1
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Wang B, Wang K, Wu D, Sahni S, Jiang P, Ruppin E. Decoupling the correlation between cytotoxic and exhausted T lymphocyte states enhances melanoma immunotherapy response prediction. iScience 2024; 27:109926. [PMID: 38832027 PMCID: PMC11145333 DOI: 10.1016/j.isci.2024.109926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/24/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Cytotoxic T lymphocyte (CTL) and terminal exhausted T lymphocyte (ETL) activities crucially influence immune checkpoint inhibitor (ICI) response. Despite this, the efficacy of ETL and CTL transcriptomic signatures for response prediction remains limited. Investigating this across the TCGA and publicly available single-cell cohorts, we find a strong positive correlation between ETL and CTL expression signatures in most cancers. We hence posited that their limited predictability arises due to their mutually canceling effects on ICI response. Thus, we developed DETACH, a computational method to identify a gene set whose expression pinpoints to a subset of melanoma patients where the CTL and ETL correlation is low. DETACH enhances CTL's prediction accuracy, outperforming existing signatures. DETACH signature genes activity also demonstrates a positive correlation with lymphocyte infiltration and the prevalence of reactive T cells in the tumor microenvironment (TME), advancing our understanding of the CTL cell state within the TME.
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Affiliation(s)
- Binbin Wang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Kun Wang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Di Wu
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Sahil Sahni
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Peng Jiang
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD USA
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2
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Yang B, Cao L, Ge K, Lv C, Zhao Z, Zheng T, Gao S, Zhang J, Wang T, Jiang J, Qin Y. FeSA‐Ir/Metallene Nanozymes Induce Sequential Ferroptosis‐Pyroptosis for Multi‐Immunogenic Responses Against Lung Metastasis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401110. [PMID: 38874051 DOI: 10.1002/smll.202401110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/01/2024] [Indexed: 06/15/2024]
Abstract
For cancer metastasis inhibition, the combining of nanozymes with immune checkpoint blockade (ICB) therapy remains the major challenge in controllable reactive oxygen species (ROS) generation for creating effective immunogenicity. Herein, new nanozymes with light-controlled ROS production in terms of quantity and variety are developed by conjugating supramolecular-wrapped Fe single atom on iridium metallene with lattice-strained nanoislands (FeSA-Ir@PF NSs). The Fenton-like catalysis of FeSA-Ir@PF NSs effectively produced •OH radicals in dark, which induced ferroptosis and apoptosis of cancer cells. While under second near-infrared (NIR-II) light irradiation, FeSA-Ir@PF NSs showed ultrahigh photothermal conversion efficiency (𝜂, 75.29%), cooperative robust •OH generation, photocatalytic O2 and 1O2 generation, and caused significant pyroptosis of cancer cells. The controllable ROS generation, sequential cancer cells ferroptosis and pyroptosis, led 99.1% primary tumor inhibition and multi-immunogenic responses in vivo. Most importantly, the inhibition of cancer lung metastasis is completely achieved by FeSA-Ir@PF NSs with immune checkpoint inhibitors, as demonstrated in different mice lung metastasis models, including circulating tumor cells (CTCs) model. This work provided new inspiration for developing nanozymes for cancer treatments and metastasis inhibition.
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Affiliation(s)
- Baochan Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- School of Biomedical Engineering, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510260, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Lingzhi Cao
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding, Hebei, 071002, China
| | - Kun Ge
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding, Hebei, 071002, China
| | - Chaofan Lv
- School of Biomedical Engineering, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510260, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Zunling Zhao
- School of Biomedical Engineering, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510260, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Tianyu Zheng
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Shutao Gao
- College of Science, Hebei Agricultural University, Baoding, 071001, China
| | - Jinchao Zhang
- State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding, Hebei, 071002, China
| | - Tianyu Wang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jianzhuang Jiang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yan Qin
- School of Biomedical Engineering, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510260, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
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3
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Kim SH, Lee BR, Kim SM, Kim S, Kim MS, Kim J, Lee I, Kim HS, Nam GH, Kim IS, Song K, Choi Y, Lee DS, Park WY. The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex. Exp Mol Med 2024:10.1038/s12276-024-01259-2. [PMID: 38866910 DOI: 10.1038/s12276-024-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
Neoantigens are ideal targets for cancer immunotherapy because they are expressed de novo in tumor tissue but not in healthy tissue and are therefore recognized as foreign by the immune system. Advances in next-generation sequencing and bioinformatics technologies have enabled the quick identification and prediction of tumor-specific neoantigens; however, only a small fraction of predicted neoantigens are immunogenic. To improve the predictability of immunogenic neoantigens, we developed the in silico neoantigen prediction workflows VACINUSpMHC and VACINUSTCR: VACINUSpMHC incorporates physical binding between peptides and MHCs (pMHCs), and VACINUSTCR integrates T cell reactivity to the pMHC complex through deep learning-based pairing with T cell receptors (TCRs) of putative tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs). We then validated our neoantigen prediction workflows both in vitro and in vivo in patients with hepatocellular carcinoma (HCC) and in a B16F10 mouse melanoma model. The predictive abilities of VACINUSpMHC and VACINUSTCR were confirmed in a validation cohort of 8 patients with HCC. Of a total of 118 neoantigen candidates predicted by VACINUSpMHC, 48 peptides were ultimately selected using VACINUSTCR. In vitro validation revealed that among the 48 predicted neoantigen candidates, 13 peptides were immunogenic. Assessment of the antitumor efficacy of the candidate neoepitopes using a VACINUSTCR in vivo mouse model suggested that vaccination with the predicted neoepitopes induced neoantigen-specific T cell responses and enabled the trafficking of neoantigen-specific CD8 + T cell clones into the tumor tissue, leading to tumor suppression. This study showed that the prediction of immunogenic neoantigens can be improved by integrating a tumor-reactive TIL TCR-pMHC ternary complex.
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Affiliation(s)
| | | | | | | | | | - Jaehyun Kim
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
| | - Inkyu Lee
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
| | | | - Gi-Hoon Nam
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul, 02841, Korea
| | - In-San Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
- Chemical & Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | | | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, 58128, Korea.
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
| | - Woong-Yang Park
- Geninus Inc., Seoul, 05836, Korea.
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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4
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Hua Y, Shen Y. Applications of self-assembled peptide hydrogels in anti-tumor therapy. NANOSCALE ADVANCES 2024; 6:2993-3008. [PMID: 38868817 PMCID: PMC11166105 DOI: 10.1039/d4na00172a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/29/2024] [Indexed: 06/14/2024]
Abstract
Peptides are a class of active substances composed of a variety of amino acids with special physiological functions. The rational design of peptide sequences at the molecular level enables their folding into diverse secondary structures. This property has garnered significant attention in the biomedical sphere owing to their favorable biocompatibility, adaptable mechanical traits, and exceptional loading capabilities. Concurrently with advancements in modern medicine, the diagnosis and treatment of tumors have increasingly embraced targeted and personalized approaches. This review explores recent applications of self-assembled peptides derived from natural amino acids in chemical therapy, immunotherapy, and other adjunctive treatments. We highlighted the utilization of peptide hydrogels as delivery systems for chemotherapeutic drugs and other bioactive molecules and then discussed the challenges and prospects for their future application.
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Affiliation(s)
- Yue Hua
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University Nanjing Jiangsu 210009 China
| | - Yang Shen
- Department of Obstetrics and Gynecology, Zhongda Hospital, School of Medicine, Southeast University Nanjing Jiangsu 210009 China
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5
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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 2024:10.1038/s41416-024-02737-0. [PMID: 38849478 DOI: 10.1038/s41416-024-02737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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6
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Liang Y, Bu Q, You W, Zhang R, Xu Z, Gan X, Zhou J, Qiao L, Huang T, Lu L. Single-cell analysis reveals hypoxia-induced immunosuppressive microenvironment in intrahepatic cholangiocarcinoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167276. [PMID: 38844114 DOI: 10.1016/j.bbadis.2024.167276] [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: 01/17/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
The role of hypoxia in the tumor microenvironment of intrahepatic cholangiocarcinoma (iCCA) remains unclear. Here, we generated a comprehensive atlas of the entire tumor microenvironment and delineated the multifaceted cell-cell interactions to decipher hypoxia-induced pro-tumor immune suppression. We discovered hypoxia is significantly associated with iCCA progression via the activation of HIF1A expression. Moreover, hypoxia-dependent PPARγ-mediated fatty acid oxidation in APOE+ TAMs promoted M2 macrophage polarization by activating the HIF1A-PPARG-CD36 axis. These polarized APOE+ TAMs recruited Treg cell infiltration via the CCL3-CCR5 pair to form an immunosuppressive microenvironment. APOE+ TAMs tended to co-localize spatially with Treg cells in the malignant tissue based on spatial transcriptome data and immunofluorescence analysis results. We identified tumor-reactive CXCL13+ CD8-PreTex with specific high expression of ENTPD1 and ITGAE, which acted as precursors of CD8-Tex and had higher cytotoxicity, lower exhaustion, and more vigorous proliferation. Consequently, CXCL13+ CD8-PreTex functioned as a positive regulator of antitumor immunity by expressing the pro-inflammatory cytokines IFNG and TNF, associated with a better survival outcome. Our study reveals the mechanisms involved in hypoxia-induced immunosuppression and suggests that targeting precursor-exhausted CXCL13+CD8+ T cells might provide a pratical immunotherapeutic approach.
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Affiliation(s)
- Yuan Liang
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, China; Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Qingfa Bu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Wenhua You
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Rui Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zibo Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaojie Gan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jinren Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Lei Qiao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tianning Huang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Ling Lu
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, China; Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
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7
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Wang AZ, Mashimo BL, Schaettler MO, Sherpa ND, Leavitt LA, Livingstone AJ, Khan SM, Li M, Anzaldua-Campos MI, Bradley JD, Leuthardt EC, Kim AH, Dowling JL, Chicoine MR, Jones PS, Choi BD, Cahill DP, Carter BS, Petti AA, Johanns TM, Dunn GP. Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population. Cancer Discov 2024; 14:1106-1131. [PMID: 38416133 DOI: 10.1158/2159-8290.cd-23-0913] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
Recent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing and single-cell RNA sequencing with paired V(D)J sequencing, respectively, on TILs from two cohorts of patients totaling 15 patients with high-grade glioma, including GBM or astrocytoma, IDH-mutant, grade 4 (G4A). Analysis of the CD8+ TIL landscape reveals an enrichment of clonally expanded GZMK+ effector T cells in the tumor compared with matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+ T-cell population in GBM TIL. These data suggest that GZMK+ effector T cells represent an important T-cell subset within the GBM microenvironment and may harbor potential therapeutic implications. SIGNIFICANCE To understand the limited efficacy of immune-checkpoint blockade in GBM, we applied a multiomics approach to understand the TIL landscape. By highlighting the enrichment of GZMK+ effector T cells and the lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Anthony Z Wang
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryce L Mashimo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maximilian O Schaettler
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ngima D Sherpa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences Graduate Program, Harvard University, Cambridge, Massachusetts
| | - Lydia A Leavitt
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurosurgery, University of Louisville, Louisville, Kentucky
| | - Alexandra J Livingstone
- Department of Medicine, Division of Medical Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Saad M Khan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mao Li
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Markus I Anzaldua-Campos
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Neuroscience Undergraduate Program, Harvard University, Cambridge, Massachusetts
| | - Joseph D Bradley
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Michael R Chicoine
- Department of Neurological Surgery, University of Missouri-Columbia, Columbia, Missouri
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Allegra A Petti
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tanner M Johanns
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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8
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Lin WP, Li H, Sun ZJ. T cell exhaustion initiates tertiary lymphoid structures and turbocharges cancer-immunity cycle. EBioMedicine 2024; 104:105154. [PMID: 38749300 PMCID: PMC11108856 DOI: 10.1016/j.ebiom.2024.105154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Immune therapies represented by immune checkpoint blockade (ICB) have significantly transformed cancer treatment. However, the effectiveness of these treatments depends on the status of T cells. T cell exhaustion, characterized by diminished effector function, increased expression of co-inhibitory receptors, and clonal deletion, emerges as a hypofunctional state resulting from chronic exposure to antigens, posing an obstacle to ICB therapy. Several studies have deeply explored T cell exhaustion, providing innovative insights and correlating T cell exhaustion with tertiary lymphoid structures (TLS) formation. TLS, lymphocyte aggregates formed in non-lymphoid tissues amid chronic inflammation, serve as pivotal reservoirs for anti-tumour immunity. Here, we underscore the pivotal role of T cell exhaustion as a signalling mechanism in reinvigorating anti-tumour immunity by turbocharging cancer-immunity (CI) cycle, particularly when tumour becomes unmanageable. Building upon this concept, we summarize emerging immunotherapeutic strategies aimed at enhancing the response rate to ICB therapy and improving patient prognosis.
