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Stephens HM, Kirkpatrick E, Mallis RJ, Reinherz EL, Lang MJ. Characterizing Biophysical Parameters of Single TCR-pMHC Interactions Using Optical Tweezers. Methods Mol Biol 2023; 2654:375-392. [PMID: 37106195 DOI: 10.1007/978-1-0716-3135-5_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
αβ T cells are mechanosensors that leverage bioforces during immune surveillance for highly sensitive and specific antigen discrimination. Single-molecule studies are used to profile the initial TCRαβ-pMHC binding event, and various biophysical parameters can be identified. Isolating purified TCRαβ and pMHC molecules on a coverslip allows for direct measurements of the kinetics and conformational changes in the system and removes cellular components along the load pathway that may interfere with or mask subtle changes. Optical tweezers provide high resolution position and force information that map the bonding profile, including catch bond, and the ability to measure distinct conformational changes driven by forces. The present method describes the single-molecule optical tweezers assay setup, considerations, and execution. This model can be used for various TCR-pMHC pairs or expanded to measure a wide variety of receptor-ligand interactions operative in multiple biological systems.
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Affiliation(s)
- Hannah M Stephens
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Evan Kirkpatrick
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Robert J Mallis
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Dermatology, Harvard Medical School, Boston, MA, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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Pettmann J, Awada L, Różycki B, Huhn A, Faour S, Kutuzov M, Limozin L, Weikl TR, van der Merwe PA, Robert P, Dushek O. Mechanical forces impair antigen discrimination by reducing differences in T-cell receptor/peptide-MHC off-rates. EMBO J 2022; 42:e111841. [PMID: 36484367 PMCID: PMC10068313 DOI: 10.15252/embj.2022111841] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
T cells use their T-cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains debated. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity TCR/pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds). This was confirmed by molecular dynamics simulations. Consistent with these findings, we show that the best-characterized catch bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination, and we suggest a role for the adhesion receptors CD2 and LFA-1 in force-shielding the TCR/pMHC interaction.
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Affiliation(s)
- Johannes Pettmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lama Awada
- Laboratoire Adhesion et Inflammation, Aix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333, Marseille, France
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Huhn
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sara Faour
- Laboratoire Adhesion et Inflammation, Aix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333, Marseille, France
| | - Mikhail Kutuzov
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Laurent Limozin
- Laboratoire Adhesion et Inflammation, Aix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333, Marseille, France
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | | | - Philippe Robert
- Laboratoire Adhesion et Inflammation, Aix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333, Marseille, France.,Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Zhang W, Zhang Q, Zhu C, Shi Z, Shao C, Chen Y, Wang N, Jiang Y, Liang Q, Wang K. The intrarenal landscape of T cell receptor repertoire in clear cell renal cell cancer. J Transl Med 2022; 20:558. [PMID: 36463235 PMCID: PMC9719196 DOI: 10.1186/s12967-022-03771-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/13/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Clear cell renal cell cancer (ccRCC) is accompanied by T-cell infiltration. In this study, we sought to determine the difference in T-cell infiltration and the T-cell receptor (TCR) immune repertoire between ccRCC and peritumour tissue. METHODS T-cell infiltration was examined using immunohistochemistry (IHC) and haematoxylin and eosin (HE) staining. The chi-squared test and Pearson correlation analysis were applied to evaluate the relationship between clinical traits and CD3, CD4, and CD8 expression. Immune repertoire sequencing (IR-Seq) was used to describe the profile of the TCR repertoire. RESULTS The adjacent tissue showed increased expression of CD3, CD4 and CD8 compared with ccRCC tissue (PCD3 = 0.033; PCD4 = 0.014; PCD8 = 0.004). Indicated CD3+ T-cell density in ccRCC tissue was positively correlated with that in peritumour tissue (P = 0.010, r = 0.514), which implied the T cells in peritumour tissue directly infect the number of cells infiltrating in ccRCC tissue. Moreover, there was a positive correlation between Vimentin expression and indicated positive T-cell marker in ccRCC tissue (PCD3 = 0.035; PCD4 = 0.020; PCD8 = 0.027). Advanced stage revealed less CD4+ T-cell infiltration in ccRCC tissue (PCD4 = 0.023). The results from IR-Seq revealed an obvious increase in VJ and VDJ segment usage, as well as higher complementarity-determining region 3 (CDR3) amino acid (aa) clonotypes in ccRCC. The matched antigen recognized by the TCR of ccRCC may be potential targets. CONCLUSIONS The current study collectively demonstrates diminished T-cell infiltration and increased CDR3 aa diversity in ccRCC, which may be associated with immunotherapeutic targets for ccRCC patients.
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Affiliation(s)
- Wei Zhang
- Department of Pathology, The 971 Hospital of People’s Liberation Army Navy, Qingdao, China
| | - Qian Zhang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chao Zhu
- grid.411525.60000 0004 0369 1599Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhiyuan Shi
- grid.12955.3a0000 0001 2264 7233Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chen Shao
- grid.12955.3a0000 0001 2264 7233Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yujie Chen
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Nan Wang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yanxia Jiang
- grid.412521.10000 0004 1769 1119Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qing Liang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Kejia Wang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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Rosati E, Rios Martini G, Pogorelyy MV, Minervina AA, Degenhardt F, Wendorff M, Sari S, Mayr G, Fazio A, Dowds CM, Hauser C, Tran F, von Schönfels W, Pochhammer J, Salnikova MA, Jaeckel C, Gigla JB, Sabet SS, Hübenthal M, Schiminsky E, Schreiber S, Rosenstiel PC, Scheffold A, Thomas PG, Lieb W, Bokemeyer B, Witte M, Aden K, Hendricks A, Schafmayer C, Egberts JH, Mamedov IZ, Bacher P, Franke A. A novel unconventional T cell population enriched in Crohn's disease. Gut 2022; 71:2194-2204. [PMID: 35264446 PMCID: PMC9554086 DOI: 10.1136/gutjnl-2021-325373] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE One of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls. DESIGN We performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq. RESULTS We identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn's disease (CD) and particularly expanded in the CD8+ T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs. CONCLUSIONS We identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany .,Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriela Rios Martini
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anastasia A Minervina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Soner Sari
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Christel Marie Dowds
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Charlotte Hauser
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Witigo von Schönfels
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Julius Pochhammer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Maria A Salnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Charlot Jaeckel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Johannes Boy Gigla
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Esther Schiminsky
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank POPGEN, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bernd Bokemeyer
- Interdisciplinary Crohn Colitis Centre Minden, Minden, Germany
| | - Maria Witte
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Alexander Hendricks
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany,Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany,Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Jan-Hendrick Egberts
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,CEITEC, Masaryk University, Brno, Czech Republic,Dmitry Rogachev National Research Center of Pediatric Hematology, Moscow, Russian Federation,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russian Federation
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
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KRAS G12V特异性T细胞受体治疗恶性肿瘤的临床前研究. Beijing Da Xue Xue Bao Yi Xue Ban 2022; 54. [PMID: 36241231 DOI: 10.19723/j.issn.1671-167X.2022.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE KRAS gene is one of the most common mutations of proto-oncogenes in human tumors, G12V is one of the most common mutation types for KRAS. It's challenging to chemically acquire the targeted drug for this mutation. Recent studies reported that this mutation peptides can form a neoepitope for T cell recognition. Our study aims to clone the T cell receptor (TCR) which specifically recognizes the neoepitope for KRAS G12V mutation and constructs TCR engineered T cells (TCR-T), and to investigate if TCR-Ts have strong antitumor response ability. METHODS In this study, tumor infiltrating lymphocytes were obtained from one colorectal cancer patient carrying KRAS G12V mutation. Tumor-reactive TCR was obtained by single-cell RT-5' rapid-amplification of cDNA ends PCR analysis and introduced into peripheral blood lymphocytes to generate TCR-Ts. RESULTS We obtained a high-affinity TCR sequence that specifically recognized the HLA-A*11:01-restricted KRAS G12V8-16 epitope: KVA11-01. KVA11-01 TCR-T could significantly kill various tumor cells such as PANC-1, SW480 and HeLa (overexpressing HLA-A*11:01 and KRAS G12V), and secreting high levels of interferon-γ (IFN-γ). Non-specific killing experiments suggested KVA11-01 specifically recognized tumor cells expressing both mutant KRAS G12V and HLA-A*11:01. In vivo assay, tumor inhibition experiments demonstrated that infusion of approximately 1E7 KVA11-01 TCR-T could significantly inhibit the growth of subcuta-neously transplanted tumors of PANC-1 and HeLa (overexpressing HLA-A*11:01 and KRAS G12V) cells in nude mice. No destruction of the morphologies of the liver, spleen and brain were observed. We also found that KVA11-01 TCR-T could significantly infiltrate into tumor tissue and had a better homing ability. CONCLUSION KVA11-01 TCR-T cells can effectively target a variety of malignant tumor cells carrying KRAS G12V mutation through in vitro and in vivo assay. KVA11-01 TCR-T cells have excellent biological activity, high specificity of target antigen and homing ability into solid tumor tissue. KVA11-01 TCR-T is expected to be an effective treatment for patients with KRAS G12V mutant solid malignancies.
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Lee B, Namkoong H, Yang Y, Huang H, Heller D, Szot GL, Davis MM, Husain SZ, Pandol SJ, Bellin MD, Habtezion A. Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis. Gut 2022; 71:1831-1842. [PMID: 34702715 PMCID: PMC9105403 DOI: 10.1136/gutjnl-2021-324546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Chronic pancreatitis (CP) is a potentially fatal disease of the exocrine pancreas, with no specific or effective approved therapies. Due to difficulty in accessing pancreas tissues, little is known about local immune responses or pathogenesis in human CP. We sought to characterise pancreatic immune responses using tissues derived from patients with different aetiologies of CP and non-CP organ donors in order to identify key signalling molecules associated with human CP. DESIGN We performed single-cell level cellular indexing of transcriptomes and epitopes by sequencing and T-cell receptor (TCR) sequencing of pancreatic immune cells isolated from organ donors, hereditary and idiopathic patients with CP who underwent total pancreatectomy. We validated gene expression data by performing flow cytometry and functional assays in a second patient with CP cohort. RESULTS Deep single-cell sequencing revealed distinct immune characteristics and significantly enriched CCR6+ CD4+ T cells in hereditary compared with idiopathic CP. In hereditary CP, a reduction in T-cell clonality was observed due to the increased CD4+ T (Th) cells that replaced tissue-resident CD8+ T cells. Shared TCR clonotype analysis among T-cell lineages also unveiled unique interactions between CCR6+ Th and Th1 subsets, and TCR clustering analysis showed unique common antigen binding motifs in hereditary CP. In addition, we observed a significant upregulation of the CCR6 ligand (CCL20) expression among monocytes in hereditary CP as compared with those in idiopathic CP. The functional significance of CCR6 expression in CD4+ T cells was confirmed by flow cytometry and chemotaxis assay. CONCLUSION Single-cell sequencing with pancreatic immune cells in human CP highlights pancreas-specific immune crosstalk through the CCR6-CCL20 axis, a signalling pathway that might be leveraged as a potential future target in human hereditary CP.
