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Moravec Z, Zhao Y, Voogd R, Cook DR, Kinrot S, Capra B, Yang H, Raud B, Ou J, Xuan J, Wei T, Ren L, Hu D, Wang J, Haanen JBAG, Schumacher TN, Chen X, Porter E, Scheper W. Discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening. Nat Biotechnol 2024:10.1038/s41587-024-02210-6. [PMID: 38653798 DOI: 10.1038/s41587-024-02210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
T cell receptor (TCR) gene therapy is a potent form of cellular immunotherapy in which patient T cells are genetically engineered to express TCRs with defined tumor reactivity. However, the isolation of therapeutic TCRs is complicated by both the general scarcity of tumor-specific T cells among patient T cell repertoires and the patient-specific nature of T cell epitopes expressed on tumors. Here we describe a high-throughput, personalized TCR discovery pipeline that enables the assembly of complex synthetic TCR libraries in a one-pot reaction, followed by pooled expression in reporter T cells and functional genetic screening against patient-derived tumor or antigen-presenting cells. We applied the method to screen thousands of tumor-infiltrating lymphocyte (TIL)-derived TCRs from multiple patients and identified dozens of CD4+ and CD8+ T-cell-derived TCRs with potent tumor reactivity, including TCRs that recognized patient-specific neoantigens.
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Affiliation(s)
- Ziva Moravec
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yue Zhao
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Rhianne Voogd
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Haiyan Yang
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Brenda Raud
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jiayu Ou
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Jiekun Xuan
- RootPath, Inc. (US), Watertown, MA, USA
- RootPath, Inc. (Hangzhou), Hangzhou, China
| | - Teng Wei
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Lili Ren
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Dandan Hu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - John B A G Haanen
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Xi Chen
- RootPath, Inc. (Guangzhou), Guangzhou, China.
- RootPath, Inc. (US), Watertown, MA, USA.
- RootPath, Inc. (Hangzhou), Hangzhou, China.
| | - Ely Porter
- RootPath, Inc. (US), Watertown, MA, USA.
| | - Wouter Scheper
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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2
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de Miranda NFCC, Scheeren FA. Immunogenetic Diversity and Cancer Immunotherapy Disparities. Cancer Discov 2024; 14:585-588. [PMID: 38571423 DOI: 10.1158/2159-8290.cd-23-1536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY The success of checkpoint blockade cancer immunotherapies has unequivocally confirmed the critical role of T cells in cancer immunity and boosted the development of immunotherapeutic strategies targeting specific antigens on cancer cells. The vast immunogenetic diversity of human leukocyte antigen (HLA) class I alleles across populations is a key factor influencing the advancement of HLA class I-restricted therapies and related research and diagnostic tools.
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Affiliation(s)
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
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3
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Slieker RC, Warmerdam DO, Vermeer MH, van Doorn R, Heemskerk MHM, Scheeren FA. Reassessing human MHC-I genetic diversity in T cell studies. Sci Rep 2024; 14:7966. [PMID: 38575727 PMCID: PMC10995142 DOI: 10.1038/s41598-024-58777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analysed (pre)clinical publications focusing on COVID-19 studies and T cell receptor (TCR)-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian, and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
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Affiliation(s)
- Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël O Warmerdam
- Centre for Future Affordable & Sustainable Therapy Development (FAST), The Hague, The Netherlands
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Dermatology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands.
