1
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Moravec Z, Zhao Y, Voogd R, Cook DR, Kinrot S, Capra B, Yang H, Raud B, Ou J, Xuan J, Wei T, Ren L, Hu D, Wang J, Haanen JBAG, Schumacher TN, Chen X, Porter E, Scheper W. Discovery of tumor-reactive T cell receptors by massively parallel library synthesis and screening. Nat Biotechnol 2024:10.1038/s41587-024-02210-6. [PMID: 38653798 DOI: 10.1038/s41587-024-02210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
T cell receptor (TCR) gene therapy is a potent form of cellular immunotherapy in which patient T cells are genetically engineered to express TCRs with defined tumor reactivity. However, the isolation of therapeutic TCRs is complicated by both the general scarcity of tumor-specific T cells among patient T cell repertoires and the patient-specific nature of T cell epitopes expressed on tumors. Here we describe a high-throughput, personalized TCR discovery pipeline that enables the assembly of complex synthetic TCR libraries in a one-pot reaction, followed by pooled expression in reporter T cells and functional genetic screening against patient-derived tumor or antigen-presenting cells. We applied the method to screen thousands of tumor-infiltrating lymphocyte (TIL)-derived TCRs from multiple patients and identified dozens of CD4+ and CD8+ T-cell-derived TCRs with potent tumor reactivity, including TCRs that recognized patient-specific neoantigens.
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Affiliation(s)
- Ziva Moravec
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yue Zhao
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Rhianne Voogd
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Haiyan Yang
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Brenda Raud
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jiayu Ou
- RootPath, Inc. (Guangzhou), Guangzhou, China
| | - Jiekun Xuan
- RootPath, Inc. (US), Watertown, MA, USA
- RootPath, Inc. (Hangzhou), Hangzhou, China
| | - Teng Wei
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Lili Ren
- Cytotherapy Laboratory, People's Hospital, Shenzhen, Guangdong, China
| | - Dandan Hu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - John B A G Haanen
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Xi Chen
- RootPath, Inc. (Guangzhou), Guangzhou, China.
- RootPath, Inc. (US), Watertown, MA, USA.
- RootPath, Inc. (Hangzhou), Hangzhou, China.
| | - Ely Porter
- RootPath, Inc. (US), Watertown, MA, USA.
| | - Wouter Scheper
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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2
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Yang Q, Patrick M, Lu J, Chen J, Zhang Y, Hemani H, Lehrmann E, De S, Weng NP. Homeodomain-only protein suppresses proliferation and contributes to differentiation- and age-related reduced CD8 + T cell expansion. Front Immunol 2024; 15:1360229. [PMID: 38410516 PMCID: PMC10895957 DOI: 10.3389/fimmu.2024.1360229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
T cell activation is a tightly controlled process involving both positive and negative regulators. The precise mechanisms governing the negative regulators in T cell proliferation remain incompletely understood. Here, we report that homeodomain-only protein (HOPX), a homeodomain-containing protein, and its most abundant isoform HOPXb, negatively regulate activation-induced proliferation of human T cells. We found that HOPX expression progressively increased from naïve (TN) to central memory (TCM) to effector memory (TEM) cells, with a notable upregulation following in vitro stimulation. Overexpression of HOPXb leads to a reduction in TN cell proliferation while HOPX knockdown promotes proliferation of TN and TEM cells. Furthermore, we demonstrated that HOPX binds to promoters and exerts repressive effects on the expression of MYC and NR4A1, two positive regulators known to promote T cell proliferation. Importantly, our findings suggest aging is associated with increased HOPX expression, and that knockdown of HOPX enhances the proliferation of CD8+ T cells in older adults. Our findings provide compelling evidence that HOPX serves as a negative regulator of T cell activation and plays a pivotal role in T cell differentiation and in age-related-reduction in T cell proliferation.
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Affiliation(s)
- Qian Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Michael Patrick
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Jian Lu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Joseph Chen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Humza Hemani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Elin Lehrmann
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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3
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Cetin M, Pinamonti V, Schmid T, Boschert T, Mellado Fuentes A, Kromer K, Lerner T, Zhang J, Herzig Y, Ehlert C, Hernandez-Hernandez M, Samaras G, Torres CM, Fisch L, Dragan V, Kouwenhoven A, Van Schoubroeck B, Wils H, Van Hove C, Platten M, Green EW, Stevenaert F, Felix NJ, Lindner JM. T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery. SCIENCE ADVANCES 2024; 10:eadk3060. [PMID: 38306432 PMCID: PMC10836725 DOI: 10.1126/sciadv.adk3060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequisite to diagnostic and therapeutic applications, yet remain underdeveloped. Here, we present T-FINDER [T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors], a system to rapidly deconvolute CD4 and CD8 TCRs and targets physiologically processed and presented by an individual's unmanipulated, complete human leukocyte antigen (HLA) haplotype. Combining a highly sensitive TCR signaling reporter with an antigen processing system to overcome previously undescribed limitations to target expression, T-FINDER both robustly identifies unknown peptide:HLA ligands from antigen libraries and rapidly screens and functionally validates the specificity of large TCR libraries against known or predicted targets. To demonstrate its capabilities, we apply the platform to multiple TCR-based applications, including diffuse midline glioma, celiac disease, and rheumatoid arthritis, providing unique biological insights and showcasing T-FINDER's potency and versatility.
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Affiliation(s)
- Miray Cetin
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Veronica Pinamonti
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Theresa Schmid
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Tamara Boschert
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Helmoltz Institute for Translational Oncology (HI-TRON), Heidelberg, Germany
| | | | - Kristina Kromer
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Taga Lerner
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Jing Zhang
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Yonatan Herzig
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | - Christopher Ehlert
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), 69118 Heidelberg, Germany
| | | | - Georgios Samaras
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
| | | | - Laura Fisch
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Valeriia Dragan
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | | | | | - Hans Wils
- Janssen Research and Development, Beerse, Belgium
| | | | - Michael Platten
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Helmoltz Institute for Translational Oncology (HI-TRON), Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | - Edward W. Green
- DKTK CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany
| | | | | | - John M. Lindner
- BioMed X GmbH, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany
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4
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Christodoulou MI, Zaravinos A. Single-Cell Analysis in Immuno-Oncology. Int J Mol Sci 2023; 24:ijms24098422. [PMID: 37176128 PMCID: PMC10178969 DOI: 10.3390/ijms24098422] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The complexity of the cellular and non-cellular milieu surrounding human tumors plays a decisive role in the course and outcome of disease. The high variability in the distribution of the immune and non-immune compartments within the tumor microenvironments (TME) among different patients governs the mode of their response or resistance to current immunotherapeutic approaches. Through deciphering this diversity, one can tailor patients' management to meet an individual's needs. Single-cell (sc) omics technologies have given a great boost towards this direction. This review gathers recent data about how multi-omics profiling, including the utilization of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (scATAC-seq), T-cell receptor sequencing (scTCR-seq), mass, tissue-based, or microfluidics cytometry, and related bioinformatics tools, contributes to the high-throughput assessment of a large number of analytes at single-cell resolution. Unravelling the exact TCR clonotype of the infiltrating T cells or pinpointing the classical or novel immune checkpoints across various cell subsets of the TME provide a boost to our comprehension of adaptive immune responses, their antigen specificity and dynamics, and grant suggestions for possible therapeutic targets. Future steps are expected to merge high-dimensional data with tissue localization data, which can serve the investigation of novel multi-modal biomarkers for the selection and/or monitoring of the optimal treatment from the current anti-cancer immunotherapeutic armamentarium.
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Affiliation(s)
- Maria-Ioanna Christodoulou
- Tumor Immunology and Biomarkers Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
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5
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Wegrecki M, Ocampo TA, Gunasinghe SD, von Borstel A, Tin SY, Reijneveld JF, Cao TP, Gully BS, Le Nours J, Moody DB, Van Rhijn I, Rossjohn J. Atypical sideways recognition of CD1a by autoreactive γδ T cell receptors. Nat Commun 2022; 13:3872. [PMID: 35790773 PMCID: PMC9256601 DOI: 10.1038/s41467-022-31443-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/16/2022] [Indexed: 01/04/2023] Open
Abstract
CD1a is a monomorphic antigen-presenting molecule on dendritic cells that presents lipids to αβ T cells. Whether CD1a represents a ligand for other immune receptors remains unknown. Here we use CD1a tetramers to show that CD1a is a ligand for Vδ1+ γδ T cells. Functional studies suggest that two γδ T cell receptors (TCRs) bound CD1a in a lipid-independent manner. The crystal structures of three Vγ4Vδ1 TCR-CD1a-lipid complexes reveal that the γδ TCR binds at the extreme far side and parallel to the long axis of the β-sheet floor of CD1a's antigen-binding cleft. Here, the γδ TCR co-recognises the CD1a heavy chain and β2 microglobulin in a manner that is distinct from all other previously observed γδ TCR docking modalities. The 'sideways' and lipid antigen independent mode of autoreactive CD1a recognition induces TCR clustering on the cell surface and proximal T cell signalling as measured by CD3ζ phosphorylation. In contrast with the 'end to end' binding of αβ TCRs that typically contact carried antigens, autoreactive γδ TCRs support geometrically diverse approaches to CD1a, as well as antigen independent recognition.