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Affiliation(s)
- Bomi Lee
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, Stanford University, Stanford, California, USA .,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, USA
| | - Hong Namkoong
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, Stanford University, Stanford, California, USA
| | - Yan Yang
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, California, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA
| | - David Heller
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota Medical Center, Minneapolis, Minnesota, USA
| | - Gregory L Szot
- Department of Surgery, Division of Transplantation, University of California San Francisco, San Francisco, California, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA,Department of Microbiology and Immunology, Stanford Medicine, Stanford, California, USA,Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
| | - Sohail Z Husain
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, School of Medicine, Stanford University, Stanford, California, USA
| | - Stephen J Pandol
- Basic and Translational Pancreatic Research, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Melena D Bellin
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota Medical Center, Minneapolis, Minnesota, USA,Department of Pediatrics, University of Minnesota Medical Center and Masonic Children’s Hospital, Minneapolis, Minnesota, USA
| | - Aida Habtezion
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, Stanford University, Stanford, California, USA .,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA
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Chung A, Banbury B, Vignali M, Huang CY, Asoori S, Johnson R, Kurtz T, Arora S, Wong SW, Shah N, Martin TG, Wolf JL. Antibody and T-cell responses by ultra-deep T-cell receptor immunosequencing after COVID-19 vaccination in patients with plasma cell dyscrasias. Br J Haematol 2022; 199:520-528. [PMID: 36041779 PMCID: PMC9538250 DOI: 10.1111/bjh.18434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022]
Abstract
We investigated antibody and coronavirus disease 2019 (COVID‐19)‐specific T‐cell mediated responses via ultra‐deep immunosequencing of the T‐cell receptor (TCR) repertoire in patients with plasma cell dyscrasias (PCD). We identified 364 patients with PCD who underwent spike antibody testing using commercially available spike‐receptor binding domain immunoglobulin G antibodies ≥2 weeks after completion of the initial two doses of mRNA vaccines or one dose of JNJ‐78436735. A total of 56 patients underwent TCR immunosequencing after vaccination. Overall, 86% tested within 6 months of vaccination had detectable spike antibodies. Increasing age, use of anti‐CD38 or anti‐B‐cell maturation antigen therapy, and receipt of BNT162b2 (vs. mRNA‐1273) were associated with lower antibody titres. We observed an increased proportion of TCRs associated with surface glycoprotein regions of the COVID‐19 genome after vaccination, consistent with spike‐specific T‐cell responses. The median spike‐specific T‐cell breadth was 3.11 × 10−5, comparable to those in healthy populations after vaccination. Although spike‐specific T‐cell breadth correlated with antibody titres, patients without antibody responses also demonstrated spike‐specific T‐cell responses. Patients receiving mRNA‐1273 had higher median spike‐specific T‐cell breadth than those receiving BNT162b2 (p = 0.01). Although patients with PCD are often immunocompromised due to underlying disease and treatments, COVID‐19 vaccination can still elicit humoral and T‐cell responses and remain an important intervention in this patient population.
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Affiliation(s)
- Alfred Chung
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | | | | | - Chiung-Yu Huang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Sireesha Asoori
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Rachel Johnson
- American University of the Caribbean School of Medicine, St. Maarten
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Shagun Arora
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Sandy W Wong
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Nina Shah
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Thomas G Martin
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey L Wolf
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
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Jiang H, Wang CW, Wang Z, Dai Y, Zhu Y, Lee YS, Cao Y, Chung WH, Ouyang S, Wang H. Functional and structural characteristics of HLA-B*13:01-mediated specific T cells reaction in dapsone-induced drug hypersensitivity. J Biomed Sci 2022; 29:58. [PMID: 35964029 DOI: 10.1186/s12929-022-00845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Severe cutaneous adverse drug reactions (SCARs) are a group of serious clinical conditions caused by immune reaction to certain drugs. The allelic variance of human leukocyte antigens of HLA-B*13:01 has been strongly associated with hypersensitivities induced by dapsone (DDS). T-cell receptor mediated activation of cytotoxic T lymphocytes (CTLs) has also been suggested to play an essential role in pathogenesis of SCARs. However, HLA-B*13:01-DDS-TCR immune synapse that plays role in drug-induced hypersensitivity syndrome (DIHS) associated T cells activation remains uncharacterized. METHODS To investigate the molecular mechanisms for HLA-B*13:01 in the pathogenesis of Dapsone-induced drug hypersensitivity (DDS-DIHS), we performed crystallization and expanded drug-specific CTLs to analyze the pathological role of DDS-DIHS. RESULTS Results showed the crystal structure of HLA-B*13:01-beta-2-microglobulin (β2M) complex at 1.5 Å resolution and performed mutation assays demonstrating that I118 or I119, and R121 of HLA-B*13:01 were the key residues that mediate the binding of DDS. Subsequent single-cell TCR and RNA sequencing indicated that TCRs composed of paired TRAV12-3/TRBV28 clonotype with shared CDR3 region specifically recognize HLA-B*13:01-DDS complex to trigger inflammatory cytokines associated with DDS-DIHS. CONCLUSION Our study identified the novel p-i-HLA/TCR as the model of interaction between HLA-B*13:01, DDS and the clonotype-specific TCR in DDS-DIHS.
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Bermick JR, Issuree P, denDekker A, Gallagher KA, Santillan D, Kunkel S, Lukacs N, Schaller M. Differences in H3K4me3 and chromatin accessibility contribute to altered T-cell receptor signaling in neonatal naïve CD4 T cells. Immunol Cell Biol 2022; 100:562-579. [PMID: 35608955 PMCID: PMC9357221 DOI: 10.1111/imcb.12561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 07/13/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Neonatal CD4+ T cells have reduced or delayed T-cell receptor (TCR) signaling responses compared with adult cells, but the mechanisms underlying this are poorly understood. This study tested the hypothesis that human neonatal naïve CD4+ TCR signaling and activation deficits are related to differences in H3K4me3 patterning and chromatin accessibility. Following initiation of TCR signaling using anti-CD3/anti-CD28 beads, adult naïve CD4+ T cells demonstrated increased CD69, phospho-CD3ε and interleukin (IL)-2, tumor necrosis factor-α (TNF-α), interferon-γ and IL-17A compared with neonatal cells. By contrast, following TCR-independent activation using phorbol myristate acetate (PMA)/ionomycin, neonatal cells demonstrated increased expression of CD69, IL-2 and TNF-α and equivalent phospho-ERK compared with adult cells. H3K4me3 chromatin immunoprecipitation-sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were performed on separate cohorts of naïve CD4+ T cells from term neonates and adults, and RNA-seq data from neonatal and adult naïve CD4+ T cells were obtained from the Blueprint Consortium. Adult cells demonstrated overall increased chromatin accessibility and a higher proportion of H3K4me3 sites associated with open chromatin and active gene transcription compared with neonatal cells. Adult cells demonstrated increased mRNA expression of the TCR-associated genes FYN, ITK, CD4, LCK and LAT, which was associated with increased H3K4me3 at the FYN and ITK gene loci and increased chromatin accessibility at the CD4, LCK and LAT loci. These findings indicate that neonatal TCR-dependent defects in activation are epigenetically regulated and provide a potentially targetable mechanism to enhance neonatal CD4+ T-cell responses.
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Affiliation(s)
- Jennifer R Bermick
- Division of Neonatology, Department of PediatricsUniversity of IowaIowa CityIAUSA
- Division of Neonatal‐Perinatal Medicine, Department of PediatricsMichigan MedicineAnn ArborMIUSA
| | - Priya Issuree
- Department of Internal MedicineUniversity of IowaIowa CityIAUSA
| | - Aaron denDekker
- Department of Vascular SurgeryMichigan MedicineAnn ArborMIUSA
| | | | - Donna Santillan
- Department of Obstetrics and GynecologyUniversity of IowaIowa CityIAUSA
| | - Steven Kunkel
- Department of PathologyMichigan MedicineAnn ArborMIUSA
| | - Nicholas Lukacs
- Department of PathologyMichigan MedicineAnn ArborMIUSA
- Mary H. Weiser Food Allergy CenterMichigan MedicineAnn ArborMIUSA
| | - Matthew Schaller
- Department of PathologyMichigan MedicineAnn ArborMIUSA
- Pulmonary, Critical Care & Sleep MedicineUniversity of FloridaGainesvilleFLUSA
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Abstract
Immunotherapy in cancer takes advantage of the exquisite specificity, potency, and flexibility of the immune system to eliminate alien tumor cells. It involves strategies to activate the entire immune defense, by unlocking mechanisms developed by tumor cells to escape from surrounding immune cells, as well as engineered antibody and cellular therapies. What is important to note is that these are therapeutics with curative potential. The earliest example of immune therapy is allogeneic stem cell transplantation, introduced in 1957, which is still an important modality in hematology, most notably in myeloid malignancies. In this review, we discuss developmental trends of immunotherapy in hematological malignancies, focusing on some of the strategies that we believe will have the most impact on future clinical practice in this field. In particular, we delineate novel developments for therapies that have already been introduced into the clinic, such as immune checkpoint inhibition and chimeric antigen receptor T-cell therapies. Finally, we discuss the therapeutic potential of emerging strategies based on T-cell receptors and adoptive transfer of allogeneic natural killer cells.
