1
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Dobrin A, Lindenbergh PL, Shi Y, Perica K, Xie H, Jain N, Chow A, Wolchok JD, Merghoub T, Sadelain M, Hamieh M. Synthetic dual co-stimulation increases the potency of HIT and TCR-targeted cell therapies. NATURE CANCER 2024; 5:760-773. [PMID: 38503896 DOI: 10.1038/s43018-024-00744-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
Chimeric antigen receptor T cells have dramatically improved the treatment of hematologic malignancies. T cell antigen receptor (TCR)-based cell therapies are yet to achieve comparable outcomes. Importantly, chimeric antigen receptors not only target selected antigens but also reprogram T cell functions through the co-stimulatory pathways that they engage upon antigen recognition. We show here that a fusion receptor comprising the CD80 ectodomain and the 4-1BB cytoplasmic domain, termed 80BB, acts as both a ligand and a receptor to engage the CD28 and 4-1BB pathways, thereby increasing the antitumor potency of human leukocyte antigen-independent TCR (HIT) receptor- or TCR-engineered T cells and tumor-infiltrating lymphocytes. Furthermore, 80BB serves as a switch receptor that provides agonistic 4-1BB co-stimulation upon its ligation by the inhibitory CTLA4 molecule. By combining multiple co-stimulatory features in a single antigen-agnostic synthetic receptor, 80BB is a promising tool to sustain CD3-dependent T cell responses in a wide range of targeted immunotherapies.
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Affiliation(s)
- Anton Dobrin
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pieter L Lindenbergh
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuzhe Shi
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karlo Perica
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongyao Xie
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nayan Jain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Chow
- Thoracic Oncology Service, Division of Solid Tumour Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Taha Merghoub
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Mohamad Hamieh
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pediatrics and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
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2
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Stefanidis E, Semilietof A, Pujol J, Seijo B, Scholten K, Zoete V, Michielin O, Sandaltzopoulos R, Coukos G, Irving M. Combining SiRPα decoy-coengineered T cells and antibodies augments macrophage-mediated phagocytosis of tumor cells. J Clin Invest 2024; 134:e161660. [PMID: 38828721 PMCID: PMC11142748 DOI: 10.1172/jci161660] [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: 05/06/2022] [Accepted: 04/16/2024] [Indexed: 06/05/2024] Open
Abstract
The adoptive transfer of T cell receptor-engineered (TCR-engineered) T cells (ACT) targeting the HLA-A2-restricted cancer-testis epitope NY-ESO-1157-165 (A2/NY) has yielded favorable clinical responses against several cancers. Two approaches to improve ACT are TCR affinity optimization and T cell coengineering to express immunomodulatory molecules that can exploit endogenous immunity. By computational design we previously developed a panel of binding-enhanced A2/NY-TCRs including A97L, which augmented the in vitro function of gene-modified T cells as compared with WT. Here, we demonstrated higher persistence and improved tumor control by A97L-T cells. In order to harness macrophages in tumors, we further coengineered A97L-T cells to secrete a high-affinity signal regulatory protein α (SiRPα) decoy (CV1) that blocks CD47. While CV1-Fc-coengineered A97L-T cells mediated significantly better control of tumor outgrowth and survival in Winn assays, in subcutaneous xenograft models the T cells, coated by CV1-Fc, were depleted. Importantly, there was no phagocytosis of CV1 monomer-coengineered T cells by human macrophages. Moreover, avelumab and cetuximab enhanced macrophage-mediated phagocytosis of tumor cells in vitro in the presence of CV1 and improved tumor control upon coadministration with A97L-T cells. Taken together, our study indicates important clinical promise for harnessing macrophages by combining CV1-coengineered TCR-T cells with targeted antibodies to direct phagocytosis against tumor cells.
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MESH Headings
- Animals
- Humans
- Mice
- Antigens, Differentiation/immunology
- Antigens, Neoplasm/immunology
- CD47 Antigen/immunology
- Cell Line, Tumor
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/genetics
- Immunotherapy, Adoptive
- Macrophages/immunology
- Macrophages/metabolism
- Phagocytosis
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Immunologic/immunology
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/genetics
- T-Lymphocytes/immunology
- Xenograft Model Antitumor Assays
- Male
- Female
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Affiliation(s)
- Evangelos Stefanidis
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Aikaterini Semilietof
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Pujol
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Bili Seijo
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Kirsten Scholten
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Michielin
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Oncology, University Hospital of Geneva (HUG), Geneva, Switzerland
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Coukos
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne (UNIL) and University Hospital of Lausanne (CHUV), Lausanne, Switzerland
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3
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Wu D, Li Y. Application of adoptive cell therapy in hepatocellular carcinoma. Immunology 2023; 170:453-469. [PMID: 37435926 DOI: 10.1111/imm.13677] [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: 01/05/2023] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC) remains a global health challenge. Novel treatment modalities are urgently needed to extend the overall survival of patients. The liver plays an immunomodulatory function due to its unique physiological structural characteristics. Therefore, following surgical resection and radiotherapy, immunotherapy regimens have shown great potential in the treatment of hepatocellular carcinoma. Adoptive cell immunotherapy is rapidly developing in the treatment of hepatocellular carcinoma. In this review, we summarize the latest research on adoptive immunotherapy for hepatocellular carcinoma. The focus is on chimeric antigen receptor (CAR)-T cells and T cell receptor (TCR) engineered T cells. Then tumour-infiltrating lymphocytes (TILs), natural killer (NK) cells, cytokine-induced killer (CIK) cells, and macrophages are briefly discussed. The main overview of the application and challenges of adoptive immunotherapy in hepatocellular carcinoma. It aims to provide the reader with a comprehensive understanding of the current status of HCC adoptive immunotherapy and offers some strategies. We hope to provide new ideas for the clinical treatment of hepatocellular carcinoma.
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Affiliation(s)
- Dengqiang Wu
- Department of Clinical Laboratory, Ningbo No. 6 Hospital, Ningbo, China
| | - Yujie Li
- Clinical Laboratory of Ningbo Medical Centre Lihuili Hospital, Ningbo University, Zhejiang, Ningbo, China
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4
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Giordano Attianese GMP, Ash S, Irving M. Coengineering specificity, safety, and function into T cells for cancer immunotherapy. Immunol Rev 2023; 320:166-198. [PMID: 37548063 DOI: 10.1111/imr.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
Adoptive T-cell transfer (ACT) therapies, including of tumor infiltrating lymphocytes (TILs) and T cells gene-modified to express either a T cell receptor (TCR) or a chimeric antigen receptor (CAR), have demonstrated clinical efficacy for a proportion of patients and cancer-types. The field of ACT has been driven forward by the clinical success of CD19-CAR therapy against various advanced B-cell malignancies, including curative responses for some leukemia patients. However, relapse remains problematic, in particular for lymphoma. Moreover, for a variety of reasons, relative limited efficacy has been demonstrated for ACT of non-hematological solid tumors. Indeed, in addition to pre-infusion challenges including lymphocyte collection and manufacturing, ACT failure can be attributed to several biological processes post-transfer including, (i) inefficient tumor trafficking, infiltration, expansion and retention, (ii) chronic antigen exposure coupled with insufficient costimulation resulting in T-cell exhaustion, (iii) a range of barriers in the tumor microenvironment (TME) mediated by both tumor cells and suppressive immune infiltrate, (iv) tumor antigen heterogeneity and loss, or down-regulation of antigen presentation machinery, (v) gain of tumor intrinsic mechanisms of resistance such as to apoptosis, and (vi) various forms of toxicity and other adverse events in patients. Affinity-optimized TCRs can improve T-cell function and innovative CAR designs as well as gene-modification strategies can be used to coengineer specificity, safety, and function into T cells. Coengineering strategies can be designed not only to directly support the transferred T cells, but also to block suppressive barriers in the TME and harness endogenous innate and adaptive immunity. Here, we review a selection of the remarkable T-cell coengineering strategies, including of tools, receptors, and gene-cargo, that have been developed in recent years to augment tumor control by ACT, more and more of which are advancing to the clinic.