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Affiliation(s)
- Marcin Wegrecki
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tonatiuh A Ocampo
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US
| | - Sachith D Gunasinghe
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shin Yi Tin
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Josephine F Reijneveld
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thinh-Phat Cao
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Benjamin S Gully
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US.
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US.
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.
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6
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Guo T, Ma D, Lu TK. Sense-and-Respond Payload Delivery Using a Novel Antigen-Inducible Promoter Improves Suboptimal CAR-T Activation. ACS Synth Biol 2022; 11:1440-1453. [PMID: 35316028 PMCID: PMC9016769 DOI: 10.1021/acssynbio.1c00236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Chimeric antigen
receptor (CAR)-T cell therapies demonstrate the
clinical potential of lymphocytes engineered with synthetic properties.
However, CAR-T cells are ineffective in most solid tumors, partly
due to inadequate activation of the infused lymphocytes at the site
of malignancy. To selectively enhance antitumor efficacy without exacerbating
off-target toxicities, CAR-T cells can be engineered to preferentially
deliver immunostimulatory payloads in tumors. Here, we report a novel
antigen-inducible promoter for conditional payload expression in primary
human T cells. In therapeutic T cell models, the novel NR4A-based
promoter induced higher reporter gene expression than the conventional
NFAT-based promoter under weakly immunogenic conditions, where payload
expression is most needed. Minimal activity was detected from the
inducible promoters in the absence of antigen and after withdrawal
of stimulation. As a functional proof-of-concept, we used the NR4A-based
promoter to express cytokines in an antimesothelin CAR-T model with
suboptimal stimulation and observed improved proliferation compared
to T cells engineered with the conventional NFAT promoter or CAR alone.
Our system achieves CAR-directed payload expression under weakly immunogenic
conditions and could enable the next generation of cell therapies
with enhanced antitumor efficacy.
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Affiliation(s)
- Tingxi Guo
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dacheng Ma
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Senti Biosciences, South San Francisco, California 94080, United States
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7
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Fahad AS, Chung CY, Lopez Acevedo SN, Boyle N, Madan B, Gutiérrez-González MF, Matus-Nicodemos R, Laflin AD, Ladi RR, Zhou J, Wolfe J, Llewellyn-Lacey S, Koup RA, Douek DC, Balfour Jr HH, Price DA, DeKosky BJ. Immortalization and functional screening of natively paired human T cell receptor repertoires. Protein Eng Des Sel 2022; 35:gzab034. [PMID: 35174859 PMCID: PMC9005053 DOI: 10.1093/protein/gzab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. We developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale, and to exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen-specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of disease-relevant antigen interactions with human TCRs.
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Affiliation(s)
- Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Cheng-Yu Chung
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Sheila N Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Nicoleen Boyle
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | | | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Rukmini R Ladi
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - John Zhou
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Jacy Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry H Balfour Jr
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66044, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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8
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Xia Q, Huang H, Davis MM. A High-Throughput Strategy for T-Cell Receptor Cloning and Expression. Methods Mol Biol 2022; 2574:251-264. [PMID: 36087206 PMCID: PMC10035758 DOI: 10.1007/978-1-0716-2712-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Expression of T-cell receptor (TCR) genes is a critical step for TCR characterization and epitope identification. The recent interest in using specific TCRs for cancer immunotherapy has further increased the demand for practical and robust methods to rapidly clone and express TCRs. We show that a recombination-based cloning protocol facilitates simple and rapid transfer of the TCR transgene into different expression systems. In this protocol, we first constructed all the human TRAV and TRBV genes into individual plasmid. To clone any TCR, we only need to ligate a short CDR3 fragment to its corresponding V gene plasmid using Golden Gate cloning. This strategy significantly improves the efficiency of individual TCR cloning and mutagenesis, providing a flexible high-throughput method for TCR analysis and TCR-mediated therapeutics.
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Affiliation(s)
- Qiong Xia
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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9
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Wahl I, Hoffmann S, Hundsdorfer R, Puchan J, Hoffman SL, Kremsner PG, Mordmüller B, Busse CE, Wardemann H. An efficient single-cell based method for linking human T cell phenotype to T cell receptor sequence and specificity. Eur J Immunol 2021; 52:237-246. [PMID: 34710239 DOI: 10.1002/eji.202149392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/16/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022]
Abstract
Single-cell antigen-receptor gene amplification and sequencing platforms have been used to characterize T cell receptor (TCR) repertoires but typically fail to generate paired full-length gene products for direct expression cloning and do not enable linking this data to cell phenotype information. To overcome these limitations, we established a high-throughput platform for the quantitative and qualitative analysis of human TCR repertoires that provides insights into the clonal and functional composition of human CD4+ and CD8+ αβ T cells at the molecular and cellular level. The strategy is a powerful tool to qualitatively assess differences between antigen receptors of phenotypically defined αβ T cell subsets, e.g. in immune responses to cancer, vaccination, or infection, and in autoimmune diseases.
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Affiliation(s)
- Ilka Wahl
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany.,Biosciences Faculty, University of Heidelberg, Heidelberg, Germany
| | - Sandro Hoffmann
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | - Julia Puchan
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter G Kremsner
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Benjamin Mordmüller
- Institute of Tropical Medicine and German Center for Infection Research, University of Tübingen, Tübingen, Germany.,Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian E Busse
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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10
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Chen L, Dong L, Ma Y, Wang J, Qiao D, Tian G, Wang M. An efficient method to identify virus-specific TCRs for TCR-T cell immunotherapy against virus-associated malignancies. BMC Immunol 2021; 22:65. [PMID: 34583647 PMCID: PMC8480097 DOI: 10.1186/s12865-021-00455-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/14/2021] [Indexed: 11/21/2022] Open
Abstract
Adoptive transfer of T cells genetically engineered with a T cell receptor (TCR) is a promising cancer treatment modality that requires the identification of TCRs with good characteristics. Most T cell cloning methods involve a stringent singularization process, which necessitates either tedious hands-on operations or high cost. We present an efficient and nonstringent cloning approach based on existing techniques. We hypothesize that after elimination of most nonspecific T cells, a clonotype with high quality could outcompete other clonotypes and finally form a predominant population. This TCR identification method can be used to clone virus-specific TCRs efficiently from cancer patients and is easily adoptable by any laboratory.
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Affiliation(s)
- Lei Chen
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Lianhua Dong
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Yipeng Ma
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Juntao Wang
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Dongjuan Qiao
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China
| | - Geng Tian
- Department of Oncology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Mingjun Wang
- Department of Research and Development, Shenzhen Institute for Innovation and Translational Medicine, Shenzhen International Biological Valley-Life Science Industrial Park, Dapeng New District, Shenzhen, China.
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11
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Almeida CF, Smith DGM, Cheng TY, Harpur CM, Batleska E, Nguyen-Robertson CV, Nguyen T, Thelemann T, Reddiex SJJ, Li S, Eckle SBG, Van Rhijn I, Rossjohn J, Uldrich AP, Moody DB, Williams SJ, Pellicci DG, Godfrey DI. Benzofuran sulfonates and small self-lipid antigens activate type II NKT cells via CD1d. Proc Natl Acad Sci U S A 2021; 118:e2104420118. [PMID: 34417291 PMCID: PMC8403964 DOI: 10.1073/pnas.2104420118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Natural killer T (NKT) cells detect lipids presented by CD1d. Most studies focus on type I NKT cells that express semi-invariant αβ T cell receptors (TCR) and recognize α-galactosylceramides. However, CD1d also presents structurally distinct lipids to NKT cells expressing diverse TCRs (type II NKT cells), but our knowledge of the antigens for type II NKT cells is limited. An early study identified a nonlipidic NKT cell agonist, phenyl pentamethyldihydrobenzofuransulfonate (PPBF), which is notable for its similarity to common sulfa drugs, but its mechanism of NKT cell activation remained unknown. Here, we demonstrate that a range of pentamethylbenzofuransulfonates (PBFs), including PPBF, activate polyclonal type II NKT cells from human donors. Whereas these sulfa drug-like molecules might have acted pharmacologically on cells, here we demonstrate direct contact between TCRs and PBF-treated CD1d complexes. Further, PBF-treated CD1d tetramers identified type II NKT cell populations expressing αβTCRs and γδTCRs, including those with variable and joining region gene usage (TRAV12-1-TRAJ6) that was conserved across donors. By trapping a CD1d-type II NKT TCR complex for direct mass-spectrometric analysis, we detected molecules that allow the binding of CD1d to TCRs, finding that both selected PBF family members and short-chain sphingomyelin lipids are present in these complexes. Furthermore, the combination of PPBF and short-chain sphingomyelin enhances CD1d tetramer staining of PPBF-reactive T cell lines over either molecule alone. This study demonstrates that nonlipidic small molecules, which resemble sulfa drugs implicated in systemic hypersensitivity and drug allergy reactions, are targeted by a polyclonal population of type II NKT cells in a CD1d-restricted manner.