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Affiliation(s)
- Luca Mazzarella
- Department of Experimental Oncology, European Institute of Oncology, Milano, Italy
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Experimental and Clinical Oncology, Uppsala University, Sweden
| | - Johanna Olweus
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mats Jerkeman
- Department of Oncology, Skane University Hospital, Lund University, Lund, Sweden
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Safarzadeh Kozani P, Shokrgozar MA, Evazalipour M, Roudkenar MH. CRISPR/Cas9-medaited knockout of endogenous T-cell receptor in Jurkat cells and generation of NY-ESO-1-specific T cells: An in vitro study. Int Immunopharmacol 2022; 110:109055. [PMID: 35853277 DOI: 10.1016/j.intimp.2022.109055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 11/27/2022]
Abstract
Adoptive transfer of T-cell receptor (TCR)-engineered T cells has been successful in mediating favorable clinical outcomes. TCR-engineered T cells can be applied for targeting cancers whose associated antigens are intracellular and presented through major histocompatibility complexes (MHC). The mispairing of the exogenous TCR chains with the endogenous TCR chains leads to functionally impaired TCR-engineered T cells. The CRISPR/Cas9 genome-editing system can be utilized for the knockout of the endogenous TCR in T cells before introducing the exogenous TCR chains. In this study, we used the lentiviral delivery of CRISPR/Cas9 for disrupting the expression of the endogenous TCR in the Jurkat cell line. Next, an exogenous TCR targeting human leukocyte antigen (HLA)-A*0201-restricted New York esophageal squamous cell carcinoma 1 (NY-ESO-1) peptide was transduced into the TCR-knockout (KO) Jurkat cells. Further, we assessed lentiviral transduction efficacy using tetramer assay and evaluated the functionality of the NY-ESO-1-specific TCR-engineered T cells by quantifying the cell surface expression of CD69 upon co-cultivation with peptide-pulsed T2 cells. We successfully knocked out the endogenous TCR in ∼40% of the Jurkat cells. TCR-KO cells were selected and subjected to express NY-ESO-1-specific TCRs using lentiviral vectors. Flow cytometry analysis confirmed that up to 55% of the cells expressed the transgenic TCR on their surface. The functionality assay demonstrated that >90% of the engineered cells expressed CD69 when co-cultured with peptide-pulsed T2 cells. Conclusively, we developed a pipeline to engineer Jurkat cells using the state-of-the-art technique CRISPR/Cas9 and generated TCR-engineered cells that can become activated by a tumor-specific antigen.
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62
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Akiyama Y, Kondou R, Iizuka A, Miyata H, Maeda C, Kanematsu A, Ashizawa T, Nagashima T, Urakami K, Shimoda Y, Ohshima K, Shiomi A, Ohde Y, Terashima M, Uesaka K, Hirashima Y, Kiyohara Y, Katagiri H, Sugino T, Notsu A, Mori K, Takahashi M, Kenmotsu H, Yamaguchi K. Characterization of the Immunological Status of Hypermutated Solid Tumors in the Cancer Genome Analysis Project HOPE. Anticancer Res 2022; 42:3537-3549. [PMID: 35790264 DOI: 10.21873/anticanres.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 03/31/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Many reports demonstrate that a high tumor mutation burden (TMB-H) is closely associated with good prognosis of cancer. However, specific studies investigating the association of various TMB statuses with overall survival in patients with solid tumors are scarce. PATIENTS AND METHODS In the present study, we investigated the association of TMB status with overall survival in 5,072 patients with cancer from the HOPE project and clarified the specific mechanism responsible for the good prognosis of the TMB-H group. All tumors were classified into one of four groups based on TMB: ultralow (UL), low (L), intermediate (I) and high (H). RESULTS The TMB-H group had a better prognosis than the TMB-I and TMB-L groups, but not than the TMB-UL group. Analyzing the expression of 293 immune response-associated genes, 17 genes were up-regulated in the TMB-H group compared to the TMB-I and TNB-L groups, and two genes [CD274 and interferon-γ (IFNG)] were identified as good prognostic factors. Analysis of immune cell populations inside tumors demonstrated that the frequencies of exhausted CD8+ T-cells, activated effector CD8+ T-cells and natural killer cells were significantly higher in the TMB-H group. The T-cell receptor repertoire numbers and the diversity evenness score (DE50) were lower in the TMB-H group than in TMB-UL group; however, no association of the DE50 value with the binding or elution affinity of epitope peptides from neoantigens was found. CONCLUSION One possible mechanism for the good prognosis of the TMB-UL group compared to the TMB-H group might be that the TMB-UL group features a balance between immunosuppression and immunostimulation.
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Affiliation(s)
- Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan;
| | - Ryota Kondou
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Haruo Miyata
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Chie Maeda
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akari Kanematsu
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Tadashi Ashizawa
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Tokyo, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuyuki Hirashima
- Division of Gynecology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yoshio Kiyohara
- Division of Dermatology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Hirohisa Katagiri
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Akifumi Notsu
- Clinical Research Center, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Keita Mori
- Clinical Research Center, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Mitsuru Takahashi
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
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Nakamura T, Kobayashi E, Hamana H, Hayakawa Y, Muraguchi A, Hayashi A, Ozawa T, Kishi H. Evaluation of chimeric antigen receptor of humanized rabbit-derived T cell receptor-like antibody. Cancer Sci 2022; 113:3321-3329. [PMID: 35766417 DOI: 10.1111/cas.15478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 12/01/2022] Open
Abstract
T-cell receptor (TCR)-like antibodies that specifically recognize antigenic peptides presented on major histocompatibility complex (MHC) molecules have been developed for next-generation cancer immunotherapy. Recently, we reported a rapid and efficient method to generate TCR-like antibodies using a rabbit system. We humanized previously generated rabbit-derived TCR-like antibodies reacting Epstein-Barr virus peptide (BRLF1p, TYPVLEEMF) in the context of HLA-A24 molecules, produced CAR-T cells, and evaluated their anti-tumor effects using in vitro and in vivo tumor models. Humanization of the rabbit-derived TCR-like antibodies using the complementarity-determining region grafting technology maintained their specificity and affinity. We prepared a second-generation chimeric antigen receptor (CAR) using scFv of the humanized TCR-like antibodies and then transduced them into human T-cells. The CAR-T cells specifically recognized BRLF1p/MHC molecules and lysed the target cells in an antigen-specific manner in vitro. They also demonstrated anti-tumor activity in a mouse xenograft model. We report the generation of CAR-T cells using humanized rabbit-derived TCR-like antibodies. Together with our established and efficient generation procedure for TCR-like antibodies using rabbits, our platform for the clinical application of humanized rabbit-derived TCR-like antibodies to CAR-T cells will help improve next-generation cancer immunotherapy.
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Affiliation(s)
- Tomoko Nakamura
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.,Department of Ophthalmology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Eiji Kobayashi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Yoshihiro Hayakawa
- Section of Host Defences, Department of Bioscience, Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Atsushi Hayashi
- Department of Ophthalmology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
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Chung CY, Gutiérrez-González M, López Acevedo SN, Fahad AS, DeKosky BJ; AIRR Community. Quality Control: Chain Pairing Precision and Monitoring of Cross-Sample Contamination: A Method by the AIRR Community. Methods Mol Biol 2022; 2453:423-37. [PMID: 35622337 DOI: 10.1007/978-1-0716-2115-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
New approaches in high-throughput analysis of immune receptor repertoires are enabling major advances in immunology and for the discovery of precision immunotherapeutics. Commensurate with growth of the field, there has been an increased need for the establishment of techniques for quality control of immune receptor data. Our laboratory has standardized the use of multiple quality control techniques in immunoglobulin (IG) and T-cell receptor (TR) sequencing experiments to ensure quality control throughout diverse experimental conditions. These quality control methods can also validate the development of new technological approaches and accelerate the training of laboratory personnel. This chapter describes multiple quality control techniques, including split-replicate cell preparations that enable repeat analyses and bioinformatic methods to quantify and ensure high sample quality. We hope that these quality control approaches can accelerate the technical adoption and validated use of unpaired and natively paired immune receptor data.
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65
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Kortleve D, van Brakel M, Wijers R, Debets R, Hammerl D. Gene Engineering T Cells with T-Cell Receptor for Adoptive Therapy. Methods Mol Biol 2022; 2453:209-29. [PMID: 35622329 DOI: 10.1007/978-1-0716-2115-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Prior to clinical testing of adoptive T-cell therapy with T-cell receptor (TCR)-engineered T cells, TCRs need to be retrieved, annotated, gene-transferred, and extensively tested in vitro to accurately assess specificity and sensitivity of target recognition. Here, we present a fundamental series of protocols that cover critical preclinical parameters, thereby enabling the selection of candidate TCRs for clinical testing.
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66
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Corrie BD, Christley S, Busse CE, Cowell LG, Neller KCM, Rubelt F, Schwab N. Data Sharing and Reuse: A Method by the AIRR Community. Methods Mol Biol 2022; 2453:447-476. [PMID: 35622339 DOI: 10.1007/978-1-0716-2115-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR ) has revolutionized the ability to study the adaptive immune response via large-scale experiments. Since 2009, AIRR sequencing (AIRR-seq) has been widely applied to survey the immune state of individuals (see "The AIRR Community Guide to Repertoire Analysis" chapter for details). One of the goals of the AIRR Community is to make the resulting AIRR-seq data FAIR (Findable, Accessible, Interoperable, and Reusable) (Wilkinson et al. Sci Data 3:1-9, 2016), with a primary goal of making it easy for the research community to reuse AIRR-seq data (Breden et al. Front Immunol 8:1418, 2017; Scott and Breden. Curr Opin Syst Biol 24:71-77, 2020). The basis for this is the MiAIRR data standard (Rubelt et al. Nat Immunol 18:1274-1278, 2017). For long-term preservation, it is recommended that researchers store their sequence read data in an INSDC repository. At the same time, the AIRR Community has established the AIRR Data Commons (Christley et al. Front Big Data 3:22, 2020), a distributed set of AIRR-compliant repositories that store the critically important annotated AIRR-seq data based on the MiAIRR standard, making the data findable, interoperable, and, because the data are annotated, more valuable in its reuse. Here, we build on the other AIRR Community chapters and illustrate how these principles and standards can be incorporated into AIRR-seq data analysis workflows. We discuss the importance of careful curation of metadata to ensure reproducibility and facilitate data sharing and reuse, and we illustrate how data can be shared via the AIRR Data Commons.
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Affiliation(s)
- Brian D Corrie
- Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.
| | | | - Lindsay G Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kira C M Neller
- Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University of Muenster, Muenster, Germany
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Galigalidou C, Zaragoza-Infante L, Chatzidimitriou A, Stamatopoulos K, Psomopoulos F, Agathangelidis A. Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis. Methods Mol Biol 2022; 2453:585-603. [PMID: 35622343 DOI: 10.1007/978-1-0716-2115-8_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The study of antigen receptor gene repertoires using next-generation sequencing (NGS) technologies has disclosed an unprecedented depth of complexity, requiring novel computational and analytical solutions. Several bioinformatics workflows have been developed to this end, including the T-cell receptor/immunoglobulin profiler (TRIP), a web application implemented in R shiny, specifically designed for the purposes of comprehensive repertoire analysis, which is the focus of this chapter. TRIP has the potential to perform robust immunoprofiling analysis through the extraction and processing of the IMGT/HighV-Quest output, via a series of functions, ensuring the analysis of high-quality, biologically relevant data through a multilevel process of data filtering. Subsequently, it provides in-depth analysis of antigen receptor gene rearrangements, including (a) clonality assessment; (b) extraction of variable (V), diversity (D), and joining (J) gene repertoires; (c) CDR3 characterization at both the nucleotide and amino acid level; and (d) somatic hypermutation analysis, in the case of immunoglobulin gene rearrangements. Relevant to mention, TRIP enables a high level of customization through the integration of various options in key aspects of the analysis, such as clonotype definition and computation, hence allowing for flexibility without compromising on accuracy.
