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Lee H, Lee M, Lim CL, Park HS, Song IH, Jeong BK, Kim DK, Kim YH, Choi S, Lee GD, Lee SB, Jung S, Gong G, Kim SB, Yoo C, Kim JY, Lee HJ. Expansion of tumor-infiltrating lymphocytes in non-small cell lung cancer: Clinical potential and efficacy in EGFR mutation subsets. Clin Immunol 2024; 265:110289. [PMID: 38908769 DOI: 10.1016/j.clim.2024.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Our study aimed to expand tumor-infiltrating lymphocytes (TILs) from primary non-small cell lung cancers (NSCLCs) and evaluate their reactivity against tumor cells. We expanded TILs from 103 primary NSCLCs using histopathological analysis, flow cytometry, IFN-γ release assays, cell-mediated cytotoxicity assays, and in vivo efficacy tests. TIL expansion was observed in all cases, regardless of EGFR mutation status. There was also an increase in the median CD4+/CD8+ ratio during expansion. In post-rapid expansion protocol (REP) TILs, 13 out of 16 cases, including all three cases with EGFR mutations, exhibited a two-fold or greater increase in IFN-γ secretion. The cytotoxicity assay revealed enhanced tumor cell death in three of the seven cases, two of which had EGFR mutations. In vivo functional testing in a patient-derived xenograft model showed a reduction in tumor volume. The anti-tumor activity of post-REP TILs underscores their potential as a therapeutic option for advanced NSCLC, irrespective of mutation status.
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Affiliation(s)
- Hyun Lee
- Department of Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Miseon Lee
- Department of Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chae Lyul Lim
- Research and Development Center, NeogenTC Corp., Seoul, Republic of Korea
| | - Hye Seon Park
- Research and Development Center, NeogenTC Corp., Seoul, Republic of Korea
| | - In Hye Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Byung-Kwan Jeong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong-Hee Kim
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sehoon Choi
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Geun Dong Lee
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sae Byul Lee
- Department of Breast Surgery, Asan Medical Center, College of Medicine, University of Ulsan, Seoul, Republic of Korea
| | - SungWook Jung
- Department of Medical Science, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Gyungyub Gong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung-Bae Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Joo Young Kim
- Department of Pathology, Chung-Ang University Hospital, College of Medicine, Chung-Ang University, Seoul, Republic of Korea.
| | - Hee Jin Lee
- Research and Development Center, NeogenTC Corp., Seoul, Republic of Korea; Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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Sim MJW, Hanada KI, Stotz Z, Yu Z, Lu J, Brennan P, Quastel M, Gillespie GM, Long EO, Yang JC, Sun PD. Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3. Eur J Immunol 2024:e2451079. [PMID: 39030753 DOI: 10.1002/eji.202451079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/22/2024]
Abstract
Mutations in KRAS are some of the most common across multiple cancer types and are thus attractive targets for therapy. Recent studies demonstrated that mutant KRAS generates immunogenic neoantigens that are targetable by adoptive T-cell therapy in metastatic diseases. To expand mutant KRAS-specific immunotherapies, it is critical to identify additional HLA-I allotypes that can present KRAS neoantigens and their cognate T-cell receptors (TCR). Here, we identified a murine TCR specific to a KRAS-G12V neoantigen (7VVVGAVGVGK16) using a vaccination approach with transgenic mice expressing HLA-A*03:01 (HLA-A3). This TCR demonstrated exquisite specificity for mutant G12V and not WT KRAS peptides. To investigate the molecular basis for neoantigen recognition by this TCR, we determined its structure in complex with HLA-A3(G12V). G12V-TCR CDR3β and CDR1β formed a hydrophobic pocket to interact with p6 Val of the G12V but not the WT KRAS peptide. To improve the tumor sensitivity of this TCR, we designed rational substitutions to improve TCR:HLA-A3 contacts. Two substitutions exhibited modest improvements in TCR binding avidity to HLA-A3 (G12V) but did not sufficiently improve T-cell sensitivity for further clinical development. Our study provides mechanistic insight into how TCRs detect neoantigens and reveals the challenges in targeting KRAS-G12V mutations.
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Affiliation(s)
- Malcolm J W Sim
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Zachary Stotz
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, NCI, NIH, Bethesda, Maryland, USA
| | - Jinghua Lu
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Paul Brennan
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Eric O Long
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - James C Yang
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Peter D Sun
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
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Li Z, Ma L, Gao Z, Wang X, Che X, Zhang P, Li Y, Zhang Q, Liu T, Sun Y, Bai Y, Deng H. Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures. Cancer Immunol Immunother 2024; 73:164. [PMID: 38954022 PMCID: PMC11219989 DOI: 10.1007/s00262-024-03749-8] [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: 03/20/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current algorithms for predicting tumor neoantigens are unreliable and many neoantigens are derived from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently needed. In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulation of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxicity of TCRs were confirmed by transferring to primary peripheral blood T cells. The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumor organoids, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner. The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes of patients with colorectal cancer, and tumor-specific TCRs can potentially be used for personalized TCR-T therapy.
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Affiliation(s)
- Zhilang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Lisha Ma
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zhaoya Gao
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, 100041, China
| | - Xiya Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xuan Che
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Pengchong Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yixian Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qianjing Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Tianxing Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100091, China
| | - Yuan Sun
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yun Bai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Hongkui Deng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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Sun H, Han X, Du Z, Chen G, Guo T, Xie F, Gu W, Shi Z. Machine learning for the identification of neoantigen-reactive CD8 + T cells in gastrointestinal cancer using single-cell sequencing. Br J Cancer 2024; 131:387-402. [PMID: 38849478 PMCID: PMC11263575 DOI: 10.1038/s41416-024-02737-0] [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: 11/13/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND It appears that tumour-infiltrating neoantigen-reactive CD8 + T (Neo T) cells are the primary driver of immune responses to gastrointestinal cancer in patients. However, the conventional method is very time-consuming and complex for identifying Neo T cells and their corresponding T cell receptors (TCRs). METHODS By mapping neoantigen-reactive T cells from the single-cell transcriptomes of thousands of tumour-infiltrating lymphocytes, we developed a 26-gene machine learning model for the identification of neoantigen-reactive T cells. RESULTS In both training and validation sets, the model performed admirably. We discovered that the majority of Neo T cells exhibited notable differences in the biological processes of amide-related signal pathways. The analysis of potential cell-to-cell interactions, in conjunction with spatial transcriptomic and multiplex immunohistochemistry data, has revealed that Neo T cells possess potent signalling molecules, including LTA, which can potentially engage with tumour cells within the tumour microenvironment, thereby exerting anti-tumour effects. By sequencing CD8 + T cells in tumour samples of patients undergoing neoadjuvant immunotherapy, we determined that the fraction of Neo T cells was significantly and positively linked with the clinical benefit and overall survival rate of patients. CONCLUSION This method expedites the identification of neoantigen-reactive TCRs and the engineering of neoantigen-reactive T cells for therapy.
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Affiliation(s)
- Hongwei Sun
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao Han
- KangChen Bio-tech., Ltd, ShangHai, China
| | - Zhengliang Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Geer Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tonglei Guo
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Fei Xie
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
| | - Weiyue Gu
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China
| | - Zhiwen Shi
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Data and Analysis Center for Genetic Diseases, Beijing Chigene Translational Medicine Research Center Co, Ltd, Tongzhou District, Beijing, China.
- Chineo Medical Technology Co., Ltd, Beijing, 100101, China.
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Zhang Y, Liu S, Guo F, Qin S, Zhou N, Liu Z, Fan X, Chen PR. Bioorthogonal Quinone Methide Decaging Enables Live-Cell Quantification of Tumor-Specific Immune Interactions. J Am Chem Soc 2024; 146:15186-15197. [PMID: 38789930 DOI: 10.1021/jacs.4c02052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Effective antitumor immunity hinges on the specific engagement between tumor and cytotoxic immune cells, especially cytotoxic T cells. Although investigating these intercellular interactions is crucial for characterizing immune responses and guiding immunotherapeutic applications, direct and quantitative detection of tumor-T cell interactions within a live-cell context remains challenging. We herein report a photocatalytic live-cell interaction labeling strategy (CAT-Cell) relying on the bioorthogonal decaging of quinone methide moieties for sensitive and selective investigation and quantification of tumor-T cell interactions. By developing quinone methide-derived probes optimized for capturing cell-cell interactions (CCIs), we demonstrated the capacity of CAT-Cell for detecting CCIs directed by various types of receptor-ligand pairs (e.g., CD40-CD40L, TCR-pMHC) and further quantified the strengths of tumor-T cell interactions that are crucial for evaluating the antitumor immune responses. We further applied CAT-Cell for ex vivo quantification of tumor-specific T cell interactions on splenocyte and solid tumor samples from mouse models. Finally, the broad compatibility and utility of CAT-Cell were demonstrated by integrating it with the antigen-specific targeting system as well as for tumor-natural killer cell interaction detection. By leveraging the bioorthogonal photocatalytic decaging chemistry on quinone methide, CAT-Cell provides a sensitive, tunable, universal, and noninvasive toolbox for unraveling and quantifying the crucial but delicate tumor-immune interactions under live-cell settings.
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Affiliation(s)
- Yan Zhang
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shibo Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fuhu Guo
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shan Qin
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Nan Zhou
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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Yang Q, Xu L, Dong W, Li X, Wang K, Dong S, Zhang X, Yang T, Jiang F, Zhang B, Luo G, Gao X, Wang G. HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses. Brief Bioinform 2024; 25:bbae302. [PMID: 38920343 PMCID: PMC11200192 DOI: 10.1093/bib/bbae302] [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: 03/19/2024] [Revised: 05/20/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
While significant strides have been made in predicting neoepitopes that trigger autologous CD4+ T cell responses, accurately identifying the antigen presentation by human leukocyte antigen (HLA) class II molecules remains a challenge. This identification is critical for developing vaccines and cancer immunotherapies. Current prediction methods are limited, primarily due to a lack of high-quality training epitope datasets and algorithmic constraints. To predict the exogenous HLA class II-restricted peptides across most of the human population, we utilized the mass spectrometry data to profile >223 000 eluted ligands over HLA-DR, -DQ, and -DP alleles. Here, by integrating these data with peptide processing and gene expression, we introduce HLAIImaster, an attention-based deep learning framework with adaptive domain knowledge for predicting neoepitope immunogenicity. Leveraging diverse biological characteristics and our enhanced deep learning framework, HLAIImaster is significantly improved against existing tools in terms of positive predictive value across various neoantigen studies. Robust domain knowledge learning accurately identifies neoepitope immunogenicity, bridging the gap between neoantigen biology and the clinical setting and paving the way for future neoantigen-based therapies to provide greater clinical benefit. In summary, we present a comprehensive exploitation of the immunogenic neoepitope repertoire of cancers, facilitating the effective development of "just-in-time" personalized vaccines.