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Affiliation(s)
- Catarina F Almeida
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dylan G M Smith
- School of Chemistry, The University of Melbourne, Melbourne, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Boston, MA 02115
| | - Chris M Harpur
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Elena Batleska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Catriona V Nguyen-Robertson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tram Nguyen
- School of Chemistry, The University of Melbourne, Melbourne, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Tamara Thelemann
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Scott J J Reddiex
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Ildiko Van Rhijn
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Boston, MA 02115
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University Utrecht, 3584CL Utrecht, Netherlands
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Adam P Uldrich
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - D Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women's Hospital, Boston, MA 02115;
| | - Spencer J Williams
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia;
- School of Chemistry, The University of Melbourne, Melbourne, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
- Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Melbourne, VIC 3010, Australia
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12
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Pertseva M, Gao B, Neumeier D, Yermanos A, Reddy ST. Applications of Machine and Deep Learning in Adaptive Immunity. Annu Rev Chem Biomol Eng 2021; 12:39-62. [PMID: 33852352 DOI: 10.1146/annurev-chembioeng-101420-125021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immunity is mediated by lymphocyte B and T cells, which respectively express a vast and diverse repertoire of B cell and T cell receptors and, in conjunction with peptide antigen presentation through major histocompatibility complexes (MHCs), can recognize and respond to pathogens and diseased cells. In recent years, advances in deep sequencing have led to a massive increase in the amount of adaptive immune receptor repertoire data; additionally, proteomics techniques have led to a wealth of data on peptide-MHC presentation. These large-scale data sets are now making it possible to train machine and deep learning models, which can be used to identify complex and high-dimensional patterns in immune repertoires. This article introduces adaptive immune repertoires and machine and deep learning related to biological sequence data and then summarizes the many applications in this field, which span from predicting the immunological status of a host to the antigen specificity of individual receptors and the engineering of immunotherapeutics.
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Affiliation(s)
- Margarita Pertseva
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; .,Life Science Zurich Graduate School, ETH Zurich and University of Zurich, 8006 Zurich, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; .,Department of Pathology and Immunology, University of Geneva, 1205 Geneva, Switzerland.,Department of Biology, Institute of Microbiology and Immunology, ETH Zurich, 8093 Zurich, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
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13
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Gohil SH, Iorgulescu JB, Braun DA, Keskin DB, Livak KJ. Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol 2021; 18:244-256. [PMID: 33277626 PMCID: PMC8415132 DOI: 10.1038/s41571-020-00449-x] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Advances in molecular biology, microfluidics and bioinformatics have empowered the study of thousands or even millions of individual cells from malignant tumours at the single-cell level of resolution. This high-dimensional, multi-faceted characterization of the genomic, transcriptomic, epigenomic and proteomic features of the tumour and/or the associated immune and stromal cells enables the dissection of tumour heterogeneity, the complex interactions between tumour cells and their microenvironment, and the details of the evolutionary trajectory of each tumour. Single-cell transcriptomics, the ability to track individual T cell clones through paired sequencing of the T cell receptor genes and high-dimensional single-cell spatial analysis are all areas of particular relevance to immuno-oncology. Multidimensional biomarker signatures will increasingly be crucial to guiding clinical decision-making in each patient with cancer. High-dimensional single-cell technologies are likely to provide the resolution and richness of data required to generate such clinically relevant signatures in immuno-oncology. In this Perspective, we describe advances made using transformative single-cell analysis technologies, especially in relation to clinical response and resistance to immunotherapy, and discuss the growing utility of single-cell approaches for answering important research questions.
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Affiliation(s)
- Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Academic Haematology, University College London Cancer Institute, London, UK
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA.
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14
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Zhang H, Sun M, Wang J, Zeng B, Cao X, Han Y, Tan S, Gao GF. Identification of NY-ESO-1 157-165 Specific Murine T Cell Receptors With Distinct Recognition Pattern for Tumor Immunotherapy. Front Immunol 2021; 12:644520. [PMID: 33833762 PMCID: PMC8021954 DOI: 10.3389/fimmu.2021.644520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
New York esophageal squamous cell carcinoma 1 (NY-ESO-1) is a promising target for T-cell receptor-engineered T cell (TCR-T) therapy, and targeting the human leukocyte antigen (HLA)-A2 restricted NY-ESO-1157-165 epitope has yielded remarkable clinical benefits in the treatment of multiple advanced malignancies. Herein, we report the identification of two NY-ESO-1157-165 epitope-specific murine TCRs obtained from HLA-A*0201 transgenic mice. NY-ESO-1157-165 specific TCRs were isolated after vaccinating HLA-A2 transgenic mice with epitope peptides. HZ6 and HZ8 TCRs could specifically bind to NY-ESO-1157-165/HLA-A2 and were capable of cytokine secretion with engineered Jurkat T cells and primary T cells upon recognition with K562 target cells expressing the single-chain trimer (SCT) of NY-ESO-1157-165/HLA-A2. The reactivity profiles of the HZ6 and HZ8 TCRs were found to be distinct from one another when co-cultured with K562 target cells carrying alanine-substituted NY-ESO-1157-165 SCTs. The binding characterization revealed that the recognition pattern of the HZ6 TCR to NY-ESO-1157-165/HLA-A2 was substantially different from the widely used 1G4 TCR. These findings would broaden the understanding of immunogenicity of the NY-ESO-1157-165, and the two identified TCRs may serve as promising candidates for the future development of TCR-T therapy for tumors.
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Affiliation(s)
- Helin Zhang
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Meng Sun
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin Zeng
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xiaoqing Cao
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Han
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shuguang Tan
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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15
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Gherardin NA, Waldeck K, Caneborg A, Martelotto LG, Balachander S, Zethoven M, Petrone PM, Pattison A, Wilmott JS, Quiñones-Parra SM, Rossello F, Posner A, Wong A, Weppler AM, Shannon KF, Hong A, Ferguson PM, Jakrot V, Raleigh J, Hatzimihalis A, Neeson PJ, Deleso P, Johnston M, Chua M, Becker JC, Sandhu S, McArthur GA, Gill AJ, Scolyer RA, Hicks RJ, Godfrey DI, Tothill RW. γδ T Cells in Merkel Cell Carcinomas Have a Proinflammatory Profile Prognostic of Patient Survival. Cancer Immunol Res 2021; 9:612-623. [PMID: 33674358 DOI: 10.1158/2326-6066.cir-20-0817] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/14/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022]
Abstract
Merkel cell carcinomas (MCC) are immunogenic skin cancers associated with viral infection or UV mutagenesis. To study T-cell infiltrates in MCC, we analyzed 58 MCC lesions from 39 patients using multiplex-IHC/immunofluorescence (m-IHC/IF). CD4+ or CD8+ T cells comprised the majority of infiltrating T lymphocytes in most tumors. However, almost half of the tumors harbored prominent CD4/CD8 double-negative (DN) T-cell infiltrates (>20% DN T cells), and in 12% of cases, DN T cells represented the majority of T cells. Flow cytometric analysis of single-cell suspensions from fresh tumors identified DN T cells as predominantly Vδ2- γδ T cells. In the context of γδ T-cell inflammation, these cells expressed PD-1 and LAG3, which is consistent with a suppressed or exhausted phenotype, and CD103, which indicates tissue residency. Furthermore, single-cell RNA sequencing (scRNA-seq) identified a transcriptional profile of γδ T cells suggestive of proinflammatory potential. T-cell receptor (TCR) analysis confirmed clonal expansion of Vδ1 and Vδ3 clonotypes, and functional studies using cloned γδ TCRs demonstrated restriction of these for CD1c and MR1 antigen-presenting molecules. On the basis of a 13-gene γδ T-cell signature derived from scRNA-seq analysis, gene-set enrichment on bulk RNA-seq data showed a positive correlation between enrichment scores and DN T-cell infiltrates. An improved disease-specific survival was evident for patients with high enrichment scores, and complete responses to anti-PD-1/PD-L1 treatment were observed in three of four cases with high enrichment scores. Thus, γδ T-cell infiltration may serve as a prognostic biomarker and should be explored for therapeutic interventions.See related Spotlight on p. 600.