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Affiliation(s)
- Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Biology and Genetics (MBG), Democritus University of Thrace, Alexandroupolis, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,First Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
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68
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Lefranc MP, Lefranc G. IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope. Methods Mol Biol 2022; 2453:533-570. [PMID: 35622341 DOI: 10.1007/978-1-0716-2115-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
T-cell receptors (TR), the antigen receptors of T cells, specifically recognize peptides presented by the major histocompatibility (MH) proteins, as peptide/MH (pMH), on the cell surface. The structure characterization of the trimolecular TR/pMH complexes is crucial to the fields of immunology, vaccination, and immunotherapy. IMGT/3Dstructure-DB is the three-dimensional (3-D) structure database of IMGT®, the international ImMunoGenetics information system®. By its creation, IMGT® marks the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. The IMGT® immunoglobulin (IG) and TR gene and allele nomenclature (CLASSIFICATION axiom) and the IMGT unique numbering and IMGT/Collier-de-Perles (NUMEROTATION axiom) are the two founding breakthroughs of immunoinformatics. IMGT-ONTOLOGY concepts and IMGT Scientific chart rules generated from these axioms allowed IMGT® bridging genes, structures, and functions. IMGT/3Dstructure-DB contains 3-D structures of IG or antibodies, TR and MH proteins of the adaptive immune responses of jawed vertebrates (gnathostomata), IG or TR complexes with antigens (IG/Ag, TR/pMH), related proteins of the immune system of any species belonging to the IG and MH superfamilies, and fusion proteins for immune applications. The focus of this chapter is on the TR V domains and MH G domains and the contact analysis comparison in TR/pMH interactions. Standardized molecular characterization includes "IMGT pMH contact sites" for peptide and MH groove interactions and "IMGT paratopes and epitopes" for TR/pMH complexes. Data are available in the IMGT/3Dstructure database, at the IMGT Home page http://www.imgt.org .
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Université de Montpellier, Montpellier cedex 5, France.
| | - Gérard Lefranc
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Université de Montpellier, Montpellier cedex 5, France.
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69
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Starza ID, Eckert C, Drandi D, Cazzaniga G. Minimal Residual Disease Analysis by Monitoring Immunoglobulin and T-Cell Receptor Gene Rearrangements by Quantitative PCR and Droplet Digital PCR. Methods Mol Biol 2022; 2453:79-89. [PMID: 35622321 DOI: 10.1007/978-1-0716-2115-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Analysis of immunoglobulin and T-cell receptor gene rearrangements by real-time quantitative polymerase chain reaction (RQ-PCR) is the gold standard for sensitive and accurate minimal residual disease (MRD) monitoring; it has been extensively standardized and guidelines have been developed within the EuroMRD consortium ( www.euromrd.org ). However, new generations of PCR-based methods are standing out as potential alternatives to RQ-PCR, such as digital PCR technology (dPCR), the third-generation implementation of conventional PCR, which has the potential to overcome some of the limitations of RQ-PCR such as allowing the absolute quantification of nucleic acid targets without the need for a calibration curve. During the last years, droplet digital PCR (ddPCR) technology has been compared to RQ-PCR in several hematologic malignancies showing its proficiency for MRD analysis. So far, no established guidelines for ddPCR MRD analysis and data interpretation have been defined and its potential is still under investigation. However, a major standardization effort is underway within the EuroMRD consortium ( www.euromrd.org ) for future application of ddPCR in standard clinical practice.
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Affiliation(s)
- Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, "Sapienza" University of Rome, Rome, Italy.,GIMEMA Foundation, Rome, Italy
| | - Cornelia Eckert
- Department of Pediatric Oncology Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | - Daniela Drandi
- Hematology Division, Department of Molecular Biotechnology and Health sciences, University of Torino, Torino, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Fondazione Tettamanti, Centro Maria Letizia Verga, Monza, Italy. .,Genetics, Department of Medicine and Surgery, University of Milan Bicocca, Monza, Italy.
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70
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Babrak L, Marquez S, Busse CE, Lees WD, Miho E, Ohlin M, Rosenfeld AM, Stervbo U, Watson CT, Schramm CA; AIRR Community. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol 2022; 2453:279-96. [PMID: 35622332 DOI: 10.1007/978-1-0716-2115-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
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71
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van der Velden VHJ, Bastian L, Brüggemann M, Hartmann AM, Darzentas N. Immunoglobulin/ T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq. Methods Mol Biol 2022; 2453:61-77. [PMID: 35622320 DOI: 10.1007/978-1-0716-2115-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation are crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. Here we describe how RNA-Seq data can be generated and subsequently analyzed with ARResT/Interrogate to identify possible MRD markers. In addition to the procedures, possible pitfalls will be discussed. Similar strategies can be employed for other lymphoid malignancies, such as lymphoma and myeloma.
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72
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Dalai SC, Dines JN, Snyder TM, Gittelman RM, Eerkes T, Vaney P, Howard S, Akers K, Skewis L, Monteforte A, Witte PR, Wolf C, Nesse H, Herndon M, Qadeer J, Duffy S, Svejnoha E, Taromino C, Kaplan IM, Alsobrook J, Manley T, Baldo L. Clinical Validation of a Novel T-Cell Receptor Sequencing Assay for Identification of Recent or Prior Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Clin Infect Dis 2022; 75:2079-2087. [PMID: 35521791 PMCID: PMC9129217 DOI: 10.1093/cid/ciac353] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/08/2022] [Accepted: 04/29/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND While diagnostic, therapeutic, and vaccine development in the coronavirus disease 2019 (COVID-19) pandemic has proceeded at unprecedented speed, critical gaps in our understanding of the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unaddressed by current diagnostic strategies. METHODS A statistical classifier for identifying prior SARS-CoV-2 infection was trained using >4000 SARS-CoV-2-associated T-cell receptor (TCR) β sequences identified by comparing 784 cases and 2447 controls from 5 independent cohorts. The T-Detect COVID (Adaptive Biotechnologies) assay applies this classifier to TCR repertoires sequenced from blood samples to yield a binary assessment of past infection. Assay performance was assessed in 2 retrospective (n = 346; n = 69) and 1 prospective cohort (n = 87) to determine positive percent agreement (PPA) and negative percent agreement (NPA). PPA was compared with 2 commercial serology assays, and pathogen cross-reactivity was evaluated. RESULTS T-Detect COVID demonstrated high PPA in individuals with prior reverse transcription-polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infection (97.1% 15+ days from diagnosis; 94.5% 15+ days from symptom onset), high NPA (∼100%) in presumed or confirmed SARS-CoV-2 negative cases, equivalent or higher PPA than 2 commercial serology tests, and no evidence of pathogen cross-reactivity. CONCLUSIONS T-Detect COVID is a novel T-cell immunosequencing assay demonstrating high clinical performance for identification of recent or prior SARS-CoV-2 infection from blood samples, with implications for clinical management, risk stratification, surveillance, and understanding of protective immunity and long-term sequelae.
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Affiliation(s)
- Sudeb C. Dalai
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer N. Dines
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | | | - Rachel M. Gittelman
- Research, Adaptive Biotechnologies, Seattle, Washington, USA,CORRESPONDING AUTHOR: Rachel M. Gittelman, PhD Adaptive Biotechnologies 1551 Eastlake Ave E Seattle, WA, 98102 USA
| | - Tera Eerkes
- Regulatory Affairs, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Pashmi Vaney
- Regulatory Affairs, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Sally Howard
- Regulatory Affairs, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Kipp Akers
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lynell Skewis
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Anthony Monteforte
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Pamela R. Witte
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Cristina Wolf
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Hans Nesse
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Megan Herndon
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Jia Qadeer
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Sarah Duffy
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Emily Svejnoha
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Caroline Taromino
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Ian M. Kaplan
- T-Detect Product Management, Adaptive Biotechnologies, Seattle, Washington, USA
| | - John Alsobrook
- Molecular Lab Management, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Thomas Manley
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lance Baldo
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
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Dessalles R, Pan Y, Xia M, Maestrini D, D'Orsogna MR, Chou T. How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation. Front Immunol 2022; 12:735135. [PMID: 35250963 PMCID: PMC8891377 DOI: 10.3389/fimmu.2021.735135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
The specificity of T cells is that each T cell has only one T cell receptor (TCR). A T cell clone represents a collection of T cells with the same TCR sequence. Thus, the number of different T cell clones in an organism reflects the number of different T cell receptors (TCRs) that arise from recombination of the V(D)J gene segments during T cell development in the thymus. TCR diversity and more specifically, the clone abundance distribution, are important factors in immune functions. Specific recombination patterns occur more frequently than others while subsequent interactions between TCRs and self-antigens are known to trigger proliferation and sustain naive T cell survival. These processes are TCR-dependent, leading to clone-dependent thymic export and naive T cell proliferation rates. We describe the heterogeneous steady-state population of naive T cells (those that have not yet been antigenically triggered) by using a mean-field model of a regulated birth-death-immigration process. After accounting for random sampling, we investigate how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells, or “clone counts”). By using reasonable physiological parameter values and fitting predicted clone counts to experimentally sampled clone abundances, we show that realistic levels of heterogeneity in immigration rates cause very little change to predicted clone-counts, but that modest heterogeneity in proliferation rates can generate the observed clone abundances. Our analysis provides constraints among physiological parameters that are necessary to yield predictions that qualitatively match the data. Assumptions of the model and potentially other important mechanistic factors are discussed.