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Affiliation(s)
- Qiang Yang
- School of Medicine and Health, Harbin Institute of Technology, Yikuang Street, Harbin 150000, China
| | - Long Xu
- School of Computer Science and Technology, Harbin Institute of Technology, West Dazhi Street, Harbin 150001, China
| | - Weihe Dong
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, Harbin 150004, China
| | - Xiaokun Li
- School of Computer Science and Technology, Harbin Institute of Technology, West Dazhi Street, Harbin 150001, China
- School of Computer Science and Technology, Heilongjiang University, Xuefu Road, Harbin 150080, China
- Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd., Xuefu Road, Harbin 150090, China
- Shandong Hengxun Technology Co., Ltd., Miaoling Road, Qingdao 266100, China
| | - Kuanquan Wang
- School of Computer Science and Technology, Harbin Institute of Technology, West Dazhi Street, Harbin 150001, China
| | - Suyu Dong
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, Harbin 150004, China
| | - Xianyu Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Haping Road, Harbin 150081, China
| | - Tiansong Yang
- Department of Rehabilitation, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, and Traditional Chinese Medicine Informatics Key Laboratory of Heilongjiang Province, Heping Road, Harbin 150040, China
| | - Feng Jiang
- School of Medicine and Health, Harbin Institute of Technology, Yikuang Street, Harbin 150000, China
| | - Bin Zhang
- Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia
| | - Gongning Luo
- Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Hexing Road, Harbin 150004, China
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Ioffe D, McSweeny M, Hall MJ. Precision Medicine in the Era of Genetic Testing: Microsatellite Instability Evolved. Clin Colon Rectal Surg 2024; 37:157-171. [PMID: 38617845 PMCID: PMC11007599 DOI: 10.1055/s-0043-1770385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The recognized importance of microsatellite instability (MSI) in cancer has evolved considerably in the past 30 years. From its beginnings as a molecular predictor for Lynch syndrome, MSI first transitioned to a universal screening test in all colorectal and endometrial cancers, substantially increasing the identification of patients with Lynch syndrome among cancer patients. More recently, MSI has been shown to be a powerful biomarker of response to immune checkpoint blockade therapy across a diversity of tumor types, and in 2017 was granted Food and Drug Administration approval as the first tumor histology-agnostic biomarker for a cancer therapy. Focusing on colorectal cancer specifically, immune checkpoint blockade therapy has been shown to be highly effective in the treatment of both MSI-high (MSI-H) colon and rectal cancer, with data increasingly suggesting an early role for immune checkpoint blockade therapy in MSI-H colorectal tumors in the neoadjuvant setting, with the potential to avoid more toxic and morbid approaches using traditional chemotherapy, radiation therapy, and surgery. The success of MSI as an immune checkpoint blockade target has inspired ongoing vigorous research to identify new similar targets for immune checkpoint blockade therapy that may help to one day expand the reach of this revolutionary cancer therapy to a wider swath of patients and indications.
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Affiliation(s)
- Dina Ioffe
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michelle McSweeny
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J. Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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8
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Guo M, Liu MYR, Brooks DG. Regulation and impact of tumor-specific CD4 + T cells in cancer and immunotherapy. Trends Immunol 2024; 45:303-313. [PMID: 38508931 DOI: 10.1016/j.it.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/22/2024]
Abstract
CD4+ T cells are crucial in generating and sustaining immune responses. They orchestrate and fine-tune mammalian innate and adaptive immunity through cell-based interactions and the release of cytokines. The role of these cells in contributing to the efficacy of antitumor immunity and immunotherapy has just started to be uncovered. Yet, many aspects of the CD4+ T cell response are still unclear, including the differentiation pathways controlling such cells during cancer progression, the external signals that program them, and how the combination of these factors direct ensuing immune responses or immune-restorative therapies. In this review, we focus on recent advances in understanding CD4+ T cell regulation during cancer progression and the importance of CD4+ T cells in immunotherapies.
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Affiliation(s)
- Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Melissa Yi Ran Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada.
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9
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Zenga J, Awan M, Frei A, Foeckler J, Kuehn R, Espinosa OV, Bruening J, Massey B, Wong S, Shreenivas A, Shukla M, Kasprzak J, Sun Y, Shaheduzzaman M, Chen F, Kearl T, Himburg HA. Tumor-specific T cells in head and neck cancer have rescuable functionality and can be identified through single-cell co-culture. Transl Oncol 2024; 42:101899. [PMID: 38320395 PMCID: PMC10851216 DOI: 10.1016/j.tranon.2024.101899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) remains a treatment-resistance disease with limited response to immunotherapy. While T cells in HNSCC are known to display phenotypic dysfunction, whether they retain rescuable functional capacity and tumor-killing capability remains unclear. METHODS To investigate the functionality and tumor-specificity of tumor-infiltrating lymphocytes (TILs) across HNSCCs, malignant cell lines and TILs were derived from 31 HPV-negative HNSCCs at the time of standard surgical resection. T cell functional capacity was evaluated through ex vivo expansion, immunophenotyping, and IsoLight single-cell proteomics. Tumor-specificity was investigated through both bulk and single-cell tumor-TIL co-culture. RESULTS TILs could be successfully generated from 24 patients (77%), including both previously untreated and radiation recurrent HNSCCs. We demonstrate that across HNSCCs, TILs express multiple exhaustion markers but maintain a predominantly effector memory phenotype. After ex vivo expansion, TILs retain immunogenic functionality even from radiation-resistant, exhausted, and T cell-depleted disease. We further demonstrate tumor-specificity of T cells across HNSCC patients through patient-matched malignant cell-T cell co-culture. Finally, we use optofluidic technology to establish an autologous single tumor cell-single T cell co-culture platform for HNSCC. Cells derived from three HNSCC patients underwent single-cell co-culture which enabled identification and visualization of individual tumor-killing TILs in real-time in all patients. CONCLUSIONS These studies show that cancer-specific T cells exist across HNSCC patients with rescuable immunogenicity and can be identified on a single-cell level. These data lay the foundation for development of patient-specific T cell immunotherapies in HNSCC.
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Affiliation(s)
- Joseph Zenga
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Musaddiq Awan
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anne Frei
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jamie Foeckler
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Rachel Kuehn
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Oscar Villareal Espinosa
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jennifer Bruening
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Becky Massey
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Stuart Wong
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Aditya Shreenivas
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Monica Shukla
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Julia Kasprzak
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Dermatology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Yunguang Sun
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Md Shaheduzzaman
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Fanghong Chen
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tyce Kearl
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Heather A Himburg
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Otolaryngology, Medical College of Wisconsin, Milwaukee, WI, United States; Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, United States.
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10
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Wu Y, Ma J, Yang X, Nan F, Zhang T, Ji S, Rao D, Feng H, Gao K, Gu X, Jiang S, Song G, Pan J, Zhang M, Xu Y, Zhang S, Fan Y, Wang X, Zhou J, Yang L, Fan J, Zhang X, Gao Q. Neutrophil profiling illuminates anti-tumor antigen-presenting potency. Cell 2024; 187:1422-1439.e24. [PMID: 38447573 DOI: 10.1016/j.cell.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing functions across cancer types. However, given their short half-life, it remains challenging to explore how neutrophils adopt specific fates in cancer. Here, we generated and integrated single-cell neutrophil transcriptomes from 17 cancer types (225 samples from 143 patients). Neutrophils exhibited extraordinary complexity, with 10 distinct states including inflammation, angiogenesis, and antigen presentation. Notably, the antigen-presenting program was associated with favorable survival in most cancers and could be evoked by leucine metabolism and subsequent histone H3K27ac modification. These neutrophils could further invoke both (neo)antigen-specific and antigen-independent T cell responses. Neutrophil delivery or a leucine diet fine-tuned the immune balance to enhance anti-PD-1 therapy in various murine cancer models. In summary, these data not only indicate the neutrophil divergence across cancers but also suggest therapeutic opportunities such as antigen-presenting neutrophil delivery.
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Affiliation(s)
- Yingcheng Wu
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaqiang Ma
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xupeng Yang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Fang Nan
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Tiancheng Zhang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shuyi Ji
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University School of Medicine, Shanghai 200123, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hua Feng
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xixi Gu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Mao Zhang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yanan Xu
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yihui Fan
- Department of Pathogenic Biology and Basic Medical Research Center, School of Medicine, Nantong University, Nantong 226001, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Jia Fan
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Qiang Gao
- Department of Liver Surgery and Transplantation and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
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11
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Srivastava PK. Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines. J Clin Invest 2024; 134:e176740. [PMID: 38426497 PMCID: PMC10904052 DOI: 10.1172/jci176740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A proportion of somatic mutations in tumors create neoepitopes that can prime T cell responses that target the MHC I-neoepitope complexes on tumor cells, mediating tumor control or rejection. Despite the compelling centrality of neoepitopes to cancer immunity, we know remarkably little about what constitutes a neoepitope that can mediate tumor control in vivo and what distinguishes such a neoepitope from the vast majority of similar candidate neoepitopes that are inefficacious in vivo. Studies in mice as well as clinical trials have begun to reveal the unexpected paradoxes in this area. Because cancer neoepitopes straddle that ambiguous ground between self and non-self, some rules that are fundamental to immunology of frankly non-self antigens, such as viral or model antigens, do not appear to apply to neoepitopes. Because neoepitopes are so similar to self-epitopes, with only small changes that render them non-self, immune response to them is regulated at least partially the way immune response to self is regulated. Therefore, neoepitopes are viewed and understood here through the clarifying lens of negative thymic selection. Here, the emergent questions in the biology and clinical applications of neoepitopes are discussed critically and a mechanistic and testable framework that explains the complexity and translational potential of these wonderful antigens is proposed.
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12
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Pounraj S, Chen S, Ma L, Mazzieri R, Dolcetti R, Rehm BHA. Targeting Tumor Heterogeneity with Neoantigen-Based Cancer Vaccines. Cancer Res 2024; 84:353-363. [PMID: 38055891 DOI: 10.1158/0008-5472.can-23-2042] [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: 07/10/2023] [Revised: 10/24/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Neoantigen-based cancer vaccines have emerged as a promising immunotherapeutic approach to treat cancer. Nevertheless, the high degree of heterogeneity in tumors poses a significant hurdle for developing a vaccine that targets the therapeutically relevant neoantigens capable of effectively stimulating an immune response as each tumor contains numerous unique putative neoantigens. Understanding the complexities of tumor heterogeneity is crucial for the development of personalized neoantigen-based vaccines, which hold the potential to revolutionize cancer treatment and improve patient outcomes. In this review, we discuss recent advancements in the design of neoantigen-based cancer vaccines emphasizing the identification, validation, formulation, and targeting of neoantigens while addressing the challenges posed by tumor heterogeneity. The review highlights the application of cutting-edge approaches, such as single-cell sequencing and artificial intelligence to identify immunogenic neoantigens, while outlining current limitations and proposing future research directions to develop effective neoantigen-based vaccines.
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Affiliation(s)
- Saranya Pounraj
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Linlin Ma
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
- School of Environment and Science, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
| | - Roberta Mazzieri
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Riccardo Dolcetti
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University (Nathan Campus), Brisbane, Queensland, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University (Gold Coast Campus), Queensland, Australia
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13
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Faghfuri E. Recent advances in personalized cancer immunotherapy with immune checkpoint inhibitors, T cells and vaccines. Per Med 2024; 21:45-57. [PMID: 38088165 DOI: 10.2217/pme-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The results of genomic and molecular profiling of cancer patients can be effectively applied to immunotherapy agents, including immune checkpoint inhibitors, to select the most appropriate treatment. In addition, accurate prediction of neoantigens facilitates the development of individualized cancer vaccines and T-cell therapy. This review summarizes the biomarker(s) predicting responses to immune checkpoint inhibitors and focuses on current strategies to identify and isolate neoantigen-reactive T cells as well as the clinical development of neoantigen-based therapeutics. The results suggest that maximal T-cell stimulation and expansion can be achieved with combination therapies that enhance antigen-presenting cells' function and optimal T-cell priming in lymph nodes.