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Affiliation(s)
- Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria, Australia
| | - Kelly Waldeck
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alex Caneborg
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Luciano G Martelotto
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Pasquale M Petrone
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sergio M Quiñones-Parra
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando Rossello
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Annie Wong
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison M Weppler
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Angela Hong
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Jeanette Raleigh
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Athena Hatzimihalis
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul J Neeson
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paolo Deleso
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Meredith Johnston
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Liverpool Hospital, Sydney, New South Wales, Australia
| | - Margaret Chua
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Juergen C Becker
- German Cancer Consortium (DKTK), Translational Skin Cancer Research, University Medicine Essen, Essen and DKFZ, Heidelberg, Germany
| | - Shahneen Sandhu
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical, Research and The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Rodney J Hicks
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Cancer Imaging Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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16
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Paria BC, Levin N, Lowery F, Pasetto A, Deniger DC, Parkhurst MR, Yossef R, Kim SP, Florentin M, Ngo L, Ray S, Krishna S, Robbins PF, Rosenberg SA. Rapid Identification and Evaluation of Neoantigen-reactive T-Cell Receptors From Single Cells. J Immunother 2021; 44:1-8. [PMID: 33086340 PMCID: PMC7725897 DOI: 10.1097/cji.0000000000000342] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Engineered T cells expressing tumor-specific T-cell receptors (TCRs) are emerging as a mode of personalized cancer immunotherapy that requires identification of TCRs against the products of known driver mutations and novel mutations in a timely fashion. We present a nonviral and non-next-generation sequencing platform for rapid, and efficient neoantigen-specific TCR identification and evaluation that does not require the use of recombinant cloning techniques. The platform includes an innovative method of TCRα detection using Sanger sequencing, TCR pairings and the use of TCRα/β gene fragments for putative TCR evaluation. Using patients' samples, we validated and compared our new methods head-to-head with conventional approaches used for TCR discovery. Development of a unique demultiplexing method for identification of TCRα, adaptation of synthetic TCRs for gene transfer, and a reliable reporter system significantly shortens TCR discovery time over conventional methods and increases throughput to facilitate testing prospective personalized TCRs for adoptive cell therapy.
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Affiliation(s)
- Biman C. Paria
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Noam Levin
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Frank Lowery
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Anna Pasetto
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Drew C. Deniger
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Maria R. Parkhurst
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Rami Yossef
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Sanghyun P. Kim
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Maria Florentin
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Lien Ngo
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Satyajit Ray
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Sri Krishna
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Paul F. Robbins
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, 20892, USA
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17
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Rollins MR, Spartz EJ, Stromnes IM. T Cell Receptor Engineered Lymphocytes for Cancer Therapy. ACTA ACUST UNITED AC 2020; 129:e97. [PMID: 32432843 DOI: 10.1002/cpim.97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
T lymphocytes are capable of specific recognition and elimination of target cells. Physiological antigen recognition is mediated by the T cell receptor (TCR), which is an alpha beta heterodimer comprising the products of randomly rearranged V, D, and J genes. The exquisite specificity and functionality of T cells can be leveraged for cancer therapy: specifically, the adoptive transfer of T cells that express tumor-reactive TCRs can induce regression of solid tumors in patients with advanced cancer. However, the isolation and expression of a tumor antigen-specific TCRs is a highly involved process that requires identifying an immunogenic epitope, ensuring human cells are of the correct haplotype, performing a laborious T cell expansion process, and carrying out downstream TCR sequencing and cloning. Recent advances in single-cell sequencing have begun to streamline this process. This protocol synthesizes and expands upon methodologies to generate, isolate, and engineer human T cells with tumor-reactive TCRs for adoptive cell therapy. Though this process is perhaps more arduous than the alternative strategy of using chimeric antigen receptors (CARs) for engineering, the ability to target intracellular proteins using TCRs substantially increases the types of antigens that can be safely targeted. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Generation of human autologous dendritic cells from monocytes Basic Protocol 2: In vitro priming and expansion of human antigen-specific T cells Basic Protocol 3: Cloning of antigen-specific T cell receptors based on single-cell VDJ sequencing data Basic Protocol 4: Validation of T cell receptor expression and functionality in vitro Basic Protocol 5: Rapid expansion of T cell receptor-transduced T cells and human T cell clones.
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Affiliation(s)
- Meagan R Rollins
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ellen J Spartz
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ingunn M Stromnes
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota.,Center for Genome Engineering, University of Minnesota Medical School, Minneapolis, Minnesota.,Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, Minnesota
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18
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Wang R, Ghumra A, Cochrane S, Fairclough L, Broughton R, Michaelson LV, Beaudoin F, Alcocer MJC. Defining lipids and T cell receptors involved in the intrinsic allergenicity of nut proteins. Clin Transl Allergy 2020; 10:54. [PMID: 33292600 PMCID: PMC7687982 DOI: 10.1186/s13601-020-00358-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/03/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Rui Wang
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ashfaq Ghumra
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Stella Cochrane
- Unilever Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, MK44 1LQ, Sharnbrook, UK.
| | - Lucy Fairclough
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Richard Broughton
- Plant Sciences Department, Rothamstead Research, Harpenden, AL5 2JQ, UK
| | | | - Frederic Beaudoin
- Plant Sciences Department, Rothamstead Research, Harpenden, AL5 2JQ, UK
| | - Marcos J C Alcocer
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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19
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Müller TR, Schuler C, Hammel M, Köhler A, Jutz S, Leitner J, Schober K, Busch DH, Steinberger P. A T-cell reporter platform for high-throughput and reliable investigation of TCR function and biology. Clin Transl Immunology 2020; 9:e1216. [PMID: 33251011 PMCID: PMC7681835 DOI: 10.1002/cti2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Transgenic re-expression enables unbiased investigation of T-cell receptor (TCR)-intrinsic characteristics detached from its original cellular context. Recent advancements in TCR repertoire sequencing and development of protocols for direct cloning of full TCRαβ constructs now facilitate large-scale transgenic TCR re-expression. Together, this offers unprecedented opportunities for the screening of TCRs for basic research as well as clinical use. However, the functional characterisation of re-expressed TCRs is still a complicated and laborious matter. Here, we propose a Jurkat-based triple parameter TCR signalling reporter endogenous TCR knockout cellular platform (TPRKO) that offers an unbiased, easy read-out of TCR functionality and facilitates high-throughput screening approaches. METHODS As a proof-of-concept, we transgenically re-expressed 59 human cytomegalovirus-specific TCRs and systematically investigated and compared TCR function in TPRKO cells versus primary human T cells. RESULTS We demonstrate that the TPRKO cell line facilitates antigen-HLA specificity screening via sensitive peptide-MHC-multimer staining, which was highly comparable to primary T cells. Also, TCR functional avidity in TPRKO cells was strongly correlating to primary T cells, especially in the absence of CD8αβ co-receptor. CONCLUSION Overall, our data show that the TPRKO cell lines can serve as a surrogate of primary human T cells for standardised and high-throughput investigation of TCR biology.
