and pharmaceutical interventions to overcome these barriers. Looking forward, we discussed the latest studies which are expected to reach the clinicals in the next few years, including CRISPR screens-based CAR modification and CAR T cells driven from progenitor-like T cells. Collectively, this review may inspire researchers and clinicians to develop clinical available strategies of CAR T cell therapies in solid tumor.
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Affiliation(s)
- Zhongguo Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Can Tao
- School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Jianting Li
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Johnny Cheuk-on Tang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- Kamford Genetics Company Limited, Hong Kong, Hong Kong SAR, China
| | - Albert Sun-chi Chan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuanyuan Zhou
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China
- *Correspondence: Yuanyuan Zhou,
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Lou H, Cao X. Antibody variable region engineering for improving cancer immunotherapy. Cancer Commun (Lond) 2022; 42:804-827. [PMID: 35822503 PMCID: PMC9456695 DOI: 10.1002/cac2.12330] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/25/2022] [Accepted: 06/22/2022] [Indexed: 04/09/2023] Open
Abstract
The efficacy and specificity of conventional monoclonal antibody (mAb) drugs in the clinic require further improvement. Currently, the development and application of novel antibody formats for improving cancer immunotherapy have attracted much attention. Variable region-retaining antibody fragments, such as antigen-binding fragment (Fab), single-chain variable fragment (scFv), bispecific antibody, and bi/trispecific cell engagers, are engineered with humanization, multivalent antibody construction, affinity optimization and antibody masking for targeting tumor cells and killer cells to improve antibody-based therapy potency, efficacy and specificity. In this review, we summarize the application of antibody variable region engineering and discuss the future direction of antibody engineering for improving cancer therapies.
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Affiliation(s)
- Hantao Lou
- Ludwig Institute of Cancer ResearchUniversity of OxfordOxfordOX3 7DRUK
- Chinese Academy for Medical Sciences Oxford InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
| | - Xuetao Cao
- Chinese Academy for Medical Sciences Oxford InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
- Department of ImmunologyCentre for Immunotherapy, Institute of Basic Medical SciencesChinese Academy of Medical SciencesBeijing100005P. R. China
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Minegishi Y, Kiyotani K, Nemoto K, Inoue Y, Haga Y, Fujii R, Saichi N, Nagayama S, Ueda K. Differential ion mobility mass spectrometry in immunopeptidomics identifies neoantigens carrying colorectal cancer driver mutations. Commun Biol 2022; 5:831. [PMID: 35982173 PMCID: PMC9388627 DOI: 10.1038/s42003-022-03807-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/05/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding the properties of human leukocyte antigen (HLA) peptides (immunopeptides) is essential for precision cancer medicine, while the direct identification of immunopeptides from small biopsies of clinical tissues by mass spectrometry (MS) is still confronted with technical challenges. Here, to overcome these hindrances, high-field asymmetric waveform ion mobility spectrometry (FAIMS) is introduced to conduct differential ion mobility (DIM)-MS by seamless gas-phase fractionation optimal for scarce samples. By established DIM-MS for immunopeptidomics analysis, on average, 42.9 mg of normal and tumor colorectal tissues from identical patients (n = 17) were analyzed, and on average 4921 immunopeptides were identified. Among these 44,815 unique immunopeptides, two neoantigens, KRAS-G12V and CPPED1-R228Q, were identified. These neoantigens were confirmed by synthetic peptides through targeted MS in parallel reaction monitoring (PRM) mode. Comparison of the tissue-based personal immunopeptidome revealed tumor-specific processing of immunopeptides. Since the direct identification of neoantigens from tumor tissues suggested that more potential neoantigens have yet to be identified, we screened cell lines with known oncogenic KRAS mutations and identified 2 more neoantigens that carry KRAS-G12V. These results indicated that the established FAIMS-assisted DIM-MS is effective in the identification of immunopeptides and potential recurrent neoantigens directly from scarce samples such as clinical tissues.
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Affiliation(s)
- Yuriko Minegishi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazuma Kiyotani
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensaku Nemoto
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Yoshimi Haga
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Risa Fujii
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naomi Saichi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Nagayama
- Development of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
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Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation. Proc Natl Acad Sci U S A 2022; 119:e2203410119. [PMID: 35878026 PMCID: PMC9351518 DOI: 10.1073/pnas.2203410119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tissue-specific antigens can serve as targets for adoptive T cell transfer-based cancer immunotherapy. Recognition of tumor by T cells is mediated by interaction between peptide-major histocompatibility complexes (pMHCs) and T cell receptors (TCRs). Revealing the identity of peptides bound to MHC is critical in discovering cognate TCRs and predicting potential toxicity. We performed multimodal immunopeptidomic analyses for human prostatic acid phosphatase (PAP), a well-recognized tissue antigen. Three physical methods, including mild acid elution, coimmunoprecipitation, and secreted MHC precipitation, were used to capture a thorough signature of PAP on HLA-A*02:01. Eleven PAP peptides that are potentially A*02:01-restricted were identified, including five predicted strong binders by NetMHCpan 4.0. Peripheral blood mononuclear cells (PBMCs) from more than 20 healthy donors were screened with the PAP peptides. Seven cognate TCRs were isolated which can recognize three distinct epitopes when expressed in PBMCs. One TCR shows reactivity toward cell lines expressing both full-length PAP and HLA-A*02:01. Our results show that a combined multimodal immunopeptidomic approach is productive in revealing target peptides and defining the cloned TCR sequences reactive with prostatic acid phosphatase epitopes.