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Affiliation(s)
- Elnaz Faghfuri
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, 5613658115, Iran
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14
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Migueles SA, Nettere DM, Gavil NV, Wang LT, Toulmin SA, Kelly EP, Ward AJ, Lin S, Thompson SA, Peterson BA, Abdeen CS, Sclafani CR, Pryal PF, Leach BG, Ludwig AK, Rogan DC, Przygonska PA, Cattani A, Imamichi H, Sachs A, Cafri G, Huang NN, Patamawenu A, Liang CJ, Hallahan CW, Kambach DM, Han EX, Coupet T, Chen J, Moir SL, Chun TW, Coates EE, Ledgerwood J, Schmidt J, Taillandier-Coindard M, Michaux J, Pak H, Bassani-Sternberg M, Frahm N, McElrath MJ, Connors M. HIV vaccines induce CD8 + T cells with low antigen receptor sensitivity. Science 2023; 382:1270-1276. [PMID: 38096385 DOI: 10.1126/science.adg0514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Current HIV vaccines designed to stimulate CD8+ T cells have failed to induce immunologic control upon infection. The functions of vaccine-induced HIV-specific CD8+ T cells were investigated here in detail. Cytotoxic capacity was significantly lower than in HIV controllers and was not a consequence of low frequency or unaccumulated functional cytotoxic proteins. Low cytotoxic capacity was attributable to impaired degranulation in response to the low antigen levels present on HIV-infected targets. The vaccine-induced T cell receptor (TCR) repertoire was polyclonal and transduction of these TCRs conferred the same reduced functions. These results define a mechanism accounting for poor antiviral activity induced by these vaccines and suggest that an effective CD8+ T cell response may require a vaccination strategy that drives further TCR clonal selection.
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Affiliation(s)
- Stephen A Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Danielle M Nettere
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Noah V Gavil
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence T Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sushila A Toulmin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth P Kelly
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Addison J Ward
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Siying Lin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah A Thompson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bennett A Peterson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cassidy S Abdeen
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carina R Sclafani
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrick F Pryal
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin G Leach
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amanda K Ludwig
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Rogan
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paulina A Przygonska
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cattani
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hiromi Imamichi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Abraham Sachs
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gal Cafri
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ning-Na Huang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andy Patamawenu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - C Jason Liang
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Claire W Hallahan
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | - Susan L Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Coates
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Ledgerwood
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Marie Taillandier-Coindard
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Nicole Frahm
- Vaccine and Infectious Disease Division and the HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division and the HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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15
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Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023; 14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [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: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Advancements in sequencing technologies and bioinformatics algorithms have expanded our ability to identify tumor-specific somatic mutation-derived antigens (neoantigens). While recent studies have shown neoantigens to be compelling targets for cancer immunotherapy due to their foreign nature and high immunogenicity, the need for increasingly accurate and cost-effective approaches to rapidly identify neoantigens remains a challenging task, but essential for successful cancer immunotherapy. Currently, gene expression analysis and algorithms for variant calling can be used to generate lists of mutational profiles across patients, but more care is needed to curate these lists and prioritize the candidate neoantigens most capable of inducing an immune response. A growing amount of evidence suggests that only a handful of somatic mutations predicted by mutational profiling approaches act as immunogenic neoantigens. Hence, unbiased screening of all candidate neoantigens predicted by Whole Genome Sequencing/Whole Exome Sequencing may be necessary to more comprehensively access the full spectrum of immunogenic neoepitopes. Once putative cancer neoantigens are identified, one of the largest bottlenecks in translating these neoantigens into actionable targets for cell-based therapies is identifying the cognate T cell receptors (TCRs) capable of recognizing these neoantigens. While many TCR-directed screening and validation assays have utilized bulk samples in the past, there has been a recent surge in the number of single-cell assays that provide a more granular understanding of the factors governing TCR-pMHC interactions. The goal of this review is to provide an overview of existing strategies to identify candidate neoantigens using genomics-based approaches and methods for assessing neoantigen immunogenicity. Additionally, applications, prospects, and limitations of some of the current single-cell technologies will be discussed. Finally, we will briefly summarize some of the recent models that have been used to predict TCR antigen specificity and analyze the TCR receptor repertoire.
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Affiliation(s)
- Ravi K. Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Cygan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Alfredo Colina
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anthony E. Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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16
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Liu L, Li Y, Song Y, Sun Z, Li W, Li B, Wang Y, Wang H, Wang B. One-step shotgun approach for antigenic specific pMHCs capture stimulated CD8 + T cell activation and proliferation. Cell Immunol 2023; 393-394:104784. [PMID: 37984278 DOI: 10.1016/j.cellimm.2023.104784] [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: 08/01/2023] [Revised: 09/27/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023]
Abstract
Antigenic peptides play a central role in immune surveillance in cancer, infectious disease, autoimmunity, and allergy. The identification and isolation of antigenic peptides for T cell immune response are crucial for successful personalized adoptive immune cell therapy. The mainly methods includes gene sequencing and bioinformatic analysis. The antigenic peptides which identified by analysis and artificially synthesized still need antigen presenting cell (APC) to deliver to T cells. However, high costs and lengthy process times have limited its application in clinical practice. In order to overcome it, this study attempted to directly capture antigenic peptide-major histocompatibility complex (MHC) class I (pMHCs) from cell lysates using streptavidin Dynabeads and biotin-labeled antibodies, then the pMHCs was co-cultured with tumor infiltrating lymphocytes (TILs) of the same tissue origin. The results indicated that the captured pMHCs were able to enrich the tumor antigen-specific CD8+ T cells, and also effectively induce proliferation and cytotoxic responses of CD8+ T cells. This study provided a novel approach for obtaining tumor antigenic pMHCs, which could enrich antigen-specific CD8+ T cells, and could also function as artificial APCs (aAPCs) to stimulate proliferation and activation of T cells. Notably, these pMHCs can stimulate the proliferation of stem-like memory T cells. In conclusion, this study describes a time-saving and low-cost method to isolate tumour antigen peptide MHC complexs, helping tumor antigen-specific T cell enrichment, activation, and proliferation.
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Affiliation(s)
- Lili Liu
- School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, China
| | - Yateng Li
- Qingdao Sino-Cell Biomedicine Co., Ltd., Qingdao, Shandong 266200, China
| | - Yu Song
- Qingdao Sino-Cell Biomedicine Co., Ltd., Qingdao, Shandong 266200, China
| | - Zhen Sun
- Qingdao Sino-Cell Biomedicine Co., Ltd., Qingdao, Shandong 266200, China
| | - Wenjing Li
- Qingdao Sino-Cell Biomedicine Co., Ltd., Qingdao, Shandong 266200, China
| | - Bin Li
- Qingdao Sino-Cell Biomedicine Co., Ltd., Qingdao, Shandong 266200, China
| | - Yongjie Wang
- Institute of Translational Research for Solid Tumor, Qingdao University, Qingdao, Shandong 266000, China; Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266200, China.
| | - Haibo Wang
- Institute of Translational Research for Solid Tumor, Qingdao University, Qingdao, Shandong 266000, China; Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266200, China.
| | - Bin Wang
- School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, China.
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17
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Chen G, Kong D, Lin Y. Neo-Antigen-Reactive T Cells Immunotherapy for Colorectal Cancer: A More Personalized Cancer Therapy Approach. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2200186. [PMID: 37970536 PMCID: PMC10632666 DOI: 10.1002/gch2.202200186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/09/2023] [Indexed: 11/17/2023]
Abstract
Colorectal cancer (CRC) is the second most common malignancy in women and the third most frequent cancer in men. Evidence has revealed that the survival of patients with metastatic CRC is very low, between one and three years. Neoantigens are known proteins encoded by mutations in tumor cells. It is theorized that recognizing neoantigens by T cells leads to T cell activation and further antitumor responses. Neoantigen-reactive T cells (NRTs) are designed against the mentioned neoantigens expressed by tumor cells. NRTs selectively kill tumor cells without damage to non-cancerous cells. Identifying patient-specific and high immunogen neoantigens is important in NRT immunotherapy of patients with CRC. However, the main challenges are the side effects and preparation of NRTs, as well as the effectiveness of these cells in vivo. This review summarized the properties of neoantigens as well as the preparation and therapeutic outcomes of NRTs for the treatment of CRC.
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Affiliation(s)
- Guan‐Liang Chen
- Department of Gastroenterology SurgeryAffiliated Hospital of Shaoxing UniversityShaoxing312000China
| | - De‐Xia Kong
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
| | - Yan Lin
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
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18
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Yarmarkovich M, Marshall QF, Warrington JM, Premaratne R, Farrel A, Groff D, Li W, di Marco M, Runbeck E, Truong H, Toor JS, Tripathi S, Nguyen S, Shen H, Noel T, Church NL, Weiner A, Kendsersky N, Martinez D, Weisberg R, Christie M, Eisenlohr L, Bosse KR, Dimitrov DS, Stevanovic S, Sgourakis NG, Kiefel BR, Maris JM. Targeting of intracellular oncoproteins with peptide-centric CARs. Nature 2023; 623:820-827. [PMID: 37938771 PMCID: PMC10665195 DOI: 10.1038/s41586-023-06706-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023]
Abstract
The majority of oncogenic drivers are intracellular proteins, constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient for generating responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins essential for tumorigenesis. We focused on targeting the unmutated peptide QYNPIRTTF discovered on HLA-A*24:02, which is derived from the neuroblastoma-dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (PC-CARs) through a counter panning strategy using predicted potentially cross-reactive peptides. We further proposed that PC-CARs can recognize peptides on additional HLA allotypes when presenting a similar overall molecular surface. Informed by our computational modelling results, we show that PHOX2B PC-CARs also recognize QYNPIRTTF presented by HLA-A*23:01, the most common non-A2 allele in people with African ancestry. Finally, we demonstrate potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that PC-CARs have the potential to expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and allow targeting through additional HLA allotypes in a clinical setting.
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Affiliation(s)
- Mark Yarmarkovich
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Quinlen F Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Warrington
- 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
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Erin Runbeck
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hau Truong
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Son Nguyen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena Shen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiffany Noel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Amber Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nathan Kendsersky
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dan Martinez
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rebecca Weisberg
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly Christie
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurence Eisenlohr
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Nikolaos G Sgourakis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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19
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Jayaraman S, Montagne JM, Nirschl TR, Marcisak E, Johnson J, Huff A, Hsiao MH, Nauroth J, Heumann T, Zarif JC, Jaffee EM, Azad N, Fertig EJ, Zaidi N, Larman HB. Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses. CELL REPORTS METHODS 2023; 3:100600. [PMID: 37776855 PMCID: PMC10626196 DOI: 10.1016/j.crmeth.2023.100600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/23/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023]
Abstract
Assays linking cellular phenotypes with T cell or B cell antigen receptor sequences are crucial for characterizing adaptive immune responses. Existing methodologies are limited by low sample throughput and high cost. Here, we present INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach that combines molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility.
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Affiliation(s)
- Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Janelle M Montagne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas R Nirschl
- Pathobiology Graduate Program, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Emily Marcisak
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeanette Johnson
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amanda Huff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Julie Nauroth
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thatcher Heumann
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Hematology Oncology, Vanderbilt-Ingram Comprehensive Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jelani C Zarif
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nilo Azad
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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20
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Ghorani E, Swanton C, Quezada SA. Cancer cell-intrinsic mechanisms driving acquired immune tolerance. Immunity 2023; 56:2270-2295. [PMID: 37820584 DOI: 10.1016/j.immuni.2023.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Immune evasion is a hallmark of cancer, enabling tumors to survive contact with the host immune system and evade the cycle of immune recognition and destruction. Here, we review the current understanding of the cancer cell-intrinsic factors driving immune evasion. We focus on T cells as key effectors of anti-cancer immunity and argue that cancer cells evade immune destruction by gaining control over pathways that usually serve to maintain physiological tolerance to self. Using this framework, we place recent mechanistic advances in the understanding of cancer immune evasion into broad categories of control over T cell localization, antigen recognition, and acquisition of optimal effector function. We discuss the redundancy in the pathways involved and identify knowledge gaps that must be overcome to better target immune evasion, including the need for better, routinely available tools that incorporate the growing understanding of evasion mechanisms to stratify patients for therapy and trials.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology and Immunotherapy Unit, Department of Surgery and Cancer, Imperial College London, London, UK; Department of Medical Oncology, Imperial College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London, UK.