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Affiliation(s)
- Renaud Dessalles
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Yunbei Pan
- Department of Mathematics, California State University at Northridge, Los Angeles, CA, United States
| | - Mingtao Xia
- Department of Mathematics, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Davide Maestrini
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Maria R D'Orsogna
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Department of Mathematics, California State University at Northridge, Los Angeles, CA, United States
| | - Tom Chou
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Department of Mathematics, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
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74
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Murray JA. Several faces of refractory coeliac disease type 2. Gut 2022; 71:449-450. [PMID: 33785554 DOI: 10.1136/gutjnl-2021-324251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 12/08/2022]
Affiliation(s)
- Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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75
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Hu J, Zhang Y, Yu Y, Yu H, Guo S, Shi D, He J, Hu C, Yang J, Fang X, Xiao Y. Encephalomyelitis Caused by Balamuthia mandrillaris in a Woman With Breast Cancer: A Case Report and Review of the Literature. Front Immunol 2022; 12:768065. [PMID: 35069540 PMCID: PMC8766823 DOI: 10.3389/fimmu.2021.768065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Balamuthia mandrillaris is one cause of a rare and severe brain infection called granulomatous amoebic encephalitis (GAE), which has a mortality rate of >90%. Diagnosis of Balamuthia GAE is difficult because symptoms are non-specific. Here, we report a case of Balamuthia amoebic encephalomyelitis (encephalitis and myelitis) in a woman with breast cancer. She sustained trauma near a garbage dump 2 years ago and subsequently developed a skin lesion with a Mycobacterium abscessus infection. She experienced dizziness, lethargy, nausea and vomiting, inability to walk, and deterioration of consciousness. Next-generation sequencing of cerebrospinal fluid (CSF) samples revealed B. mandrillaris, and MRI of both brain and spinal cord showed abnormal signals. T-cell receptor (TCR) sequencing of the CSF identified the Top1 TCR. A combination of amphotericin B, flucytosine, fluconazole, sulfamethoxazole, trimethoprim, clarithromycin, pentamidine, and miltefosine was administrated, but she deteriorated gradually and died on day 27 post-admission.
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Affiliation(s)
- Juan Hu
- Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiqi Zhang
- Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongwei Yu
- Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huili Yu
- Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Siruo Guo
- Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ding Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianqin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chi Hu
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiqi Yang
- Department of Neurosurgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueling Fang
- Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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76
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Li Y, Hu J, Wang Y, Liu D, Shi Y, Zhang J, Liu Y, Lin D, Lin J, Hu W, He H, Wang W, Fan W, Li L, Wang D, Wang K, Xu J. T-Cell Repertoire Characteristics of Asymptomatic and Re-Detectable Positive COVID-19 Patients. Front Immunol 2022; 12:769442. [PMID: 35154070 PMCID: PMC8828559 DOI: 10.3389/fimmu.2021.769442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/24/2021] [Indexed: 01/01/2023] Open
Abstract
The prevention of the COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear. Here we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different courses, including asymptomatic, symptomatic, convalescent, and re-detectable positive cases. We identified a set of V-J gene combinations characterizing the upward immune responses through asymptomatic and symptomatic courses. Furthermore, some of these V-J combinations could be awakened in the re-detectable positive cases, which may help predict the risk of recurrent infection. Therefore, TCR repertoire examination has the potential to strengthen the clinical surveillance and the immunotherapy development for COVID-19.
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Affiliation(s)
- Yizhe Li
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jian Hu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongsi Wang
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dongdong Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaling Shi
- Department of Laboratory Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaqi Zhang
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongzi Lin
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Jing Lin
- Department of Clinical Laboratory, The First People’s Hospital of Foshan, Foshan, China
| | - Wei Hu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Haolan He
- Department of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Wentao Fan
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Linlin Li
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dawei Wang
- Department of Pulmonary and Critical Care Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Kejian Wang
- The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jianhua Xu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
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77
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Christley S, Stervbo U, Cowell LG. Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community. Methods Mol Biol 2022; 2453:439-446. [PMID: 35622338 PMCID: PMC9761903 DOI: 10.1007/978-1-0716-2115-8_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
AIRR-seq data sets are usually large and require specialized analysis methods and software tools. A typical Illumina MiSeq sequencing run generates 20-30 million 2 × 300 bp paired-end sequence reads, which roughly corresponds to 15 GB of sequence data to be processed. Other platforms like NextSeq, which is useful in projects where the full V gene is not needed, create about 400 million 2 × 150 bp paired-end reads. Because of the size of the data sets, the analysis can be computationally expensive, particularly the early analysis steps like preprocessing and gene annotation that process the majority of the sequence data. A standard desktop PC may take 3-5 days of constant processing for a single MiSeq run, so dedicated high-performance computational resources may be required.VDJServer provides free access to high-performance computing (HPC) at the Texas Advanced Computing Center (TACC) through a graphical user interface (Christley et al. Front Immunol 9:976, 2018). VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provides access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene assignment, repertoire characterization, and repertoire comparison. Furthermore, VDJServer has parallelized execution for tools such as IgBLAST, so more compute resources are utilized as the size of the input data grows. Analysis that takes days on a desktop PC might take only a few hours on VDJServer. VDJServer is a free, publicly available, and open-source licensed resource. Here, we describe the workflow for performing immune repertoire analysis on VDJServer's high-performance computing.
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Affiliation(s)
- Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Lindsay G Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA.
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78
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Abstract
The immune system is constantly protecting its host from the invasion of pathogens and the development of cancer cells. The specific CD8+ T-cell immune response against virus-infected cells and tumor cells is based on the T-cell receptor recognition of antigenic peptides bound to class I major histocompatibility complexes (MHC) at the surface of antigen presenting cells. Consequently, the peptide binding specificities of the highly polymorphic MHC have important implications for the design of vaccines, for the treatment of autoimmune diseases, and for personalized cancer immunotherapy. Evidence-based machine-learning approaches have been successfully used for the prediction of peptide binders and are currently being developed for the prediction of peptide immunogenicity. However, understanding and modeling the structural details of peptide/MHC binding is crucial for a better understanding of the molecular mechanisms triggering the immunological processes, estimating peptide/MHC affinity using universal physics-based approaches, and driving the design of novel peptide ligands. Unfortunately, due to the large diversity of MHC allotypes and possible peptides, the growing number of 3D structures of peptide/MHC (pMHC) complexes in the Protein Data Bank only covers a small fraction of the possibilities. Consequently, there is a growing need for rapid and efficient approaches to predict 3D structures of pMHC complexes. Here, we review the key characteristics of the 3D structure of pMHC complexes before listing databases and other sources of information on pMHC structures and MHC specificities. Finally, we discuss some of the most prominent pMHC docking software.
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Affiliation(s)
- Marta A S Perez
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michel A Cuendet
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland.
| | - Vincent Zoete
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, Lausanne, Switzerland.
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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79
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Edes I, Clauss J, Stahn R, Japp AS, Lorenz FKM. TCR and CAR Engineering of Primary Human T Cells. Methods Mol Biol 2022; 2521:85-93. [PMID: 35732994 DOI: 10.1007/978-1-0716-2441-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The efficient expression of T-cell receptors (TCRs) or chimeric antigen receptors (CARs) in primary human T cells is crucial for preclinical testing of receptor properties for adoptive T-cell therapies. Multiple streams of technological platforms have been developed in the recent decades to genetically modify primary T cells including nonviral platforms such as transposon-based systems (PiggyBac, Sleeping Beauty), TALENs, or CRISPR-Cas9). The production of CAR- or TCR-encoding retroviral vectors, however, is still the most commonly used technique both in preclinical as well as in clinical settings.In this chapter we describe a comprehensive 12-day protocol for (a) generating high-titered gamma-retroviral vector particles containing the transgene of interest (e.g., TCR , CAR ), (b) the isolation, activation and rapid expansion of primary T cells and (c) the stable genetic engineering of these T cells with the transgene for subsequent characterization.
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Affiliation(s)
- Inan Edes
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Julian Clauss
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Rainer Stahn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Alberto Sada Japp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Felix K M Lorenz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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80
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Pasetto A, Buggert M. T-Cell Repertoire Characterization. Methods Mol Biol 2022; 2574:209-219. [PMID: 36087203 DOI: 10.1007/978-1-0716-2712-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
T-cell repertoire characterization is a methodology that enables the identification of T-cell receptor (TCR) gene sequences in a T-cell population. TCR genes are composed of modular gene segments V (D) J that undergo somatic recombination, resulting in unique and unpredictable sequences that can be utilized to identify each T-cell clone. The analysis of the TCR composition in a T-cell population can give information on the biological phenomenon such as antigen-driven expansion and heterogeneity of T-cell responses. Bulk TCR analysis can give useful information on the clonality and can help track a specific clonotype over time or in different compartments, although the information about pairing cannot be provided. Single-cell TCR sequencing, on the other hand, can provide pairing information that are necessary to reconstruct the TCR and confirm antigen specificity.Here we describe common methods to characterize T-cell repertoires based on both bulk and single-cell next-generation sequencing.
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Affiliation(s)
- Anna Pasetto
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), Karolinska Institutet, Stockholm, Sweden.
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81
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Stephens HM, Brazin KN, Mallis RJ, Feng Y, Banik D, Reinherz EL, Lang MJ. Measuring αβ T-Cell Receptor-Mediated Mechanosensing Using Optical Tweezers Combined with Fluorescence Imaging. Methods Mol Biol 2022; 2478:727-753. [PMID: 36063340 DOI: 10.1007/978-1-0716-2229-2_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
T-cell antigen receptors (TCRs) are mechanosensors, which initiate a signaling cascade upon ligand recognition resulting in T-cell differentiation, homeostasis, effector and regulatory functions. An optical trap combined with fluorescence permits direct monitoring of T-cell triggering in response to force application at various concentrations of peptide-bound major histocompatibility complex molecules (pMHC). The technique mimics physiological shear forces applied as cells crawl across antigen-presenting surfaces during immune surveillance. True single molecule studies performed on single cells profile force-bond lifetime, typically seen as a catch bond, and conformational change at the TCR-pMHC bond on the surface of the cell upon force loading. Together, activation and single molecule single cell studies provide chemical and physical triggering thresholds as well as insight into catch bond formation and quaternary structural changes of single TCRs. The present methods detail assay design, preparation, and execution, as well as data analysis. These methods may be applied to a wide range of pMHC-TCR interactions and have potential for adaptation to other receptor-ligand systems.