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Affiliation(s)
- Thomas R Müller
- Institute for Medical Microbiology, Immunology and HygieneTechnical University of Munich (TUM)MunichGermany
- German Center for Infection Research (DZIF)MunichGermany
| | - Corinna Schuler
- Institute for Medical Microbiology, Immunology and HygieneTechnical University of Munich (TUM)MunichGermany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and HygieneTechnical University of Munich (TUM)MunichGermany
| | - Amelie Köhler
- Institute for Medical Microbiology, Immunology and HygieneTechnical University of Munich (TUM)MunichGermany
| | - Sabrina Jutz
- Division of Immune Receptors and T Cell ActivationCenter for Pathophysiology, Infectiology, and ImmunologyInstitute of ImmunologyMedical University of ViennaViennaAustria
| | - Judith Leitner
- Division of Immune Receptors and T Cell ActivationCenter for Pathophysiology, Infectiology, and ImmunologyInstitute of ImmunologyMedical University of ViennaViennaAustria
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and HygieneTechnical University of Munich (TUM)MunichGermany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and HygieneTechnical University of Munich (TUM)MunichGermany
- German Center for Infection Research (DZIF)MunichGermany
- Focus Group ‘Clinical Cell Processing and Purification’Institute for Advanced StudyTUMMunichGermany
| | - Peter Steinberger
- Division of Immune Receptors and T Cell ActivationCenter for Pathophysiology, Infectiology, and ImmunologyInstitute of ImmunologyMedical University of ViennaViennaAustria
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20
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Cox KS, Zhang L, Freed DC, Tang A, Zhang S, Zhou Y, Wang IM, Rupp RE, Adler SP, Musey LK, Wang D, Vora KA, Fu TM. Functional Evaluation and Genetic Evolution of Human T-Cell Responses After Vaccination With a Conditionally Replication-Defective Cytomegalovirus Vaccine. J Infect Dis 2020; 223:2001-2012. [PMID: 33031517 DOI: 10.1093/infdis/jiaa631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) can cause congenital infection and is the leading cause of nongenetic newborn disabilities. V160, a conditionally replication-defective virus, is an investigational vaccine under evaluation for prevention of congenital CMV. The vaccine was well tolerated and induced both humoral and cellular immunity in CMV-seronegative trial participants. T-cell-mediated immunity is important for immune control of CMV. Here we describe efforts to understand the quality attributes of the T-cell responses induced by vaccination. METHODS Using multicolor flow cytometry, we analyzed vaccine-induced T cells for memory phenotype, antigen specificity, cytokine profiles, and cytolytic potential. Moreover, antigen-specific T cells were sorted from 4 participants, and next-generation sequencing was used to trace clonal lineage development during the course of vaccination using T-cell receptor β-chain sequences as identifiers. RESULTS The results demonstrated that vaccination elicited polyfunctional CD4 and CD8 T cells to 2 dominant antigens, pp65 and IE1, with a predominantly effector phenotype. Analysis of T-cell receptor repertoires showed polyclonal expansion of pp65- and IE1-specific T cells after vaccination. CONCLUSION V160 induced a genetically diverse and polyfunctional T-cell response and the data support further clinical development of V160 for prevention of CMV infection and congenital transmission. CLINICAL TRIALS REGISTRATION NCT01986010.
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Affiliation(s)
- Kara S Cox
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - Lu Zhang
- Department of Strategic Planning and Research Informatics, MSD, Beijing, China
| | - Daniel C Freed
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - Aimin Tang
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | | | - Yu Zhou
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - I-Ming Wang
- Department of Genetics and Pharmacogenomics, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - Richard E Rupp
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Luwy K Musey
- Department of Clinical Research, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - Dai Wang
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - Kalpit A Vora
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
| | - Tong-Ming Fu
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc. Kenilworth, New Jersey, USA
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21
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Abstract
γδ T cells form an abundant part of the human cellular immune system, where they respond to tissue damage, infection, and cancer. The spectrum of known molecular targets recognized by Vδ1-expressing γδ T cells is becoming increasingly diverse. Here we describe human γδ T cells that recognize CD1b, a lipid antigen-presenting molecule, which is inducibly expressed on monocytes and dendritic cells. Using CD1b tetramers to study multiple donors, we found that many CD1b-specific γδ T cells use Vδ1. Despite their common use of Vδ1, three CD1b-specific γδ T cell receptors (TCRs) showed clear differences in the surface of CD1b recognized, the requirement for lipid antigens, and corecognition of butryophilin-like proteins. Several Vγ segments were present among the CD1b-specific TCRs, but chain swap experiments demonstrated that CD1b specificity was mediated by the Vδ1 chain. One of the CD1b-specific Vδ1+ TCRs paired with Vγ4 and shows dual reactivity to CD1b and butyrophilin-like proteins. αβ TCRs typically recognize the peptide display platform of MHC proteins. In contrast, our results demonstrate the use of rearranged receptors to mediate diverse modes of recognition across the surface of CD1b in ways that do and do not require carried lipids.
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22
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Mann SE, Zhou Z, Landry LG, Anderson AM, Alkanani AK, Fischer J, Peakman M, Mallone R, Campbell K, Michels AW, Nakayama M. Multiplex T Cell Stimulation Assay Utilizing a T Cell Activation Reporter-Based Detection System. Front Immunol 2020; 11:633. [PMID: 32328071 PMCID: PMC7160884 DOI: 10.3389/fimmu.2020.00633] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Recent advancements in single cell sequencing technologies allow for identification of numerous immune-receptors expressed by T cells such as tumor-specific and autoimmune T cells. Determining antigen specificity of those cells holds immense therapeutic promise. Therefore, the purpose of this study was to develop a method that can efficiently test antigen reactivity of multiple T cell receptors (TCRs) with limited cost, time, and labor. Nuclear factor of activated T cells (NFAT) is a transcription factor involved in producing cytokines and is often utilized as a reporter system for T cell activation. Using a NFAT-based fluorescent reporter system, we generated T-hybridoma cell lines that express intensely fluorescent proteins in response to antigen stimulation and constitutively express additional fluorescent proteins, which serve as identifiers of each T-hybridoma expressing a unique TCR. This allows for the combination of multiple T-hybridoma lines within a single reaction. Sensitivity to stimulation is not decreased by adding fluorescent proteins or multiplexing T cells. In multiplexed reactions, response by one cell line does not induce response in others, thus preserving specificity. This multiplex assay system will be a useful tool for antigen discovery research in a variety of contexts, including using combinatorial peptide libraries to determine T cell epitopes.
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Affiliation(s)
- Sarah E. Mann
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Zhicheng Zhou
- CNRS, INSERM, Institut Cochin, Université de Paris, Paris, France
| | - Laurie G. Landry
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Amanda M. Anderson
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aimon K. Alkanani
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jeremy Fischer
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Mark Peakman
- Department of Immunobiology, School of Immunology & Microbial Sciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
| | - Roberto Mallone
- CNRS, INSERM, Institut Cochin, Université de Paris, Paris, France
- Assistance Publique - Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
| | - Kristen Campbell
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aaron W. Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
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23
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Spindler MJ, Nelson AL, Wagner EK, Oppermans N, Bridgeman JS, Heather JM, Adler AS, Asensio MA, Edgar RC, Lim YW, Meyer EH, Hawkins RE, Cobbold M, Johnson DS. Massively parallel interrogation and mining of natively paired human TCRαβ repertoires. Nat Biotechnol 2020; 38:609-619. [PMID: 32393905 PMCID: PMC7224336 DOI: 10.1038/s41587-020-0438-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022]
Abstract
T cells engineered to express antigen-specific T cell receptors (TCRs) are potent therapies for viral infections and cancer. However, efficient identification of clinical candidate TCRs is complicated by the size and complexity of T cell repertoires and the challenges of working with primary T cells. Here, we present a high-throughput method to identify TCRs with high functional avidity from diverse human T cell repertoires. The approach uses massively parallel microfluidics to generate libraries of natively paired, full-length TCRαβ clones, from millions of primary T cells, which are then expressed in Jurkat cells. The TCRαβ-Jurkat libraries enable repeated screening and panning for antigen-reactive TCRs using peptide:MHC binding and cellular activation. We captured >2.9 million natively paired TCRαβ clonotypes from six healthy human donors and identified rare (<0.001% frequency) viral antigen–reactive TCRs. We also mined a tumor-infiltrating lymphocyte (TIL) sample from a melanoma patient and identified several tumor-specific TCRs, which, after expression in primary T cells, led to tumor cell killing.
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Affiliation(s)
| | | | | | - Natasha Oppermans
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | | | - James M Heather
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Everett H Meyer
- Stanford Diabetes Research Center, Stanford University Medical Center, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University Medical Center, Stanford, CA, USA
| | - Robert E Hawkins
- Division of Cancer Sciences, University of Manchester, Manchester, UK.,Immetacyte Ltd, Manchester, UK
| | - Mark Cobbold
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, MA, USA.,AstraZeneca, Cambridge, MA, USA
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24
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Eggesbø LM, Risnes LF, Neumann RS, Lundin KEA, Christophersen A, Sollid LM. Single-cell TCR sequencing of gut intraepithelial γδ T cells reveals a vast and diverse repertoire in celiac disease. Mucosal Immunol 2020; 13:313-321. [PMID: 31728027 DOI: 10.1038/s41385-019-0222-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 02/04/2023]
Abstract
A hallmark of celiac disease (CeD), a chronic condition driven by cereal gluten exposure, is increase of gut intraepithelial γδ T cells. This may indicate pathogenic involvement of γδ T cells and existence of disease-specific γδ T-cell receptors (TCRs) recognizing defined antigen(s). We performed high-throughput and paired γδ TCR sequencing of single intraepithelial γδ T cells of untreated CeD patients (n = 8; 1821 cells), CeD patients treated with a gluten-free diet (n = 5; 436 cells) and controls (n = 7; 1068 cells). We found that CeD patients, both untreated and treated, had larger and more diverse γδ TCR repertoires, more frequent usage of TRDV1 and TRDV3 and different patterns of TCRγ/TCRδ-pairing compared with controls. Although we observed no public CDR3δ sequences, there were several public CDR3γ sequences-many of which were shared by not only the CeD patients, but also by the controls. These public CDR3s were characterized by few N/P nucleotide insertions with germline and near-germline configuration, hence being easy to generate. Previous findings of CeD-specific CDR3 motifs were not replicated. Thus, being unable to raise evidence for CeD-specific γδ TCRs in this first large, paired γδ TCR single-cell sequencing study, we project challenges for identification of CeD-relevant γδ TCR ligands.