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Affiliation(s)
- Wen-Ping Lin
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430079, PR China
| | - Hao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430079, PR China; Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China.
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430079, PR China; Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China.
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9
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Yang K, Lu R, Mei J, Cao K, Zeng T, Hua Y, Huang X, Li W, Yin Y. The war between the immune system and the tumor - using immune biomarkers as tracers. Biomark Res 2024; 12:51. [PMID: 38816871 PMCID: PMC11137916 DOI: 10.1186/s40364-024-00599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
Nowadays, immunotherapy is one of the most promising anti-tumor therapeutic strategy. Specifically, immune-related targets can be used to predict the efficacy and side effects of immunotherapy and monitor the tumor immune response. In the past few decades, increasing numbers of novel immune biomarkers have been found to participate in certain links of the tumor immunity to contribute to the formation of immunosuppression and have entered clinical trials. Here, we systematically reviewed the oncogenesis and progression of cancer in the view of anti-tumor immunity, particularly in terms of tumor antigen expression (related to tumor immunogenicity) and tumor innate immunity to complement the cancer-immune cycle. From the perspective of integrated management of chronic cancer, we also appraised emerging factors affecting tumor immunity (including metabolic, microbial, and exercise-related markers). We finally summarized the clinical studies and applications based on immune biomarkers. Overall, immune biomarkers participate in promoting the development of more precise and individualized immunotherapy by predicting, monitoring, and regulating tumor immune response. Therefore, targeting immune biomarkers may lead to the development of innovative clinical applications.
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Affiliation(s)
- Kai Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Rongrong Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Jie Mei
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Kai Cao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Tianyu Zeng
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Yijia Hua
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
- Gusu School, Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
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10
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Levin N, Kim SP, Marquardt CA, Vale NR, Yu Z, Sindiri S, Gartner JJ, Parkhurst M, Krishna S, Lowery FJ, Zacharakis N, Levy L, Prickett TD, Benzine T, Ray S, Masi RV, Gasmi B, Li Y, Islam R, Bera A, Goff SL, Robbins PF, Rosenberg SA. Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes. J Immunother Cancer 2024; 12:e008645. [PMID: 38816232 PMCID: PMC11141192 DOI: 10.1136/jitc-2023-008645] [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: 04/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Tumor-infiltrating lymphocytes (TILs) targeting neoantigens can effectively treat a selected set of metastatic solid cancers. However, harnessing TILs for cancer treatments remains challenging because neoantigen-reactive T cells are often rare and exhausted, and ex vivo expansion can further reduce their frequencies. This complicates the identification of neoantigen-reactive T-cell receptors (TCRs) and the development of TIL products with high reactivity for patient treatment. METHODS We tested whether TILs could be in vitro stimulated against neoantigens to achieve selective expansion of neoantigen-reactive TILs. Given their prevalence, mutant p53 or RAS were studied as models of human neoantigens. An in vitro stimulation method, termed "NeoExpand", was developed to provide neoantigen-specific stimulation to TILs. 25 consecutive patient TILs from tumors harboring p53 or RAS mutations were subjected to NeoExpand. RESULTS We show that neoantigenic stimulation achieved selective expansion of neoantigen-reactive TILs and broadened the neoantigen-reactive CD4+ and CD8+ TIL clonal repertoire. This allowed the effective isolation of novel neoantigen-reactive TCRs. Out of the 25 consecutive TIL samples, neoantigenic stimulation enabled the identification of 16 unique reactivities and 42 TCRs, while conventional TIL expansion identified 9 reactivities and 14 TCRs. Single-cell transcriptome analysis revealed that neoantigenic stimulation increased neoantigen-reactive TILs with stem-like memory phenotypes expressing IL-7R, CD62L, and KLF2. Furthermore, neoantigenic stimulation improved the in vivo antitumor efficacy of TILs relative to the conventional OKT3-induced rapid TIL expansion in p53-mutated or KRAS-mutated xenograft mouse models. CONCLUSIONS Taken together, neoantigenic stimulation of TILs selectively expands neoantigen-reactive TILs by frequencies and by their clonal repertoire. NeoExpand led to improved phenotypes and functions of neoantigen-reactive TILs. Our data warrant its clinical evaluation. TRIAL REGISTRATION NUMBER NCT00068003, NCT01174121, and NCT03412877.
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Affiliation(s)
- Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sanghyun P Kim
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Charles A Marquardt
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Maria Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Todd D Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Tiffany Benzine
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert V Masi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Yong Li
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Rafiqul Islam
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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11
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Zhang C, Li S, Shen L, Teng X, Xiao Y, Yang W, Lu Z. Single-cell sequencing of tumour infiltrating T cells efficiently identifies tumour-specific T cell receptors based on the T cell activation score. Cancer Immunol Immunother 2024; 73:123. [PMID: 38727812 PMCID: PMC11087383 DOI: 10.1007/s00262-024-03710-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Adoptively transferred T cell receptor-engineered T cells are a promising cancer treatment strategy, and the identification of tumour-specific TCRs is essential. Previous studies reported that tumour-reactive T cells and TCRs could be isolated based on the expression of activation markers. However, since T cells with different cell states could not respond uniformly to activation but show a heterogeneous expression profile of activation and effector molecules, isolation of tumour-reactive T cells based on single activation or effector molecules could result in the absence of tumour-reactive T cells; thus, combinations of multiple activation and effector molecules could improve the efficiency of isolating tumour-specific TCRs. We enrolled two patients with lung adenocarcinoma and obtained their tumour infiltrating lymphocytes (TILs) and autologous tumour cells (ATCs). TILs were cocultured with the corresponding ATCs for 12 h and subjected to single-cell RNA sequencing. First, we identified three TCRs with the highest expression levels of IFNG and TNFRSF9 mRNA for each patient, yet only the top one or two recognized the corresponding ATCs in each patient. Next, we defined the activation score based on normalized expression levels of IFNG, IL2, TNF, IL2RA, CD69, TNFRSF9, GZMB, GZMA, GZMK, and PRF1 mRNA for each T cell and then identified three TCRs with the highest activation score for each patient. We found that all three TCRs in each patient could specifically identify corresponding ATCs. In conclusion, we established an efficient approach to isolate tumour-reactive TCRs based on combinations of multiple activation and effector molecules through single-cell RNA sequencing.
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Affiliation(s)
- Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Shance Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Luyan Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xia Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yefei Xiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Wenjun Yang
- The Department of Pathology, the First Affiliated Hospital, Hainan Medical University, Haikou, 570102, China.
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Basic Medicine and Life Sciences, Hainan Medical University, Haikou, 571199, China.
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
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12
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Du Y, Zhao X, He F, Gong H, Yang J, Wu L, Cui X, Gai S, Yang P, Lin J. A Vacancy-Engineering Ferroelectric Nanomedicine for Cuproptosis/Apoptosis Co-Activated Immunotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2403253. [PMID: 38703184 DOI: 10.1002/adma.202403253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/14/2024] [Indexed: 05/06/2024]
Abstract
Low efficacy of immunotherapy due to the poor immunogenicity of most tumors and their insufficient infiltration by immune cells highlights the importance of inducing immunogenic cell death and activating immune system for achieving better treatment outcomes. Herein, ferroelectric Bi2CuO4 nanoparticles with rich copper vacancies (named BCO-VCu) are rationally designed and engineered for ferroelectricity-enhanced apoptosis, cuproptosis, and the subsequently evoked immunotherapy. In this structure, the suppressed recombination of the electron-hole pairs by the vacancies and the band bending by the ferroelectric polarization lead to high catalytic activity, triggering reactive oxygen species bursts and inducing apoptosis. The cell fragments produced by apoptosis serve as antigens to activate T cells. Moreover, due to the generated charge by the ferroelectric catalysis, this nanomedicine can act as "a smart switch" to open the cell membrane, promote nanomaterial endocytosis, and shut down the Cu+ outflow pathway to evoke cuproptosis, and thus a strong immune response is triggered by the reduced content of adenosine triphosphate. Ribonucleic acid transcription tests reveal the pathways related to immune response activation. Thus, this study firstly demonstrates a feasible strategy for enhancing the efficacy of immunotherapy using single ferroelectric semiconductor-induced apoptosis and cuproptosis.
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Affiliation(s)
- Yaqian Du
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Xudong Zhao
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
- State Key Laboratory of Rare Earth Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Fei He
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Haijiang Gong
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Jiani Yang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150001, P. R. China
| | - Linzhi Wu
- College of Aerospace and Civil Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Xianchang Cui
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Shili Gai
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Piaoping Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, P. R. China
| | - Jun Lin
- State Key Laboratory of Rare Earth Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
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13
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Morotti M, Grimm AJ, Hope HC, Arnaud M, Desbuisson M, Rayroux N, Barras D, Masid M, Murgues B, Chap BS, Ongaro M, Rota IA, Ronet C, Minasyan A, Chiffelle J, Lacher SB, Bobisse S, Murgues C, Ghisoni E, Ouchen K, Bou Mjahed R, Benedetti F, Abdellaoui N, Turrini R, Gannon PO, Zaman K, Mathevet P, Lelievre L, Crespo I, Conrad M, Verdeil G, Kandalaft LE, Dagher J, Corria-Osorio J, Doucey MA, Ho PC, Harari A, Vannini N, Böttcher JP, Dangaj Laniti D, Coukos G. PGE 2 inhibits TIL expansion by disrupting IL-2 signalling and mitochondrial function. Nature 2024; 629:426-434. [PMID: 38658764 PMCID: PMC11078736 DOI: 10.1038/s41586-024-07352-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Expansion of antigen-experienced CD8+ T cells is critical for the success of tumour-infiltrating lymphocyte (TIL)-adoptive cell therapy (ACT) in patients with cancer1. Interleukin-2 (IL-2) acts as a key regulator of CD8+ cytotoxic T lymphocyte functions by promoting expansion and cytotoxic capability2,3. Therefore, it is essential to comprehend mechanistic barriers to IL-2 sensing in the tumour microenvironment to implement strategies to reinvigorate IL-2 responsiveness and T cell antitumour responses. Here we report that prostaglandin E2 (PGE2), a known negative regulator of immune response in the tumour microenvironment4,5, is present at high concentrations in tumour tissue from patients and leads to impaired IL-2 sensing in human CD8+ TILs via the PGE2 receptors EP2 and EP4. Mechanistically, PGE2 inhibits IL-2 sensing in TILs by downregulating the IL-2Rγc chain, resulting in defective assembly of IL-2Rβ-IL2Rγc membrane dimers. This results in impaired IL-2-mTOR adaptation and PGC1α transcriptional repression, causing oxidative stress and ferroptotic cell death in tumour-reactive TILs. Inhibition of PGE2 signalling to EP2 and EP4 during TIL expansion for ACT resulted in increased IL-2 sensing, leading to enhanced proliferation of tumour-reactive TILs and enhanced tumour control once the cells were transferred in vivo. Our study reveals fundamental features that underlie impairment of human TILs mediated by PGE2 in the tumour microenvironment. These findings have therapeutic implications for cancer immunotherapy and cell therapy, and enable the development of targeted strategies to enhance IL-2 sensing and amplify the IL-2 response in TILs, thereby promoting the expansion of effector T cells with enhanced therapeutic potential.