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21
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Hall MS, Teer JK, Yu X, Branthoover H, Snedal S, Rodriguez-Valentin M, Nagle L, Scott E, Schachner B, Innamarato P, Hall AM, Blauvelt J, Rich CJ, Richards AD, Ceccarelli J, Langer TJ, Yoder SJ, Beatty MS, Cox CA, Messina JL, Abate-Daga D, Mule JJ, Mullinax JE, Sarnaik AA, Pilon-Thomas S. Neoantigen-specific CD4 + tumor-infiltrating lymphocytes are potent effectors identified within adoptive cell therapy products for metastatic melanoma patients. J Immunother Cancer 2023; 11:e007288. [PMID: 37802604 PMCID: PMC10565316 DOI: 10.1136/jitc-2023-007288] [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] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TILs) is a promising immunotherapeutic approach for patients with advanced solid tumors. While numerous advances have been made, the contribution of neoantigen-specific CD4+T cells within TIL infusion products remains underexplored and therefore offers a significant opportunity for progress. METHODS We analyzed infused TIL products from metastatic melanoma patients previously treated with ACT for the presence of neoantigen-specific T cells. TILs were enriched on reactivity to neoantigen peptides derived and prioritized from patient sample-directed mutanome analysis. Enriched TILs were further investigated to establish the clonal neoantigen response with respect to function, transcriptomics, and persistence following ACT. RESULTS We discovered that neoantigen-specific TIL clones were predominantly CD4+ T cells and were present in both therapeutic responders and non-responders. CD4+ TIL demonstrated an effector T cell response with cytotoxicity toward autologous tumor in a major histocompatibility complex class II-dependent manner. These results were validated by paired TCR and single cell RNA sequencing, which elucidated transcriptomic profiles distinct to neoantigen-specific CD4+ TIL. CONCLUSIONS Despite methods which often focus on CD8+T cells, our study supports the importance of prospective identification of neoantigen-specific CD4+ T cells within TIL products as they are a potent source of tumor-specific effectors. We further advocate for the inclusion of neoantigen-specific CD4+ TIL in future ACT protocols as a strategy to improve antitumor immunity.
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Affiliation(s)
- MacLean S Hall
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Cancer Biology PhD Program, University of South Florida, Tampa, Florida, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Holly Branthoover
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Sebastian Snedal
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - Luz Nagle
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Ellen Scott
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Ben Schachner
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Patrick Innamarato
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Amy M Hall
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jamie Blauvelt
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Carolyn J Rich
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Allison D Richards
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - T J Langer
- Turnstone Biologics, Inc, San Diego, California, USA
| | - Sean J Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Matthew S Beatty
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Cheryl A Cox
- Cell Therapies Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jane L Messina
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Daniel Abate-Daga
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - James J Mule
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - John E Mullinax
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Sarcoma, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Amod A Sarnaik
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Shari Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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22
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Davis L, Miller RE, Wong YNS. The Landscape of Adoptive Cellular Therapies in Ovarian Cancer. Cancers (Basel) 2023; 15:4814. [PMID: 37835509 PMCID: PMC10571827 DOI: 10.3390/cancers15194814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Ovarian cancers are typically poorly immunogenic and have demonstrated disappointing responses to immune checkpoint inhibitor (ICI) therapy. Adoptive cellular therapy (ACT) offers an alternative method of harnessing the immune system that has shown promise, especially with the success of chimeric antigen receptor T-cell (CAR-T) therapy in haematologic malignancies. So far, ACT has led to modest results in the treatment of solid organ malignancies. This review explores the possibility of ACT as an effective alternative or additional treatment to current standards of care in ovarian cancer. We will highlight the potential of ACTs, such as CAR-T, T-cell receptor therapy (TCR-T), tumour-infiltrating lymphocytes (TILs) and cell-based vaccines, whilst also discussing their challenges. We will present clinical studies for these approaches in the treatment of immunologically 'cold' ovarian cancer and consider the rationale for future research.
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Affiliation(s)
- Lucy Davis
- Royal Free Hospital, London NW3 2QG, UK;
| | - Rowan E Miller
- Department of Medical Oncology, University College London Hospital, London NW1 3PG, UK;
- Department of Medical Oncology, St Bartholomew’s Hospital, London EC1A 7BE, UK
| | - Yien Ning Sophia Wong
- Royal Free Hospital, London NW3 2QG, UK;
- Department of Medical Oncology, University College London Hospital, London NW1 3PG, UK;
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23
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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24
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Ade CM, Sporn MJ, Das S, Yu Z, Hanada KI, Qi YA, Maity T, Zhang X, Guha U, Andresson T, Yang JC. Identification of neoepitope reactive T-cell receptors guided by HLA-A*03:01 and HLA-A*11:01 immunopeptidomics. J Immunother Cancer 2023; 11:e007097. [PMID: 37758652 PMCID: PMC10537849 DOI: 10.1136/jitc-2023-007097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Tumor-specific mutated proteins can create immunogenic non-self, mutation-containing 'neoepitopes' that are attractive targets for adoptive T-cell therapies. To avoid the complexity of defining patient-specific, private neoepitopes, there has been major interest in targeting common shared mutations in driver genes using off-the-shelf T-cell receptors (TCRs) engineered into autologous lymphocytes. However, identifying the precise naturally processed neoepitopes to pursue is a complex and challenging process. One method to definitively demonstrate whether an epitope is presented at the cell surface is to elute peptides bound to a specific major histocompatibility complex (MHC) allele and analyze them by mass spectrometry (MS). These MS data can then be prospectively applied to isolate TCRs specific to the neoepitope. METHODS We created mono-allelic cell lines expressing one class I HLA allele and one common mutated oncogene in order to eliminate HLA deconvolution requirements and increase the signal of recovered peptides. MHC-bound peptides on the surface of these cell lines were immunoprecipitated, purified, and analyzed using liquid chromatography-tandem mass spectrometry, producing a list of mutation-containing minimal epitopes. To validate the immunogenicity of these neoepitopes, HLA-transgenic mice were vaccinated using the minimal peptides identified by MS in order to generate neoepitope-reactive TCRs. Specificity of these candidate TCRs was confirmed by peptide titration and recognition of transduced targets. RESULTS We identified precise neoepitopes derived from mutated isoforms of KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates. From our MS data, we were able to successfully isolate murine TCRs that specifically recognize four HLA-A*11:01 restricted neoepitopes (KRAS G13D, PIK3CA E545K, EGFR L858R and BRAF V600E) and three HLA-A*03:01 restricted neoepitopes (KRAS G12V, EGFR L858R and BRAF V600E). CONCLUSIONS Our data show that an MS approach can be used to demonstrate which shared oncogene-derived neoepitopes are processed and presented by common HLA alleles, and those MS data can rapidly be used to develop TCRs against these common tumor-specific antigens. Although further characterization of these neoepitope-specific murine TCRs is required, ultimately, they have the potential to be used clinically for adoptive cell therapy.
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Affiliation(s)
- Catherine M Ade
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Matthew J Sporn
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Sudipto Das
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Yue A Qi
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Tapan Maity
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA
| | - Xu Zhang
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- NextCure Inc, Beltsville, MD, USA
| | - Thorkell Andresson
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - James C Yang
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
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25
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Koya T, Yoshida K, Togi M, Niida Y, Togi S, Ura H, Mizuta S, Kato T, Yamada S, Shibata T, Liu YC, Yuan SS, Wu DC, Kobayashi H, Utsugisawa T, Kanno H, Shimodaira S. Clinical Trial on the Safety and Tolerability of Personalized Cancer Vaccines Using Human Platelet Lysate-Induced Antigen-Presenting Cells. Cancers (Basel) 2023; 15:3627. [PMID: 37509288 PMCID: PMC10377585 DOI: 10.3390/cancers15143627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Research and development of personalized cancer vaccines as precision medicine are ongoing. We predicted human leukocyte antigen (HLA)-compatible cancer antigen candidate peptides based on patient-specific cancer genomic profiles and performed a Phase I clinical trial for the safety and tolerability of cancer vaccines with human platelet lysate-induced antigen-presenting cells (HPL-APCs) from peripheral monocytes. Among the five enrolled patients, two patients completed six doses per course (2-3 × 107 cells per dose), and an interim analysis was performed based on the immune response. An immune response was detected by enzyme-linked immunosorbent spot (ELISpot) assays to HLA-A*33:03-matched KRASWT, HLA-DRB1*09:01-compliant KRASWT or G12D, or HLA-A*31:01-matched SMAD4WT, and HLA-DRB1*04:01-matched SMAD4G365D peptides in two completed cases, respectively. Moreover, SMAD4WT-specific CD8+ effector memory T cells were amplified. However, an attenuation of the acquired immune response was observed 6 months after one course of cancer vaccination as the disease progressed. This study confirmed the safety and tolerability of HPL-APCs in advanced and recurrent cancers refractory to standard therapy and is the first clinical report to demonstrate the immunoinducibility of personalized cancer vaccines using HPL-APCs. Phase II clinical trials to determine immune responses with optimized adjuvant drugs and continued administration are expected to demonstrate efficacy.
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Affiliation(s)
- Terutsugu Koya
- Department of Regenerative Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
| | - Kenichi Yoshida
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
| | - Misa Togi
- Department of Regenerative Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
| | - Yo Niida
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Sumihito Togi
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Hiroki Ura
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Shuichi Mizuta
- Department of Hematology and Immunology, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Tomohisa Kato
- Division of Stem Cell Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Sohsuke Yamada
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Takeo Shibata
- Department of Obstetrics and Gynecology, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Yi-Chang Liu
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shyng-Shiou Yuan
- Office of Research & Development, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Deng-Chyang Wu
- Internal Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hirohito Kobayashi
- Division of Transfusion and Cell Therapy, Tokyo Women's Medical University, Adachi Medical Center, Adachi 123-8558, Tokyo, Japan
| | - Taiju Utsugisawa
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Shinjuku 162-8666, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Shinjuku 162-8666, Tokyo, Japan
| | - Shigetaka Shimodaira
- Department of Regenerative Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
- Division of Stem Cell Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Shinjuku 162-8666, Tokyo, Japan
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26
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Fahad AS, Chung CY, López Acevedo SN, Boyle N, Madan B, Gutiérrez-González MF, Matus-Nicodemos R, Laflin AD, Ladi RR, Zhou J, Wolfe J, Llewellyn-Lacey S, Koup RA, Douek DC, Balfour HH, Price DA, DeKosky BJ. Cell activation-based screening of natively paired human T cell receptor repertoires. Sci Rep 2023; 13:8011. [PMID: 37198258 PMCID: PMC10192375 DOI: 10.1038/s41598-023-31858-4] [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: 05/02/2022] [Accepted: 03/20/2023] [Indexed: 05/19/2023] Open
Abstract
Adoptive immune therapies based on the transfer of antigen-specific T cells have been used successfully to treat various cancers and viral infections, but improved techniques are needed to identify optimally protective human T cell receptors (TCRs). Here we present a high-throughput approach to the identification of natively paired human TCRα and TCRβ (TCRα:β) genes encoding heterodimeric TCRs that recognize specific peptide antigens bound to major histocompatibility complex molecules (pMHCs). We first captured and cloned TCRα:β genes from individual cells, ensuring fidelity using a suppression PCR. We then screened TCRα:β libraries expressed in an immortalized cell line using peptide-pulsed antigen-presenting cells and sequenced activated clones to identify the cognate TCRs. Our results validated an experimental pipeline that allows large-scale repertoire datasets to be annotated with functional specificity information, facilitating the discovery of therapeutically relevant TCRs.