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Affiliation(s)
- Linn M Eggesbø
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424, Oslo, Norway.
| | - Louise F Risnes
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital- Rikshospitalet, 0372, Oslo, Norway
| | - Ralf S Neumann
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424, Oslo, Norway
| | - Knut E A Lundin
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, 0372, Oslo, Norway
| | - Asbjørn Christophersen
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424, Oslo, Norway
| | - Ludvig M Sollid
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo, 0424, Oslo, Norway. .,Department of Immunology, University of Oslo and Oslo University Hospital- Rikshospitalet, 0372, Oslo, Norway.
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25
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Zong S, Mi T, Flores LG, Alpert A, Olivares S, Patel K, Maiti S, Mcnamara G, Cooper LJN, Torikai H. Very rapid cloning, expression and identifying specificity of T-cell receptors for T-cell engineering. PLoS One 2020; 15:e0228112. [PMID: 32040512 PMCID: PMC7010234 DOI: 10.1371/journal.pone.0228112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/07/2020] [Indexed: 11/29/2022] Open
Abstract
Neoantigens can be predicted and in some cases identified using the data obtained from the whole exome sequencing and transcriptome sequencing of tumor cells. These sequencing data can be coupled with single-cell RNA sequencing for the direct interrogation of the transcriptome, surfaceome, and pairing of αβ T-cell receptors (TCRαβ) from hundreds of single T cells. Using these 2 large datasets, we established a platform for identifying antigens recognized by TCRαβs obtained from single T cells. Our approach is based on the rapid expression of cloned TCRαβ genes as Sleeping Beauty transposons and the determination of the introduced TCRαβs’ antigen specificity and avidity using a reporter cell line. The platform enables the very rapid identification of tumor-reactive TCRs for the bioengineering of T cells with redirected specificity.
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Affiliation(s)
- Shan Zong
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Tiejuan Mi
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Leo G. Flores
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Amir Alpert
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Simon Olivares
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Krina Patel
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Sourindra Maiti
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - George Mcnamara
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Laurence J. N. Cooper
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Ziopharm Oncology, Inc., Boston, Massachusetts, United States of America
| | - Hiroki Torikai
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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26
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Sant S, Jenkins MR, Dash P, Watson KA, Wang Z, Pizzolla A, Koutsakos M, Nguyen TH, Lappas M, Crowe J, Loudovaris T, Mannering SI, Westall GP, Kotsimbos TC, Cheng AC, Wakim L, Doherty PC, Thomas PG, Loh L, Kedzierska K. Human γδ T-cell receptor repertoire is shaped by influenza viruses, age and tissue compartmentalisation. Clin Transl Immunology 2019; 8:e1079. [PMID: 31559018 PMCID: PMC6756999 DOI: 10.1002/cti2.1079] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/16/2019] [Accepted: 08/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background Although γδ T cells comprise up to 10% of human peripheral blood T cells, questions remain regarding their role in disease states and T‐cell receptor (TCR) clonal expansions. We dissected anti‐viral functions of human γδ T cells towards influenza viruses and defined influenza‐reactive γδ TCRs in the context of γδ‐TCRs across the human lifespan. Methods We performed 51Cr‐killing assay and single‐cell time‐lapse live video microscopy to define mechanisms underlying γδ T‐cell‐mediated killing of influenza‐infected targets. We assessed cytotoxic profiles of γδ T cells in influenza‐infected patients and IFN‐γ production towards influenza‐infected lung epithelial cells. Using single‐cell RT‐PCR, we characterised paired TCRγδ clonotypes for influenza‐reactive γδ T cells in comparison with TCRs from healthy neonates, adults, elderly donors and tissues. Results We provide the first visual evidence of γδ T‐cell‐mediated killing of influenza‐infected targets and show distinct features to those reported for CD8+ T cells. γδ T cells displayed poly‐cytotoxic profiles in influenza‐infected patients and produced IFN‐γ towards influenza‐infected cells. These IFN‐γ‐producing γδ T cells were skewed towards the γ9δ2 TCRs, particularly expressing the public GV9‐TCRγ, capable of pairing with numerous TCR‐δ chains, suggesting their significant role in γδ T‐cell immunity. Neonatal γδ T cells displayed extensive non‐overlapping TCRγδ repertoires, while adults had enriched γ9δ2‐pairings with diverse CDR3γδ regions. Conversely, the elderly showed distinct γδ‐pairings characterised by large clonal expansions, a profile also prominent in adult tissues. Conclusion Human TCRγδ repertoire is shaped by age, tissue compartmentalisation and the individual's history of infection, suggesting that these somewhat enigmatic γδ T cells indeed respond to antigen challenge.
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Affiliation(s)
- Sneha Sant
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Misty R Jenkins
- Immunology Division Walter and Eliza Hall Institute Melbourne VIC Australia.,LaTrobe Institute for Molecular Science La Trobe University Melbourne VIC Australia.,Department of Medical Biology The University of Melbourne Melbourne VIC Australia
| | - Pradyot Dash
- Department of Immunology St Jude Children's Research Hospital Memphis TN USA
| | - Katherine A Watson
- Immunology Division Walter and Eliza Hall Institute Melbourne VIC Australia
| | - Zhongfang Wang
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Angela Pizzolla
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Thi Ho Nguyen
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group Department of Obstetrics & Gynaecology Mercy Hospital for Women University of Melbourne Melbourne VIC Australia
| | | | - Tom Loudovaris
- Immunology and Diabetes Unit St Vincent's Institute of Medical Research Fitzroy VIC Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit St Vincent's Institute of Medical Research Fitzroy VIC Australia
| | - Glen P Westall
- Lung Transplant Unit Alfred Hospital Melbourne VIC Australia
| | - Tom C Kotsimbos
- Department of Allergy, Immunology and Respiratory Medicine The Alfred Hospital Melbourne VIC Australia.,Department of Medicine Central Clinical School The Alfred Hospital Melbourne Monash University Melbourne VIC Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine Monash University Melbourne VIC Australia.,Infection Prevention and Healthcare Epidemiology Unit Alfred Health Melbourne VIC Australia
| | - Linda Wakim
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Peter C Doherty
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia.,Immunology Division Walter and Eliza Hall Institute Melbourne VIC Australia
| | - Paul G Thomas
- Department of Immunology St Jude Children's Research Hospital Memphis TN USA
| | - Liyen Loh
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology University of Melbourne at The Peter Doherty Institute for Infection and Immunity Melbourne VIC Australia
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27
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Wang R, Pscheid R, Ghumra A, Kan LYL, Cochrane S, Fairclough L, Alcocer MJC. Towards a surrogate system to express human lipid binding TCRs. Biotechnol Lett 2019; 41:1095-1104. [PMID: 31346817 DOI: 10.1007/s10529-019-02713-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/20/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Previously we reported that natural nut lipids were necessary for sensitization and that natural killer T cells (NKTs) must play a critical role in the development of food allergic responses. A major bottleneck in further understanding the interaction of nut lipids with the cells of the human immune system is the lack of well-characterized lipid responsive human cell lines. OBJECTIVE In the present study, we engineered human T cell receptor (TCR) sequences TRAV10 and TRBV25 responsive to α-GalCer into a stable murine iNKT hybridoma and surrogate human T cell lines. RESULTS The murine hybridoma system has shown to be problematic. To overcome this limitation, the expression of human TCR α/β sequences has been achieved driven by a bidirectional promoter on a plasmids or a lentivirus system, employing stable DC cell lines as lipid presenting cells, and a stable T cell line as a surrogate system. Further, a commercial human Jurkat T cell line containing an inducible secreted luciferase reporter construct was shown to be functional and can be used for a transient expression of human TCRs in a lipid screening program. The transfection efficiencies were improved using the lentivirus polycistronic constructs containing the P2A sequence in a TCR αβ/γδ null cell line (Jurkat 76). CONCLUSIONS The results suggest that the mis-pairing of the endogenous α/β TCR during ER folding in the presence of the new human TCR sequences could be impairing the functionality of the TCR lipid receptors. The surrogate systems presented here are important first steps in the establishment of human cell-specific lipid responsive libraries for the study of natural lipid substances.