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MESH Headings
- Animals
- Humans
- Mice
- CD8-Positive T-Lymphocytes/cytology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Proliferation
- Dinoprostone/metabolism
- Down-Regulation
- Ferroptosis
- Interleukin Receptor Common gamma Subunit/biosynthesis
- Interleukin Receptor Common gamma Subunit/deficiency
- Interleukin Receptor Common gamma Subunit/metabolism
- Interleukin-2/antagonists & inhibitors
- Interleukin-2/immunology
- Interleukin-2/metabolism
- Interleukin-2 Receptor beta Subunit/metabolism
- Lymphocytes, Tumor-Infiltrating/cytology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mitochondria/metabolism
- Oxidative Stress
- Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism
- Receptors, Prostaglandin E, EP2 Subtype/metabolism
- Receptors, Prostaglandin E, EP2 Subtype/antagonists & inhibitors
- Receptors, Prostaglandin E, EP4 Subtype/metabolism
- Receptors, Prostaglandin E, EP4 Subtype/antagonists & inhibitors
- Signal Transduction
- TOR Serine-Threonine Kinases/metabolism
- Tumor Microenvironment/immunology
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Affiliation(s)
- Matteo Morotti
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Alizee J Grimm
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Helen Carrasco Hope
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Mathieu Desbuisson
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Nicolas Rayroux
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Maria Masid
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Baptiste Murgues
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Bovannak S Chap
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Marco Ongaro
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Ioanna A Rota
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Catherine Ronet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Aspram Minasyan
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Sebastian B Lacher
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Clément Murgues
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Eleonora Ghisoni
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Khaoula Ouchen
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Ribal Bou Mjahed
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Naoill Abdellaoui
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Riccardo Turrini
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Philippe O Gannon
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Khalil Zaman
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Patrice Mathevet
- Department of Gynaecology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Loic Lelievre
- Department of Gynaecology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Marcus Conrad
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Centre, Helmholtz Munich, Neuherberg, Germany
| | - Gregory Verdeil
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Lana E Kandalaft
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Julien Dagher
- Unit of Translational Oncopathology, Institute of Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Jesus Corria-Osorio
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Marie-Agnes Doucey
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ping-Chih Ho
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Center, Lausanne, Switzerland
| | - Nicola Vannini
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Jan P Böttcher
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland.
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
- Agora Cancer Research Center, Lausanne, Switzerland.
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne (UNIL), Lausanne, Switzerland.
- Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
- Agora Cancer Research Center, Lausanne, Switzerland.
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14
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Li Y, Zheng Y, Liu T, Liao C, Shen G, He Z. The potential and promise for clinical application of adoptive T cell therapy in cancer. J Transl Med 2024; 22:413. [PMID: 38693513 PMCID: PMC11064426 DOI: 10.1186/s12967-024-05206-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024] Open
Abstract
Adoptive cell therapy has revolutionized cancer treatment, especially for hematologic malignancies. T cells are the most extensively utilized cells in adoptive cell therapy. Currently, tumor-infiltrating lymphocytes, T cell receptor-transgenic T cells and chimeric antigen receptor T cells are the three main adoptive T cell therapies. Tumor-infiltrating lymphocytes kill tumors by reinfusing enlarged lymphocytes that naturally target tumor-specific antigens into the patient. T cell receptor-transgenic T cells have the ability to specifically destroy tumor cells via the precise recognition of exogenous T cell receptors with major histocompatibility complex. Chimeric antigen receptor T cells transfer genes with specific antigen recognition structural domains and T cell activation signals into T cells, allowing T cells to attack tumors without the assistance of major histocompatibility complex. Many barriers have been demonstrated to affect the clinical efficacy of adoptive T cell therapy, such as tumor heterogeneity and antigen loss, hard trafficking and infiltration, immunosuppressive tumor microenvironment and T cell exhaustion. Several strategies to improve the efficacy of adoptive T cell therapy have been explored, including multispecific chimeric antigen receptor T cell therapy, combination with immune checkpoint blockade, targeting the immunosuppressive tumor microenvironment, etc. In this review, we will summarize the current status and clinical application, followed by major bottlenecks in adoptive T cell therapy. In addition, we will discuss the promising strategies to improve adoptive T cell therapy. Adoptive T cell therapy will result in even more incredible advancements in solid tumors if the aforementioned problems can be handled.
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Affiliation(s)
- Yinqi Li
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Yeteng Zheng
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Taiqing Liu
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Chuanyun Liao
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China
| | - Guobo Shen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China.
| | - Zhiyao He
- Department of Pharmacy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, 610041, China.
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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15
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Upadhye A, Meza Landeros KE, Ramírez-Suástegui C, Schmiedel BJ, Woo E, Chee SJ, Malicki D, Coufal NG, Gonda D, Levy ML, Greenbaum JA, Seumois G, Crawford J, Roberts WD, Schoenberger SP, Cheroutre H, Ottensmeier CH, Vijayanand P, Ganesan AP. Intra-tumoral T cells in pediatric brain tumors display clonal expansion and effector properties. NATURE CANCER 2024; 5:791-807. [PMID: 38228835 DOI: 10.1038/s43018-023-00706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Brain tumors in children are a devastating disease in a high proportion of patients. Owing to inconsistent results in clinical trials in unstratified patients, the role of immunotherapy remains unclear. We performed an in-depth survey of the single-cell transcriptomes and clonal relationship of intra-tumoral T cells from children with brain tumors. Our results demonstrate that a large fraction of T cells in the tumor tissue are clonally expanded with the potential to recognize tumor antigens. Such clonally expanded T cells display enrichment of transcripts linked to effector function, tissue residency, immune checkpoints and signatures of neoantigen-specific T cells and immunotherapy response. We identify neoantigens in pediatric brain tumors and show that neoantigen-specific T cell gene signatures are linked to better survival outcomes. Notably, among the patients in our cohort, we observe substantial heterogeneity in the degree of clonal expansion and magnitude of T cell response. Our findings suggest that characterization of intra-tumoral T cell responses may enable selection of patients for immunotherapy, an approach that requires prospective validation in clinical trials.
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Affiliation(s)
- Aditi Upadhye
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kevin E Meza Landeros
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | | | | | - Edwin Woo
- Southampton University Hospitals NHS Trust, Southampton, UK
| | - Serena J Chee
- Department of Respiratory Medicine, Liverpool Heart and Chest Hospital NHS Foundation Trust, Liverpool, UK
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Denise Malicki
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- Rady Children's Hospital, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - David Gonda
- Rady Children's Hospital, San Diego, CA, USA
- Department of Neurological Surgery, University of California San Diego, La Jolla, CA, USA
| | - Michael L Levy
- Rady Children's Hospital, San Diego, CA, USA
- Department of Neurological Surgery, University of California San Diego, La Jolla, CA, USA
| | | | | | - John Crawford
- Rady Children's Hospital, San Diego, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California Irvine, Irvine, CA, USA
- Children's Hospital Orange County, Irvine, CA, USA
| | - William D Roberts
- Rady Children's Hospital, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | | | - Christian H Ottensmeier
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Anusha-Preethi Ganesan
- La Jolla Institute for Immunology, La Jolla, CA, USA.
- Rady Children's Hospital, San Diego, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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16
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Wang X, Dai Z, Lin X, Zou X, Wang R, Tasiheng Y, Yan Y, Ma M, Chen Y, Cheng H, Liu C, Yu X. Antigen/HLA-agnostic strategies for Characterizing Tumor-responsive T cell receptors in PDAC patients via single-cell sequencing and autologous organoid application. Cancer Lett 2024; 588:216741. [PMID: 38395378 DOI: 10.1016/j.canlet.2024.216741] [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: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024]
Abstract
Characterization of tumor-responsive T cell receptors (TCRs) is a critical step in personalized TCR-T cell therapy, and remains challenging for pancreatic ductal adenocarcinoma (PDAC). Here we report a proof-of-concept study to identify and validate antitumor TCRs in two representative PDAC patients using ultradeep single-cell TCR/RNA sequencing and autologous organoids, and reveal the phenotypic dynamics of TCR repertoire in different T cell expansions from the same patient. We first performed comparative sequencing on freshly harvested peripheral blood mononuclear cells (PBMCs) and uncultured tumor infiltrating lymphocytes (TILs), followed by reactivity tests of TIL-enriched TCRs with autologous organoids, in which two tumor-responsive TCRs were successfully characterized and the corresponding TILs were mostly tissue-resident memory-like T cells, and partially expressed both naïve and exhausted T cell markers. For the PDAC patient without high-quality TILs, PBMCs were cultured with neoantigen peptide (KRASG12D), organoids, or anti-CD3 antibody in presence, and experienced extensive clonal expansions within ten days. All derived PBMCs were sequenced in parallel (>82,000 cells), and TCRs enriched in both peptide- and organoid-experienced, but not anti-CD3-treated CD8 T cells, were assessed for their reactivity to antigen-presenting cells (APCs) and organoids, in which three neoantigen-reactive TCRs were identified as tumor-responsive, and the corresponding T cells were characterized by mixed transcriptional signatures including but not limited to typical exhausted T cell markers. Together, our study revealed that the combination of ultradeep single-cell sequencing and organoid techniques enabled rapid characterization of tumor-responsive TCRs for developing practical personalized TCR-T therapy in an antigen/human leukocyte antigen (HLA)-agnostic manner.
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Affiliation(s)
- Xu Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China; Cancer Institute, Shanghai Key Laboratory of Radiation Oncology, Cancer Research Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhengjie Dai
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xuan Lin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xuan Zou
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Ruijie Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yesboli Tasiheng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yu Yan
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Mingjian Ma
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yusheng Chen
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - He Cheng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Chen Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Precise Diagnosis and Treatment of Pancreatic Cancer, Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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17
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Moravec Z, Zhao Y, Voogd R, Cook DR, Kinrot S, Capra B, Yang H, Raud B, Ou J, Xuan J, Wei T, Ren L, Hu D, Wang J, Haanen JBAG, Schumacher TN, Chen X, Porter E, Scheper W. Discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening. Nat Biotechnol 2024:10.1038/s41587-024-02210-6. [PMID: 38653798 DOI: 10.1038/s41587-024-02210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
T cell receptor (TCR) gene therapy is a potent form of cellular immunotherapy in which patient T cells are genetically engineered to express TCRs with defined tumor reactivity. However, the isolation of therapeutic TCRs is complicated by both the general scarcity of tumor-specific T cells among patient T cell repertoires and the patient-specific nature of T cell epitopes expressed on tumors. Here we describe a high-throughput, personalized TCR discovery pipeline that enables the assembly of complex synthetic TCR libraries in a one-pot reaction, followed by pooled expression in reporter T cells and functional genetic screening against patient-derived tumor or antigen-presenting cells. We applied the method to screen thousands of tumor-infiltrating lymphocyte (TIL)-derived TCRs from multiple patients and identified dozens of CD4+ and CD8+ T-cell-derived TCRs with potent tumor reactivity, including TCRs that recognized patient-specific neoantigens.
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Affiliation(s)
- Ziva Moravec
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yue Zhao
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Rhianne Voogd
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Haiyan Yang
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Brenda Raud
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jiayu Ou
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Jiekun Xuan
- RootPath, Inc. (US), Watertown, MA, USA
- RootPath, Inc. (Hangzhou), Hangzhou, China
| | - Teng Wei
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Lili Ren
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Dandan Hu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - John B A G Haanen
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Xi Chen
- RootPath, Inc. (Guangzhou), Guangzhou, China.
- RootPath, Inc. (US), Watertown, MA, USA.
- RootPath, Inc. (Hangzhou), Hangzhou, China.
| | - Ely Porter
- RootPath, Inc. (US), Watertown, MA, USA.
| | - Wouter Scheper
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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18
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Ehrenfried AR, Zens S, Steffens LK, Kehm H, Paul A, Lauenstein C, Volkmar M, Poschke I, Meng Z, Offringa R. T-Cell-Based Platform for Functional Screening of T-Cell Receptors Identified in Single-Cell RNA Sequencing Data Sets of Tumor-Infiltrating T-Cells. Bio Protoc 2024; 14:e4972. [PMID: 38686347 PMCID: PMC11056003 DOI: 10.21769/bioprotoc.4972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 05/02/2024] Open
Abstract
The advent of single-cell RNA sequencing (scRNAseq) has enabled in-depth gene expression analysis of several thousand cells isolated from tissues. We recently reported the application of scRNAseq toward the dissection of the tumor-infiltrating T-cell repertoire in human pancreatic cancer samples. In this study, we demonstrated that combined whole transcriptome and T-cell receptor (TCR) sequencing provides an effective way to identify tumor-reactive TCR clonotypes on the basis of gene expression signatures. An important aspect in this respect was the experimental validation of TCR-mediated anti-tumor reactivity by means of an in vitro functional assay, which is the subject of the present protocol. This assay involves the transient transfection of mRNA gene constructs encoding TCRα/β pairs into a well-defined human T-cell line, followed by co-cultivation with the tumor cells of interest and detection of T-cell activation by flow cytometry. Due to the high transfectability and the low background reactivity of the mock-transfected T-cell line to a wide variety of tumor cells, this assay offers a highly robust and versatile platform for the functional screening of large numbers of TCR clonotypes as identified in scRNAseq data sets. Whereas the assay was initially developed to test TCRs of human origin, it was more recently also applied successfully for the screening of TCRs of murine origin. Key features • Efficient functional screening of-and discrimination between-TCRs isolated from tumor-reactive vs. bystander T-cell clones. • Applicable to TCRs from CD8+ and CD4+ tumor-infiltrating T-cells originating from patient-derived tumor samples and syngeneic mouse tumor models. • Rapid flow cytometric detection of T-cell activation by means of TNFα and CD107a expression after a 5 h T-cell/tumor cell co-cultivation.