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Affiliation(s)
- Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Cheng Yu Chung
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Sheila N López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Nicoleen Boyle
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | | | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Rukmini R Ladi
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - John Zhou
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Jacy Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Henry H Balfour
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, 66044, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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27
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Camperi J, Devarajan S, McKay A, Tarighat S, Chen D, Hu Z. Assessing TCR identity, knock-in efficiency, and potency for individualized TCR-T cell therapy. J Immunol Methods 2023; 517:113491. [PMID: 37187316 DOI: 10.1016/j.jim.2023.113491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/17/2023]
Abstract
Advances in mass spectrometry, genome sequencing techniques, and bioinformatic strategies have accelerated the discovery of cancer-specific neoantigens. Tumors express multiple immunogenic neoantigens, and neoantigen-specific T cell receptors (TCRs) can be identified in peripheral blood's mononuclear cells in cancer patients. Therefore, individualized TCR-based therapies are a promising approach whereby multiple neoantigen-specific TCRs can be selected in each patient, potentially leading to a highly effective treatment for cancer patients. We developed three multiplex analytical assays to determine the quality attributes of the TCR-T cell drug product with a mixture of five engineered TCRs. The identity of each TCR was determined by two NGS-based methods, Illumina MiSeq and PacBio platforms. This approach not only confirms the expected TCR sequences but also differentiates them by their variable regions. The five individual TCR and total TCR knock-in efficiencies were measured by droplet digital PCR using specific reverse primers. A potency assay based on transfection of antigen-encoding-RNA was developed to assess the dose-dependent activation of T cells for each TCR by measuring the surface activation marker CD137 expression and cytokine secretion. This work provides new assays to characterize individualized TCR-T cell products and insights into quality attributes for the control strategy.
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Affiliation(s)
- Julien Camperi
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Srinidhi Devarajan
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Andrew McKay
- Molecular Oncology, Genentech, 1 DNA Way, South San Francisco, CA 04080, USA
| | - Somayeh Tarighat
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Dayue Chen
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zhilan Hu
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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28
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Chatani PD, Lowery FJ, Parikh NB, Hitscherich KJ, Yossef R, Hill V, Gartner JJ, Paria B, Florentin M, Ray S, Bera A, Parkhust M, Robbins P, Krishna S, Rosenberg SA. Cell surface marker-based capture of neoantigen-reactive CD8 + T-cell receptors from metastatic tumor digests. J Immunother Cancer 2023; 11:jitc-2022-006264. [PMID: 37258038 DOI: 10.1136/jitc-2022-006264] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Cellular immunotherapies using autologous tumor-infiltrating lymphocytes (TIL) can induce durable regression of epithelial cancers in selected patients with treatment-refractory metastatic disease. As the genetic engineering of T cells with tumor-reactive T-cell receptors (TCRs) comes to the forefront of clinical investigation, the rapid, scalable, and cost-effective detection of patient-specific neoantigen-reactive TIL remains a top priority. METHODS We analyzed the single-cell transcriptomic states of 31 neoantigen-specific T-cell clonotypes to identify cell surface dysfunction markers that best identified the metastatic transcriptional states enriched with antitumor TIL. We developed an efficient method to capture neoantigen-reactive TCRs directly from resected human tumors based on cell surface co-expression of CD39, programmed cell death protein-1, and TIGIT dysfunction markers (CD8+ TILTP). RESULTS TILTP TCR isolation achieved a high degree of correlation with single-cell transcriptomic signatures that identify neoantigen-reactive TCRs, making it a cost-effective strategy using widely available resources. Reconstruction of additional TILTP TCRs from tumors identified known and novel antitumor TCRs, showing that at least 39.5% of TILTP TCRs are neoantigen-reactive or tumor-reactive. Despite their substantial enrichment for neoantigen-reactive TCR clonotypes, clonal dynamics of 24 unique antitumor TILTP clonotypes from four patients indicated that most in vitro expanded TILTP populations failed to demonstrate neoantigen reactivity, either by loss of neoantigen-reactive clones during TIL expansion, or through functional impairment during cognate neoantigen recognition. CONCLUSIONS While direct usage of in vitro-expanded CD8+ TILTP as a source for cellular therapy might be precluded by profound TIL dysfunction, isolating TILTP represents a streamlined effective approach to rapidly identify neoantigen-reactive TCRs to design engineered cellular immunotherapies against cancer.
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Affiliation(s)
- Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Biman Paria
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Florentin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Parkhust
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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29
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Yu L, Lanqing G, Huang Z, Xin X, Minglin L, Fa-hui L, Zou H, Min J. T cell immunotherapy for cervical cancer: challenges and opportunities. Front Immunol 2023; 14:1105265. [PMID: 37180106 PMCID: PMC10169584 DOI: 10.3389/fimmu.2023.1105265] [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: 11/22/2022] [Accepted: 02/27/2023] [Indexed: 05/15/2023] Open
Abstract
Cancer cellular immunotherapy has made inspiring therapeutic effects in clinical practices, which brings new hope for the cure of cervical cancer. CD8+T cells are the effective cytotoxic effector cells against cancer in antitumor immunity, and T cells-based immunotherapy plays a crucial role in cellular immunotherapy. Tumor infiltrated Lymphocytes (TIL), the natural T cells, is approved for cervical cancer immunotherapy, and Engineered T cells therapy also has impressive progress. T cells with natural or engineered tumor antigen binding sites (CAR-T, TCR-T) are expanded in vitro, and re-infused back into the patients to eradicate tumor cells. This review summarizes the preclinical research and clinical applications of T cell-based immunotherapy for cervical cancer, and the challenges for cervical cancer immunotherapy.
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Affiliation(s)
- Lingfeng Yu
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Gong Lanqing
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziyu Huang
- School of Arts and Sciences, Brandeis University, Boston, MA, United States
| | - Xiaoyan Xin
- School of Arts and Sciences, Brandeis University, Boston, MA, United States
| | - Liang Minglin
- School of Arts and Sciences, Brandeis University, Boston, MA, United States
| | - Lv Fa-hui
- Department of Obstetrics and Gynecology, The Second People’s Hospital of Hefei, Hefei, Anhui, China
| | - Hongmei Zou
- Department of Obstetrics, Qianjiang Central Hospital, Qianjiang, Hubei, China
| | - Jie Min
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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30
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Ohta S, Misawa A, Kyi-Tha-Thu C, Matsumoto N, Hirose Y, Kawakami Y. Melanoma antigens recognized by T cells and their use for immunotherapy. Exp Dermatol 2023; 32:297-305. [PMID: 36607252 DOI: 10.1111/exd.14741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Melanoma has been a prototype for cancer immunology research, and the mechanisms of anti-tumor T-cell responses have been extensively investigated in patients treated with various immunotherapies. Individual differences in cancer-immune status are defined mainly by cancer cell characteristics such as DNA mutations generating immunogenic neo-antigens, and oncogene activation causing immunosuppression, but also by patients' genetic backgrounds such as HLA types and genetic polymorphisms of immune related molecules, and environmental and lifestyle factors such as UV rays, smoking, gut microbiota and concomitant medications; these factors have an influence on the efficacy of immunotherapy. Recent comparative studies on responders and non-responders in immune-checkpoint inhibitor therapy using various new technologies including multi-omics analyses on genomic DNA, mRNA, metabolites and microbiota and single cell analyses of various immune cells have led to the advance of human tumor immunology and the development of new immunotherapy. Based on the new findings from these investigations, personalized cancer immunotherapies along with appropriate biomarkers and therapeutic targets are being developed for patients with melanoma. Here, we will discuss one of the essential subjects in tumor immunology: identification of immunogenic tumor antigens and their effective use in various immunotherapies including cancer vaccines and adoptive T-cell therapy.
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Affiliation(s)
- Shigeki Ohta
- Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Aya Misawa
- Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Chaw Kyi-Tha-Thu
- Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Naomi Matsumoto
- Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Yoshie Hirose
- Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
| | - Yutaka Kawakami
- Department of Immunology, School of Medicine, International University of Health and Welfare, Chiba, Japan
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
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31
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van den Bulk J, van der Ploeg M, Ijsselsteijn ME, Ruano D, van der Breggen R, Duhen R, Peeters KCMJ, Fariña-Sarasqueta A, Verdegaal EME, van der Burg SH, Duhen T, de Miranda NFCC. CD103 and CD39 coexpression identifies neoantigen-specific cytotoxic T cells in colorectal cancers with low mutation burden. J Immunother Cancer 2023; 11:jitc-2022-005887. [PMID: 36792124 PMCID: PMC9933759 DOI: 10.1136/jitc-2022-005887] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Expression of CD103 and CD39 has been found to pinpoint tumor-reactive CD8+ T cells in a variety of solid cancers. We aimed to investigate whether these markers specifically identify neoantigen-specific T cells in colorectal cancers (CRCs) with low mutation burden. EXPERIMENTAL DESIGN Whole-exome and RNA sequencing of 11 mismatch repair-proficient (MMR-proficient) CRCs and corresponding healthy tissues were performed to determine the presence of putative neoantigens. In parallel, tumor-infiltrating lymphocytes (TILs) were cultured from the tumor fragments and, in parallel, CD8+ T cells were flow-sorted from their respective tumor digests based on single or combined expression of CD103 and CD39. Each subset was expanded and subsequently interrogated for neoantigen-directed reactivity with synthetic peptides. Neoantigen-directed reactivity was determined by flow cytometric analyses of T cell activation markers and ELISA-based detection of IFN-γ and granzyme B release. Additionally, imaging mass cytometry was applied to investigate the localization of CD103+CD39+ cytotoxic T cells in tumors. RESULTS Neoantigen-directed reactivity was only encountered in bulk TIL populations and CD103+CD39+ (double positive, DP) CD8+ T cell subsets but never in double-negative or single-positive subsets. Neoantigen-reactivity detected in bulk TIL but not in DP CD8+ T cells could be attributed to CD4+ T cells. CD8+ T cells that were located in direct contact with cancer cells in tumor tissues were enriched for CD103 and CD39 expression. CONCLUSION Coexpression of CD103 and CD39 is characteristic of neoantigen-specific CD8+ T cells in MMR-proficient CRCs with low mutation burden. The exploitation of these subsets in the context of adoptive T cell transfer or engineered T cell receptor therapies is a promising avenue to extend the benefits of immunotherapy to an increasing number of CRC patients.