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Affiliation(s)
- Rui Wang
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ronja Pscheid
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ashfaq Ghumra
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ling Yu Lea Kan
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Stella Cochrane
- Unilever Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, MK44 1LQ, UK
| | - Lucy Fairclough
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marcos J C Alcocer
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
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28
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Abstract
The ability to express and study a single T cell receptor (TCR) in vivo is an important aspect of both basic and translational immunological research. Traditionally, this was achieved by using TCR transgenic mice. In the past decade, a more efficient approach for single TCR expression was developed. This relatively rapid and accessible method utilizes retrovirus-mediated stem cell-based gene transfer and is commonly referred to as the TCR retrogenic approach. In this approach, hematopoietic bone marrow precursors are transduced with retroviral vector carrying both alpha and beta chains of a T cell receptor. After successful transduction, bone marrow is injected into recipient mice, in which T cell development is driven by expression of the vector-encoded TCR. This article details the materials and methods required to generate TCR retrogenic mice. It is divided into three sections and provides detailed methods for generation of stable retroviral producer cell lines, isolation and optimal transduction of hematopoietic bone marrow cells, and subsequent analysis of TCR retrogenic T cells. A detailed example of such analysis is provided. The current protocol is a culmination of many years of optimization and is the most efficient approach to date. Bone marrow transduction and transfer into recipient mice can now be achieved in a short period of four days. The protocol can be followed in most laboratories with standard biomedical equipment, and is supported by a troubleshooting guide that covers potential pitfalls and unexpected results. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yuelin Kong
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Yi Jing
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Maria Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas.,McNair Medical Institute, Houston, Texas
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29
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Ludwig J, Huber AK, Bartsch I, Busse CE, Wardemann H. High-throughput single-cell sequencing of paired TCRα and TCRβ genes for the direct expression-cloning and functional analysis of murine T-cell receptors. Eur J Immunol 2019; 49:1269-1277. [PMID: 31017295 PMCID: PMC6767390 DOI: 10.1002/eji.201848030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/11/2019] [Accepted: 04/15/2019] [Indexed: 12/01/2022]
Abstract
Precise clonal and functional assessments of the T cell receptor (TCR) repertoire diversity require paired TCRα and TCRβ gene sequence information at monoclonal level. However, available single‐cell strategies are typically limited in throughput and often do not provide full‐length DNA templates for direct gene cloning. Here, we describe a high‐throughput strategy for the unbiased amplification and automated sequence analysis of paired TCRα and TCRβ genes from primary mouse T cells. The platform links cell phenotype and TCR gene sequence information at single‐cell level. Furthermore, it enables direct functional analyses through the efficient cloning of both genes and the generation of stable TCR expressing cell lines. This highly efficient workflow is a powerful tool to determine the diversity and quality of the murine T‐cell repertoire in various settings, for example in vaccine development, infectious diseases, autoimmunity, or cancer.
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Affiliation(s)
- Julia Ludwig
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ann-Kathrin Huber
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ilka Bartsch
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Christian E Busse
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Hedda Wardemann
- Department of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
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30
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Ajina R, Zamalin D, Weiner LM. Functional genomics: paving the way for more successful cancer immunotherapy. Brief Funct Genomics 2019; 18:86-98. [PMID: 29762641 PMCID: PMC6430032 DOI: 10.1093/bfgp/ely017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immunotherapies have revolutionized cancer treatment. Immunotherapy is effective for the treatment of a wide range of cancer types and can mediate complete and durable tumor regression. Nonetheless, the field still faces many significant challenges, such as the need for personalized therapeutic strategies and better biomarkers, the difficulty of selecting the right combination therapy, and resistance to currently available immunotherapies. Both cancer and host immunity comprise significantly diverse and complex ecosystems, making immunogenomics an ideal field for functional genomics analysis. In this review, we describe the cancer-immunity cycle, how cancer cells manage to evade immune attack and the current hurdles in the path of cancer immunotherapy. Then, we discuss how functional genomics approaches can pave the way for more successful cancer immunotherapies.
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31
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Arruda LCM, Gaballa A, Uhlin M. Graft γδ TCR Sequencing Identifies Public Clonotypes Associated with Hematopoietic Stem Cell Transplantation Efficacy in Acute Myeloid Leukemia Patients and Unravels Cytomegalovirus Impact on Repertoire Distribution. THE JOURNAL OF IMMUNOLOGY 2019; 202:1859-1870. [DOI: 10.4049/jimmunol.1801448] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/10/2019] [Indexed: 12/19/2022]
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32
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Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens. Blood 2018; 132:1911-1921. [PMID: 30150207 PMCID: PMC6213317 DOI: 10.1182/blood-2018-04-843763] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/19/2018] [Indexed: 12/23/2022] Open
Abstract
Recent studies have highlighted the promise of targeting tumor neoantigens to generate potent antitumor immune responses and provide strong motivation for improving our understanding of antigen-T-cell receptor (TCR) interactions. Advances in single-cell sequencing technologies have opened the door for detailed investigation of the TCR repertoire, providing paired information from TCRα and TCRβ, which together determine specificity. However, a need remains for efficient methods to assess the specificity of discovered TCRs. We developed a streamlined approach for matching TCR sequences with cognate antigen through on-demand cloning and expression of TCRs and screening against candidate antigens. Here, we first demonstrate the system's capacity to identify viral-antigen-specific TCRs and compare the functional avidity of TCRs specific for a given antigen target. We then apply this system to identify neoantigen-specific TCR sequences from patients with melanoma treated with personalized neoantigen vaccines and characterize functional avidity of neoantigen-specific TCRs. Furthermore, we use a neoantigen-prediction pipeline to show that an insertion-deletion mutation in a putative chronic lymphocytic leukemia (CLL) driver gives rise to an immunogenic neoantigen mut-MGA, and use this approach to identify the mut-MGA-specific TCR sequence. This approach provides a means to identify and express TCRs, and then rapidly assess antigen specificity and functional avidity of a reconstructed TCR, which can be applied for monitoring antigen-specific T-cell responses, and potentially for guiding the design of effective T-cell-based immunotherapies.
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MESH Headings
- Antigens, Neoplasm/immunology
- Cancer Vaccines/therapeutic use
- Cells, Cultured
- Cloning, Molecular/methods
- HEK293 Cells
- Humans
- Jurkat Cells
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Melanoma/immunology
- Melanoma/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- T-Cell Antigen Receptor Specificity
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Affiliation(s)
- Zhuting Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annabelle J Anandappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jintaek Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Donna E Leet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - David J Bozym
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Christina Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Diana Tabbaa
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Oriol Olive
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kenneth J Livak
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA
| | - Hiroyuki Kishi
- Department of Immunology, University of Toyama, Toyama, Japan
| | | | - Indira Guleria
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - William J Lane
- Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Ute E Burkhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Edward F Fritsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; and
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; and
| | - Nir Hacohen
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Massachusetts General Hospital, Boston, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; and
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33
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Guo XZJ, Dash P, Crawford JC, Allen EK, Zamora AE, Boyd DF, Duan S, Bajracharya R, Awad WA, Apiwattanakul N, Vogel P, Kanneganti TD, Thomas PG. Lung γδ T Cells Mediate Protective Responses during Neonatal Influenza Infection that Are Associated with Type 2 Immunity. Immunity 2018; 49:531-544.e6. [PMID: 30170813 DOI: 10.1016/j.immuni.2018.07.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 04/25/2018] [Accepted: 07/20/2018] [Indexed: 12/25/2022]
Abstract
Compared to adults, infants suffer higher rates of hospitalization, severe clinical complications, and mortality due to influenza infection. We found that γδ T cells protected neonatal mice against mortality during influenza infection. γδ T cell deficiency did not alter viral clearance or interferon-γ production. Instead, neonatal influenza infection induced the accumulation of interleukin-17A (IL-17A)-producing γδ T cells, which was associated with IL-33 production by lung epithelial cells. Neonates lacking IL-17A-expressing γδ T cells or Il33 had higher mortality upon influenza infection. γδ T cells and IL-33 promoted lung infiltration of group 2 innate lymphoid cells and regulatory T cells, resulting in increased amphiregulin secretion and tissue repair. In influenza-infected children, IL-17A, IL-33, and amphiregulin expression were correlated, and increased IL-17A levels in nasal aspirates were associated with better clinical outcomes. Our results indicate that γδ T cells are required in influenza-infected neonates to initiate protective immunity and mediate lung homeostasis.