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Affiliation(s)
- Aaron Rodriguez Ehrenfried
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz-Institute for Translational Oncology by DKFZ (HI-TRON), Mainz, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Stefan Zens
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Laura K. Steffens
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Hannes Kehm
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alina Paul
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Claudia Lauenstein
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Volkmar
- Helmholtz-Institute for Translational Oncology by DKFZ (HI-TRON), Mainz, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Zibo Meng
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Wuhan, China
| | - Rienk Offringa
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Wuhan, China
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19
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Minnie SA, Waltner OG, Zhang P, Takahashi S, Nemychenkov NS, Ensbey KS, Schmidt CR, Legg SRW, Comstock M, Boiko JR, Nelson E, Bhise SS, Wilkens AB, Koyama M, Dhodapkar MV, Chesi M, Riddell SR, Green DJ, Spencer A, Furlan SN, Hill GR. TIM-3 + CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies. Sci Immunol 2024; 9:eadg1094. [PMID: 38640253 PMCID: PMC11093588 DOI: 10.1126/sciimmunol.adg1094] [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: 12/02/2022] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Chronic antigen stimulation is thought to generate dysfunctional CD8 T cells. Here, we identify a CD8 T cell subset in the bone marrow tumor microenvironment that, despite an apparent terminally exhausted phenotype (TPHEX), expressed granzymes, perforin, and IFN-γ. Concurrent gene expression and DNA accessibility revealed that genes encoding these functional proteins correlated with BATF expression and motif accessibility. IFN-γ+ TPHEX effectively killed myeloma with comparable efficacy to transitory effectors, and disease progression correlated with numerical deficits in IFN-γ+ TPHEX. We also observed IFN-γ+ TPHEX within CD19-targeted chimeric antigen receptor T cells, which killed CD19+ leukemia cells. An IFN-γ+ TPHEX gene signature was recapitulated in TEX cells from human cancers, including myeloma and lymphoma. Here, we characterize a TEX subset in hematological malignancies that paradoxically retains function and is distinct from dysfunctional TEX found in chronic viral infections. Thus, IFN-γ+ TPHEX represent a potential target for immunotherapy of blood cancers.
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Affiliation(s)
- Simone A. Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Olivia G. Waltner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shuichiro Takahashi
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Nicole S. Nemychenkov
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Kathleen S. Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Christine R. Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Samuel RW. Legg
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Melissa Comstock
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Julie R. Boiko
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Ethan Nelson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Shruti S. Bhise
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Alec B. Wilkens
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Atlanta, GA, UNITED STATES
- Winship Cancer Institute, Emory University, Atlanta, GA, UNITED STATES
| | - Marta Chesi
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, UNITED STATES
| | - Stanley R. Riddell
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Damian J. Green
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University/The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Malignant Haematology and Stem Cell Transplantation, The Alfred Hospital, Melbourne, VIC, AUSTRALIA
- Department of Clinical Haematology, Monash University, Melbourne, VIC
| | - Scott N. Furlan
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Department of Pediatrics, University of Washington; WA, UNITED STATES
| | - Geoffrey R. Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center; Seattle, WA, UNITED STATES
- Division of Medical Oncology, University of Washington; Seattle, WA, UNITED STATES
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20
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Leonard-Murali S, Bhaskarla C, Yadav GS, Maurya SK, Galiveti CR, Tobin JA, Kann RJ, Ashwat E, Murphy PS, Chakka AB, Soman V, Cantalupo PG, Zhuo X, Vyas G, Kozak DL, Kelly LM, Smith E, Chandran UR, Hsu YMS, Kammula US. Uveal melanoma immunogenomics predict immunotherapy resistance and susceptibility. Nat Commun 2024; 15:2863. [PMID: 38627362 PMCID: PMC11021475 DOI: 10.1038/s41467-024-46906-4] [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: 06/20/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Immune checkpoint inhibition has shown success in treating metastatic cutaneous melanoma but has limited efficacy against metastatic uveal melanoma, a rare variant arising from the immune privileged eye. To better understand this resistance, we comprehensively profile 100 human uveal melanoma metastases using clinicogenomics, transcriptomics, and tumor infiltrating lymphocyte potency assessment. We find that over half of these metastases harbor tumor infiltrating lymphocytes with potent autologous tumor specificity, despite low mutational burden and resistance to prior immunotherapies. However, we observe strikingly low intratumoral T cell receptor clonality within the tumor microenvironment even after prior immunotherapies. To harness these quiescent tumor infiltrating lymphocytes, we develop a transcriptomic biomarker to enable in vivo identification and ex vivo liberation to counter their growth suppression. Finally, we demonstrate that adoptive transfer of these transcriptomically selected tumor infiltrating lymphocytes can promote tumor immunity in patients with metastatic uveal melanoma when other immunotherapies are incapable.
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Affiliation(s)
- Shravan Leonard-Murali
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chetana Bhaskarla
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ghanshyam S Yadav
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sudeep K Maurya
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chenna R Galiveti
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joshua A Tobin
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rachel J Kann
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eishan Ashwat
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patrick S Murphy
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anish B Chakka
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vishal Soman
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul G Cantalupo
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinming Zhuo
- UPMC Genome Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gopi Vyas
- UPMC Genome Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dara L Kozak
- UPMC Genome Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lindsey M Kelly
- UPMC Genome Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ed Smith
- UPMC Genome Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Uma R Chandran
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yen-Michael S Hsu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Immunologic Monitoring and Cellular Products Laboratory, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Udai S Kammula
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
- Solid Tumor Cellular Immunotherapy Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA.
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21
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Pan H, Yu M, Tang X, Mao X, Liu M, Zhang K, Qian C, Wang J, Xie H, Qiu W, Ding Q, Wang S, Zhou W. Preoperative single-dose camrelizumab and/or microwave ablation in women with early-stage breast cancer: A window-of-opportunity trial. MED 2024; 5:291-310.e5. [PMID: 38417440 DOI: 10.1016/j.medj.2024.01.015] [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: 11/20/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 03/01/2024]
Abstract
BACKGROUND Immune checkpoint blockade has shown low response rates for advanced breast cancer, and combination strategies are needed. Microwave ablation (MWA) may be a trigger of antitumor immunity. This window-of-opportunity trial (ClinicalTrials.gov: NCT04805736) was conducted to determine the safety and feasibility of preoperative camrelizumab (an anti-PD-1 antibody) combined with MWA in the treatment of early-stage breast cancer. METHODS Sixty participants were randomized to preoperatively receive single-dose camrelizumab alone (n = 20), MWA alone (n = 20), or camrelizumab+MWA (n = 20). A random number table was used to allocate interventions. The primary outcome was the safety and feasibility of MWA combined with camrelizumab. FINDINGS Camrelizumab and MWA were well tolerated alone and in combination without delays in prescheduled surgery. No treatment-related grade III/IV adverse events were observed. Different from in the single-dose camrelizumab or MWA group, participants showed stable counts of blood cells after combination therapy. After combination therapy, peripheral CD8+ T cells showed enhanced cytotoxic and effect-memory functions. Clonal expansional CD8+ T cells showed higher cytotoxic activity and effector memory- and tumor-specific signatures than emergent clones after combination therapy. Enhanced interactions between clonal expansional CD8+ T cells and monocytes were observed, suggesting that monocytes contributed to the enhanced functions of clonal expansional CD8+ T cells. Major histocompatibility complex (MHC) class I-related pathways and interferon signaling pathways were activated in monocytes by combination therapy. CONCLUSIONS Camrelizumab combined with MWA was feasible for early-stage breast cancer. Peripheral CD8+ T cells were activated after combination therapy, dependent on monocytes with activated MHC class I pathways. FUNDING This study was supported by the Natural Science Foundation of Jiangsu Province (BK20230017).
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Affiliation(s)
- Hong Pan
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Muxin Yu
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xinyu Tang
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Xinrui Mao
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Mingduo Liu
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Kai Zhang
- Pancreas Center & Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China; Pancreas Institute of Nanjing Medical University, Nanjing 210029, China
| | - Chao Qian
- Department of General Surgery, Sir Run Run Hospital, Nanjing Medical University, Nanjing 211112, China
| | - Ji Wang
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hui Xie
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Wen Qiu
- Department of Immunology, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Antibody Technology of the Ministry of Health, Nanjing Medical University, Nanjing 211166, China
| | - Qiang Ding
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Shui Wang
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
| | - Wenbin Zhou
- Department of Breast Surgery & General Surgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention, and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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22
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Chen X, Zhao J, Yue S, Li Z, Duan X, Lin Y, Yang Y, He J, Gao L, Pan Z, Yang X, Su X, Huang M, Li X, Zhao Y, Zhang X, Li Z, Hu L, Tang J, Hao Y, Tian Q, Wang Y, Xu L, Huang Q, Cao Y, Chen Y, Zhu B, Li Y, Bai F, Zhang G, Ye L. An oncolytic virus delivering tumor-irrelevant bystander T cell epitopes induces anti-tumor immunity and potentiates cancer immunotherapy. NATURE CANCER 2024:10.1038/s43018-024-00760-x. [PMID: 38609488 DOI: 10.1038/s43018-024-00760-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/15/2024] [Indexed: 04/14/2024]
Abstract
Tumor-specific T cells are crucial in anti-tumor immunity and act as targets for cancer immunotherapies. However, these cells are numerically scarce and functionally exhausted in the tumor microenvironment (TME), leading to inefficacious immunotherapies in most patients with cancer. By contrast, emerging evidence suggested that tumor-irrelevant bystander T (TBYS) cells are abundant and preserve functional memory properties in the TME. To leverage TBYS cells in the TME to eliminate tumor cells, we engineered oncolytic virus (OV) encoding TBYS epitopes (OV-BYTE) to redirect the antigen specificity of tumor cells to pre-existing TBYS cells, leading to effective tumor inhibition in multiple preclinical models. Mechanistically, OV-BYTE induced epitope spreading of tumor antigens to elicit more diverse tumor-specific T cell responses. Remarkably, the OV-BYTE strategy targeting human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell memory efficiently inhibited tumor progression in a human tumor cell-derived xenograft model, providing important insights into the improvement of cancer immunotherapies in a large population with a history of SARS-CoV-2 infection or coronavirus disease 2019 (COVID-19) vaccination.
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Affiliation(s)
- Xiangyu Chen
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China
- Changping Laboratory, Beijing, China
| | - Jing Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuai Yue
- Institute of Immunology, Third Military Medical University, Chongqing, China
- Cancer Center, Daping Hospital and Army Medical Center of PLA, Third Military Medical University, Chongqing, China
| | - Ziyu Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Xiang Duan
- The State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Yao Lin
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Yang Yang
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Junjian He
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Leiqiong Gao
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Zhiwei Pan
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Xiaofan Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Xingxing Su
- Department of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Min Huang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiao Li
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xuehui Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhirong Li
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Li Hu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jianfang Tang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Yaxing Hao
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qin Tian
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yifei Wang
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China
| | - Lifan Xu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Qizhao Huang
- Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing, China
| | - Yingjiao Cao
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yan Li
- The State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China.
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China.
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Lilin Ye
- Changping Laboratory, Beijing, China.
- Institute of Immunology, Third Military Medical University, Chongqing, China.
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23
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Shao W, Yao Y, Yang L, Li X, Ge T, Zheng Y, Zhu Q, Ge S, Gu X, Jia R, Song X, Zhuang A. Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy. Exp Hematol Oncol 2024; 13:37. [PMID: 38570883 PMCID: PMC10988985 DOI: 10.1186/s40164-024-00504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Adoptive immunotherapy in the T cell landscape exhibits efficacy in cancer treatment. Over the past few decades, genetically modified T cells, particularly chimeric antigen receptor T cells, have enabled remarkable strides in the treatment of hematological malignancies. Besides, extensive exploration of multiple antigens for the treatment of solid tumors has led to clinical interest in the potential of T cells expressing the engineered T cell receptor (TCR). TCR-T cells possess the capacity to recognize intracellular antigen families and maintain the intrinsic properties of TCRs in terms of affinity to target epitopes and signal transduction. Recent research has provided critical insight into their capability and therapeutic targets for multiple refractory solid tumors, but also exposes some challenges for durable efficacy. In this review, we describe the screening and identification of available tumor antigens, and the acquisition and optimization of TCRs for TCR-T cell therapy. Furthermore, we summarize the complete flow from laboratory to clinical applications of TCR-T cells. Last, we emerge future prospects for improving therapeutic efficacy in cancer world with combination therapies or TCR-T derived products. In conclusion, this review depicts our current understanding of TCR-T cell therapy in solid neoplasms, and provides new perspectives for expanding its clinical applications and improving therapeutic efficacy.