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4
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Shao W, Yao Y, Yang L, Li X, Ge T, Zheng Y, Zhu Q, Ge S, Gu X, Jia R, Song X, Zhuang A. Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy. Exp Hematol Oncol 2024; 13:37. [PMID: 38570883 PMCID: PMC10988985 DOI: 10.1186/s40164-024-00504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Adoptive immunotherapy in the T cell landscape exhibits efficacy in cancer treatment. Over the past few decades, genetically modified T cells, particularly chimeric antigen receptor T cells, have enabled remarkable strides in the treatment of hematological malignancies. Besides, extensive exploration of multiple antigens for the treatment of solid tumors has led to clinical interest in the potential of T cells expressing the engineered T cell receptor (TCR). TCR-T cells possess the capacity to recognize intracellular antigen families and maintain the intrinsic properties of TCRs in terms of affinity to target epitopes and signal transduction. Recent research has provided critical insight into their capability and therapeutic targets for multiple refractory solid tumors, but also exposes some challenges for durable efficacy. In this review, we describe the screening and identification of available tumor antigens, and the acquisition and optimization of TCRs for TCR-T cell therapy. Furthermore, we summarize the complete flow from laboratory to clinical applications of TCR-T cells. Last, we emerge future prospects for improving therapeutic efficacy in cancer world with combination therapies or TCR-T derived products. In conclusion, this review depicts our current understanding of TCR-T cell therapy in solid neoplasms, and provides new perspectives for expanding its clinical applications and improving therapeutic efficacy.
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Affiliation(s)
- Weihuan Shao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiaoran Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Tongxin Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yue Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Qiuyi Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
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5
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Klobuch S, Seijkens TTP, Schumacher TN, Haanen JBAG. Tumour-infiltrating lymphocyte therapy for patients with advanced-stage melanoma. Nat Rev Clin Oncol 2024; 21:173-184. [PMID: 38191921 DOI: 10.1038/s41571-023-00848-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Immunotherapy with immune-checkpoint inhibitors (ICIs) and targeted therapy with BRAF and MEK inhibitors have revolutionized the treatment of melanoma over the past decade. Despite these breakthroughs, the 5-year survival rate of patients with advanced-stage melanoma is at most 50%, emphasizing the need for additional therapeutic strategies. Adoptive cell therapy with tumour-infiltrating lymphocytes (TILs) is a therapeutic modality that has, in the past few years, demonstrated long-term clinical benefit in phase II/III trials involving patients with advanced-stage melanoma, including those with disease progression on ICIs and/or BRAF/MEK inhibitors. In this Review, we summarize the current status of TIL therapies for patients with advanced-stage melanoma, including potential upcoming marketing authorization, the characteristics of TIL therapy products, as well as future strategies that are expected to increase the efficacy of this promising cellular immunotherapy.
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Affiliation(s)
- Sebastian Klobuch
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tom T P Seijkens
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - John B A G Haanen
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands.
- Melanoma Clinic, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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6
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Srivastava PK. Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines. J Clin Invest 2024; 134:e176740. [PMID: 38426497 PMCID: PMC10904052 DOI: 10.1172/jci176740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A proportion of somatic mutations in tumors create neoepitopes that can prime T cell responses that target the MHC I-neoepitope complexes on tumor cells, mediating tumor control or rejection. Despite the compelling centrality of neoepitopes to cancer immunity, we know remarkably little about what constitutes a neoepitope that can mediate tumor control in vivo and what distinguishes such a neoepitope from the vast majority of similar candidate neoepitopes that are inefficacious in vivo. Studies in mice as well as clinical trials have begun to reveal the unexpected paradoxes in this area. Because cancer neoepitopes straddle that ambiguous ground between self and non-self, some rules that are fundamental to immunology of frankly non-self antigens, such as viral or model antigens, do not appear to apply to neoepitopes. Because neoepitopes are so similar to self-epitopes, with only small changes that render them non-self, immune response to them is regulated at least partially the way immune response to self is regulated. Therefore, neoepitopes are viewed and understood here through the clarifying lens of negative thymic selection. Here, the emergent questions in the biology and clinical applications of neoepitopes are discussed critically and a mechanistic and testable framework that explains the complexity and translational potential of these wonderful antigens is proposed.