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Affiliation(s)
- Jitske van den Bulk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruud van der Breggen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rebekka Duhen
- Basic Immunology Lab, Earle A Chiles Research Institute, Portland, Oregon, USA
| | - Koen C M J Peeters
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Els M E Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Duhen
- Anti-Cancer Immune Response Lab, Earle A Chiles Research Institute, Portland, Oregon, USA
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32
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Sun H, Zhang Y, Wang G, Yang W, Xu Y. mRNA-Based Therapeutics in Cancer Treatment. Pharmaceutics 2023; 15:pharmaceutics15020622. [PMID: 36839944 PMCID: PMC9964383 DOI: 10.3390/pharmaceutics15020622] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 02/15/2023] Open
Abstract
Over the past two decades, significant technological innovations have led to messenger RNA (mRNA) becoming a promising option for developing prophylactic and therapeutic vaccines, protein replacement therapies, and genome engineering. The success of the two COVID-19 mRNA vaccines has sparked new enthusiasm for other medical applications, particularly in cancer treatment. In vitro-transcribed (IVT) mRNAs are structurally designed to resemble naturally occurring mature mRNA. Delivery of IVT mRNA via delivery platforms such as lipid nanoparticles allows host cells to produce many copies of encoded proteins, which can serve as antigens to stimulate immune responses or as additional beneficial proteins for supplements. mRNA-based cancer therapeutics include mRNA cancer vaccines, mRNA encoding cytokines, chimeric antigen receptors, tumor suppressors, and other combination therapies. To better understand the current development and research status of mRNA therapies for cancer treatment, this review focused on the molecular design, delivery systems, and clinical indications of mRNA therapies in cancer.
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Affiliation(s)
- Han Sun
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ge Wang
- Department of Oral Maxillofacial & Head and Neck Oncology, National Center of Stomatology, National Clinical Research Center for Oral Disease, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Wen Yang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence:
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33
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Qiu S, Zhao Z, Wu M, Xue Q, Yang Y, Ouyang S, Li W, Zhong L, Wang W, Yang R, Wu P, Li JP. Use of intercellular proximity labeling to quantify and decipher cell-cell interactions directed by diversified molecular pairs. SCIENCE ADVANCES 2022; 8:eadd2337. [PMID: 36542702 PMCID: PMC9770995 DOI: 10.1126/sciadv.add2337] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
FucoID is an intercellular proximity labeling technique for studying cell-cell interactions (CCIs) via fucosyltransferase (FT)-meditated fucosyl-biotinylation, which has been applied to probe antigen-specific dendritic cell (DC)-T cell interactions. In this system, bait cells of interest with cell surface-anchored FT are used to capture the interacting prey cells by transferring a biotin-modified substrate to prey cells. Here, we leveraged FucoID to study CCIs directed by different molecular pairs, e.g., programmed cell death protein-1(PD-1)/programmed cell death protein-ligand-1 (PD-L1), and identify unknown or little studied CCIs, e.g., the interaction of DCs and B cells. To expand the application of FucoID to complex systems, we also synthesized site-specific antibody-based FT conjugate, which substantially improves the ability of FucoID to probe molecular signatures of specific CCI when cells of interest (bait cells) cannot be purified, e.g., in clinical samples. Collectively, these studies demonstrate the general applicability of FucoID to study unknown CCIs in complex systems at a molecular resolution.
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Affiliation(s)
- Shuang Qiu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Zihan Zhao
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Mengyao Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Qi Xue
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yang Yang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Shian Ouyang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wannan Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Lingyu Zhong
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wenjian Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rong Yang
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jie P. Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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34
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Hall MS, Mullinax JE, Cox CA, Hall AM, Beatty MS, Blauvelt J, Innamarato P, Nagle L, Branthoover H, Wiener D, Schachner B, Martinez AJ, Richards AD, Rich CJ, Colón Colón M, Schell MJ, Teer JK, Khushalani NI, Weber JS, Mulé JJ, Sondak VK, Pilon-Thomas S, Sarnaik AA. Combination Nivolumab, CD137 Agonism, and Adoptive Cell Therapy with Tumor-Infiltrating Lymphocytes for Patients with Metastatic Melanoma. Clin Cancer Res 2022; 28:5317-5329. [PMID: 36215121 DOI: 10.1158/1078-0432.ccr-22-2103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/25/2022] [Accepted: 10/06/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Metastatic melanoma is a tumor amenable to immunotherapy in part due to the presence of antigen-specific tumor-infiltrating lymphocytes (TIL). These T cells can be activated and expanded for adoptive cell transfer (ACT), which has resulted in relatively high rates of clinical responses. Similarly, immune checkpoint inhibitors, specifically programmed cell death protein 1 (PD-1) blocking antibodies, augment antitumor immunity and increase the influx of T cells into tumors. Thus, we hypothesized that addition of PD-1 inhibition may improve the outcomes for patients undergoing ACT with TILs. PATIENTS AND METHODS Patients with stage III/IV metastatic melanoma with unresectable disease who were anti-PD-1 treatment-naïve were enrolled. TILs were generated in the presence of anti-4-1BB antibody in vitro and expanded for ACT. Patients in cohort 1 received TIL infusion followed by nivolumab. Patients in cohort 2 also received nivolumab prior to surgical harvest and during TIL production. RESULTS A total of 11 patients were enrolled, all of whom were evaluated for response, and nine completed ACT. Predominantly CD8+ TILs were successfully expanded from all ACT-treated patients and were tumor reactive in vitro. The trial met its safety endpoint, as there were no protocol-defined dose-limiting toxicity events. The objective response rate was 36%, and median progression-free survival was 5 months. Two nonresponders who developed new metastatic lesions were analyzed to determine potential mechanisms of therapeutic resistance, which included clonal divergence and intrinsic TIL dysfunction. CONCLUSIONS Combination therapy with TILs and nivolumab was safe and feasible for patients with metastatic melanoma and provides important insights for future therapeutic developments in ACT with TILs.
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Affiliation(s)
- MacLean S Hall
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - John E Mullinax
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Cheryl A Cox
- Cell Therapies Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Amy M Hall
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Matthew S Beatty
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie Blauvelt
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Patrick Innamarato
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Luz Nagle
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Holly Branthoover
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Doris Wiener
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Benjamin Schachner
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alberto J Martinez
- Cell Therapies Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Allison D Richards
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Carolyn J Rich
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Marjorie Colón Colón
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nikhil I Khushalani
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jeffrey S Weber
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - James J Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Vernon K Sondak
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Shari Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Amod A Sarnaik
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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Balta E, Janzen N, Kirchgessner H, Toufaki V, Orlik C, Liang J, Lairikyengbam D, Abken H, Niesler B, Müller-Decker K, Ruppert T, Samstag Y. Expression of TRX1 optimizes the antitumor functions of human CAR T cells and confers resistance to a pro-oxidative tumor microenvironment. Front Immunol 2022; 13:1063313. [PMID: 36591284 PMCID: PMC9794734 DOI: 10.3389/fimmu.2022.1063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022] Open
Abstract
Use of chimeric antigen receptor (CAR) T cells to treat B cell lymphoma and leukemia has been remarkably successful. Unfortunately, the therapeutic efficacy of CAR T cells against solid tumors is very limited, with immunosuppression by the pro-oxidative tumor microenvironment (TME) a major contributing factor. High levels of reactive oxygen species are well-tolerated by tumor cells due to their elevated expression of antioxidant proteins; however, this is not the case for T cells, which consequently become hypo-responsive. The aim of this study was to improve CAR T cell efficacy in solid tumors by empowering the antioxidant capacity of CAR T cells against the pro-oxidative TME. To this end, HER2-specific human CAR T cells stably expressing two antioxidant systems: thioredoxin-1 (TRX1), and glutaredoxin-1 (GRX1) were generated and characterized. Thereafter, antitumor functions of CAR T cells were evaluated under control or pro-oxidative conditions. To provide insights into the role of antioxidant systems, gene expression profiles as well as global protein oxidation were analyzed. Our results highlight that TRX1 is pivotal for T cell redox homeostasis. TRX1 expression allows CAR T cells to retain their cytolytic immune synapse formation, cytokine release, proliferation, and tumor cell-killing properties under pro-oxidative conditions. Evaluation of differentially expressed genes and the first comprehensive redoxosome analysis of T cells by mass spectrometry further clarified the underlying mechanisms. Taken together, enhancement of the key antioxidant TRX1 in human T cells opens possibilities to increase the efficacy of CAR T cell treatment against solid tumors.
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Affiliation(s)
- Emre Balta
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany,*Correspondence: Emre Balta, ; Yvonne Samstag,
| | - Nina Janzen
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Henning Kirchgessner
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Vasiliki Toufaki
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Orlik
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jie Liang
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Divya Lairikyengbam
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hinrich Abken
- Leibniz Institute for Immunotherapy, Division of Genetic Immunotherapy, University Regensburg, Regensburg, Germany
| | - Beate Niesler
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany,Counter Core Facility, Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Karin Müller-Decker
- Core Facility Tumor Models, German Cancer Research Center, Heidelberg, Germany
| | - Thomas Ruppert
- Mass Spectrometry Core Facility, Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
| | - Yvonne Samstag
- Section of Molecular Immunology, Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany,*Correspondence: Emre Balta, ; Yvonne Samstag,
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36
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Greenberg J, Limberg J, Verma A, Kim D, Chen X, Lee YJ, Moore MD, Ullmann TM, Thiesmeyer JW, Loewenstein Z, Chen KJ, Egan CE, Stefanova D, Bareja R, Zarnegar R, Finnerty BM, Scognamiglio T, Du YCN, Elemento O, Fahey TJ, Min IM. Metastatic pancreatic neuroendocrine tumors feature elevated T cell infiltration. JCI Insight 2022; 7:160130. [PMID: 36301668 PMCID: PMC9746918 DOI: 10.1172/jci.insight.160130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/26/2022] [Indexed: 01/12/2023] Open
Abstract
Pancreatic neuroendocrine tumors (PNETs) are malignancies arising from the islets of Langerhans. Therapeutic options are limited for the over 50% of patients who present with metastatic disease. We aimed to identify mechanisms to remodel the PNET tumor microenvironment (TME) to ultimately enhance susceptibility to immunotherapy. The TMEs of localized and metastatic PNETs were investigated using an approach that combines RNA-Seq, cancer and T cell profiling, and pharmacologic perturbations. RNA-Seq analysis indicated that the primary tumors of metastatic PNETs showed significant activation of inflammatory and immune-related pathways. We determined that metastatic PNETs featured increased numbers of tumor-infiltrating T cells compared with localized tumors. T cells isolated from both localized and metastatic PNETs showed evidence of recruitment and antigen-dependent activation, suggestive of an immune-permissive microenvironment. A computational analysis suggested that vorinostat, a histone deacetylase inhibitor, may perturb the transcriptomic signature of metastatic PNETs. Treatment of PNET cell lines with vorinostat increased chemokine CCR5 expression by NF-κB activation. Vorinostat treatment of patient-derived metastatic PNET tissues augmented recruitment of autologous T cells, and this augmentation was substantiated in a mouse model of PNET. Pharmacologic induction of chemokine expression may represent a promising approach for enhancing the immunogenicity of metastatic PNET TMEs.
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Affiliation(s)
| | | | - Akanksha Verma
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and
| | - David Kim
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Xiang Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | | | | | | | | | | | - Rohan Bareja
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and
| | | | | | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and
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Abstract
Significance: Immune cell therapy involves the administration of immune cells into patients, and it has emerged as one of the most common type of immunotherapy for cancer treatment. Knowledge on the biology and metabolism of the adoptively transferred immune cells and the metabolic requirements of different cell types in the tumor is fundamental for the development of immune cell therapy with higher efficacy. Recent Advances: Adoptive T cell therapy has been shown to be effective in limited types of cancer. Different types and generations of adoptive T cell therapies have evolved in the recent decade. This review covers the basic principles and development of these therapies in cancer treatment. Critical Issues: Our review provides an overview on the basic concepts on T cell metabolism and highlights the metabolic requirements of T and adoptively transferred T cells. Future Directions: Integrating the knowledge just cited will facilitate the development of strategies to maximize the expansion of adoptively transferred T cells ex vivo and in vivo and to promote their durability and antitumor effects. Antioxid. Redox Signal. 37, 1303-1324.