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Affiliation(s)
- Greta Maria Paola Giordano Attianese
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sarah Ash
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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5
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T. RR, Smith JC. Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors. Proteins 2022; 90:1645-1654. [DOI: 10.1002/prot.26343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/12/2022] [Accepted: 03/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Rajitha Rajeshwar T.
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
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6
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Baumgaertner P, Schmidt J, Costa-Nunes CM, Bordry N, Guillaume P, Luescher I, Speiser DE, Rufer N, Hebeisen M. CD8 T cell function and cross-reactivity explored by stepwise increased peptide-HLA versus TCR affinity. Front Immunol 2022; 13:973986. [PMID: 36032094 PMCID: PMC9399405 DOI: 10.3389/fimmu.2022.973986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/22/2022] [Indexed: 12/05/2022] Open
Abstract
Recruitment and activation of CD8 T cells occur through specific triggering of T cell receptor (TCR) by peptide-bound human leucocyte antigen (HLA) ligands. Within the generated trimeric TCR-peptide:HLA complex, the molecular binding affinities between peptide and HLA, and between TCR and peptide:HLA both impact T cell functional outcomes. However, how their individual and combined effects modulate immunogenicity and overall T cell responsiveness has not been investigated systematically. Here, we established two panels of human tumor peptide variants differing in their affinity to HLA. For precise characterization, we developed the “blue peptide assay”, an upgraded cell-based approach to measure the peptide:HLA affinity. These peptide variants were then used to investigate the cross-reactivity of tumor antigen-specific CD8 T cell clonotypes derived from blood of cancer patients after vaccination with either the native or an affinity-optimized Melan-A/MART-1 epitope, or isolated from tumor infiltrated lymph nodes (TILNs). Vaccines containing the native tumor epitope generated T cells with better functionality, and superior cross-reactivity against potential low affinity escape epitopes, as compared to T cells induced by vaccines containing an HLA affinity-optimized epitope. Comparatively, Melan-A/MART-1-specific TILN cells displayed functional and cross-reactive profiles that were heterogeneous and clonotype-dependent. Finally, we took advantage of a collection of T cells expressing affinity-optimized NY-ESO-1-specific TCRs to interrogate the individual and combined impact of peptide:HLA and TCR-pHLA affinities on overall CD8 T cell responses. We found profound and distinct effects of both biophysical parameters, with additive contributions and absence of hierarchical dominance. Altogether, the biological impact of peptide:HLA and TCR-pHLA affinities on T cell responses was carefully dissected in two antigenic systems, frequently targeted in human cancer immunotherapy. Our technology and stepwise comparison open new insights into the rational design and selection of vaccine-associated tumor-specific epitopes and highlight the functional and cross-reactivity profiles that endow T cells with best tumor control capacity.
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Affiliation(s)
- Petra Baumgaertner
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
- *Correspondence: Michael Hebeisen, ; Petra Baumgaertner,
| | - Julien Schmidt
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Carla-Marisa Costa-Nunes
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Natacha Bordry
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Immanuel Luescher
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Daniel E. Speiser
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
| | - Michael Hebeisen
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Epalinges, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne, Epalinges, Switzerland
- *Correspondence: Michael Hebeisen, ; Petra Baumgaertner,
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7
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Bhatt D, Kang B, Sawant D, Zheng L, Perez K, Huang Z, Sekirov L, Wolak D, Huang JY, Liu X, DeVoss J, Manzanillo PS, Pierce N, Zhang Z, Symons A, Ouyang W. STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets. J Exp Med 2021; 218:212026. [PMID: 33900375 PMCID: PMC8077174 DOI: 10.1084/jem.20201329] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/18/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8+ cells, CD4+ Th1 cells, and T reg cells. In addition, large amounts of paired TCRα/β sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti–PD-1 treatment in MC38 and B16F10 tumor models.
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Affiliation(s)
- Dev Bhatt
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Boxi Kang
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China
| | - Deepali Sawant
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Liangtao Zheng
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China
| | - Kristy Perez
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Zhiyu Huang
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Laura Sekirov
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Dan Wolak
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Julie Y Huang
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Xian Liu
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Jason DeVoss
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Paolo S Manzanillo
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Nathan Pierce
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Zemin Zhang
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China
| | - Antony Symons
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Wenjun Ouyang
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
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8
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Zhang H, Sun M, Wang J, Zeng B, Cao X, Han Y, Tan S, Gao GF. Identification of NY-ESO-1 157-165 Specific Murine T Cell Receptors With Distinct Recognition Pattern for Tumor Immunotherapy. Front Immunol 2021; 12:644520. [PMID: 33833762 PMCID: PMC8021954 DOI: 10.3389/fimmu.2021.644520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
New York esophageal squamous cell carcinoma 1 (NY-ESO-1) is a promising target for T-cell receptor-engineered T cell (TCR-T) therapy, and targeting the human leukocyte antigen (HLA)-A2 restricted NY-ESO-1157-165 epitope has yielded remarkable clinical benefits in the treatment of multiple advanced malignancies. Herein, we report the identification of two NY-ESO-1157-165 epitope-specific murine TCRs obtained from HLA-A*0201 transgenic mice. NY-ESO-1157-165 specific TCRs were isolated after vaccinating HLA-A2 transgenic mice with epitope peptides. HZ6 and HZ8 TCRs could specifically bind to NY-ESO-1157-165/HLA-A2 and were capable of cytokine secretion with engineered Jurkat T cells and primary T cells upon recognition with K562 target cells expressing the single-chain trimer (SCT) of NY-ESO-1157-165/HLA-A2. The reactivity profiles of the HZ6 and HZ8 TCRs were found to be distinct from one another when co-cultured with K562 target cells carrying alanine-substituted NY-ESO-1157-165 SCTs. The binding characterization revealed that the recognition pattern of the HZ6 TCR to NY-ESO-1157-165/HLA-A2 was substantially different from the widely used 1G4 TCR. These findings would broaden the understanding of immunogenicity of the NY-ESO-1157-165, and the two identified TCRs may serve as promising candidates for the future development of TCR-T therapy for tumors.