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Affiliation(s)
- Weihuan Shao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiaoran Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Tongxin Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yue Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Qiuyi Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
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24
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Lei X, de Groot DC, Welters MJP, de Wit T, Schrama E, van Eenennaam H, Santegoets SJ, Oosenbrug T, van der Veen A, Vos JL, Zuur CL, de Miranda NFCC, Jacobs H, van der Burg SH, Borst J, Xiao Y. CD4 + T cells produce IFN-I to license cDC1s for induction of cytotoxic T-cell activity in human tumors. Cell Mol Immunol 2024; 21:374-392. [PMID: 38383773 PMCID: PMC10978876 DOI: 10.1038/s41423-024-01133-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024] Open
Abstract
CD4+ T cells can "help" or "license" conventional type 1 dendritic cells (cDC1s) to induce CD8+ cytotoxic T lymphocyte (CTL) anticancer responses, as proven in mouse models. We recently identified cDC1s with a transcriptomic imprint of CD4+ T-cell help, specifically in T-cell-infiltrated human cancers, and these cells were associated with a good prognosis and response to PD-1-targeting immunotherapy. Here, we delineate the mechanism of cDC1 licensing by CD4+ T cells in humans. Activated CD4+ T cells produce IFNβ via the STING pathway, which promotes MHC-I antigen (cross-)presentation by cDC1s and thereby improves their ability to induce CTL anticancer responses. In cooperation with CD40 ligand (L), IFNβ also optimizes the costimulatory and other functions of cDC1s required for CTL response induction. IFN-I-producing CD4+ T cells are present in diverse T-cell-infiltrated cancers and likely deliver "help" signals to CTLs locally, according to their transcriptomic profile and colocalization with "helped/licensed" cDCs and tumor-reactive CD8+ T cells. In agreement with this scenario, the presence of IFN-I-producing CD4+ T cells in the TME is associated with overall survival and the response to PD-1 checkpoint blockade in cancer patients.
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Affiliation(s)
- Xin Lei
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël C de Groot
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom de Wit
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Ellen Schrama
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Saskia J Santegoets
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Timo Oosenbrug
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Joris L Vos
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Charlotte L Zuur
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Leiden University Medical Center, Leiden, The Netherlands
| | | | - Heinz Jacobs
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sjoerd H van der Burg
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Jannie Borst
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands.
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.
| | - Yanling Xiao
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands.
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.
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25
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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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26
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Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol 2024; 25:644-658. [PMID: 38503922 DOI: 10.1038/s41590-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 02/15/2024] [Indexed: 03/21/2024]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7+PD-1+CD8+ T cells, activated CCR7+LAMP3+ dendritic cells and CCL19+ fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10+ macrophages and TCF7-CD8+ T cells as well as between mature regulatory dendritic cells and TCF7+CD4+ and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
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Affiliation(s)
- Jonathan H Chen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Department of Pathology, MGH, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Linda T Nieman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Maxwell Spurrell
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vjola Jorgji
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Liad Elmelech
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Peter Richieri
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Katherine H Xu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Roopa Madhu
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA
| | - Milan Parikh
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Izabella Zamora
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Arnav Mehta
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Christopher S Nabel
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua D Pirl
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Chenyue Lu
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
| | - Catherine B Meador
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Hematology/Oncology, MGH, HMS, Boston, MA, USA
| | | | | | - Alexander L Tang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Matan Hofree
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Lautenberg Center for Immunology and Cancer Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Angela Shih
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Genevieve M Boland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, MGH, Boston, MA, USA
| | - Karin Pelka
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, Gladstone Institutes, San Francisco, CA, USA
| | - Martin J Aryee
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mari Mino-Kenudson
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA
- Department of Pathology, MGH, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Center for Thoracic Cancers, MGH, Boston, MA, USA.
| | - Ilya Korsunsky
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Boston, MA, USA.
| | - Nir Hacohen
- Massachusetts General Hospital (MGH) Cancer Center, Harvard Medical School (HMS), Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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27
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Pal S, Chaudhari R, Baurceanu I, Hill BJ, Nagy BA, Wolf MT. Extracellular Matrix Scaffold-Assisted Tumor Vaccines Induce Tumor Regression and Long-Term Immune Memory. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309843. [PMID: 38302823 PMCID: PMC11009079 DOI: 10.1002/adma.202309843] [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: 09/22/2023] [Revised: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Injectable scaffold delivery is a strategy to enhance the efficacy of cancer vaccine immunotherapy. The choice of scaffold biomaterial is crucial, impacting both vaccine release kinetics and immune stimulation via the host response. Extracellular matrix (ECM) scaffolds prepared from decellularized tissues facilitate a pro-healing inflammatory response that promotes local cancer immune surveillance. Here, an ECM scaffold-assisted therapeutic cancer vaccine that maintains an immune microenvironment consistent with tissue reconstruction is engineered. Several immune-stimulating adjuvants are screened to develop a cancer vaccine formulated with decellularized small intestinal submucosa (SIS) ECM scaffold co-delivery. It is found that the STING pathway agonist cyclic di-AMP most effectively induces cytotoxic immunity in an ECM scaffold vaccine, without compromising key interleukin 4 (IL-4) mediated immune pathways associated with healing. ECM scaffold delivery enhances therapeutic vaccine efficacy, curing 50-75% of established E.G-7OVA lymphoma tumors in mice, while none are cured with soluble vaccine. SIS-ECM scaffold-assisted vaccination prolonged antigen exposure is dependent on CD8+ cytotoxic T cells and generates long-term antigen-specific immune memory for at least 10 months post-vaccination. This study shows that an ECM scaffold is a promising delivery vehicle to enhance cancer vaccine efficacy while being orthogonal to characteristics of pro-healing immune hallmarks.
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Affiliation(s)
- Sanjay Pal
- Cancer Biomaterial Engineering Section, Cancer Innovation
Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
21702
| | - Rohan Chaudhari
- Cancer Biomaterial Engineering Section, Cancer Innovation
Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
21702
- OHSU School of Medicine, Oregon Health & Science
University, Portland, OR 97239
| | - Iris Baurceanu
- Cancer Biomaterial Engineering Section, Cancer Innovation
Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
21702
| | - Brenna J. Hill
- AIDS and Cancer Virus Program, Frederick National
Laboratory for Cancer Research, Frederick, MD 21702
| | - Bethany A. Nagy
- Laboratory Animal Sciences Program (LASP), National Cancer
Institute, Frederick, MD 21702
| | - Matthew T. Wolf
- Cancer Biomaterial Engineering Section, Cancer Innovation
Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD
21702
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28
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Donia M, Svane IM. Harnessing neoantigen-specific T cells for precision cancer immunotherapy. Nat Rev Clin Oncol 2024; 21:253-254. [PMID: 38243022 DOI: 10.1038/s41571-024-00860-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Affiliation(s)
- Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Copenhagen, Denmark.
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Copenhagen, Denmark.
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29
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Ke Y, Xin K, Tao Y, Li L, Chen A, Shao J, Zhu J, Zhang D, Cen L, Chu Y, Yu L, Liu B, Liu Q. A Thermosensitive Bi-Adjuvant Hydrogel Triggers Epitope Spreading to Promote the Anti-Tumor Efficacy of Frameshift Neoantigens. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306889. [PMID: 38308098 PMCID: PMC11005695 DOI: 10.1002/advs.202306889] [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: 09/20/2023] [Revised: 01/09/2024] [Indexed: 02/04/2024]
Abstract
Tumor-specific frameshift mutations encoding peptides (FSPs) are highly immunogenic neoantigens for personalized cancer immunotherapy, while their clinical efficacy is limited by immunosuppressive tumor microenvironment (TME) and self-tolerance. Here, a thermosensitive hydrogel (FSP-RZ-BPH) delivering dual adjuvants R848 (TLR7/8 agonist) + Zn2+ (cGAS-STING agonist) is designed to promote the efficacy of FSPs on murine forestomach cancer (MFC). After peritumoral injection, FSP-RZ-BPH behaves as pH-responsive sustained drug release at sites near the tumor to effectively transform the immunosuppressive TME into an inflammatory type. FSP-RZ-BPH orchestrates innate and adaptive immunity to activate dendritic cells in tumor-draining lymph nodes and increase the number of FSPs-reactive effector memory T cells (TEM) in tumor by 2.9 folds. More importantly, these TEM also exhibit memory responses to nonvaccinated neoantigens on MFC. This epitope spreading effect contributes to reduce self-tolerance to maintain long-lasting anti-tumor immunity. In MFC suppressive model, FSP-RZ-BPH achieves 84.8% tumor inhibition rate and prolongs the survival of tumor-bearing mice with 57.1% complete response rate. As a preventive tumor vaccine, FSP-RZ-BPH can also significantly delay tumor growth. Overall, the work identifies frameshift MFC neoantigens for the first time and demonstrates the thermosensitive bi-adjuvant hydrogel as an effective strategy to boost bystander anti-tumor responses of frameshift neoantigens.
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Affiliation(s)
- Yaohua Ke
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
| | - Kai Xin
- Department of OncologyNanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine321 Zhongshan RoadNanjing210008China
| | - Yaping Tao
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
| | - Lin Li
- Department of OncologyNanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine321 Zhongshan RoadNanjing210008China
| | - Aoxing Chen
- Department of OncologyNanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine321 Zhongshan RoadNanjing210008China
| | - Jingyi Shao
- Department of OncologyNanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine321 Zhongshan RoadNanjing210008China
| | - Junmeng Zhu
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
| | - Dinghu Zhang
- Zhejiang Cancer HospitalHangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhou310022China
| | - Lanqi Cen
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
| | - Yanhong Chu
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
| | - Lixia Yu
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
| | - Baorui Liu
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
- Department of OncologyNanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine321 Zhongshan RoadNanjing210008China
| | - Qin Liu
- The Comprehensive Cancer CentreNanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing University321 Zhongshan RoadNanjing210008China
- Department of OncologyNanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine321 Zhongshan RoadNanjing210008China
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30
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Manoutcharian K, Gevorkian G. Are we getting closer to a successful neoantigen cancer vaccine? Mol Aspects Med 2024; 96:101254. [PMID: 38354548 DOI: 10.1016/j.mam.2024.101254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Although significant advances in immunotherapy have revolutionized the treatment of many cancer types over the past decade, the field of vaccine therapy, an important component of cancer immunotherapy, despite decades-long intense efforts, is still transmitting signals of promises and awaiting strong data on efficacy to proceed with regulatory approval. The field of cancer vaccines faces standard challenges, such as tumor-induced immunosuppression, immune response in inhibitory tumor microenvironment (TME), intratumor heterogeneity (ITH), permanently evolving cancer mutational landscape leading to neoantigens, and less known obstacles: neoantigen gain/loss upon immunotherapy, the timing and speed of appearance of neoantigens and responding T cell clonotypes and possible involvement of immune interference/heterologous immunity, in the complex interplay between evolving tumor epitopes and the immune system. In this review, we discuss some key issues related to challenges hampering the development of cancer vaccines, along with the current approaches focusing on neoantigens. We summarize currently well-known ideas/rationales, thus revealing the need for alternative vaccine approaches. Such a discussion should stimulate vaccine researchers to apply out-of-box, unconventional thinking in search of new avenues to deal with critical, often yet unaddressed challenges on the road to a new generation of therapeutics and vaccines.
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Affiliation(s)
- Karen Manoutcharian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), CDMX, Apartado Postal 70228, Cuidad Universitaria, Mexico DF, CP, 04510, Mexico.
| | - Goar Gevorkian
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), CDMX, Apartado Postal 70228, Cuidad Universitaria, Mexico DF, CP, 04510, Mexico.