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Affiliation(s)
- Hannah M Stephens
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kristine N Brazin
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robert J Mallis
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yinnian Feng
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Debasis Banik
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
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82
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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83
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Eugster A, Bostick ML, Gupta N, Mariotti-Ferrandiz E, Kraus G, Meng W, Soto C, Trück J, Stervbo U, Luning Prak ET; AIRR Community. AIRR Community Guide to Planning and Performing AIRR-Seq Experiments. Methods Mol Biol 2022; 2453:261-78. [PMID: 35622331 DOI: 10.1007/978-1-0716-2115-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
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84
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Dutta D, Santhanam SK, Parween F, Ismaeel S, Qadri A. Membrane prohibitin forms a dynamic complex with p56 lck to regulate T cell receptor signaling. Immunol Lett 2021; 241:49-54. [PMID: 34942191 DOI: 10.1016/j.imlet.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/24/2021] [Accepted: 12/17/2021] [Indexed: 11/29/2022]
Abstract
Prohibitin is a highly conserved ubiquitously expressed protein involved in several key cellular functions. Targeting of this protein in the membrane by the virulence polysaccharide, Vi, of human typhoid-causing pathogen, Salmonella enterica serovar Typhi (S. Typhi), results in suppression of IL-2 secretion from T cells activated through the T-cell receptor (TCR). However, the mechanism of this suppression remains unclear. Here, using Vi as a probe, we show that membrane prohibitin associates with the src-tyrosine kinase, p56lck (Lck), and actin in human model T cell line, Jurkat. Activation with anti-CD3 antibody brings about dissociation of this complex, which coincides with downstream ERK activation. The trimolecular complex reappears towards culmination of proximal TCR signaling. Engagement of cells with Vi prevents TCR-triggered activation of Lck and ERK by inhibiting dissociation of the former from prohibitin. These findings suggest a regulatory role for membrane prohibitin in Lck activation and TCR signaling.
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Affiliation(s)
- Debjani Dutta
- Hybridoma Laboratory, National Institute of Immunology, Aruna Asaf ali marg, New Delhi, 110067 India
| | - Srikanth K Santhanam
- Hybridoma Laboratory, National Institute of Immunology, Aruna Asaf ali marg, New Delhi, 110067 India
| | - Farhat Parween
- Hybridoma Laboratory, National Institute of Immunology, Aruna Asaf ali marg, New Delhi, 110067 India
| | - Sana Ismaeel
- Hybridoma Laboratory, National Institute of Immunology, Aruna Asaf ali marg, New Delhi, 110067 India
| | - Ayub Qadri
- Hybridoma Laboratory, National Institute of Immunology, Aruna Asaf ali marg, New Delhi, 110067 India.
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85
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Kawamoto H, Masuda K, Nagano S. Regeneration of antigen-specific T cells by using induced pluripotent stem cell (iPSC) technology. Int Immunol 2021; 33:827-833. [PMID: 34661676 DOI: 10.1093/intimm/dxab091] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/15/2021] [Indexed: 01/20/2023] Open
Abstract
In currently ongoing adoptive T-cell therapies, T cells collected from the patient are given back to the patient after ex vivo cell activation and expansion. In some cases, T cells are transduced with chimeric antigen receptor (CAR) or T-cell receptor (TCR) genes during the ex vivo culture period. Although such strategies have been shown to be effective in some types of cancer, there remain issues to be solved; these methods (i) are time-consuming, (ii) are costly and (iii) it is difficult to guarantee the quality because the products depend on patient-derived T cells. To address these issues, several groups including ours have developed methods in which cytotoxic cells are mass-produced by using induced pluripotent stem cell (iPSC) technology. For the regeneration of T cells, the basic idea is as follows: iPSCs produced from T cells inherit rearranged TCR genes, and thus all regenerated T cells should express the same TCR. Based on this idea, various types of T cells have been regenerated, including conventional cytotoxic T lymphocytes (CTLs), γδT cells, NKT cells and mucosal-associated invariant T (MAIT) cells. On the other hand, any cytotoxic cells can be used as the base cells into which CAR is introduced, and thus iPSC-derived NK cells have been developed. To apply the iPSC-based cell therapy in an allogeneic setting, the authors' group developed a method in which non-T-cell-derived iPSCs are transduced with exogenous TCR genes (TCR-iPSC method). This approach is being prepared for a clinical trial to be realized in Kyoto University Hospital, in which acute myeloid leukemia patients will be treated by the regenerated WT1 antigen-specific CTLs.
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Affiliation(s)
- Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of Regenerative Immunology, International Center for Cell and Gene Therapy, Fujita Health University, Toyoake, Japan
| | - Kyoko Masuda
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Seiji Nagano
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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86
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Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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87
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Chen BJ, Wang RC, Jhuang JY, Chen SW, Su YZ, Tseng CE, Chiang CT, Wu YT, Chuang SS. Primary cutaneous gamma/delta T-cell lymphoma in Taiwan: A series of six cases with frequent solitary presentation and relatively indolent behavior. J Cutan Pathol 2021; 49:350-357. [PMID: 34778979 DOI: 10.1111/cup.14169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/22/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Primary cutaneous gamma/delta T-cell lymphoma (PCDG-TCL) is aggressive, frequently presenting as multiple plaques, tumors, and/or subcutaneous nodules. METHODS In this study, we conducted a retrospective study in a tertiary center in Taiwan to characterize this rare tumor. RESULTS We identified six patients. Five presented with a solitary lesion, including two with clinical impression of epidermal inclusion cyst or lipoma. Two of four evaluable cases exhibited epidermotropism, with one mimicking Pautrier microabscess. The neoplastic cells were pleomorphic and mostly medium- to large-sized. In all cases, the neoplastic cells expressed T-cell receptor (TCR)-γ and/or TCR-δ, with four co-expressing βF1. Two of these βF1+ cases co-expressed TCR-γ but not TCR-δ (two different clones). All were negative for Epstein-Barr virus (EBV), low stage, and treated with radiotherapy alone or combined chemotherapy and radiotherapy. In two patients, lymphoma relapsed in 3 and 7 months, respectively, and one patient died of the disease in 7 months. Four other patients were free of disease for 6 to 126 months. CONCLUSION PCGD-TCL cases in Taiwan are more commonly solitary, frequently with indolent courses. The two currently available TCR-δ clones alone might be insufficient to detect all tumors.
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Affiliation(s)
- Bo-Jung Chen
- Department of Pathology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ren Ching Wang
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Nursing, College of Nursing, HungKuang University, Taichung, Taiwan
| | - Jie-Yang Jhuang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Shang-Wen Chen
- Division of Hemato-Oncology, Department of Internal Medicine, Lioying Chi-Mei Hospital, Tainan, Taiwan
| | - Ying-Zhen Su
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan
| | - Chih-En Tseng
- Department of Anatomic Pathology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chia-Yi, Taiwan.,School of Medicine, Tzu Chi University, Hualian, Taiwan
| | - Chien-Ta Chiang
- Department of Anatomic Pathology, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - You-Ting Wu
- Department of Pathology, Chia-Yi Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Chia-Yi, Taiwan
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88
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Velas L, Brameshuber M, Huppa JB, Kurz E, Dustin ML, Zelger P, Jesacher A, Schütz GJ. Three-Dimensional Single Molecule Localization Microscopy Reveals the Topography of the Immunological Synapse at Isotropic Precision below 15 nm. Nano Lett 2021; 21:9247-9255. [PMID: 34709845 PMCID: PMC8587899 DOI: 10.1021/acs.nanolett.1c03160] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
T-cells engage with antigen-presenting cells in search for antigenic peptides and form transient interfaces termed immunological synapses. Synapse topography affects receptor binding rates and the mutual segregation of proteins due to size exclusion effects. It is hence important to determine the 3D topography of the immunological synapse at high precision. Current methods provide only rather coarse images of the protein distribution within the synapse. Here, we applied supercritical angle fluorescence microscopy combined with defocused imaging, which allows three-dimensional single molecule localization microscopy (3D-SMLM) at an isotropic localization precision below 15 nm. Experiments were performed on hybrid synapses between primary T-cells and functionalized glass-supported lipid bilayers. We used 3D-SMLM to quantify the cleft size within the synapse by mapping the position of the T-cell receptor (TCR) with respect to the supported lipid bilayer, yielding average distances of 18 nm up to 31 nm for activating and nonactivating bilayers, respectively.
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Affiliation(s)
- Lukas Velas
- Institute
of Applied Physics, TU Wien, 1040 Vienna, Austria
| | | | - Johannes B. Huppa
- Institute
for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology
and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, OX3 7FY Oxford, United Kingdom
| | - Michael L. Dustin
- Kennedy
Institute of Rheumatology, University of
Oxford, OX3 7FY Oxford, United Kingdom
| | - Philipp Zelger
- Division
for Biomedical Physics, Medical University
of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Jesacher
- Division
for Biomedical Physics, Medical University
of Innsbruck, 6020 Innsbruck, Austria
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89
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Aschauer C, Jelencsics K, Hu K, Heinzel A, Gregorich MG, Vetter J, Schaller S, Winkler SM, Weinberger J, Pimenov L, Gualdoni GA, Eder M, Kainz A, Troescher AR, Regele H, Reindl-Schwaighofer R, Wekerle T, Huppa JB, Sykes M, Oberbauer R. Prospective Tracking of Donor-Reactive T-Cell Clones in the Circulation and Rejecting Human Kidney Allografts. Front Immunol 2021; 12:750005. [PMID: 34721420 PMCID: PMC8552542 DOI: 10.3389/fimmu.2021.750005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Antigen recognition of allo-peptides and HLA molecules leads to the activation of donor-reactive T-cells following transplantation, potentially causing T-cell-mediated rejection (TCMR). Sequencing of the T-cell receptor (TCR) repertoire can be used to track the donor-reactive repertoire in blood and tissue of patients after kidney transplantation. Methods/Design In this prospective cohort study, 117 non-sensitized kidney transplant recipients with anti-CD25 induction were included. Peripheral mononuclear cells (PBMCs) were sampled pre-transplant and at the time of protocol or indication biopsies together with graft tissue. Next-generation sequencing (NGS) of the CDR3 region of the TCRbeta chain was performed after donor stimulation in mixed lymphocyte reactions to define the donor-reactive TCR repertoire. Blood and tissue of six patients experiencing a TCMR and six patients without rejection on protocol biopsies were interrogated for these TCRs. To elucidate common features of T-cell clonotypes, a network analysis of the TCR repertoires was performed. Results After transplantation, the frequency of circulating donor-reactive CD4 T-cells increased significantly from 0.86 ± 0.40% to 2.06 ± 0.40% of all CD4 cells (p < 0.001, mean dif.: -1.197, CI: -1.802, -0.593). The number of circulating donor-reactive CD4 clonotypes increased from 0.72 ± 0.33% to 1.89 ± 0.33% (p < 0.001, mean dif.: -1.168, CI: -1.724, -0.612). No difference in the percentage of donor-reactive T-cells in the circulation at transplant biopsy was found between subjects experiencing a TCMR and the control group [p = 0.64 (CD4+), p = 0.52 (CD8+)]. Graft-infiltrating T-cells showed an up to six-fold increase of donor-reactive T-cell clonotypes compared to the blood at the same time (3.7 vs. 0.6% and 2.4 vs. 1.5%), but the infiltrating TCR repertoire was not reflected by the composition of the circulating TCR repertoire despite some overlap. Network analysis showed a distinct segregation of the donor-reactive repertoire with higher modularity than the overall TCR repertoire in the blood. These findings indicate an unchoreographed process of diverse T-cell clones directed against numerous non-self antigens found in the allograft. Conclusion Donor-reactive T-cells are enriched in the kidney allograft during a TCMR episode, and dominant tissue clones are also found in the blood. Trial Registration Clinicaltrials.gov: NCT: 03422224 (https://clinicaltrials.gov/ct2/show/NCT03422224).