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Alternative CAR Therapies: Recent Approaches in Engineering Chimeric Antigen Receptor Immune Cells to Combat Cancer. Biomedicines 2022; 10:biomedicines10071493. [PMID: 35884798 PMCID: PMC9313317 DOI: 10.3390/biomedicines10071493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/08/2023] Open
Abstract
For nearly three decades, chimeric antigen receptors (CARs) have captivated the interest of researchers seeking to find novel immunotherapies to treat cancer. CARs were first designed to work with T cells, and the first CAR T cell therapy was approved to treat B cell lymphoma in 2017. Recent advancements in CAR technology have led to the development of modified CARs, including multi-specific CARs and logic gated CARs. Other immune cell types, including natural killer (NK) cells and macrophages, have also been engineered to express CARs to treat cancer. Additionally, CAR technology has been adapted in novel approaches to treating autoimmune disease and other conditions and diseases. In this article, we review these recent advancements in alternative CAR therapies and design, as well as their mechanisms of action, challenges in application, and potential future directions.
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Marhelava K, Krawczyk M, Firczuk M, Fidyt K. CAR-T Cells Shoot for New Targets: Novel Approaches to Boost Adoptive Cell Therapy for B Cell-Derived Malignancies. Cells 2022; 11:1804. [PMID: 35681499 PMCID: PMC9180412 DOI: 10.3390/cells11111804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/27/2022] [Indexed: 12/10/2022] Open
Abstract
Chimeric antigen receptor (CAR)-T cell therapy is undeniably a promising tool in combating various types of hematological malignancies. However, it is not yet optimal and a significant number of patients experience a lack of response or relapse after the treatment. Therapy improvement requires careful analysis of the occurring problems and a deeper understanding of the reasons that stand behind them. In this review, we summarize the recent knowledge about CAR-T products' clinical performance and discuss diversified approaches taken to improve the major shortcomings of this therapy. Especially, we prioritize the challenges faced by CD19 CAR-T cell-based treatment of B cell-derived malignancies and revise the latest insights about mechanisms mediating therapy resistance. Since the loss of CD19 is one of the major obstacles to the success of CAR-T cell therapy, we present antigens that could be alternatively used for the treatment of various types of B cell-derived cancers.
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Affiliation(s)
- Katsiaryna Marhelava
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.M.); (M.K.); (M.F.)
| | - Marta Krawczyk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.M.); (M.K.); (M.F.)
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Doctoral School of Translational Medicine, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Malgorzata Firczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.M.); (M.K.); (M.F.)
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Klaudyna Fidyt
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (K.M.); (M.K.); (M.F.)
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Jiang M, Sun W, Lu D, He J, Wang J, Tan S, Gao F. Wilms tumor 1 (WT1)抗原HLA-A11限制性T细胞表位鉴定及特异性TCR筛选. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Challenges and Advances in Chimeric Antigen Receptor Therapy for Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14030497. [PMID: 35158765 PMCID: PMC8833567 DOI: 10.3390/cancers14030497] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
The advent of chimeric antigen receptor (CAR) T-cell therapy has led to dramatic remission rates in multiple relapsed/refractory hematologic malignancies. While CAR T-cell therapy has been particularly successful as a treatment for B-cell malignancies, effectively treating acute myeloid leukemia (AML) with CARs has posed a larger challenge. AML not only creates an immunosuppressive tumor microenvironment that dampens CAR T-cell responses, but it also lacks many unique tumor-associated antigens, making leukemic-specific targeting difficult. One advantage of CAR T-cell therapy compared to alternative treatment options is the ability to provide prolonged antigen-specific immune effector and surveillance functions. Since many AML CAR targets under investigation including CD33, CD117, and CD123 are also expressed on hematopoietic stem cells, CAR T-cell therapy can lead to severe and potentially lethal myeloablation. Novel strategies to combat these issues include creation of bispecific CARs, CAR T-cell "safety switches", TCR-like CARs, NK CARs, and universal CARs, but all vary in their ability to provide a sustained remission, and consolidation with an allogeneic hematopoietic cell transplantation (allo-HCT) will be necessary in most cases This review highlights the delicate balance between effectively eliminating AML blasts and leukemic stem cells, while preserving the ability for bone marrow to regenerate. The impact of CAR therapy on treatment landscape of AML and changing scope of allo-HCT is discussed. Continued advances in AML CAR therapy would be of great benefit to a disease that still has high morbidity and mortality.
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Zhang A, Piechocka-Trocha A, Li X, Walker BD. A Leucine Zipper Dimerization Strategy to Generate Soluble T Cell Receptors Using the Escherichia coli Expression System. Cells 2022; 11:cells11030312. [PMID: 35159122 PMCID: PMC8834513 DOI: 10.3390/cells11030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/10/2022] Open
Abstract
T cell-mediated adaptive immunity plays a key role in immunological surveillance and host control of infectious diseases. A better understanding of T cell receptor (TCR) recognition of pathogen-derived epitopes or cancer-associated neoantigens is the basis for developing T cell-based vaccines and immunotherapies. Studies on the interaction between soluble TCR α:β heterodimers and peptide-bound major histocompatibility complexes (pMHCs) inform underlying mechanisms driving TCR recognition, but not every isolated TCR can be prepared in soluble form for structural and functional studies using conventional methods. Here, taking a challenging HIV-specific TCR as a model, we designed a general leucine zipper (LZ) dimerization strategy for soluble TCR preparation using the Escherichia coli expression system. We report details of TCR construction, inclusion body expression and purification, and protein refolding and purification. Measurements of binding affinity between the TCR and its specific pMHC using surface plasmon resonance (SPR) verify its activity. We conclude that this is a feasible approach to produce challenging TCRs in soluble form, needed for studies related to T cell recognition.
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Affiliation(s)
- Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Correspondence: (X.L.); (B.D.W.)
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science (IMES) and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (X.L.); (B.D.W.)
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