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7
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O'Brien H, Salm M, Morton LT, Szukszto M, O'Farrell F, Boulton C, Becker PD, Samuels Y, Swanton C, Mansour MR, Reker Hadrup S, Quezada SA. Breaking the performance ceiling for neoantigen immunogenicity prediction. Nat Cancer 2023; 4:1618-1621. [PMID: 38102360 DOI: 10.1038/s43018-023-00675-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Affiliation(s)
| | - Max Salm
- Achilles Therapeutics Ltd, London, UK.
| | | | - Maciej Szukszto
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Charlotte Boulton
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | | | | | - Marc R Mansour
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Sergio A Quezada
- Achilles Therapeutics Ltd, London, UK.
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
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8
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Pang Z, Lu MM, Zhang Y, Gao Y, Bai JJ, Gu JY, Xie L, Wu WZ. Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges. Biomark Res 2023; 11:104. [PMID: 38037114 PMCID: PMC10690996 DOI: 10.1186/s40364-023-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Adoptive cell therapy using T cell receptor-engineered T cells (TCR-T) is a promising approach for cancer therapy with an expectation of no significant side effects. In the human body, mature T cells are armed with an incredible diversity of T cell receptors (TCRs) that theoretically react to the variety of random mutations generated by tumor cells. The outcomes, however, of current clinical trials using TCR-T cell therapies are not very successful especially involving solid tumors. The therapy still faces numerous challenges in the efficient screening of tumor-specific antigens and their cognate TCRs. In this review, we first introduce TCR structure-based antigen recognition and signaling, then describe recent advances in neoantigens and their specific TCR screening technologies, and finally summarize ongoing clinical trials of TCR-T therapies against neoantigens. More importantly, we also present the current challenges of TCR-T cell-based immunotherapies, e.g., the safety of viral vectors, the mismatch of T cell receptor, the impediment of suppressive tumor microenvironment. Finally, we highlight new insights and directions for personalized TCR-T therapy.
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Affiliation(s)
- Zhi Pang
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Man-Man Lu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yu Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yuan Gao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Jin-Jin Bai
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jian-Ying Gu
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| | - Wei-Zhong Wu
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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9
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Scheper W. Mapping the landscape of T cell-recognized neoantigens in cancer patients. Genes Immun 2023; 24:287-288. [PMID: 38066338 DOI: 10.1038/s41435-023-00230-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
Affiliation(s)
- Wouter Scheper
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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10
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Cattaneo CM. Identification of personalized cancer neoantigens with HANSolo. Nat Rev Cancer 2023; 23:800. [PMID: 37704741 DOI: 10.1038/s41568-023-00624-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
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11
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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12
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Phulphagar KM, Ctortecka C, Jacome ASV, Klaeger S, Verzani EK, Hernandez GM, Udeshi ND, Clauser KR, Abelin JG, Carr SA. Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry. Mol Cell Proteomics 2023:100563. [PMID: 37142057 DOI: 10.1016/j.mcpro.2023.100563] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
Comprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is powerful technology for direct identification of HLA peptides from patient derived tumor samples or cell lines. However, achieving sufficient coverage to detect rare, clinically relevant antigens requires highly sensitive MS-based acquisition methods and large amounts of sample. While immunopeptidome depth can be increased by off-line fractionation prior to MS, its use is impractical when analyzing limited amounts of primary tissue biopsies. To address this challenge, we developed and applied a high throughput, sensitive, single-shot MS-based immunopeptidomics workflow that leverages trapped ion mobility time-of-flight mass spectrometry on the Bruker timsTOF SCP. We demonstrate >2-fold improved coverage of HLA immunopeptidomes relative to prior methods with up to 15,000 distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS acquisition method on the timsTOF SCP maintains high coverage, eliminates the need for off-line fractionation and reduces input requirements to as few as 1e6 A375 cells for > 800 distinct HLA-I peptides. This depth is sufficient to identify HLA-I peptides derived from cancer-testis antigen, and non-canonical proteins. We also apply our optimized single-shot SCP acquisition methods to tumor derived samples, enabling sensitive, high throughput and reproducible immunopeptidome profiling with detection of clinically relevant peptides from less than 4e7 cells or 15 mg wet weight tissue.
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