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Affiliation(s)
- Helin Zhang
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Meng Sun
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin Zeng
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xiaoqing Cao
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Han
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shuguang Tan
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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9
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Merkle PS, Trabjerg E, Hongjian S, Ferber M, Cuendet MA, Jørgensen TJD, Luescher I, Irving M, Zoete V, Michielin O, Rand KD. Probing the Conformational Dynamics of Affinity-Enhanced T Cell Receptor Variants upon Binding the Peptide-Bound Major Histocompatibility Complex by Hydrogen/Deuterium Exchange Mass Spectrometry. Biochemistry 2021; 60:859-872. [PMID: 33689297 DOI: 10.1021/acs.biochem.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of the T cell receptor (TCR) to its cognate, peptide antigen-loaded major histocompatibility complex (pMHC) is a key interaction for triggering T cell activation and ultimately elimination of the target cell. Despite the importance of this interaction for cellular immunity, a comprehensive molecular understanding of TCR specificity and affinity is lacking. We conducted hydrogen/deuterium exchange mass spectrometry (HDX-MS) analyses of individual affinity-enhanced TCR variants and clinically relevant pMHC class I molecules (HLA-A*0201/NY-ESO-1157-165) to investigate the causality between increased binding affinity and conformational dynamics in TCR-pMHC complexes. Differential HDX-MS analyses of TCR variants revealed that mutations for affinity enhancement in TCR CDRs altered the conformational response of TCR to pMHC ligation. Improved pMHC binding affinity was in general observed to correlate with greater differences in HDX upon pMHC binding in modified TCR CDR loops, thereby providing new insights into the TCR-pMHC interaction. Furthermore, a specific point mutation in the β-CDR3 loop of the NY-ESO-1 TCR associated with a substantial increase in binding affinity resulted in a substantial change in pMHC binding kinetics (i.e., very slow kon, revealed by the detection of EX1 HDX kinetics), thus providing experimental evidence for a slow induced-fit binding mode. We also examined the conformational impact of pMHC binding on an unrelated TRAV12-2 gene-encoded TCR directed against the immunodominant MART-126-35 cancer antigen restricted by HLA-A*0201. Our findings provide a molecular basis for the observed TRAV12-2 gene bias in natural CD8+ T cell-based immune responses against the MART-1 antigen, with potential implications for general ligand discrimination and TCR cross-reactivity processes.
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Affiliation(s)
- Patrick S Merkle
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esben Trabjerg
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Song Hongjian
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland.,Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Immanuel Luescher
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland.,Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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10
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Radiation induces dynamic changes to the T cell repertoire in renal cell carcinoma patients. Proc Natl Acad Sci U S A 2020; 117:23721-23729. [PMID: 32900949 PMCID: PMC7519245 DOI: 10.1073/pnas.2001933117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Clinical studies combining radiation and immunotherapy have shown promising response rates, strengthening efforts to sensitize tumors to immune-mediated attack. Thus, there is an ongoing surge in trials using preconditioning regimens with immunotherapy. Yet, due to the scarcity of resected tumors treated in situ with radiotherapy, there has been little investigation of radiation's sole contributions to local and systemic antitumor immunity in patients. Without this access, translational studies have been limited to evaluating circulating immune subsets and systemic remodeling of peripheral T cell receptor repertoires. This constraint has left gaps in how radiation impacts intratumoral responses and whether tumor-resident T cell clones are amplified following treatment. Therefore, to interrogate the immune impact of radiation on the tumor microenvironment and test the hypothesis that radiation initiates local and systemic expansion of tumor-resident clones, we analyzed renal cell carcinomas from patients treated with stereotactic body radiation therapy. Transcriptomic comparisons were evaluated by bulk RNA sequencing. T cell receptor sequencing monitored repertoires during treatment. Pathway analysis showed radiation-specific enrichment of immune-related processes, and T cell receptor sequencing revealed increased clonality in radiation-treated tumors. The frequency of identified, tumor-enriched clonotypes was tracked across serial blood samples. We observed increased abundance of tumor-enriched clonotypes at 2 wk postradiation compared with pretreatment levels; however, this expansion was not sustained, and levels contracted toward baseline by 4 wk posttreatment. Taken together, these results indicate robust intratumoral immune remodeling and a window of tumor-resident T cell expansion following radiation that may be leveraged for the rational design of combinatorial strategies.
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11
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Coles CH, Mulvaney RM, Malla S, Walker A, Smith KJ, Lloyd A, Lowe KL, McCully ML, Martinez Hague R, Aleksic M, Harper J, Paston SJ, Donnellan Z, Chester F, Wiederhold K, Robinson RA, Knox A, Stacey AR, Dukes J, Baston E, Griffin S, Jakobsen BK, Vuidepot A, Harper S. TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. THE JOURNAL OF IMMUNOLOGY 2020; 204:1943-1953. [PMID: 32102902 DOI: 10.4049/jimmunol.1900915] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022]
Abstract
The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1157-165-HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.
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Affiliation(s)
- Charlotte H Coles
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Rachel M Mulvaney
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sunir Malla
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Walker
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kathrine J Smith
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Angharad Lloyd
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kate L Lowe
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | | | | | - Milos Aleksic
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Jane Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Samantha J Paston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Zoe Donnellan
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Fiona Chester
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Katrin Wiederhold
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Ross A Robinson
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Knox
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrea R Stacey
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Joseph Dukes
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Emma Baston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sue Griffin
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Bent K Jakobsen
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Annelise Vuidepot
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Stephen Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
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12
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Gilfillan CB, Wang C, Mohsen MO, Rufer N, Hebeisen M, Allard M, Verdeil G, Irvine DJ, Bachmann MF, Speiser DE. Murine CD8 T-cell functional avidity is stable in vivo but not in vitro: Independence from homologous prime/boost time interval and antigen density. Eur J Immunol 2019; 50:505-514. [PMID: 31785153 PMCID: PMC7187562 DOI: 10.1002/eji.201948355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/17/2019] [Accepted: 11/27/2019] [Indexed: 01/13/2023]
Abstract
It is known that for achieving high affinity antibody responses, vaccines must be optimized for antigen dose/density, and the prime/boost interval should be at least 4 weeks. Similar knowledge is lacking for generating high avidity T‐cell responses. The functional avidity (FA) of T cells, describing responsiveness to peptide, is associated with the quality of effector function and the protective capacity in vivo. Despite its importance, the FA is rarely determined in T‐cell vaccination studies. We addressed the question whether different time intervals for short‐term homologous vaccinations impact the FA of CD8 T‐cell responses. Four‐week instead of 2‐week intervals between priming and boosting with potent subunit vaccines in C57BL/6 mice did not improve FA. Equally, similar FA was observed after vaccination with virus‐like particles displaying low versus high antigen densities. Interestingly, FA was stable in vivo but not in vitro, depending on the antigen dose and the time interval since T‐cell activation, as observed in murine monoclonal T cells. Our findings suggest dynamic in vivo modulation for equal FA. We conclude that low antigen density vaccines or a minimal 4‐week prime/boost interval are not crucial for the T‐cell's FA, in contrast to antibody responses.