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31
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Kirk AM, Crawford JC, Chou CH, Guy C, Pandey K, Kozlik T, Shah RK, Chung S, Nguyen P, Zhang X, Wang J, Bell M, Mettelman RC, Allen EK, Pogorelyy MV, Kim H, Minervina AA, Awad W, Bajracharya R, White T, Long D, Gordon B, Morrison M, Glazer ES, Murphy AJ, Jiang Y, Fitzpatrick EA, Yarchoan M, Sethupathy P, Croft NP, Purcell AW, Federico SM, Stewart E, Gottschalk S, Zamora AE, DeRenzo C, Strome SE, Thomas PG. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med 2024; 5:101469. [PMID: 38508137 PMCID: PMC10983114 DOI: 10.1016/j.xcrm.2024.101469] [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: 08/23/2023] [Revised: 11/29/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Fibrolamellar carcinoma (FLC) is a liver tumor with a high mortality burden and few treatment options. A promising therapeutic vulnerability in FLC is its driver mutation, a conserved DNAJB1-PRKACA gene fusion that could be an ideal target neoantigen for immunotherapy. In this study, we aim to define endogenous CD8 T cell responses to this fusion in FLC patients and evaluate fusion-specific T cell receptors (TCRs) for use in cellular immunotherapies. We observe that fusion-specific CD8 T cells are rare and that FLC patient TCR repertoires lack large clusters of related TCR sequences characteristic of potent antigen-specific responses, potentially explaining why endogenous immune responses are insufficient to clear FLC tumors. Nevertheless, we define two functional fusion-specific TCRs, one of which has strong anti-tumor activity in vivo. Together, our results provide insights into the fragmented nature of neoantigen-specific repertoires in humans and indicate routes for clinical development of successful immunotherapies for FLC.
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Affiliation(s)
- Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ravi K Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shanzou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyu Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jin Wang
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyunjin Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Toni White
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald Long
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Brittney Gordon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michelle Morrison
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan S Glazer
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew J Murphy
- Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yixing Jiang
- Department of Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth A Fitzpatrick
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott E Strome
- College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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32
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Tan CL, Lindner K, Boschert T, Meng Z, Rodriguez Ehrenfried A, De Roia A, Haltenhof G, Faenza A, Imperatore F, Bunse L, Lindner JM, Harbottle RP, Ratliff M, Offringa R, Poschke I, Platten M, Green EW. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy. Nat Biotechnol 2024:10.1038/s41587-024-02161-y. [PMID: 38454173 DOI: 10.1038/s41587-024-02161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
The identification of patient-derived, tumor-reactive T cell receptors (TCRs) as a basis for personalized transgenic T cell therapies remains a time- and cost-intensive endeavor. Current approaches to identify tumor-reactive TCRs analyze tumor mutations to predict T cell activating (neo)antigens and use these to either enrich tumor infiltrating lymphocyte (TIL) cultures or validate individual TCRs for transgenic autologous therapies. Here we combined high-throughput TCR cloning and reactivity validation to train predicTCR, a machine learning classifier that identifies individual tumor-reactive TILs in an antigen-agnostic manner based on single-TIL RNA sequencing. PredicTCR identifies tumor-reactive TCRs in TILs from diverse cancers better than previous gene set enrichment-based approaches, increasing specificity and sensitivity (geometric mean) from 0.38 to 0.74. By predicting tumor-reactive TCRs in a matter of days, TCR clonotypes can be prioritized to accelerate the manufacture of personalized T cell therapies.
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Affiliation(s)
- C L Tan
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - K Lindner
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
| | - T Boschert
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
| | - Z Meng
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - A Rodriguez Ehrenfried
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Helmholtz Institute for Translational Oncology, Mainz, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
| | - A De Roia
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- DNA Vector Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - G Haltenhof
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | | | | | - L Bunse
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany
| | | | - R P Harbottle
- DNA Vector Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - M Ratliff
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - R Offringa
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - I Poschke
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany
| | - M Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany.
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany.
- Immune Monitoring Unit, National Center for Tumor Diseases, Heidelberg, Germany.
- Helmholtz Institute for Translational Oncology, Mainz, Germany.
- German Cancer Research Center-Hector Cancer Institute at the Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.
| | - E W Green
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany.
- German Cancer Consortium, Core Center Heidelberg, Heidelberg, Germany.
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience, Heidelberg University, Mannheim, Germany.
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Los C, Klobuch S, Haanen JBAG. Tumor-Infiltrating Lymphocyte and Other Cell Therapies for Metastatic Melanoma. Cancer J 2024; 30:113-119. [PMID: 38527265 DOI: 10.1097/ppo.0000000000000705] [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: 03/27/2024]
Abstract
ABSTRACT Major progress in prolonging survival of patients with advanced melanoma has been made in the past decade because of the development and approval of immune checkpoint inhibitor and targeted therapies. However, for nonresponding or relapsing patients, their prognosis is still dismal. Based on clinical trial data, treatment with adoptive cell therapies holds great promise. In patients with metastatic melanoma progressing on or nonresponsive to single-agent anti-programmed cell death 1, infusion of tumor-infiltrating lymphocytes can produce responses in up to half of patients, with durable complete responses in up to 20%. Genetic modification of peripheral blood T cells with T-cell receptors derived from tumor-specific T cells, or with chimeric antigen receptors, has the potential to further improve treatment outcomes in this refractory population. In this review, we will discuss the historical development, current status, and future perspectives of adoptive T-cell therapies in melanoma.
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Affiliation(s)
- Christy Los
- From the Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute
| | - Sebastian Klobuch
- Department of Medical Oncology, Antoni van Leeuwenhoek/Netherlands Cancer Institute, Amsterdam
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Tan J, Egelston CA, Guo W, Stark JM, Lee PP. STING signalling compensates for low tumour mutation burden to drive anti-tumour immunity. EBioMedicine 2024; 101:105035. [PMID: 38401418 PMCID: PMC10904200 DOI: 10.1016/j.ebiom.2024.105035] [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: 05/20/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND While mutation-derived neoantigens are well recognized in generating anti-tumour T cell response, increasing evidences highlight the complex association between tumour mutation burden (TMB) and tumour infiltrating lymphocytes (TILs). The exploration of non-TMB determinants of active immune response could improve the prognosis prediction and provide guidance for current immunotherapy. METHODS The transcriptomic and whole exome sequence data in The Cancer Genome Atlas were used to examine the relationship between TMB and exhausted CD8+ T cells (Tex), as an indicator of tumour antigen-specific T cells across nine major cancer types. Computational clustering analysis was performed on 4510 tumours to identify different immune profiles. NanoString gene expression analysis and single cell RNA-seq analysis using fresh human breast cancer were performed for finding validation. FINDINGS TMB was found to be poorly correlated with active immune response in various cancer types. Patient clustering analysis revealed a group of tumours with abundant Tex but low TMB. In those tumours, we observed significantly higher expression of the stimulator of interferon genes (STING) signalling. Dendritic cells, particularly those of BATF3+ lineage, were also found to be essential for accumulation of Tex within tumours. Mechanistically, loss of genomic and cellular integrity, marked by decreased DNA damage repair, defective replication stress response, and increased apoptosis were shown to drive STING activation. INTERPRETATION These results highlight that TMB alone does not fully predict tumour immune profiles, with STING signalling compensating for low TMB in non-hypermutated tumours to enhance anti-tumour immunity. Translating these results, STING agonists may benefit patients with non-hypermutated tumours. STING activation may serve as an additional biomarker to predict response to immune checkpoint blockades alongside TMB. Our research also unravelled the interplay between genomic instability and STING activation, informing potential combined chemotherapy targeting the axis of genomic integrity and immunotherapy. FUNDING City of Hope Christopher Family Endowed Innovation Fund for Alzheimer's Disease and Breast Cancer Research in honor of Vineta Christopher; Breast Cancer Alliance Early Career Investigator Award; National Cancer Institute of the National Institutes of Health under award number R01CA256989 and R01CA240392.
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Affiliation(s)
- Jiayi Tan
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Colt A Egelston
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Weihua Guo
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Peter P Lee
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
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Klobuch S, Seijkens TTP, Schumacher TN, Haanen JBAG. Tumour-infiltrating lymphocyte therapy for patients with advanced-stage melanoma. Nat Rev Clin Oncol 2024; 21:173-184. [PMID: 38191921 DOI: 10.1038/s41571-023-00848-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Immunotherapy with immune-checkpoint inhibitors (ICIs) and targeted therapy with BRAF and MEK inhibitors have revolutionized the treatment of melanoma over the past decade. Despite these breakthroughs, the 5-year survival rate of patients with advanced-stage melanoma is at most 50%, emphasizing the need for additional therapeutic strategies. Adoptive cell therapy with tumour-infiltrating lymphocytes (TILs) is a therapeutic modality that has, in the past few years, demonstrated long-term clinical benefit in phase II/III trials involving patients with advanced-stage melanoma, including those with disease progression on ICIs and/or BRAF/MEK inhibitors. In this Review, we summarize the current status of TIL therapies for patients with advanced-stage melanoma, including potential upcoming marketing authorization, the characteristics of TIL therapy products, as well as future strategies that are expected to increase the efficacy of this promising cellular immunotherapy.
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Affiliation(s)
- Sebastian Klobuch
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tom T P Seijkens
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - John B A G Haanen
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Division of Molecular Oncology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands.
- Melanoma Clinic, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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Xiong P, Liang A, Cai X, Xia T. APTAnet: an atom-level peptide-TCR interaction affinity prediction model. BIOPHYSICS REPORTS 2024; 10:1-14. [PMID: 38737473 PMCID: PMC11079603 DOI: 10.52601/bpr.2023.230037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/26/2024] [Indexed: 05/14/2024] Open
Abstract
The prediction of affinity between TCRs and peptides is crucial for the further development of TIL (Tumor-Infiltrating Lymphocytes) immunotherapy. Inspired by the broader research of drug-protein interaction (DPI), we propose an atom-level peptide-TCR interaction (PTI) affinity prediction model APTAnet using natural language processing methods. APTAnet model achieved an average ROC-AUC and PR-AUC of 0.893 and 0.877, respectively, in ten-fold cross-validation on 25,675 pairs of PTI data. Furthermore, experimental results on an independent test set from the McPAS database showed that APTAnet outperformed the current mainstream models. Finally, through the validation on 11 cases of real tumor patient data, we found that the APTAnet model can effectively identify tumor peptides and screen tumor-specific TCRs.
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Affiliation(s)
- Peng Xiong
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Anyi Liang
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xunhui Cai
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tian Xia
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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37
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Hafler D, Lu B, Lucca L, Lewis W, Wang J, Nogeuira C, Heer S, Axisa PP, Buitrago-Pocasangre N, Pham G, Kojima M, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski J, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle A, Kisielow J, Obermair FJ, Kluger H. Circulating Tumor Reactive KIR+CD8+ T cells Suppress Anti-Tumor Immunity in Patients with Melanoma. RESEARCH SQUARE 2024:rs.3.rs-3956671. [PMID: 38464315 PMCID: PMC10925449 DOI: 10.21203/rs.3.rs-3956671/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Effective anti-tumor immunity is largely driven by cytotoxic CD8+ T cells that can specifically recognize tumor antigens. However, the factors which ultimately dictate successful tumor rejection remain poorly understood. Here we identify a subpopulation of CD8+ T cells which are tumor antigen-specific in patients with melanoma but resemble KIR+CD8+ T cells with a regulatory function (Tregs). These tumor antigen-specific KIR+CD8+ T cells are detectable in both the tumor and the blood, and higher levels of this population are associated with worse overall survival. Our findings therefore suggest that KIR+CD8+ Tregs are tumor antigen-specific but uniquely suppress anti-tumor immunity in patients with melanoma.
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Zhou W, Kawashima S, Ishino T, Kawase K, Ueda Y, Yamashita K, Watanabe T, Kawazu M, Dansako H, Suzuki Y, Nishikawa H, Inozume T, Nagasaki J, Togashi Y. Stem-like progenitor and terminally differentiated T FH-like CD4 + T cell exhaustion in the tumor microenvironment. Cell Rep 2024; 43:113797. [PMID: 38363680 DOI: 10.1016/j.celrep.2024.113797] [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: 11/29/2022] [Revised: 03/13/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Immune checkpoint inhibitors exert clinical efficacy against various types of cancer through reinvigoration of exhausted CD8+ T cells that attack cancer cells directly in the tumor microenvironment (TME). Using single-cell sequencing and mouse models, we show that CXCL13, highly expressed in tumor-infiltrating exhausted CD8+ T cells, induces CD4+ follicular helper T (TFH) cell infiltration, contributing to anti-tumor immunity. Furthermore, a part of the TFH cells in the TME exhibits cytotoxicity and directly attacks major histocompatibility complex-II-expressing tumors. TFH-like cytotoxic CD4+ T cells have high LAG-3/BLIMP1 and low TCF1 expression without self-renewal ability, whereas non-cytotoxic TFH cells express low LAG-3/BLIMP1 and high TCF1 with self-renewal ability, closely resembling the relationship between terminally differentiated and stem-like progenitor exhaustion in CD8+ T cells, respectively. Our findings provide deep insights into TFH-like CD4+ T cell exhaustion with helper progenitor and cytotoxic differentiated functions, mediating anti-tumor immunity orchestrally with CD8+ T cells.