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Affiliation(s)
- Ge Hui Tan
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Carmen Chak-Lui Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Center for Oncology and Immunology, Hong Kong Science Park, Hong Kong, SAR, China
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38
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Expansion of KRAS hotspot mutations reactive T cells from human pancreatic tumors using autologous T cells as the antigen-presenting cells. Cancer Immunol Immunother 2022; 72:1301-1313. [PMID: 36436020 DOI: 10.1007/s00262-022-03335-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/18/2022] [Indexed: 11/28/2022]
Abstract
Adoptive cell therapy (ACT) with expanded tumor-infiltrating lymphocytes (TIL) or TCR gene-modified T cells (TCR-T) that recognize mutant KRAS neo-antigens can mediate tumor regression in patients with advanced pancreatic ductal adenocarcinoma (PDAC) (Tran et al in N Engl J Med, 375:2255-2262, 2016; Leidner et al in N Engl J Med, 386:2112-2119, 2022). The mutant KRAS-targeted ACT holds great potential to achieve durable clinical responses for PDAC, which has had no meaningful improvement over 40 years. However, the wide application of mutant KRAS-centric ACT is currently limited by the rarity of TIL that recognize the mutant KRAS. In addition, PDAC is generally recognized as a poorly immunogenic tumor, and TILs in PDAC are less abundant than in immunogenic tumors such as melanoma. To increase the success rate of TIL production, we adopted a well-utilized K562-based artificial APC (aAPC) that expresses 4-1BBL as the costimulatory molecules to enhance the TIL production from PDCA. However, stimulation with K562-based aAPC led to a rapid loss of specificity to mutant KRAS. To selectively expand neo-antigen-specific T cells, particularly mKRAS, from the TILs, we used tandem mini gene-modified autologous T cells (TMG-T) as the novel aAPC. Using this modified IVS protocol, we successfully generated TIL cultures specifically reactive to mKRAS (G12V). We believe that autologous TMG-T cells provide a reliable source of autologous APC to expand a rare population of neoantigen-specific T cells in TILs.
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39
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Ge W, Dong Y, Deng Y, Chen L, Chen J, Liu M, Wu J, Wang W, Ma X. Potential biomarkers: Identifying powerful tumor specific T cells in adoptive cellular therapy. Front Immunol 2022; 13:1003626. [PMID: 36451828 PMCID: PMC9702804 DOI: 10.3389/fimmu.2022.1003626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/27/2022] [Indexed: 12/01/2023] Open
Abstract
Tumor-specific T cells (TSTs) are essential components for the success of personalized tumor-infiltrating lymphocyte (TIL)-based adoptive cellular therapy (ACT). Therefore, the selection of a common biomarker for screening TSTs in different tumor types, followed by ex vivo expansion to clinical number levels can generate the greatest therapeutic effect. However, studies on shared biomarkers for TSTs have not been realized yet. The present review summarizes the similarities and differences of a number of biomarkers for TSTs in several tumor types studied in the last 5 years, and the advantages of combining biomarkers. In addition, the review discusses the possible shortcomings of current biomarkers and highlights strategies to identify TSTs accurately using intercellular interactions. Finally, the development of TSTs in personalized TIL-based ACT for broader clinical applications is explored.
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Affiliation(s)
- Wu Ge
- Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yuqian Dong
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yao Deng
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lujuan Chen
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Juan Chen
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Muqi Liu
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jianmin Wu
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Wei Wang
- Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoqian Ma
- Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
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40
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Palmer DC, Webber BR, Patel Y, Johnson MJ, Kariya CM, Lahr WS, Parkhurst MR, Gartner JJ, Prickett TD, Lowery FJ, Kishton RJ, Gurusamy D, Franco Z, Vodnala SK, Diers MD, Wolf NK, Slipek NJ, McKenna DH, Sumstad D, Viney L, Henley T, Bürckstümmer T, Baker O, Hu Y, Yan C, Meerzaman D, Padhan K, Lo W, Malekzadeh P, Jia L, Deniger DC, Patel SJ, Robbins PF, McIvor RS, Choudhry M, Rosenberg SA, Moriarity BS, Restifo NP. Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade. MED 2022; 3:682-704.e8. [PMID: 36007524 PMCID: PMC9847506 DOI: 10.1016/j.medj.2022.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/28/2022] [Accepted: 07/26/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Adoptive transfer of tumor-infiltrating lymphocytes (TIL) fails to consistently elicit tumor rejection. Manipulation of intrinsic factors that inhibit T cell effector function and neoantigen recognition may therefore improve TIL therapy outcomes. We previously identified the cytokine-induced SH2 protein (CISH) as a key regulator of T cell functional avidity in mice. Here, we investigate the mechanistic role of CISH in regulating human T cell effector function in solid tumors and demonstrate that CRISPR/Cas9 disruption of CISH enhances TIL neoantigen recognition and response to checkpoint blockade. METHODS Single-cell gene expression profiling was used to identify a negative correlation between high CISH expression and TIL activation in patient-derived TIL. A GMP-compliant CRISPR/Cas9 gene editing process was developed to assess the impact of CISH disruption on the molecular and functional phenotype of human peripheral blood T cells and TIL. Tumor-specific T cells with disrupted Cish function were adoptively transferred into tumor-bearing mice and evaluated for efficacy with or without checkpoint blockade. FINDINGS CISH expression was associated with T cell dysfunction. CISH deletion using CRISPR/Cas9 resulted in hyper-activation and improved functional avidity against tumor-derived neoantigens without perturbing T cell maturation. Cish knockout resulted in increased susceptibility to checkpoint blockade in vivo. CONCLUSIONS CISH negatively regulates human T cell effector function, and its genetic disruption offers a novel avenue to improve the therapeutic efficacy of adoptive TIL therapy. FUNDING This study was funded by Intima Bioscience, U.S. and in part through the Intramural program CCR at the National Cancer Institute.
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Affiliation(s)
- Douglas C Palmer
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA.
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
| | - Yogin Patel
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Matthew J Johnson
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Christine M Kariya
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Maria R Parkhurst
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Frank J Lowery
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Rigel J Kishton
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Devikala Gurusamy
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Zulmarie Franco
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Suman K Vodnala
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Miechaleen D Diers
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Natalie K Wolf
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - David H McKenna
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Darin Sumstad
- Molecular and Cellular Therapeutics, University of Minnesota, Saint Paul, MN, USA
| | | | - Tom Henley
- Intima Bioscience, Inc., New York, NY, USA
| | | | | | - Ying Hu
- The Center for Biomedical Informatics and Information Technology (CBIIT), National Institutes of Health, Bethesda, MD, USA
| | - Chunhua Yan
- The Center for Biomedical Informatics and Information Technology (CBIIT), National Institutes of Health, Bethesda, MD, USA
| | - Daoud Meerzaman
- The Center for Biomedical Informatics and Information Technology (CBIIT), National Institutes of Health, Bethesda, MD, USA
| | - Kartik Padhan
- National Institute of Allergy and Infectious Disease (NIAID), National Institutes of Health, Bethesda, MD, USA
| | - Winnie Lo
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Parisa Malekzadeh
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Li Jia
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Drew C Deniger
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Shashank J Patel
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA
| | - R Scott McIvor
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA; Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | | | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA.
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
| | - Nicholas P Restifo
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD, USA.
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41
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Research progress of neoantigens in gynecologic cancers. Int Immunopharmacol 2022; 112:109236. [PMID: 36113318 DOI: 10.1016/j.intimp.2022.109236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022]
Abstract
The incidence and mortality of gynecological cancers have increased over the past decade. In the absence of effective treatment strategies, many advanced patients develop resistance to conventional therapies and have poor prognosis. Neoantigens have emerged as a novel tumor-specific antigen (TSA) that arises from genomic mutations in tumor cells. With higher immunogenicity than tumor-associated antigens (TAA), they have no risk of developing autoimmune response, leading them an attractive candidate for tumor therapeutic vaccines. With the development of next-generation sequencing (NGS) technology, the identification of neoantigens has been gradually improved, and the scope of application of neoantigen vaccines has continued to expand. Combined with other therapies such as immune-checkpoint inhibitors (ICIs) or adoptive cell therapy (ACT), the application of neoantigen in gynecological cancers has extended to clinical practice. Here, we reviewed the preclinical and clinical studies of neoantigens in gynecological cancers.
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42
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de Mey W, De Schrijver P, Autaers D, Pfitzer L, Fant B, Locy H, Esprit A, Lybaert L, Bogaert C, Verdonck M, Thielemans K, Breckpot K, Franceschini L. A synthetic DNA template for fast manufacturing of versatile single epitope mRNA. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:943-954. [PMID: 36159589 PMCID: PMC9464653 DOI: 10.1016/j.omtn.2022.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/14/2022] [Indexed: 11/30/2022]
Abstract
A flexible, affordable, and rapid vaccine platform is necessary to unlock the potential of personalized cancer vaccines in order to achieve full clinical efficiency. mRNA cancer vaccine manufacture relies on the rigid sequence design of multiepitope constructs produced by laborious bacterial cloning and time-consuming plasmid preparation. Here, we introduce a synthetic DNA template (SDT) assembly process, which allows cost- and time-efficient manufacturing of single (neo)epitope mRNA. We benchmarked SDT-derived mRNA against mRNA derived from a plasmid DNA template (PDT), showing that monocyte-derived dendritic cells (moDCs) electroporated with SDT-mRNA or PDT-mRNA, encoding HLA-I- or HLA-II-restricted (neo)epitopes, equally activated T cells that were modified to express the cognate T cell receptors. Furthermore, we validated the SDT-mRNA platform for neoepitope immunogenicity screening using the characterized HLA-A2-restricted neoepitope DHX40B and four new candidate HLA-A2-restricted melanoma neoepitopes. Finally, we compared SDT-mRNA with PDT-mRNA for vaccine development purposes. moDCs electroporated with mRNA encoding the HLA-A2-restricted, mutated Melan-A/Mart-1 epitope together with TriMix mRNA-generated high levels of functional Melan-A/Mart-1-specific CD8+ T cells. In conclusion, SDT single epitope mRNA can be manufactured in a more flexible, cost-efficient, and time-efficient way compared with PDT-mRNA, allowing prompt neoepitope immunogenicity screening, and might be exploited for the development of personalized cancer vaccines.
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Affiliation(s)
- Wout de Mey
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Phaedra De Schrijver
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Dorien Autaers
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lena Pfitzer
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | - Bruno Fant
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | - Hanne Locy
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Arthur Esprit
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lien Lybaert
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
- myNEO, Ottergemsesteenweg-Zuid 808, 9000 Ghent, Belgium
| | | | - Magali Verdonck
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
| | - Lorenzo Franceschini
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium
- Corresponding author Lorenzo Franceschini, Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103/E, 1090 Brussels, Belgium.
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Füchsl F, Krackhardt AM. Paving the Way to Solid Tumors: Challenges and Strategies for Adoptively Transferred Transgenic T Cells in the Tumor Microenvironment. Cancers (Basel) 2022; 14:4192. [PMID: 36077730 PMCID: PMC9454442 DOI: 10.3390/cancers14174192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 01/10/2023] Open
Abstract
T cells are important players in the antitumor immune response. Over the past few years, the adoptive transfer of genetically modified, autologous T cells-specifically redirected toward the tumor by expressing either a T cell receptor (TCR) or a chimeric antigen receptor (CAR)-has been adopted for use in the clinic. At the moment, the therapeutic application of CD19- and, increasingly, BCMA-targeting-engineered CAR-T cells have been approved and have yielded partly impressive results in hematologic malignancies. However, employing transgenic T cells for the treatment of solid tumors remains more troublesome, and numerous hurdles within the highly immunosuppressive tumor microenvironment (TME) need to be overcome to achieve tumor control. In this review, we focused on the challenges that these therapies must face on three different levels: infiltrating the tumor, exerting efficient antitumor activity, and overcoming T cell exhaustion and dysfunction. We aimed to discuss different options to pave the way for potent transgenic T cell-mediated tumor rejection by engineering either the TME or the transgenic T cell itself, which responds to the environment.