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Affiliation(s)
| | - Chensu Wang
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Mona O Mohsen
- Inselspital, Universitaetsklinik RIA, Immunologie, Bern, Switzerland.,Jenner Institute, University of Oxford, Oxford, UK
| | - Nathalie Rufer
- Department of Oncology, University of Lausanne, Switzerland.,Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | | | | | | | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Martin F Bachmann
- Inselspital, Universitaetsklinik RIA, Immunologie, Bern, Switzerland.,Jenner Institute, University of Oxford, Oxford, UK
| | - Daniel E Speiser
- Department of Oncology, University of Lausanne, Switzerland.,Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
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13
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Hall CE, Koparde VN, Jameson-Lee M, Elnasseh AG, Scalora AF, Kobulnicky DJ, Serrano MG, Roberts CH, Buck GA, Neale MC, Nixon DE, Toor AA. Sequence homology between HLA-bound cytomegalovirus and human peptides: A potential trigger for alloreactivity. PLoS One 2017; 12:e0178763. [PMID: 28800601 PMCID: PMC5553991 DOI: 10.1371/journal.pone.0178763] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 05/18/2017] [Indexed: 11/18/2022] Open
Abstract
Human cytomegalovirus (hCMV) reactivation may often coincide with the development of graft-versus-host-disease (GVHD) in stem cell transplantation (SCT). Seventy seven SCT donor-recipient pairs (DRP) (HLA matched unrelated donor (MUD), n = 50; matched related donor (MRD), n = 27) underwent whole exome sequencing to identify single nucleotide polymorphisms (SNPs) generating alloreactive peptide libraries for each DRP (9-mer peptide-HLA complexes); Human CMV CROSS (Cross-Reactive Open Source Sequence) database was compiled from NCBI; HLA class I binding affinity for each DRPs HLA was calculated by NetMHCpan 2.8 and hCMV- derived 9-mers algorithmically compared to the alloreactive peptide-HLA complex libraries. Short consecutive (≥6) amino acid (AA) sequence homology matching hCMV to recipient peptides was considered for HLA-bound-peptide (IC50<500nM) cross reactivity. Of the 70,686 hCMV 9-mers contained within the hCMV CROSS database, an average of 29,658 matched the MRD DRP alloreactive peptides and 52,910 matched MUD DRP peptides (p<0.001). In silico analysis revealed multiple high affinity, immunogenic CMV-Human peptide matches (IC50<500 nM) expressed in GVHD-affected tissue-specific manner. hCMV+GVHD was found in 18 patients, 13 developing hCMV viremia before GVHD onset. Analysis of patients with GVHD identified potential cross reactive peptide expression within affected organs. We propose that hCMV peptide sequence homology with human alloreactive peptides may contribute to the pathophysiology of GVHD.
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Affiliation(s)
- Charles E. Hall
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Vishal N. Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Maximilian Jameson-Lee
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Abdelrhman G. Elnasseh
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Allison F. Scalora
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - David J. Kobulnicky
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Myrna G. Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Catherine H. Roberts
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Gregory A. Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael C. Neale
- Departments of Psychiatry and Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel E. Nixon
- Division of Infectious Diseases, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Amir A. Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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14
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Allard M, Couturaud B, Carretero-Iglesia L, Duong MN, Schmidt J, Monnot GC, Romero P, Speiser DE, Hebeisen M, Rufer N. TCR-ligand dissociation rate is a robust and stable biomarker of CD8+ T cell potency. JCI Insight 2017; 2:92570. [PMID: 28724801 DOI: 10.1172/jci.insight.92570] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022] Open
Abstract
Despite influencing many aspects of T cell biology, the kinetics of T cell receptor (TCR) binding to peptide-major histocompatibility molecules (pMHC) remain infrequently determined in patient monitoring or for adoptive T cell therapy. Using specifically designed reversible fluorescent pMHC multimeric complexes, we performed a comprehensive study of TCR-pMHC off-rates combined with various functional assays on large libraries of self/tumor- and virus-specific CD8+ T cell clones from melanoma patients and healthy donors. We demonstrate that monomeric TCR-pMHC dissociation rates accurately predict the extent of cytotoxicity, cytokine production, polyfunctionality, cell proliferation, activating/inhibitory receptor expression, and in vivo antitumor potency of naturally occurring antigen-specific CD8+ T cells. Our data also confirm the superior binding avidities of virus-specific T cells as compared with self/tumor-specific T cell clonotypes (n > 300). Importantly, the TCR-pMHC off-rate is a more stable and robust biomarker of CD8+ T cell potency than the frequently used functional assays/metrics that depend on the T cell's activation state, and therefore show major intra- and interexperimental variability. Taken together, our data show that the monomeric TCR-pMHC off-rate is highly useful for the ex vivo high-throughput functional assessment of antigen-specific CD8+ T cell responses and a strong candidate as a biomarker of T cell therapeutic efficacy.
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Affiliation(s)
- Mathilde Allard
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland
| | - Barbara Couturaud
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland
| | - Laura Carretero-Iglesia
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland
| | - Minh Ngoc Duong
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland
| | - Julien Schmidt
- Ludwig Cancer Research, University of Lausanne, Epalinges, Switzerland
| | | | - Pedro Romero
- Ludwig Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland.,Ludwig Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Michael Hebeisen
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital Center (CHUV) and University of Lausanne, Epalinges, Switzerland.,Ludwig Cancer Research, University of Lausanne, Epalinges, Switzerland
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15
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Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites. Biochemistry 2017; 56:3945-3961. [DOI: 10.1021/acs.biochem.7b00385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Patrick S. Merkle
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Song Hongjian
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Kirsten Scholten
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - George Coukos
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A. Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Department
of Physiology and Biophysics, Weill Cornell Medical College, 1300
York Avenue, New York, New
York 10065, United States
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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16
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Hebeisen M, Schmidt J, Guillaume P, Baumgaertner P, Speiser DE, Luescher I, Rufer N. Identification of Rare High-Avidity, Tumor-Reactive CD8+ T Cells by Monomeric TCR-Ligand Off-Rates Measurements on Living Cells. Cancer Res 2015; 75:1983-91. [PMID: 25808864 DOI: 10.1158/0008-5472.can-14-3516] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/20/2015] [Indexed: 11/16/2022]
Abstract
The avidity of the T-cell receptor (TCR) for antigenic peptides presented by the peptide-MHC (pMHC) on cells is a key parameter for cell-mediated immunity. Yet a fundamental feature of most tumor antigen-specific CD8(+) T cells is that this avidity is low. In this study, we addressed the need to identify and select tumor-specific CD8(+) T cells of highest avidity, which are of the greatest interest for adoptive cell therapy in patients with cancer. To identify these rare cells, we developed a peptide-MHC multimer technology, which uses reversible Ni(2+)-nitrilotriacetic acid histidine tags (NTAmers). NTAmers are highly stable but upon imidazole addition, they decay rapidly to pMHC monomers, allowing flow-cytometric-based measurements of monomeric TCR-pMHC dissociation rates of living CD8(+) T cells on a wide avidity spectrum. We documented strong correlations between NTAmer kinetic results and those obtained by surface plasmon resonance. Using NTAmers that were deficient for CD8 binding to pMHC, we found that CD8 itself stabilized the TCR-pMHC complex, prolonging the dissociation half-life several fold. Notably, our NTAmer technology accurately predicted the function of large panels of tumor-specific T cells that were isolated prospectively from patients with cancer. Overall, our results demonstrated that NTAmers are effective tools to isolate rare high-avidity cytotoxic T cells from patients for use in adoptive therapies for cancer treatment.
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Affiliation(s)
- Michael Hebeisen
- Department of Oncology, Lausanne University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland. TCMetrix Sàrl., Epalinges, Switzerland
| | - Philippe Guillaume
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland. TCMetrix Sàrl., Epalinges, Switzerland
| | - Petra Baumgaertner
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Lausanne University Hospital Center and University of Lausanne, Lausanne, Switzerland. Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Immanuel Luescher
- Department of Oncology, Lausanne University Hospital Center and University of Lausanne, Lausanne, Switzerland. Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland. TCMetrix Sàrl., Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, Lausanne University Hospital Center and University of Lausanne, Lausanne, Switzerland. Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland.