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Affiliation(s)
- Xi-Zhi J Guo
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David F Boyd
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Susu Duan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid A Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nopporn Apiwattanakul
- Division of Infectious Diseases, Department of Pediatrics Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Peter Vogel
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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34
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Davey MS, Willcox CR, Baker AT, Hunter S, Willcox BE. Recasting Human Vδ1 Lymphocytes in an Adaptive Role. Trends Immunol 2018; 39:446-459. [PMID: 29680462 PMCID: PMC5980997 DOI: 10.1016/j.it.2018.03.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/21/2018] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
γδ T cells are unconventional lymphocytes commonly described as 'innate-like' in function, which can respond in both a T cell receptor (TCR)-independent and also major histocompatibility complex (MHC)-unrestricted TCR-dependent manner. While the relative importance of TCR recognition had remained unclear, recent studies revealed that human Vδ1 T cells display unexpected parallels with adaptive αβ T cells. Vδ1 T cells undergo profound and highly focussed clonal expansion from an initially diverse and private TCR repertoire, most likely in response to specific immune challenges. Concomitantly, they differentiate from a Vδ1 T cell naïve (Tnaïve) to a Vδ1 T cell effector (Teffector) phenotype, marked by the downregulation of lymphoid homing receptors and upregulation of peripheral homing receptors and effector markers. This suggests that an adaptive paradigm applies to Vδ1 T cells, likely involving TCR-dependent but MHC-unrestricted responses to microbial and non-microbial challenges.
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Affiliation(s)
- Martin S Davey
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, School of Medicine and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; These authors contributed equally
| | - Carrie R Willcox
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, School of Medicine and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; These authors contributed equally
| | - Alfie T Baker
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, School of Medicine and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stuart Hunter
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, School of Medicine and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Centre for Liver Research and NIHR Biomedical Research Unit in Liver Disease, Institute of Immunology and Immunotherapy, School of Medicine and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Benjamin E Willcox
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, School of Medicine and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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35
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Izraelson M, Nakonechnaya TO, Moltedo B, Egorov ES, Kasatskaya SA, Putintseva EV, Mamedov IZ, Staroverov DB, Shemiakina II, Zakharova MY, Davydov AN, Bolotin DA, Shugay M, Chudakov DM, Rudensky AY, Britanova OV. Comparative analysis of murine T-cell receptor repertoires. Immunology 2017; 153:133-144. [PMID: 29080364 DOI: 10.1111/imm.12857] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
For understanding the rules and laws of adaptive immunity, high-throughput profiling of T-cell receptor (TCR) repertoires becomes a powerful tool. The structure of TCR repertoires is instructive even before the antigen specificity of each particular receptor becomes available. It embodies information about the thymic and peripheral selection of T cells; the readiness of an adaptive immunity to withstand new challenges; the character, magnitude and memory of immune responses; and the aetiological and functional proximity of T-cell subsets. Here, we describe our current analytical approaches for the comparative analysis of murine TCR repertoires, and show several examples of how these approaches can be applied for particular experimental settings. We analyse the efficiency of different metrics used for estimation of repertoire diversity, repertoire overlap, V-gene and J-gene segments usage similarity, and amino acid composition of CDR3. We discuss basic differences of these metrics and their advantages and limitations in different experimental models, and we provide guidelines for choosing an efficient way to lead a comparative analysis of TCR repertoires. Applied to the various known and newly developed mouse models, such analysis should allow us to disentangle multiple sophisticated puzzles in adaptive immunity.
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Affiliation(s)
- Mark Izraelson
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Bruno Moltedo
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evgeniy S Egorov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Ilgar Z Mamedov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy B Staroverov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina I Shemiakina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria Y Zakharova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Dmitriy A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Mikhail Shugay
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Dmitriy M Chudakov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olga V Britanova
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
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36
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Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, Crawford JC, Clemens EB, Nguyen THO, Kedzierska K, La Gruta NL, Bradley P, Thomas PG. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 2017. [PMID: 28636592 DOI: 10.1038/nature22383] [Citation(s) in RCA: 500] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 1015 (ref. 1) to as high as 1061 (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific TCR repertoires of CD8+ T cells from mice and humans, representing over 4,600 in-frame single-cell-derived TCRαβ sequence pairs from 110 subjects. We developed analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analyses demonstrate that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse 'outlier' sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.
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Affiliation(s)
- Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andrew J Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - George C Wang
- Division of Geriatric Medicine and Gerontology, Biology of Healthy Aging Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
| | - Shalini Sharma
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Aisha Souquette
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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37
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MR1-restricted mucosal-associated invariant T (MAIT) cells respond to mycobacterial vaccination and infection in nonhuman primates. Mucosal Immunol 2017; 10:802-813. [PMID: 27759023 PMCID: PMC5397382 DOI: 10.1038/mi.2016.91] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/03/2016] [Indexed: 02/07/2023]
Abstract
Studies on mucosal-associated invariant T cells (MAITs) in nonhuman primates (NHP), a physiologically relevant model of human immunity, are handicapped due to a lack of macaque MAIT-specific reagents. Here we show that while MR1 ligand-contact residues are conserved between human and multiple NHP species, three T-cell receptor contact-residue mutations in NHP MR1 diminish binding of human MR1 tetramers to macaque MAITs. Construction of naturally loaded macaque MR1 tetramers facilitated identification and characterization of macaque MR1-binding ligands and MAITs, both of which mirrored their human counterparts. Using the macaque MR1 tetramer we show that NHP MAITs activated in vivo in response to both Bacillus Calmette-Guerin vaccination and Mycobacterium tuberculosis infection. These results demonstrate that NHP and human MR1 and MAITs function analogously, and establish a preclinical animal model to test MAIT-targeted vaccines and therapeutics for human infectious and autoimmune disease.
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38
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Lindau P, Robins HS. Advances and applications of immune receptor sequencing in systems immunology. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Sprouse ML, Blahnik G, Lee T, Tully N, Banerjee P, James EA, Redondo MJ, Bettini ML, Bettini M. Rapid identification and expression of human TCRs in retrogenic mice. J Immunol Methods 2016; 439:29-36. [PMID: 27589924 DOI: 10.1016/j.jim.2016.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 10/21/2022]
Abstract
Single-cell paired TCR identification is a powerful tool, but has been limited in its previous incompatibility with further functional analysis. The current protocol describes a method to clone and functionally evaluate in vivo TCRs derived from single antigen-responsive human T cells and monoclonal T cell lines. We have improved upon current PCR-based TCR sequencing protocols by developing primers that allow amplification of human TCRα and TCRβ variable regions, while incorporating specific restriction cut sites for direct subcloning into the template retroviral vector. This streamlined approach for generating human:mouse chimeric TCR vectors allows for rapid TCR expression in humanized-retrogenic (hu-Rg) mice through retroviral mediated stem cell gene transfer. Using widely available techniques and equipment, this method is easily adaptable by most laboratories. This is the first TCR identification protocol that is efficiently combined with subsequent in vivo TCR expression.
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Affiliation(s)
- Maran L Sprouse
- Department of Pediatrics, Section of Diabetes and Endocrinology, McNair Medical Institute, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | | | - Thomas Lee
- Department of Pediatrics, Section of Diabetes and Endocrinology, McNair Medical Institute, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Natalie Tully
- Department of Pediatrics, Section of Diabetes and Endocrinology, McNair Medical Institute, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Pinaki Banerjee
- Center for Human Immunobiology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Eddie A James
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Maria J Redondo
- Department of Pediatrics, Section of Diabetes and Endocrinology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Matthew L Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, McNair Medical Institute, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Maria Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, McNair Medical Institute, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA.
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Hamana H, Shitaoka K, Kishi H, Ozawa T, Muraguchi A. A novel, rapid and efficient method of cloning functional antigen-specific T-cell receptors from single human and mouse T-cells. Biochem Biophys Res Commun 2016; 474:709-714. [PMID: 27155153 DOI: 10.1016/j.bbrc.2016.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 01/21/2023]
Abstract
T-cell receptor (TCR) gene therapy is a promising approach for the treatment of infectious diseases and cancers. However, the paired cloning and functional assays of antigen-specific TCRα and TCRβ is time-consuming and laborious. In this study, we developed a novel, rapid and efficient antigen-specific TCR-cloning system by combining three technologies: multiplex one-step RT-PCR, transcriptionally active PCR (TAP) and luciferase reporter assays. Multiplex one-step RT-PCR with leader primers designed from leader peptide sequences of TCRs enabled us to amplify cDNAs of TCRα and β pairs from single T-cells with remarkably high efficiency. The combination of TAP fragments and HEK293T-based NFAT-luciferase reporter cells allowed for a rapid functional assay without the need to construct expression vectors. Using this system, we cloned human TCRs specific for Epstein-Barr virus BRLF-1-derived peptide as well as mouse TCRs specific for melanoma-associated antigen tyrosinase-related protein 2 (TRP-2) within four days. These results suggest that our system provides rapid and efficient cloning of functional antigen-specific human and mouse TCRs and contributes to TCR-based immunotherapy for cancers and infectious diseases.
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Affiliation(s)
- Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan
| | - Kiyomi Shitaoka
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.
| | - Tatsuhiko Ozawa
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan
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