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Affiliation(s)
- Franziska Füchsl
- Klinik und Poliklinik für Innere Medizin III, School of Medicine, Technische Universität München, Klinikum rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
| | - Angela M. Krackhardt
- Klinik und Poliklinik für Innere Medizin III, School of Medicine, Technische Universität München, Klinikum rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
- German Cancer Consortium of Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, 81675 Munich, Germany
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Kim SP, Vale NR, Zacharakis N, Krishna S, Yu Z, Gasmi B, Gartner JJ, Sindiri S, Malekzadeh P, Deniger DC, Lowery FJ, Parkhurst MR, Ngo LT, Ray S, Li YF, Hill V, Florentin M, Masi RV, Paria BC, Levin N, Bera A, Hedges EA, Choi A, Chatani PD, Parikh AY, Levi S, Seitter S, Lu YC, Zheng Z, Prickett TD, Jia L, Hernandez JM, Hoang CD, Robbins PF, Goff SL, Sherry RM, Yang JC, Rosenberg SA. Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor-Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors. Cancer Immunol Res 2022; 10:932-946. [PMID: 35749374 PMCID: PMC9357191 DOI: 10.1158/2326-6066.cir-22-0040] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/21/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022]
Abstract
Adoptive cellular therapy (ACT) targeting neoantigens can achieve durable clinical responses in patients with cancer. Most neoantigens arise from patient-specific mutations, requiring highly individualized treatments. To broaden the applicability of ACT targeting neoantigens, we focused on TP53 mutations commonly shared across different cancer types. We performed whole-exome sequencing on 163 patients with metastatic solid cancers, identified 78 who had TP53 missense mutations, and through immunologic screening, identified 21 unique T-cell reactivities. Here, we report a library of 39 T-cell receptors (TCR) targeting TP53 mutations shared among 7.3% of patients with solid tumors. These TCRs recognized tumor cells in a TP53 mutation- and human leucocyte antigen (HLA)-specific manner in vitro and in vivo. Twelve patients with chemorefractory epithelial cancers were treated with ex vivo-expanded autologous tumor-infiltrating lymphocytes (TIL) that were naturally reactive against TP53 mutations. However, limited clinical responses (2 partial responses among 12 patients) were seen. These infusions contained low frequencies of mutant p53-reactive TILs that had exhausted phenotypes and showed poor persistence. We also treated one patient who had chemorefractory breast cancer with ACT comprising autologous peripheral blood lymphocytes transduced with an allogeneic HLA-A*02-restricted TCR specific for p53R175H. The infused cells exhibited an improved immunophenotype and prolonged persistence compared with TIL ACT and the patient experienced an objective tumor regression (-55%) that lasted 6 months. Collectively, these proof-of-concept data suggest that the library of TCRs targeting shared p53 neoantigens should be further evaluated for the treatment of patients with advanced human cancers. See related Spotlight by Klebanoff, p. 919.
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Affiliation(s)
- Sanghyun P. Kim
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nolan R. Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Billel Gasmi
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland
| | - Jared J. Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Parisa Malekzadeh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Drew C. Deniger
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Frank J. Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria R. Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lien T. Ngo
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yong F. Li
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Victoria Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria Florentin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Robert V. Masi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Biman C. Paria
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth A. Hedges
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Agnes Choi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Praveen D. Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Anup Y. Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Shoshana Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Samantha Seitter
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yong-Chen Lu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Zhili Zheng
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Todd D. Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Li Jia
- National Institutes of Health Library, Office of Director, National Institutes of Health, Bethesda, Maryland
| | - Jonathan M. Hernandez
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Chuong D. Hoang
- Thoracic Surgery Branch, National Cancer Institute, NIH, CCR and The Clinical Center, Bethesda, Maryland
| | - Paul F. Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephanie L. Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Richard M. Sherry
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - James C. Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven A. Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Current State of Cell Therapies for Gastrointestinal Cancers. Cancer J 2022; 28:310-321. [PMID: 35880941 DOI: 10.1097/ppo.0000000000000611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Adoptive cell therapies include multiple cell-based therapies to harness the immune system's power to mount a robust anticancer effect. Early successes in solid tumors with checkpoint inhibition have increased the research and development of immunotherapy. The utilization of cell-based therapy for gastrointestinal malignancies is still in its infancy because of challenges of antigen specificity and access to the tumor microenvironment. In this review, we discuss the current state of adoptive cell therapies in terms of challenges and early successes in preclinical and clinical studies.
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Abstract
ABSTRACT The holy grail of cancer therapeutics is the destruction of cancer cells while avoiding harm to normal cells. Cancer is unique from normal tissues because of the presence of somatic mutations that accumulate during tumorigenesis. Some nonsynonymous mutations can give rise to mutated peptide antigens (hereafter referred to as neoantigens) that can be specifically recognized by T cells. Thus, the immunological targeting of neoantigens represents a safe and promising strategy to treat patients with cancer. This article reviews the clinical application of adoptive cell therapy targeting neoantigens in patients with epithelial cancers.
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Abstract
The protocol describes the procedure of antigen-specific T cell generation and TCR identification for the use in adoptive T cell therapy. We describe two paths of generating antigen-specific T cells, first, T cell stimulation with autologous dendritic cells pulsed with antigen peptide, second, in vivo T cell stimulation with peptide or DNA by gene gun application in a suitable mouse model followed by in vitro enrichment of peptide-reactive T cells. Peptide-stimulated T cells are sorted by fluorescence-activated cell sorting for CD107α or IFNγ expression and subsequently isolated RNA is used in a 5' rapid amplification of cDNA ends (RACE )-PCR specific for TCR for TCR chain identification. After retroviral cloning, it is re-expressed on human T cells to test its applicability in adoptive T cell therapy.
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48
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Duhen R, Fesneau O, Samson KA, Frye AK, Beymer M, Rajamanickam V, Ross D, Tran E, Bernard B, Weinberg AD, Duhen T. PD-1 and ICOS coexpression identifies tumor-reactive CD4+ T cells in human solid tumors. J Clin Invest 2022; 132:156821. [PMID: 35439168 PMCID: PMC9197519 DOI: 10.1172/jci156821] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/14/2022] [Indexed: 12/20/2022] Open
Abstract
CD4+ Th cells play a key role in orchestrating immune responses, but the identity of the CD4+ Th cells involved in the antitumor immune response remains to be defined. We analyzed the immune cell infiltrates of head and neck squamous cell carcinoma and colorectal cancers and identified a subset of CD4+ Th cells distinct from FOXP3+ Tregs that coexpressed programmed cell death 1 (PD-1) and ICOS. These tumor-infiltrating lymphocyte CD4+ Th cells (CD4+ Th TILs) had a tissue-resident memory phenotype, were present in MHC class II–rich areas, and proliferated in the tumor, suggesting local antigen recognition. The T cell receptor repertoire of the PD-1+ICOS+ CD4+ Th TILs was oligoclonal, with T cell clones expanded in the tumor, but present at low frequencies in the periphery. Finally, these PD-1+ICOS+ CD4+ Th TILs were shown to recognize both tumor-associated antigens and tumor-specific neoantigens. Our findings provide an approach for isolating tumor-reactive CD4+ Th TILs directly ex vivo that will help define their role in the antitumor immune response and potentially improve future adoptive T cell therapy approaches.
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Affiliation(s)
- Rebekka Duhen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Olivier Fesneau
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Kimberly A Samson
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Alexandra K Frye
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Michael Beymer
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | | | - David Ross
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Eric Tran
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Brady Bernard
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Andrew D Weinberg
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA.,AgonOx Inc., Portland, Oregon, USA
| | - Thomas Duhen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
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49
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Leidner R, Sanjuan Silva N, Huang H, Sprott D, Zheng C, Shih YP, Leung A, Payne R, Sutcliffe K, Cramer J, Rosenberg SA, Fox BA, Urba WJ, Tran E. Neoantigen T-Cell Receptor Gene Therapy in Pancreatic Cancer. N Engl J Med 2022; 386:2112-2119. [PMID: 35648703 PMCID: PMC9531755 DOI: 10.1056/nejmoa2119662] [Citation(s) in RCA: 228] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A patient with progressive metastatic pancreatic cancer was treated with a single infusion of 16.2×109 autologous T cells that had been genetically engineered to clonally express two allogeneic HLA-C*08:02-restricted T-cell receptors (TCRs) targeting mutant KRAS G12D expressed by the tumors. The patient had regression of visceral metastases (overall partial response of 72% according to the Response Evaluation Criteria in Solid Tumors, version 1.1); the response was ongoing at 6 months. The engineered T cells constituted more than 2% of all the circulating peripheral-blood T cells 6 months after the cell transfer. In this patient, TCR gene therapy targeting the KRAS G12D driver mutation mediated the objective regression of metastatic pancreatic cancer. (Funded by the Providence Portland Medical Foundation.).
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Affiliation(s)
- Rom Leidner
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Nelson Sanjuan Silva
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Huayu Huang
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - David Sprott
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Chunhong Zheng
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Yi-Ping Shih
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Amy Leung
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Roxanne Payne
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Kim Sutcliffe
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Julie Cramer
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Steven A Rosenberg
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Bernard A Fox
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Walter J Urba
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Eric Tran
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
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50
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Gao Q, Wang S, Li F, Lian J, Cheng S, Yue D, Zhang Z, Liu S, Ren F, Zhang D, Wang S, Wang L, Zhang Y. High mobility group protein B1 decreases surface localization of PD-1 to augment T-cell activation. Cancer Immunol Res 2022; 10:844-855. [PMID: 35580259 DOI: 10.1158/2326-6066.cir-21-0652] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 01/13/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
Abstract
High-mobility group protein B1 (HMGB1) is a danger signaling molecule that has been found to trigger an effective antitumor immune response. However, the mechanisms underlying its antitumor effects are not fully understood. Here, we found that HMGB1 release induced by chemotherapy in patients with non-small cell lung cancer (NSCLC) was negatively correlated with PD-1 expression on CD8+ T cells. In vitro analysis indicated that treatment with HMGB1 led to a significant decrease in the level of expression of PD-1 on CD8+ T cells. Further analysis demonstrated that HMGB1 reduced PD-1 expression by inducing dynamin-mediated internalization of the protein, leading to early endocytosis in the cytoplasm, and subsequently degradation in the lysosomes. In a xenograft model, HER2-targeted chimeric-antigen receptor (CAR) T cells had enhanced function in the presence of HMGB1. These data identify a role for HMGB1 as a negative regulator of PD-1 signaling in lung cancer cells and the observed antitumor effect of HMGB1 on chimeric-antigen receptor (CAR) T cells may provide a theoretical foundation for a new immunotherapy combination.
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Affiliation(s)
- Qun Gao
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shumin Wang
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Li
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jingyao Lian
- First Affiliated Hospital of Zhengzhou University, China
| | - Shaoyan Cheng
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, ZhengZhou, China
| | - Dongli Yue
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhen Zhang
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shasha Liu
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Feifei Ren
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Daiqun Zhang
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | | | - Liping Wang
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Zhang
- First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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