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17
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Clemens EB, Doherty PC, La Gruta NL, Turner SJ. Fixed expression of single influenza virus-specific TCR chains demonstrates the capacity for TCR α- and β-chain diversity in the face of peptide-MHC class I specificity. THE JOURNAL OF IMMUNOLOGY 2014; 194:898-910. [PMID: 25535284 DOI: 10.4049/jimmunol.1401792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The characteristics of the TCR repertoire expressed by epitope-specific CD8(+) T cells can be an important determinant of the quality of immune protection against virus infection. Most studies of epitope-specific TCR repertoires focus solely on an analysis of TCR β-chains, rather than the combined TCRαβ heterodimers that confer specificity. Hence, the importance of complementary α- and β-chain pairing in determining TCR specificity and T cell function is not well understood. Our earlier study of influenza-specific TCR repertoires in a C57BL/6J mouse model described a structural basis for preferred TCRαβ pairing that determined exquisite specificity for the D(b)PA224 epitope from influenza A virus. We have now extended this analysis using retrogenic mice engineered to express single TCR α- or β-chains specific for the D(b)NP366 or D(b)PA224 epitopes derived from influenza A virus. We found that particular TCRαβ combinations were selected for recognition of these epitopes following infection, indicating that pairing of certain α- and β-chain sequences is key for determining TCR specificity. Furthermore, we demonstrated that some TCRαβ heterodimers were preferentially expanded from the naive repertoire in response to virus infection, suggesting that appropriate αβ pairing confers optimal T cell responsiveness to Ag.
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Affiliation(s)
- E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
| | - Peter C Doherty
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
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18
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Combining next-generation sequencing and immune assays: a novel method for identification of antigen-specific T cells. PLoS One 2013; 8:e74231. [PMID: 24069285 PMCID: PMC3778005 DOI: 10.1371/journal.pone.0074231] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
In this study, we combined a novel sequencing method, which can identify individual clonotypes based on their unique T cell receptor (TCR) rearrangement, with existing immune assays to characterize antigen-specific T cell responses. We validated this approach using three types of assays routinely used to measure antigen-specific responses: pentamers which enable identification of T cells bearing specific TCRs, activation marker expression following antigen stimulation and antigen-induced proliferation to identify cytomegalovirus (CMV) specific clonotypes. In one individual, 8 clonotypes were identified using a pentamer reagent derived from the CMV pp65 protein. The same 8 clonotypes were also identified following sequencing of cells that upregulated an activation marker following incubation with an identical peptide derived from pp65. These 8 and an additional 8 clonotypes were identified using a more sensitive CFSE-based proliferation assay. We found clear sequence homology among some of the clonotypes identified, and the CDR3 region in one clonotype was identical to a previously published pp65-specific clonotype sequence. Many of these CMV-specific clonotypes were present at frequencies below 10(-5) which are undetectable using standard flow-cytometric methods. These studies suggest that an immune response is comprised of a diverse set of clones, many of which are present at very low frequencies. Thus, the combination of immune assays and sequencing depicts the richness and diversity of an immune response at a level that is not possible using standard immune assays alone. The methods articulated in this work provide an enhanced understanding of T cell-mediated immune responses at the clonal level.
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19
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Zoete V, Irving M, Ferber M, Cuendet MA, Michielin O. Structure-Based, Rational Design of T Cell Receptors. Front Immunol 2013; 4:268. [PMID: 24062738 PMCID: PMC3770923 DOI: 10.3389/fimmu.2013.00268] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157–165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, KD = ∼1 − 5 μM. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function, in line with the “half-life” model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.
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Affiliation(s)
- V Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics , Lausanne , Switzerland
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20
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Dudda JC, Salaun B, Ji Y, Palmer DC, Monnot GC, Merck E, Boudousquie C, Utzschneider DT, Escobar TM, Perret R, Muljo SA, Hebeisen M, Rufer N, Zehn D, Donda A, Restifo NP, Held W, Gattinoni L, Romero P. MicroRNA-155 is required for effector CD8+ T cell responses to virus infection and cancer. Immunity 2013; 38:742-53. [PMID: 23601686 PMCID: PMC3788592 DOI: 10.1016/j.immuni.2012.12.006] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 12/18/2012] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) regulate the function of several immune cells, but their role in promoting CD8(+) T cell immunity remains unknown. Here we report that miRNA-155 is required for CD8(+) T cell responses to both virus and cancer. In the absence of miRNA-155, accumulation of effector CD8(+) T cells was severely reduced during acute and chronic viral infections and control of virus replication was impaired. Similarly, Mir155(-/-) CD8(+) T cells were ineffective at controlling tumor growth, whereas miRNA-155 overexpression enhanced the antitumor response. miRNA-155 deficiency resulted in accumulation of suppressor of cytokine signaling-1 (SOCS-1) causing defective cytokine signaling through STAT5. Consistently, enforced expression of SOCS-1 in CD8(+) T cells phenocopied the miRNA-155 deficiency, whereas SOCS-1 silencing augmented tumor destruction. These findings identify miRNA-155 and its target SOCS-1 as key regulators of effector CD8(+) T cells that can be modulated to potentiate immunotherapies for infectious diseases and cancer.
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Affiliation(s)
- Jan C Dudda
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
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21
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Singh SK, Tummers B, Schumacher TN, Gomez R, Franken KLMC, Verdegaal EM, Laske K, Gouttefangeas C, Ottensmeier C, Welters MJP, Britten CM, van der Burg SH. The development of standard samples with a defined number of antigen-specific T cells to harmonize T cell assays: a proof-of-principle study. Cancer Immunol Immunother 2013; 62:489-501. [PMID: 22986454 PMCID: PMC3589624 DOI: 10.1007/s00262-012-1351-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/02/2012] [Indexed: 11/05/2022]
Abstract
The validation of assays that quantify antigen-specific T cell responses is critically dependent on cell samples that contain clearly defined measurable numbers of antigen-specific T cells. An important requirement is that such cell samples are handled and analyzed in a comparable fashion to peripheral blood mononuclear cells (PBMC). We performed a proof-of-principle study to show that retrovirally TCR-transduced T cells spiked at defined numbers in autologous PBMC can be used as standard samples for HLA/peptide multimer staining. NY-ESO-1157-165-specific, TCR-transduced CD8+ T cell batches were successfully generated from PBMC of several HLA-A*0201 healthy donors, purified by magnetic cell sorting on the basis of HLA tetramer (TM) staining and expanded with specific antigen in vitro. When subsequently spiked into autologous PBMC, the detection of these CD3+CD8+TM+ T cells was highly accurate with a mean accuracy of 91.6 %. The standard cells can be preserved for a substantial period of time in liquid nitrogen. Furthermore, TM staining of fresh and cryopreserved standard samples diluted at decreasing concentrations into autologous cryopreserved unspiked PBMC revealed that the spiked CD3+CD8+TM+ T cells could be accurately detected at all dilutions in a linear fashion with a goodness-of-fit of over 0.99 at a frequency of at least 0.02 % among the CD3+CD8+ T cell population. Notably, the CD3+CD8+TM+ cells of the standard samples were located exactly within the gates used to analyze patient samples and displayed a similar scatter pattern. The performance of the cryopreserved standard samples in the hands of 5 external investigators was good with an inter-laboratory variation of 32.9 % and the doubtless identification of one outlier.