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Affiliation(s)
- Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Kira Jelencsics
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mariella Gloria Gregorich
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.,Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Stephan M Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Johannes Weinberger
- Research Laboratory of Infection Biology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisabeth Pimenov
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Eder
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Heinz Regele
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Thomas Wekerle
- Department of General Surgery, Division of Transplantation, Section of Transplantation Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes Bernhard Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Megan Sykes
- Columbian Center for Translational Immunology, Department of Medicine, Columbia University, New York City, NY, United States
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
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90
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Brunk F, Moritz A, Nelde A, Bilich T, Casadei N, Fraschka SAK, Heitmann JS, Hörber S, Peter A, Rammensee H, Singh H, Walz J, Maurer D, Wagner C. SARS-CoV-2-reactive T-cell receptors isolated from convalescent COVID-19 patients confer potent T-cell effector function. Eur J Immunol 2021; 51:2651-2664. [PMID: 34424997 PMCID: PMC8646365 DOI: 10.1002/eji.202149290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/25/2021] [Indexed: 11/25/2022]
Abstract
Both B cells and T cells are involved in an effective immune response to SARS-CoV-2, the disease-causing virus of COVID-19. While B cells-with the indispensable help of CD4+ T cells-are essential to generate neutralizing antibodies, T cells on their own have been recognized as another major player in effective anti-SARS-CoV-2 immunity. In this report, we provide insights into the characteristics of individual HLA-A*02:01- and HLA-A*24:02-restricted SARS-CoV-2-reactive TCRs, isolated from convalescent COVID-19 patients. We observed that SARS-CoV-2-reactive T-cell populations were clearly detectable in convalescent samples and that TCRs isolated from these T cell clones were highly functional upon ectopic re-expression. The SARS-CoV-2-reactive TCRs described in this report mediated potent TCR signaling in reporter assays with low nanomolar EC50 values. We further demonstrate that these SARS-CoV-2-reactive TCRs conferred powerful T-cell effector function to primary CD8+ T cells as evident by a robust anti-SARS-CoV-2 IFN-γ response and in vitro cytotoxicity. We also provide an example of a long-lasting anti-SARS-CoV-2 memory response by reisolation of one of the retrieved TCRs 5 months after initial sampling. Taken together, these findings contribute to a better understanding of anti-SARS-CoV-2 T-cell immunity and may contribute to paving the way toward immunotherapeutics approaches targeting SARS-CoV-2.
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Affiliation(s)
| | | | - Annika Nelde
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Nicolas Casadei
- NGS Competence Center TübingenTübingenGermany
- Institute of Medical Genetics and Applied GenomicsUniversity Hospital TübingenTübingenGermany
| | - Sabine A. K. Fraschka
- NGS Competence Center TübingenTübingenGermany
- Institute of Medical Genetics and Applied GenomicsUniversity Hospital TübingenTübingenGermany
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Sebastian Hörber
- Department for Diagnostic Laboratory MedicineInstitute for Clinical Chemistry and PathobiochemistryUniversity Hospital TübingenTübingenGermany
| | - Andreas Peter
- Department for Diagnostic Laboratory MedicineInstitute for Clinical Chemistry and PathobiochemistryUniversity Hospital TübingenTübingenGermany
| | - Hans‐Georg Rammensee
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Partner Site TübingenTübingenGermany
| | | | - Juliane Walz
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
- Dr. Margarete Fischer‐Bosch Institute of Clinical Pharmacology, Robert Bosch Center for Tumor Diseases (RBCT)StuttgartGermany
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91
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Dalai SC, Baldo L. Letter to the editor regarding 'perspective: diagnostic laboratories should urgently develop T cell assays for SARS-CoV-2 infection'. Expert Rev Clin Immunol 2021; 17:1155-1157. [PMID: 34547963 PMCID: PMC8477584 DOI: 10.1080/1744666x.2021.1982385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/15/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Sudeb C. Dalai
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, WA, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lance Baldo
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, WA, USA
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92
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Hou X, Wang G, Fan W, Chen X, Mo C, Wang Y, Gong W, Wen X, Chen H, He D, Mo L, Jiang S, Ou M, Guo H, Liu H. T-cell receptor repertoires as potential diagnostic markers for patients with COVID-19. Int J Infect Dis 2021; 113:308-317. [PMID: 34688948 PMCID: PMC8530772 DOI: 10.1016/j.ijid.2021.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/25/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Objective Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health emergency. T-cell receptors (TCRs) are crucial mediators of antiviral adaptive immunity. This study sought to comprehensively characterize the TCR repertoire changes in patients with COVID-19. Methods A large sample size multi-center randomized controlled trial was implemented to study the features of the TCR repertoire and identify COVID-19 disease-related TCR sequences. Results It was found that some T-cell receptor beta chain (TCRβ) features differed markedly between COVID-19 patients and healthy controls, including decreased repertoire diversity, longer complementarity-determining region 3 (CDR3) length, skewed utilization of the TCRβ variable gene/joining gene (TRBV/J), and a high degree of TCRβ sharing in COVID-19 patients. Moreover, this analysis showed that TCR repertoire diversity declines with aging, which may be a cause of the higher infection and mortality rates in elderly patients. Importantly, a set of TCRβ clones that can distinguish COVID-19 patients from healthy controls with high accuracy was identified. Notably, this diagnostic model demonstrates 100% specificity and 82.68% sensitivity at 0–3 days post diagnosis. Conclusions This study lays the foundation for immunodiagnosis and the development of medicines and vaccines for COVID-19 patients.
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Affiliation(s)
- Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Guangyu Wang
- College of Laboratory Medicine, Guilin Medical University, Guilin, 541199, China
| | - Wentao Fan
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Xiaoyan Chen
- Department of State Owned Assets Management, Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Chune Mo
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Yongsi Wang
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Weiwei Gong
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Xuyan Wen
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Hui Chen
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Dan He
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Lijun Mo
- Clinical Laboratory, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Shaofeng Jiang
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, 541199, China
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Haonan Guo
- Department of Clinical Laboratory, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China.
| | - Hongbo Liu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
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93
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Gong M, Li X, Zheng A, Xu H, Xie S, Yan R, Wu H, Wang Z. Age-related changes in the TRB and IGH repertoires in healthy adult males and females. Immunol Lett 2021; 240:71-6. [PMID: 34666136 DOI: 10.1016/j.imlet.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/27/2021] [Accepted: 10/08/2021] [Indexed: 11/22/2022]
Abstract
A diverse immune repertoire is capable of recognizing the enormous universe of foreign antigens encountered over life. Aging has a profound impact on the immune repertoires. However, whether continuous age-related changes in the immune repertoires differ between sexes is unclear. In this study, the characteristics of immune repertoires stratified by sex during aging are deciphered by analyzing T-cell receptor β-chain (TRB) and immunoglobulin heavy chain (IGH) sequences in 361 healthy adults. A similar change was observed between males and females across their lifespan, whereas age-subgroup analysis revealed sex-specific signatures in TRB and IGH repertoires. In regard to TRB, in males, repertoire richness and evenness increases slightly before the age of 32 years and 45 years respectively, and decreases sharply thereafter. Intriguingly, in females, they decrease significantly until around the age 57 years old, and subsequently undergo a stable stage up to the age of 83 years. Although IGH repertoire evenness increases significantly with age in both sexes, richness decreases significantly with age in males but remains stable in females. Moreover, average length of IGH CDR3 increases with age. In conclusion, these findings provide fundamental insights into the mechanisms underlying sex differences in adaptive immunity.
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94
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Zhou H, Ma L, Liu L, Yao X. TR Locus Annotation and Characteristics of Rhinolophus ferrumequinum. Front Immunol 2021; 12:741408. [PMID: 34659234 PMCID: PMC8514952 DOI: 10.3389/fimmu.2021.741408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
T-cell antigen receptors (TRs) in vertebrates can be divided into αβ or γδ, encoded by TRA/D, TRG, or TRB loci. TRs play a central role in mammal cellular immunity, which occurs by rearrangement of V, D, J, and C genes in the loci. The bat is the only mammal with flying ability and is considered the main host of zoonotic viruses, an important public health concern. However, at present, little is known about the composition of bat TR genes. Based on the whole genome sequence of the greater horseshoe bat (Rhinolophus ferrumequinum) and referring to the TR/IG annotation rules formulated by the international ImMunoGeneTics information system (IMGT), we present a complete annotation of TRA/D, TRG, and TRB loci of R. ferrumequinum. A total of 128 V segments, three D segments, 85 J segments, and 6 C segments were annotated and compared with other known mammalian data. The characteristics of the TR locus and germline genes of R. ferrumequinum are analyzed.
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Affiliation(s)
- Hao Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Longyu Liu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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95
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Campillo-Davo D, Anguille S, Lion E. Trial Watch: Adoptive TCR-Engineered T-Cell Immunotherapy for Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:4519. [PMID: 34572745 DOI: 10.3390/cancers13184519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Acute myeloid leukemia (AML) is a type of blood cancer with an extremely grim prognosis. This is due to the fact that the majority of patients will relapse after frontline treatment. Overall survival of relapsed AML is very low, and treatment options are few. T lymphocytes harnessed with antitumor T-cell receptors (TCRs) can produce objective clinical responses in certain cancers, such as melanoma, but have not entered the main road for AML. In this review, we describe the current status of the field of TCR-T-cell therapies for AML. Abstract Despite the advent of novel therapies, acute myeloid leukemia (AML) remains associated with a grim prognosis. This is exemplified by 5-year overall survival rates not exceeding 30%. Even with frontline high-intensity chemotherapy regimens and allogeneic hematopoietic stem cell transplantation, the majority of patients with AML will relapse. For these patients, treatment options are few, and novel therapies are urgently needed. Adoptive T-cell therapies represent an attractive therapeutic avenue due to the intrinsic ability of T lymphocytes to recognize tumor cells with high specificity and efficiency. In particular, T-cell therapies focused on introducing T-cell receptors (TCRs) against tumor antigens have achieved objective clinical responses in solid tumors such as synovial sarcoma and melanoma. However, contrary to chimeric antigen receptor (CAR)-T cells with groundbreaking results in B-cell malignancies, the use of TCR-T cells for hematological malignancies is still in its infancy. In this review, we provide an overview of the status and clinical advances in adoptive TCR-T-cell therapy for the treatment of AML.