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Affiliation(s)
- Wenhao Zhou
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Department of Urology Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Shusuke Kawashima
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan
| | - Takamasa Ishino
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan; Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Katsushige Kawase
- Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan; Department of Otorhinolaryngology/Head & Neck Surgery, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Youki Ueda
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | | | - Tomofumi Watanabe
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-0932, Japan
| | - Masahito Kawazu
- Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan
| | - Hiromichi Dansako
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Kashiwa 277-8568, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Division of Cancer Immunology, National Cancer Center, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), Tokyo 104-0045, Kashiwa 277-8577, Japan
| | - Takashi Inozume
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan
| | - Joji Nagasaki
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan.
| | - Yosuke Togashi
- Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; Chiba Cancer Center, Research Institute, Division of Cell Therapy, Chiba 260-8717, Japan; Division of Cancer Immunology, National Cancer Center, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), Tokyo 104-0045, Kashiwa 277-8577, Japan.
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Pulliam T, Jani S, Jing L, Ryu H, Jojic A, Shasha C, Zhang J, Kulikauskas R, Church C, Garnett-Benson C, Gooley T, Chapuis A, Paulson K, Smith KN, Pardoll DM, Newell EW, Koelle DM, Topalian SL, Nghiem P. Circulating cancer-specific CD8 T cell frequency is associated with response to PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101412. [PMID: 38340723 PMCID: PMC10897614 DOI: 10.1016/j.xcrm.2024.101412] [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: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Understanding cancer immunobiology has been hampered by difficulty identifying cancer-specific T cells. Merkel cell polyomavirus (MCPyV) causes most Merkel cell carcinomas (MCCs). All patients with virus-driven MCC express MCPyV oncoproteins, facilitating identification of virus (cancer)-specific T cells. We studied MCPyV-specific T cells from 27 patients with MCC using MCPyV peptide-HLA-I multimers, 26-color flow cytometry, single-cell transcriptomics, and T cell receptor (TCR) sequencing. In a prospective clinical trial, higher circulating MCPyV-specific CD8 T cell frequency before anti-PD-1 treatment was strongly associated with 2-year recurrence-free survival (75% if detectable, 0% if undetectable, p = 0.0018; ClinicalTrial.gov: NCT02488759). Intratumorally, such T cells were typically present, but their frequency did not significantly associate with response. Circulating MCPyV-specific CD8 T cells had increased stem/memory and decreased exhaustion signatures relative to their intratumoral counterparts. These results suggest that cancer-specific CD8 T cells in the blood may play a role in anti-PD-1 responses. Thus, strategies that augment their number or mobilize them into tumors could improve outcomes.
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Affiliation(s)
- Thomas Pulliam
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Saumya Jani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ana Jojic
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn Shasha
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jiajia Zhang
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rima Kulikauskas
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Ted Gooley
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aude Chapuis
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Paulson
- Paul G. Allen Research Center, Providence-Swedish Cancer Institute, Seattle, WA 98104, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Kellie N Smith
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Evan W Newell
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Suzanne L Topalian
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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Weber JS, Carlino MS, Khattak A, Meniawy T, Ansstas G, Taylor MH, Kim KB, McKean M, Long GV, Sullivan RJ, Faries M, Tran TT, Cowey CL, Pecora A, Shaheen M, Segar J, Medina T, Atkinson V, Gibney GT, Luke JJ, Thomas S, Buchbinder EI, Healy JA, Huang M, Morrissey M, Feldman I, Sehgal V, Robert-Tissot C, Hou P, Zhu L, Brown M, Aanur P, Meehan RS, Zaks T. Individualised neoantigen therapy mRNA-4157 (V940) plus pembrolizumab versus pembrolizumab monotherapy in resected melanoma (KEYNOTE-942): a randomised, phase 2b study. Lancet 2024; 403:632-644. [PMID: 38246194 DOI: 10.1016/s0140-6736(23)02268-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Checkpoint inhibitors are standard adjuvant treatment for stage IIB-IV resected melanoma, but many patients recur. Our study aimed to evaluate whether mRNA-4157 (V940), a novel mRNA-based individualised neoantigen therapy, combined with pembrolizumab, improved recurrence-free survival and distant metastasis-free survival versus pembrolizumab monotherapy in resected high-risk melanoma. METHODS We did an open-label, randomised, phase 2b, adjuvant study of mRNA-4157 plus pembrolizumab versus pembrolizumab monotherapy in patients, enrolled from sites in the USA and Australia, with completely resected high-risk cutaneous melanoma. Patients with completely resected melanoma (stage IIIB-IV) were assigned 2:1 to receive open-label mRNA-4157 plus pembrolizumab or pembrolizumab monotherapy. mRNA-4157 was administered intramuscularly (maximum nine doses) and pembrolizumab intravenously (maximum 18 doses) in 3-week cycles. The primary endpoint was recurrence-free survival in the intention-to-treat population. This ongoing trial is registered at ClinicalTrials.gov, NCT03897881. FINDINGS From July 18, 2019, to Sept 30, 2021, 157 patients were assigned to mRNA-4157 plus pembrolizumab combination therapy (n=107) or pembrolizumab monotherapy (n=50); median follow-up was 23 months and 24 months, respectively. Recurrence-free survival was longer with combination versus monotherapy (hazard ratio [HR] for recurrence or death, 0·561 [95% CI 0·309-1·017]; two-sided p=0·053), with lower recurrence or death event rate (24 [22%] of 107 vs 20 [40%] of 50); 18-month recurrence-free survival was 79% (95% CI 69·0-85·6) versus 62% (46·9-74·3). Most treatment-related adverse events were grade 1-2. Grade ≥3 treatment-related adverse events occurred in 25% of patients in the combination group and 18% of patients in the monotherapy group, with no mRNA-4157-related grade 4-5 events. Immune-mediated adverse event frequency was similar for the combination (37 [36%]) and monotherapy (18 [36%]) groups. INTERPRETATION Adjuvant mRNA-4157 plus pembrolizumab prolonged recurrence-free survival versus pembrolizumab monotherapy in patients with resected high-risk melanoma and showed a manageable safety profile. These results provide evidence that an mRNA-based individualised neoantigen therapy might be beneficial in the adjuvant setting. FUNDING Moderna in collaboration with Merck Sharp & Dohme, a subsidiary of Merck & Co, Rahway, NJ, USA.
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Affiliation(s)
- Jeffrey S Weber
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA.
| | - Matteo S Carlino
- Westmead and Blacktown Hospitals, Melanoma Institute Australia, Sydney, NSW, Australia
| | - Adnan Khattak
- Hollywood Private Hospital, Perth, WA, Australia; Edith Cowan University, Perth, WA, Australia
| | - Tarek Meniawy
- Saint John of God Subiaco Hospital, Subiaco, WA, Australia
| | - George Ansstas
- Washington University School of Medicine, St Louis, MO, USA
| | - Matthew H Taylor
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Meredith McKean
- Sarah Cannon Research Institute at Tennessee Oncology, Nashville, TN, USA
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Ryan J Sullivan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark Faries
- The Angeles Clinic and Research Institute, a Cedars-Sinai affiliate, Los Angeles, CA, USA
| | - Thuy T Tran
- Smilow Cancer Center at Yale New Haven Hospital, New Haven, CT, USA
| | | | - Andrew Pecora
- Hackensack University Medical Center, Hackensack, NJ, USA
| | - Montaser Shaheen
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | | | | | | | - Geoffrey T Gibney
- Georgetown-Lombardi Comprehensive Cancer Center, Washington, DC, USA
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Barras D, Ghisoni E, Chiffelle J, Orcurto A, Dagher J, Fahr N, Benedetti F, Crespo I, Grimm AJ, Morotti M, Zimmermann S, Duran R, Imbimbo M, de Olza MO, Navarro B, Homicsko K, Bobisse S, Labes D, Tsourti Z, Andriakopoulou C, Herrera F, Pétremand R, Dummer R, Berthod G, Kraemer AI, Huber F, Thevenet J, Bassani-Sternberg M, Schaefer N, Prior JO, Matter M, Aedo V, Dromain C, Corria-Osorio J, Tissot S, Kandalaft LE, Gottardo R, Pittet M, Sempoux C, Michielin O, Dafni U, Trueb L, Harari A, Laniti DD, Coukos G. Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8 + T-myeloid cell networks in melanoma. Sci Immunol 2024; 9:eadg7995. [PMID: 38306416 DOI: 10.1126/sciimmunol.adg7995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 12/06/2023] [Indexed: 02/04/2024]
Abstract
Adoptive cell therapy (ACT) using ex vivo-expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell-intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8+ TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor-reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network-based biomarkers that could improve patient selection and guide the design of ACT clinical trials.
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Affiliation(s)
- David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Eleonora Ghisoni
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Angela Orcurto
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Dagher
- Unit of Translational Oncopathology, Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Noémie Fahr
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
| | - Alizée J Grimm
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
| | - Matteo Morotti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
| | - Stefan Zimmermann
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Rafael Duran
- Department of Radiology and Interventional Radiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Martina Imbimbo
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Maria Ochoa de Olza
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Blanca Navarro
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Krisztian Homicsko
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Danny Labes
- Flow Cytometry Facility, Department of Formation and Research, University of Lausanne, Epalinges, Switzerland
| | - Zoe Tsourti
- Scientific Research Consulting Hellas, Athens, Greece
| | | | - Fernanda Herrera
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Service of Radiation Oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Rémy Pétremand
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Gregoire Berthod
- Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Anne I Kraemer
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Jonathan Thevenet
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Department of Oncology, Center of Experimental Therapeutics, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Niklaus Schaefer
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital, Lausanne, Switzerland
| | - John O Prior
- Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital, Lausanne, Switzerland
| | - Maurice Matter
- Department of Visceral Surgery, Lausanne University Hospital, and University of Lausanne, Lausannne, Switzerland
| | - Veronica Aedo
- Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Clarisse Dromain
- Department of Radiology and Interventional Radiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Jesus Corria-Osorio
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Stéphanie Tissot
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Department of Oncology, Center of Experimental Therapeutics, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Department of Oncology, Center of Experimental Therapeutics, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Raphael Gottardo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Biomedical Data Science Center and Swiss Institute of Bioinformatics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Mikaël Pittet
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Christine Sempoux
- Unit of Translational Oncopathology, Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Olivier Michielin
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Urania Dafni
- Faculty of Nursing, National and Kapodistrian University of Athens, Athens, Greece
| | - Lionel Trueb
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Agora Cancer Research Center, Lausanne, Switzerland
- Center for Cell Therapy, CHUV-Ludwig Institute, Lausanne, Switzerland
- Service of Immuno-oncology, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
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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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Keshari S, Shavkunov AS, Miao Q, Saha A, Williams CD, Highsmith AM, Pineda JE, Alspach E, Hu KH, Pauken KE, Chen K, Gubin MM. Neoantigen Cancer Vaccines and Different Immune Checkpoint Therapies Each Utilize Both Converging and Distinct Mechanisms that in Combination Enable Synergistic Therapeutic Efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.570816. [PMID: 38187708 PMCID: PMC10769249 DOI: 10.1101/2023.12.20.570816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to eliminate cancer by expanding and/or sustaining T cells with anti-tumor capabilities. However, whether cancer vaccines and ICT enhance anti-tumor immunity by distinct or overlapping mechanisms remains unclear. Here, we compared effective therapeutic tumor-specific mutant neoantigen (NeoAg) cancer vaccines with anti-CTLA-4 and/or anti-PD-1 ICT in preclinical models. Both NeoAg vaccines and ICT induce expansion of intratumoral NeoAg-specific CD8 T cells, though the degree of expansion and acquisition of effector activity was much more substantial following NeoAg vaccination. Further, we found that NeoAg vaccines are particularly adept at inducing proliferating and stem-like NeoAg-specific CD8 T cells. Single cell T cell receptor (TCR) sequencing revealed that TCR clonotype expansion and diversity of NeoAg-specific CD8 T cells relates to their phenotype and functional state associated with specific immunotherapies employed. Effective NeoAg vaccines and ICT required both CD8 and CD4 T cells. While NeoAg vaccines and anti-PD-1 affected the CD4 T cell compartment, it was to less of an extent than observed with anti-CTLA-4, which notably induced ICOS+Bhlhe40+ Th1-like CD4 T cells and, when combined with anti-PD-1, a small subset of Th2-like CD4 T cells. Although effective NeoAg vaccines or ICT expanded intratumoral M1-like iNOS+ macrophages, NeoAg vaccines expanded rather than suppressed (as observed with ICT) M2-like CX3CR1+CD206+ macrophages, associated with the vaccine adjuvant. Further, combining NeoAg vaccination with ICT induced superior efficacy compared to either therapy in isolation, highlighting the utility of combining these modalities to eliminate cancer.