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Affiliation(s)
- Satwinder Kaur Singh
- Department of Clinical Oncology, Leiden University Medical Center, Building 1, K1-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Bart Tummers
- Department of Clinical Oncology, Leiden University Medical Center, Building 1, K1-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Ton N. Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Raquel Gomez
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kees L. M. C. Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Els M. Verdegaal
- Department of Clinical Oncology, Leiden University Medical Center, Building 1, K1-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Karoline Laske
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | | | | | - Marij J. P. Welters
- Department of Clinical Oncology, Leiden University Medical Center, Building 1, K1-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Cedrik M. Britten
- Department of the Translational Oncology, University Medical Center of the Johannes-Gutenberg-University, Mainz, Germany
| | - Sjoerd H. van der Burg
- Department of Clinical Oncology, Leiden University Medical Center, Building 1, K1-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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22
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Ferber M, Zoete V, Michielin O. T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions. PLoS One 2012; 7:e51943. [PMID: 23251658 PMCID: PMC3522592 DOI: 10.1371/journal.pone.0051943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/08/2012] [Indexed: 11/19/2022] Open
Abstract
Crystallographic data about T-Cell Receptor - peptide - major histocompatibility complex class I (TCRpMHC) interaction have revealed extremely diverse TCR binding modes triggering antigen recognition. Understanding the molecular basis that governs TCR orientation over pMHC is still a considerable challenge. We present a simplified rigid approach applied on all non-redundant TCRpMHC crystal structures available. The CHARMM force field in combination with the FACTS implicit solvation model is used to study the role of long-distance interactions between the TCR and pMHC. We demonstrate that the sum of the coulomb interactions and the electrostatic solvation energies is sufficient to identify two orientations corresponding to energetic minima at 0° and 180° from the native orientation. Interestingly, these results are shown to be robust upon small structural variations of the TCR such as changes induced by Molecular Dynamics simulations, suggesting that shape complementarity is not required to obtain a reliable signal. Accurate energy minima are also identified by confronting unbound TCR crystal structures to pMHC. Furthermore, we decompose the electrostatic energy into residue contributions to estimate their role in the overall orientation. Results show that most of the driving force leading to the formation of the complex is defined by CDR1,2/MHC interactions. This long-distance contribution appears to be independent from the binding process itself, since it is reliably identified without considering neither short-range energy terms nor CDR induced fit upon binding. Ultimately, we present an attempt to predict the TCR/pMHC binding mode for a TCR structure obtained by homology modeling. The simplicity of the approach and the absence of any fitted parameters make it also easily applicable to other types of macromolecular protein complexes.
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Affiliation(s)
- Mathias Ferber
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail: (VZ); (OM)
| | - Olivier Michielin
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail: (VZ); (OM)
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23
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Irving M, Zoete V, Hebeisen M, Schmid D, Baumgartner P, Guillaume P, Romero P, Speiser D, Luescher I, Rufer N, Michielin O. Interplay between T cell receptor binding kinetics and the level of cognate peptide presented by major histocompatibility complexes governs CD8+ T cell responsiveness. J Biol Chem 2012; 287:23068-78. [PMID: 22549784 DOI: 10.1074/jbc.m112.357673] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Through a rational design approach, we generated a panel of HLA-A*0201/NY-ESO-1(157-165)-specific T cell receptors (TCR) with increasing affinities of up to 150-fold from the wild-type TCR. Using these TCR variants which extend just beyond the natural affinity range, along with an extreme supraphysiologic one having 1400-fold enhanced affinity, and a low-binding one, we sought to determine the effect of TCR binding properties along with cognate peptide concentration on CD8(+) T cell responsiveness. Major histocompatibility complexes (MHC) expressed on the surface of various antigen presenting cells were peptide-pulsed and used to stimulate human CD8(+) T cells expressing the different TCR via lentiviral transduction. At intermediate peptide concentration we measured maximum cytokine/chemokine secretion, cytotoxicity, and Ca(2+) flux for CD8(+) T cells expressing TCR within a dissociation constant (K(D)) range of ∼1-5 μM. Under these same conditions there was a gradual attenuation in activity for supraphysiologic affinity TCR with K(D) < ∼1 μM, irrespective of CD8 co-engagement and of half-life (t(1/2) = ln 2/k(off)) values. With increased peptide concentration, however, the activity levels of CD8(+) T cells expressing supraphysiologic affinity TCR were gradually restored. Together our data support the productive hit rate model of T cell activation arguing that it is not the absolute number of TCR/pMHC complexes formed at equilibrium, but rather their productive turnover, that controls levels of biological activity. Our findings have important implications for various immunotherapies under development such as adoptive cell transfer of TCR-engineered CD8(+) T cells, as well as for peptide vaccination strategies.
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Affiliation(s)
- Melita Irving
- Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Lausanne, Switzerland
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24
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Ochsenreither S, Fusi A, Geikowski A, Stather D, Busse A, Stroux A, Letsch A, Keilholz U. Wilms' tumor protein 1 (WT1) peptide vaccination in AML patients: predominant TCR CDR3β sequence associated with remission in one patient is detectable in other vaccinated patients. Cancer Immunol Immunother 2012; 61:313-22. [PMID: 21898091 PMCID: PMC11029123 DOI: 10.1007/s00262-011-1099-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 08/13/2011] [Indexed: 12/01/2022]
Abstract
BACKGROUND Clinically effective T-cell responses can be elicited by single peptide vaccination with Wilms' tumor 1 (WT1) epitope 126-134 in patients with acute myeloid leukemia (AML). We recently showed that a predominant T-cell receptor (TCR) β chain was associated with vaccine-induced complete remission in an AML patient (patient 1). In this study, we address the question of whether this predominant clone or the accompanying Vβ11 restriction could be found in other AML patients vaccinated with the same WT1 peptide. MATERIALS AND METHODS For assessment of Vβ usage, cytotoxic T lymphocytes (CTLs) from four vaccinated patients were divided into specific and non-specific by epitope-specific enrichment. Vβ families were quantified in both fractions using reverse transcribed quantitative PCR. Vβ11-positive 'complementary determining region 3' (CDR3) sequences were amplified from these samples, from bone marrow samples of 17 other vaccination patients, and from peripheral blood of six healthy controls, cloned and sequenced. RESULTS We observed a clear bias towards Vβ11 usage of the WT1-specific CTL populations in all four patients. The predominant CDR3β amino acid (AA) sequence of patient 1 was detected in two other patients. CDR3β loops with closely related AA sequences were only found in patient 1. There were no CDR3β AA sequences with side chains of identical chemical properties detected in any patient. CONCLUSION We provide the first data addressing TCR Vβ chain usage in WT1-specific T-cell populations after HLA A*0201-restricted single peptide vaccination. We demonstrate both shared Vβ restriction and the sharing of a TCR β transcript with proven clinical impact in one patient.