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96
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Zhou Y, Maldini CR, Jadlowsky J, Riley JL. Challenges and Opportunities of Using Adoptive T-Cell Therapy as Part of an HIV Cure Strategy. J Infect Dis 2021; 223:38-45. [PMID: 33586770 DOI: 10.1093/infdis/jiaa223] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
HIV-infected individuals successfully controlling viral replication via antiretroviral therapy often have a compromised HIV-specific T-cell immune response due to the lack of CD4 T-cell help, viral escape, T-cell exhaustion, and reduction in numbers due to the withdrawal of cognate antigen. A successful HIV cure strategy will likely involve a durable and potent police force that can effectively recognize and eliminate remaining virus that may emerge decades after an individual undergoes an HIV cure regimen. T cells are ideally suited to serve in this role, but given the state of the HIV-specific T-cell response, it is unclear how to best restore HIV-specific T-cell activity prior initiation of a HIV cure strategy. Here, we review several strategies of generating HIV-specific T cells ex vivo that are currently being tested in the clinic and discuss how infused T cells can be part of an HIV cure strategy.
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Affiliation(s)
- Yuqi Zhou
- Department of Microbiology, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Colby R Maldini
- Department of Microbiology, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie Jadlowsky
- Department of Microbiology, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James L Riley
- Department of Microbiology, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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97
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Lamacchia C, Calderin Sollet Z, Courvoisier D, Mongin D, Palmer G, Studer O, Gabay C, Villard J, Buhler S, Finckh A. Detection of circulating highly expanded T-cell clones in at-risk individuals for rheumatoid arthritis before the clinical onset of the disease. Rheumatology (Oxford) 2021; 60:3451-3460. [PMID: 33291148 DOI: 10.1093/rheumatology/keaa790] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/19/2020] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES To quantitatively profile the T-cell repertoire in the peripheral blood of individuals genetically at risk for RA, namely first-degree relatives of RA patients (RA-FDR) at different phases of disease development. METHODS Next-generation sequencing of the TCR CDR3β repertoire was performed on genomic DNA isolated from whole blood samples of RA-FDR selected at three different pre-clinical stages and of matched RA patients (n = 20/group). T-cell clones were identified by their unique sequence and their degree of expansion (frequency) within each sample was characterized. Clones with a frequency over 0.5% were considered highly expanded clones (HEC). RESULTS The absolute number of HEC was significantly higher in established RA patients (mean 4.65) and tended to be higher in symptomatic RA-FDR (mean 3.4) compared with asymptomatic RA-FDR (mean 1.55, P =0.003 and P =0.07, respectively). Asymptomatic individuals with high levels of ACPA did not differ from asymptomatic RA-FDR in terms of absolute number and frequency of clones. The number of HEC tended to be slightly higher at the time of RA onset (P =0.055). Neither clones shared by several patients, nor clones previously associated with RA, were preferentially present within or between the different groups. Finally, a longitudinal analysis did not allow to uncover a kinetic expansion of RA-specific clones closely correlated with disease development. CONCLUSIONS HEC were detected in the peripheral blood before the clinical onset of RA, in particular in the later pre-clinical phase of RA development, and their presence increased over time.
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Affiliation(s)
- Céline Lamacchia
- Division of Rheumatology, Department of Internal Medicine Specialities
| | - Zuleika Calderin Sollet
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals
| | | | - Denis Mongin
- Division of Rheumatology, Department of Internal Medicine Specialities
| | - Gaby Palmer
- Division of Rheumatology, Department of Internal Medicine Specialities.,Department of Pathology-Immunology, University of Geneva School of Medicine, Geneva, Switzerland
| | - Oliva Studer
- Division of Rheumatology, Department of Internal Medicine Specialities
| | - Cem Gabay
- Division of Rheumatology, Department of Internal Medicine Specialities.,Department of Pathology-Immunology, University of Geneva School of Medicine, Geneva, Switzerland
| | - Jean Villard
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals
| | - Stéphane Buhler
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals
| | - Axel Finckh
- Division of Rheumatology, Department of Internal Medicine Specialities
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98
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Moris P, De Pauw J, Postovskaya A, Gielis S, De Neuter N, Bittremieux W, Ogunjimi B, Laukens K, Meysman P. Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. Brief Bioinform 2021; 22:bbaa318. [PMID: 33346826 PMCID: PMC8294552 DOI: 10.1093/bib/bbaa318] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The prediction of epitope recognition by T-cell receptors (TCRs) has seen many advancements in recent years, with several methods now available that can predict recognition for a specific set of epitopes. However, the generic case of evaluating all possible TCR-epitope pairs remains challenging, mainly due to the high diversity of the interacting sequences and the limited amount of currently available training data. In this work, we provide an overview of the current state of this unsolved problem. First, we examine appropriate validation strategies to accurately assess the generalization performance of generic TCR-epitope recognition models when applied to both seen and unseen epitopes. In addition, we present a novel feature representation approach, which we call ImRex (interaction map recognition). This approach is based on the pairwise combination of physicochemical properties of the individual amino acids in the CDR3 and epitope sequences, which provides a convolutional neural network with the combined representation of both sequences. Lastly, we highlight various challenges that are specific to TCR-epitope data and that can adversely affect model performance. These include the issue of selecting negative data, the imbalanced epitope distribution of curated TCR-epitope datasets and the potential exchangeability of TCR alpha and beta chains. Our results indicate that while extrapolation to unseen epitopes remains a difficult challenge, ImRex makes this feasible for a subset of epitopes that are not too dissimilar from the training data. We show that appropriate feature engineering methods and rigorous benchmark standards are required to create and validate TCR-epitope predictive models.
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MESH Headings
- Animals
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Humans
- Macaca mulatta
- Mice
- Models, Genetic
- Models, Immunological
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pieter Meysman
- Corresponding author: Pieter Meysman, Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, 2020, Belgium. E-mail:
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99
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Al-Akioui-Sanz K, Moraru M, Vilches C. A simple genotyping method for CD247 3'-untranslated region polymorphism rs1052231 and characterization of a reference cell panel. HLA 2021; 98:218-222. [PMID: 34233083 PMCID: PMC9291556 DOI: 10.1111/tan.14361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
CD247 (or CD3‐ζ chain) is an essential adaptor and signal‐transducing molecule of the T‐cell antigen receptor (TCR) complex, and it also couples to NK‐cell activating receptors such as NKp46, NKp30 and CD16A (FcγRIII). Noncoding sequence polymorphisms and variations in CD247 expression, a tightly regulated process, have been related with an altered immune response in multiple health conditions. A single nucleotide polymorphism (T > A) at nucleotide 844 of the CD247 3′‐untranslated region, rs1052231, has been related with lower CD247 gene expression and it has been investigated as a potential biomarker of autoimmune disease. We present here a simple, accurate, reliable, time‐efficient, and cost‐effective method for CD247‐rs1052231 genotyping. Using this method, based on polymerase chain reaction with confronting two‐pair primers (PCR‐CTPP), we have also characterized the CD247‐rs1052231 genotypes in a panel of worldwide available cell lines, which should facilitate study of the role of this polymorphism in immunity and human health.
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Affiliation(s)
- Karima Al-Akioui-Sanz
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| | - Manuela Moraru
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| | - Carlos Vilches
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
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100
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de Sousa E, Lérias JR, Beltran A, Paraschoudi G, Condeço C, Kamiki J, António PA, Figueiredo N, Carvalho C, Castillo-Martin M, Wang Z, Ligeiro D, Rao M, Maeurer M. Targeting Neoepitopes to Treat Solid Malignancies: Immunosurgery. Front Immunol 2021; 12:592031. [PMID: 34335558 PMCID: PMC8320363 DOI: 10.3389/fimmu.2021.592031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
Successful outcome of immune checkpoint blockade in patients with solid cancers is in part associated with a high tumor mutational burden (TMB) and the recognition of private neoantigens by T-cells. The quality and quantity of target recognition is determined by the repertoire of ‘neoepitope’-specific T-cell receptors (TCRs) in tumor-infiltrating lymphocytes (TIL), or peripheral T-cells. Interferon gamma (IFN-γ), produced by T-cells and other immune cells, is essential for controlling proliferation of transformed cells, induction of apoptosis and enhancing human leukocyte antigen (HLA) expression, thereby increasing immunogenicity of cancer cells. TCR αβ-dependent therapies should account for tumor heterogeneity and availability of the TCR repertoire capable of reacting to neoepitopes and functional HLA pathways. Immunogenic epitopes in the tumor-stroma may also be targeted to achieve tumor-containment by changing the immune-contexture in the tumor microenvironment (TME). Non protein-coding regions of the tumor-cell genome may also contain many aberrantly expressed, non-mutated tumor-associated antigens (TAAs) capable of eliciting productive anti-tumor immune responses. Whole-exome sequencing (WES) and/or RNA sequencing (RNA-Seq) of cancer tissue, combined with several layers of bioinformatic analysis is commonly used to predict possible neoepitopes present in clinical samples. At the ImmunoSurgery Unit of the Champalimaud Centre for the Unknown (CCU), a pipeline combining several tools is used for predicting private mutations from WES and RNA-Seq data followed by the construction of synthetic peptides tailored for immunological response assessment reflecting the patient’s tumor mutations, guided by MHC typing. Subsequent immunoassays allow the detection of differential IFN-γ production patterns associated with (intra-tumoral) spatiotemporal differences in TIL or peripheral T-cells versus TIL. These bioinformatics tools, in addition to histopathological assessment, immunological readouts from functional bioassays and deep T-cell ‘adaptome’ analyses, are expected to advance discovery and development of next-generation personalized precision medicine strategies to improve clinical outcomes in cancer in the context of i) anti-tumor vaccination strategies, ii) gauging mutation-reactive T-cell responses in biological therapies and iii) expansion of tumor-reactive T-cells for the cellular treatment of patients with cancer.
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Affiliation(s)
- Eric de Sousa
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Joana R Lérias
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Antonio Beltran
- Department of Pathology, Champalimaud Clinical Centre, Lisbon, Portugal
| | | | - Carolina Condeço
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Jéssica Kamiki
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | - Nuno Figueiredo
- Digestive Unit, Champalimaud Clinical Centre, Lisbon, Portugal
| | - Carlos Carvalho
- Digestive Unit, Champalimaud Clinical Centre, Lisbon, Portugal
| | | | - Zhe Wang
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China
| | - Dário Ligeiro
- Lisbon Centre for Blood and Transplantation, Instituto Português do Sangue e Transplantação (IPST), Lisbon, Portugal
| | - Martin Rao
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal.,I Medical Clinic, Johannes Gutenberg University of Mainz, Mainz, Germany
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