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Affiliation(s)
- Sunita Keshari
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander S. Shavkunov
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akata Saha
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charmelle D. Williams
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna M. Highsmith
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Josué E. Pineda
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elise Alspach
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Kenneth H. Hu
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristen E. Pauken
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew M. Gubin
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Bawden EG, Wagner T, Schröder J, Effern M, Hinze D, Newland L, Attrill GH, Lee AR, Engel S, Freestone D, de Lima Moreira M, Gressier E, McBain N, Bachem A, Haque A, Dong R, Ferguson AL, Edwards JJ, Ferguson PM, Scolyer RA, Wilmott JS, Jewell CM, Brooks AG, Gyorki DE, Palendira U, Bedoui S, Waithman J, Hochheiser K, Hölzel M, Gebhardt T. CD4 + T cell immunity against cutaneous melanoma encompasses multifaceted MHC II-dependent responses. Sci Immunol 2024; 9:eadi9517. [PMID: 38241401 DOI: 10.1126/sciimmunol.adi9517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Whereas CD4+ T cells conventionally mediate antitumor immunity by providing help to CD8+ T cells, recent clinical studies have implied an important role for cytotoxic CD4+ T cells in cancer immunity. Using an orthotopic melanoma model, we provide a detailed account of antitumoral CD4+ T cell responses and their regulation by major histocompatibility complex class II (MHC II) in the skin. Intravital imaging revealed prominent interactions of CD4+ T cells with tumor debris-laden MHC II+ host antigen-presenting cells that accumulated around tumor cell nests, although direct recognition of MHC II+ melanoma cells alone could also promote CD4+ T cell control. CD4+ T cells stably suppressed or eradicated tumors even in the absence of other lymphocytes by using tumor necrosis factor-α and Fas ligand (FasL) but not perforin-mediated cytotoxicity. Interferon-γ was critical for protection, acting both directly on melanoma cells and via induction of nitric oxide synthase in myeloid cells. Our results illustrate multifaceted and context-specific aspects of MHC II-dependent CD4+ T cell immunity against cutaneous melanoma, emphasizing modulation of this axis as a potential avenue for immunotherapies.
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Affiliation(s)
- Emma G Bawden
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn 53105, Germany
| | - Teagan Wagner
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jan Schröder
- Computational Sciences Initiative, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Maike Effern
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn 53105, Germany
| | - Daniel Hinze
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn 53105, Germany
| | - Lewis Newland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn 53105, Germany
| | - Grace H Attrill
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Ariane R Lee
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sven Engel
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David Freestone
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Marcela de Lima Moreira
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Elise Gressier
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Nathan McBain
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ashraful Haque
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ruining Dong
- Computational Sciences Initiative, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Angela L Ferguson
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
- Centenary Institute, University of Sydney, Sydney, NSW, Australia
- Infection, Immunity and Inflammation theme, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Jarem J Edwards
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
- Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- NSW Health Pathology, Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Christopher M Jewell
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
- United States Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD, USA
- Robert E. Fischell Institute for Biomedical Devices, College Park, MD, USA
- Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD, USA
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David E Gyorki
- Division of Cancer Surgery, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre Melbourne, Melbourne, VIC, Australia
| | - Umaimainthan Palendira
- Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jason Waithman
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Katharina Hochheiser
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre Melbourne, Melbourne, VIC, Australia
| | - Michael Hölzel
- Institute of Experimental Oncology (IEO), Medical Faculty, University Hospital Bonn, University of Bonn, Bonn 53105, Germany
| | - Thomas Gebhardt
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [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] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Shiao SL, Gouin KH, Ing N, Ho A, Basho R, Shah A, Mebane RH, Zitser D, Martinez A, Mevises NY, Ben-Cheikh B, Henson R, Mita M, McAndrew P, Karlan S, Giuliano A, Chung A, Amersi F, Dang C, Richardson H, Shon W, Dadmanesh F, Burnison M, Mirhadi A, Zumsteg ZS, Choi R, Davis M, Lee J, Rollins D, Martin C, Khameneh NH, McArthur H, Knott SRV. Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer. Cancer Cell 2024; 42:70-84.e8. [PMID: 38194915 DOI: 10.1016/j.ccell.2023.12.012] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/05/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Strategies are needed to better identify patients that will benefit from immunotherapy alone or who may require additional therapies like chemotherapy or radiotherapy to overcome resistance. Here we employ single-cell transcriptomics and spatial proteomics to profile triple negative breast cancer biopsies taken at baseline, after one cycle of pembrolizumab, and after a second cycle of pembrolizumab given with radiotherapy. Non-responders lack immune infiltrate before and after therapy and exhibit minimal therapy-induced immune changes. Responding tumors form two groups that are distinguishable by a classifier prior to therapy, with one showing high major histocompatibility complex expression, evidence of tertiary lymphoid structures, and displaying anti-tumor immunity before treatment. The other responder group resembles non-responders at baseline and mounts a maximal immune response, characterized by cytotoxic T cell and antigen presenting myeloid cell interactions, only after combination therapy, which is mirrored in a murine model of triple negative breast cancer.
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Affiliation(s)
- Stephen L Shiao
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Kenneth H Gouin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nathan Ing
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alice Ho
- Breast Cancer Clinical Research Unit, Duke University Medical Center, Raleigh, NC, USA.
| | - Reva Basho
- Ellison Institute of Technology, Los Angeles, CA, USA
| | - Aagam Shah
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard H Mebane
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David Zitser
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Martinez
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Natalie-Ya Mevises
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bassem Ben-Cheikh
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Regina Henson
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Monica Mita
- Department of Medicine, Division of Hematology-Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Philomena McAndrew
- Department of Medicine, Division of Hematology-Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Scott Karlan
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Armando Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alice Chung
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Farin Amersi
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Catherine Dang
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heather Richardson
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wonwoo Shon
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Farnaz Dadmanesh
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michele Burnison
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amin Mirhadi
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zachary S Zumsteg
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rachel Choi
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Madison Davis
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph Lee
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dustin Rollins
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cynthia Martin
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Negin H Khameneh
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heather McArthur
- Department of Internal Medicine, Division of Hematology-Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Simon R V Knott
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Collier C, Wucherer K, McWhorter M, Jenkins C, Bartlett A, Roychoudhuri R, Eil R. Intracellular K+ Limits T-cell Exhaustion and Preserves Antitumor Function. Cancer Immunol Res 2024; 12:36-47. [PMID: 38063845 PMCID: PMC10765769 DOI: 10.1158/2326-6066.cir-23-0319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/08/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
T cells are often compromised within cancers, allowing disease progression. We previously found that intratumoral elevations in extracellular K+, related to ongoing cell death, constrained CD8+ T-cell Akt-mTOR signaling and effector function. To alleviate K+-mediated T-cell dysfunction, we pursued genetic means to lower intracellular K+. CD8+ T cells robustly and dynamically express the Na+/K+ ATPase, among other K+ transporters. CRISPR-Cas9-mediated disruption of the Atp1a1 locus lowered intracellular K+ and elevated the resting membrane potential (i.e., Vm, Ψ). Despite compromised Ca2+ influx, Atp1a1-deficient T cells harbored tonic hyperactivity in multiple signal transduction cascades, along with a phenotype of exhaustion in mouse and human CD8+ T cells. Provision of exogenous K+ restored intracellular levels in Atp1a1-deficient T cells and prevented damaging levels of reactive oxygen species (ROS), and both antioxidant treatment and exogenous K+ prevented Atp1a1-deficient T-cell exhaustion in vitro. T cells lacking Atp1a1 had compromised persistence and antitumor activity in a syngeneic model of orthotopic murine melanoma. Translational application of these findings will require balancing the beneficial aspects of intracellular K+ with the ROS-dependent nature of T-cell effector function. See related Spotlight by Banuelos and Borges da Silva, p. 6.
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Affiliation(s)
- Camille Collier
- Division of Surgical Oncology, Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Kelly Wucherer
- Division of Surgical Oncology, Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Matthew McWhorter
- Division of Surgical Oncology, Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Chelsea Jenkins
- Division of Surgical Oncology, Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Alexandra Bartlett
- Division of Surgical Oncology, Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Rahul Roychoudhuri
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Robert Eil
- Division of Surgical Oncology, Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Department of Cell, Developmental, & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
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48
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Li X, You J, Hong L, Liu W, Guo P, Hao X. Neoantigen cancer vaccines: a new star on the horizon. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0395. [PMID: 38164734 PMCID: PMC11033713 DOI: 10.20892/j.issn.2095-3941.2023.0395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Immunotherapy represents a promising strategy for cancer treatment that utilizes immune cells or drugs to activate the patient's own immune system and eliminate cancer cells. One of the most exciting advances within this field is the targeting of neoantigens, which are peptides derived from non-synonymous somatic mutations that are found exclusively within cancer cells and absent in normal cells. Although neoantigen-based therapeutic vaccines have not received approval for standard cancer treatment, early clinical trials have yielded encouraging outcomes as standalone monotherapy or when combined with checkpoint inhibitors. Progress made in high-throughput sequencing and bioinformatics have greatly facilitated the precise and efficient identification of neoantigens. Consequently, personalized neoantigen-based vaccines tailored to each patient have been developed that are capable of eliciting a robust and long-lasting immune response which effectively eliminates tumors and prevents recurrences. This review provides a concise overview consolidating the latest clinical advances in neoantigen-based therapeutic vaccines, and also discusses challenges and future perspectives for this innovative approach, particularly emphasizing the potential of neoantigen-based therapeutic vaccines to enhance clinical efficacy against advanced solid tumors.
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Affiliation(s)
- Xiaoling Li
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Jian You
- Department of Thoracic Oncology, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- Department of Thoracic Oncology Surgery, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Liping Hong
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Weijiang Liu
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Peng Guo
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Xishan Hao
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
- Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
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49
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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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50
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Yossef R, Krishna S, Sindiri S, Lowery FJ, Copeland AR, Gartner JJ, Parkhurst MR, Parikh NB, Hitscherich KJ, Levi ST, Chatani PD, Zacharakis N, Levin N, Vale NR, Nah SK, Dinerman A, Hill VK, Ray S, Bera A, Levy L, Jia L, Kelly MC, Goff SL, Robbins PF, Rosenberg SA. Phenotypic signatures of circulating neoantigen-reactive CD8 + T cells in patients with metastatic cancers. Cancer Cell 2023; 41:2154-2165.e5. [PMID: 38039963 PMCID: PMC10843665 DOI: 10.1016/j.ccell.2023.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 08/07/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Circulating T cells from peripheral blood (PBL) can provide a rich and noninvasive source for antitumor T cells. By single-cell transcriptomic profiling of 36 neoantigen-specific T cell clones from 6 metastatic cancer patients, we report the transcriptional and cell surface signatures of antitumor PBL-derived CD8+ T cells (NeoTCRPBL). Comparison of tumor-infiltrating lymphocyte (TIL)- and PBL-neoantigen-specific T cells revealed that NeoTCRPBL T cells are low in frequency and display less-dysfunctional memory phenotypes relative to their TIL counterparts. Analysis of 100 antitumor TCR clonotypes indicates that most NeoTCRPBL populations target the same neoantigens as TILs. However, NeoTCRPBL TCR repertoire is only partially shared with TIL. Prediction and testing of NeoTCRPBL signature-derived TCRs from PBL of 6 prospective patients demonstrate high enrichment of clonotypes targeting tumor mutations, a viral oncogene, and patient-derived tumor. Thus, the NeoTCRPBL signature provides an alternative source for identifying antitumor T cells from PBL of cancer patients, enabling immune monitoring and immunotherapies.
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Affiliation(s)
- Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Copeland
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shoshana T Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirley K Nah
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Dinerman
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria K Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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