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MESH Headings
- Acute Disease
- Adult
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Cancer Vaccines/administration & dosage
- Cancer Vaccines/immunology
- Clone Cells/immunology
- Clone Cells/metabolism
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Epitopes/immunology
- Female
- HLA-A2 Antigen/immunology
- Humans
- Leukemia, Myeloid/immunology
- Leukemia, Myeloid/therapy
- Male
- Middle Aged
- Molecular Sequence Data
- Peptide Fragments/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Remission Induction
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Vaccination
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/immunology
- WT1 Proteins/chemistry
- WT1 Proteins/immunology
- Young Adult
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Affiliation(s)
- Sebastian Ochsenreither
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Alberto Fusi
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anne Geikowski
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - David Stather
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Antonia Busse
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Andrea Stroux
- Institute for Biometry and Clinical Epidemiology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Anne Letsch
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
| | - Ulrich Keilholz
- Department of Hematology and Oncology, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
- Department of Medicine III, Charité Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany
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25
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Abstract
Historically, sharing T cell receptors (TCRs) between individuals has been speculated to be impossible, considering the dramatic discrepancy between the potential enormity of the TCR repertoire and the limited number of T cells generated in each individual. However, public T cell response, in which multiple individuals share identical TCRs in responding to a same antigenic epitope, has been extensively observed in a variety of immune responses across many species. Public T cell responses enable individuals within a population to generate similar antigen-specific TCRs against certain ubiquitous pathogens, leading to favorable biological outcomes. However, the relatively concentrated feature of TCR repertoire may limit T cell response in a population to some other pathogens. It could be a great benefit for human health if public T cell responses can be manipulated. Therefore, the mechanistic insight of public TCR generation is important to know. Recently, high-throughput DNA sequencing has revolutionized the study of immune receptor repertoires, which allows a much better understanding of the factors that determine the overlap of TCR repertoire among individuals. Here, we summarize the current knowledge on public T-cell response and discuss future challenges in this field.
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Affiliation(s)
- Hanjie Li
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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26
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Goodyear OC, Pearce H, Pratt G, Moss P. Dominant responses with conservation of T-cell receptor usage in the CD8+ T-cell recognition of a cancer testis antigen peptide presented through HLA-Cw7 in patients with multiple myeloma. Cancer Immunol Immunother 2011; 60:1751-61. [PMID: 21785964 PMCID: PMC11028534 DOI: 10.1007/s00262-011-1070-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 07/04/2011] [Indexed: 10/18/2022]
Abstract
Cancer testis antigens exhibit physiological expression within germ cells and are frequently expressed in malignant tissue. Interestingly, immunological tolerance to cancer testis proteins does not appear to be established, and the expression of CTAg proteins within malignant cells can therefore lead to induction of cellular and humoral immunity. A considerable body of evidence now indicates that CD8-specific immunity plays an important role in the control of cancer cell growth, and a number of vaccine studies are in progress to boost CTAg-specific cellular immune responses. We have previously identified CTAg-specific immune responses in patients with multiple myeloma and reported that recognition of the MAGE-A1(289-298) peptide, which is described as being restricted by HLA-B*0702, was the most frequent response seen with our peptide panel. Here, we studied seven CD8+ T-cell clones specific for this peptide which were isolated from three patients with myeloma at several time-points. The affinity of peptide recognition was high with 50% maximal interferon-γ production observed at a peptide concentration of 10(-10) M and variation of only one order of magnitude between the affinities of the clones. Importantly, all the clones were able to recognise and kill multiple myeloma cell lines. Interestingly, one patient did not express HLA-B*0702, but three clones from this patient recognised the MAGE-A1(289-298) peptide on a lymphoblastoid cell line (LCLs) expressing HLA-Cw7, and we now show evidence that the MAGE-A1(289-298) peptide is expressed and recognised through Cw7. The T-cell receptor gene usage was determined in five clones and showed conserved features in both the α and the β chain genes indicating correlation between T-cell receptor usage and peptide specificity of cancer testis antigen-specific T-cell clones.
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Affiliation(s)
- Oliver C Goodyear
- School of Cancer Studies, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK.
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27
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Connelley TK, MacHugh ND, Pelle R, Weir W, Morrison WI. Escape from CD8+ T cell response by natural variants of an immunodominant epitope from Theileria parva is predominantly due to loss of TCR recognition. THE JOURNAL OF IMMUNOLOGY 2011; 187:5910-20. [PMID: 22058411 DOI: 10.4049/jimmunol.1102009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polymorphism of immunodominant CD8(+) T cell epitopes can facilitate escape from immune recognition of pathogens, leading to strain-specific immunity. In this study, we examined the TCR β-chain (TRB) diversity of the CD8(+) T cell responses of cattle against two immunodominant epitopes from Theileria parva (Tp1(214-224) and Tp2(49-59)) and investigated the role of TCR recognition and MHC binding in determining differential recognition of a series of natural variants of the highly polymorphic Tp2(49-59) epitope by CD8(+) T cell clones of defined TRB genotype. Our results show that both Tp1(214-224) and Tp2(49-59) elicited CD8(+) T cell responses using diverse TRB repertoires that showed a high level of stability following repeated pathogenic challenge over a 3-y period. Analysis of single-alanine substituted versions of the Tp2(49-59) peptide demonstrated that Tp2(49-59)-specific clonotypes had a broad range of fine specificities for the epitope. Despite this diversity, all natural variants exhibited partial or total escape from immune recognition, which was predominantly due to abrogation of TCR recognition, with mutation resulting in loss of the lysine residue at P8, playing a particularly dominant role in escape. The levels of heterozygosity in individual Tp2(49-59) residues correlated closely with loss of immune recognition, suggesting that immune selection has contributed to epitope polymorphism.
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Affiliation(s)
- Timothy K Connelley
- The Roslin Institute and The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, Scotland, United Kingdom.
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28
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Leimgruber A, Ferber M, Irving M, Hussain-Kahn H, Wieckowski S, Derré L, Rufer N, Zoete V, Michielin O. TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires. PLoS One 2011; 6:e26301. [PMID: 22053188 PMCID: PMC3203878 DOI: 10.1371/journal.pone.0026301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.
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Affiliation(s)
- Antoine Leimgruber
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
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29
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Miles JJ, Douek DC, Price DA. Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol Cell Biol 2011; 89:375-87. [PMID: 21301479 DOI: 10.1038/icb.2010.139] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The naïve T-cell repertoire is vast, containing millions of unique T-cell receptor (TCR) structures. Faced with such diversity, the mobilization of TCR structures from this enormous pool was once thought to be a stochastic, even chaotic, process. However, steady and systematic dissection over the last 20 years has revealed that this is not the case. Instead, the TCR repertoire deployed against individual antigens is routinely ordered and biased. Often, identical and near-identical TCR repertoires can be observed across different individuals, suggesting that the system encompasses an element of predictability. This review provides a catalog of αβ TCR bias by disease and by species, and discusses the mechanisms that govern this inherent and widespread phenomenon.
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Affiliation(s)
- John J Miles
- T Cell Modulation Laboratory, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, UK.
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30
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Abstract
For the last two decades the immunotherapy of patients with solid and hematopoietic tumors has met with variable success. We have reviewed the field of tumor vaccines to examine what has worked and what has not, why this has been the case, how the anti-tumor responses were examined, and how we can make tumor immunity successful for the majority of individuals rather than for the exceptional patients who currently show successful immune responses against their tumors.
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Affiliation(s)
- Jan Joseph Melenhorst
- Stem Cell Allogeneic Transplant Section, Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Profile of a serial killer: cellular and molecular approaches to study individual cytotoxic T-cells following therapeutic vaccination. J Biomed Biotechnol 2010; 2011:452606. [PMID: 21113290 PMCID: PMC2989374 DOI: 10.1155/2011/452606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 09/29/2010] [Indexed: 12/28/2022] Open
Abstract
T-cell vaccination may prevent or treat cancer and infectious diseases, but further progress is required to increase clinical efficacy. Step-by-step improvements of T-cell vaccination in phase I/II clinical studies combined with very detailed analysis of T-cell responses at the single cell level are the strategy of choice for the identification of the most promising vaccine candidates for testing in subsequent large-scale phase III clinical trials. Major aims are to fully identify the most efficient T-cells in anticancer therapy, to characterize their TCRs, and to pinpoint the mechanisms of T-cell recruitment and function in well-defined clinical situations. Here we discuss novel strategies for the assessment of human T-cell responses, revealing in part unprecedented insight into T-cell biology and novel structural principles that govern TCR-pMHC recognition. Together, the described approaches advance our knowledge of T-cell mediated-protection from human diseases.
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32
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Targeting B cell leukemia with highly specific allogeneic T cells with a public recognition motif. Leukemia 2010; 24:1901-9. [DOI: 10.1038/leu.2010.186] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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33
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Palermo B, Del Bello D, Sottini A, Serana F, Ghidini C, Gualtieri N, Ferraresi V, Catricalà C, Belardelli F, Proietti E, Natali PG, Imberti L, Nisticò P. Dacarbazine Treatment before Peptide Vaccination Enlarges T-Cell Repertoire Diversity of Melan-A–Specific, Tumor-Reactive CTL in Melanoma Patients. Cancer Res 2010; 70:7084-92. [DOI: 10.1158/0008-5472.can-10-1326] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Schmid DA, Irving MB, Posevitz V, Hebeisen M, Posevitz-Fejfar A, Sarria JCF, Gomez-Eerland R, Thome M, Schumacher TNM, Romero P, Speiser DE, Zoete V, Michielin O, Rufer N. Evidence for a TCR affinity threshold delimiting maximal CD8 T cell function. THE JOURNAL OF IMMUNOLOGY 2010; 184:4936-46. [PMID: 20351194 DOI: 10.4049/jimmunol.1000173] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Protective adaptive immune responses rely on TCR-mediated recognition of Ag-derived peptides presented by self-MHC molecules. However, self-Ag (tumor)-specific TCRs are often of too low affinity to achieve best functionality. To precisely assess the relationship between TCR-peptide-MHC binding parameters and T cell function, we tested a panel of sequence-optimized HLA-A(*)0201/NY-ESO-1(157-165)-specific TCR variants with affinities lying within physiological boundaries to preserve antigenic specificity and avoid cross-reactivity, as well as two outliers (i.e., a very high- and a low-affinity TCR). Primary human CD8 T cells transduced with these TCRs demonstrated robust correlations between binding measurements of TCR affinity and avidity and the biological response of the T cells, such as TCR cell-surface clustering, intracellular signaling, proliferation, and target cell lysis. Strikingly, above a defined TCR-peptide-MHC affinity threshold (K(D) < approximately 5 muM), T cell function could not be further enhanced, revealing a plateau of maximal T cell function, compatible with the notion that multiple TCRs with slightly different affinities participate equally (codominantly) in immune responses. We propose that rational design of improved self-specific TCRs may not need to be optimized beyond a given affinity threshold to achieve both optimal T cell function and avoidance of the unpredictable risk of cross-reactivity.
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Affiliation(s)
- Daphné A Schmid
- Multidisciplinary Oncology Center, Lausanne University Hospital, Switzerland
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35
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Wieckowski S, Baumgaertner P, Corthesy P, Voelter V, Romero P, Speiser DE, Rufer N. Fine structural variations of alphabetaTCRs selected by vaccination with natural versus altered self-antigen in melanoma patients. THE JOURNAL OF IMMUNOLOGY 2009; 183:5397-406. [PMID: 19786555 DOI: 10.4049/jimmunol.0901460] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Immunotherapy of cancer is often performed with altered "analog" peptide Ags optimized for HLA class I binding, resulting in enhanced immunogenicity, but the induced T cell responses require further evaluation. Recently, we demonstrated fine specificity differences and enhanced recognition of naturally presented Ag by T cells after vaccination with natural Melan-A/MART-1 peptide, as compared with analog peptide. In this study, we compared the TCR primary structures of 1489 HLA-A*0201/Melan-A(26-35)-specific CD8 T cells derived from both cohorts of patients. Although a strong preference for TRAV12-2 segment usage was present in nearly all patients, usage of particular TRAJ gene segments and CDR3alpha composition differed slightly after vaccination with natural vs analog peptide. Moreover, TCR beta-chain repertoires were broader after natural than analog peptide vaccination. In all patients, we observed a marked conservation of the CDR3beta amino acid composition with recurrent sequences centered on a glycyl-leucyl/valyl/alanyl-glycyl motif. In contrast to viral-specific TCR repertoires, such "public" motifs were primarily expressed by nondominant T cell clonotypes, which contrasted with "private" CDR3beta signatures frequently found in T cell clonotypes that dominated repertoires of individual patients. Interestingly, no differences in functional avidity were observed between public and private T cell clonotypes. Collectively, our data indicate that T cell repertoires generated against natural or analog Melan-A peptide exhibited slightly distinct but otherwise overlapping and structurally conserved TCR features, suggesting that the differences in binding affinity/avidity of TCRs toward pMHC observed in the two cohorts of patients are caused by subtle structural TCR variations.
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Affiliation(s)
- Sébastien Wieckowski
- Division of Experimental Oncology, Multidisciplinary Oncology Center, Lausanne University Hospital, Lausanne, Switzerland
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Rational development of high-affinity T-cell receptor-like antibodies. Proc Natl Acad Sci U S A 2009; 106:5784-8. [PMID: 19307587 DOI: 10.1073/pnas.0901425106] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
T-cell interaction with a target cell is a key event in the adaptive immune response and primarily driven by T-cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes. TCR avidity for a given pMHC is determined by number of MHC molecules, availability of coreceptors, and TCR affinity for MHC or peptide, respectively, with peptide recognition being the most important factor to confer target specificity. Here we present high-resolution crystal structures of 2 Fab antibodies in complex with the immunodominant NY-ESO-1(157-165) peptide analogue (SLLMWITQV) presented by HLA-A*0201 and compare them with a TCR recognizing the same pMHC. Binding to the central methionine-tryptophan peptide motif and orientation of binding were almost identical for Fabs and TCR. As the MW "peg" dominates the contacts between Fab and peptide, we estimated the contributions of individual amino acids between the Fab and peptide to provide the rational basis for a peptide-focused second-generation, high-affinity antibody library. The final Fab candidate achieved better peptide binding by 2 light-chain mutations, giving a 20-fold affinity improvement to 2-4 nM, exceeding the affinity of the TCR by 1,000-fold. The high-affinity Fab when grafted as recombinant TCR on T cells conferred specific killing of HLA-A*0201/NY-ESO-1(157-165) target cells. In summary, we prove that affinity maturation of antibodies mimicking a TCR is possible and provide a strategy for engineering high-affinity antibodies that can be used in targeting specific pMHC complexes for diagnostic and therapeutic purposes.
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