1
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Li G, Li J, Zhang H, Zhang Y, Liu D, Hao Y, Han J, Du J, Zhu L, Zeng Y, Li B, Li R, Song C, Zhang F, Chen C, Zhao H, Zeng H. Partial recovery of disturbed V-J pairing profiles of T-cell receptor in people living with HIV receiving long-term antiretroviral therapy. SCIENCE CHINA-LIFE SCIENCES 2020; 64:152-161. [PMID: 32567004 PMCID: PMC7306449 DOI: 10.1007/s11427-020-1718-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023]
Abstract
Chronic human immunodeficiency virus (HIV) infection not only causes a gradual loss of CD4+ T cells but also leads to a disturbance of the T cell receptor (TCR) repertoire. In people living with HIV (PLWH), monitoring TCR repertoire is challenged by the inconsistency of complementarity determining region 3 (CDR3) and limited cell numbers in clinical samples. Thus, a quantitative method is necessary for monitoring the TCR repertoire in PLWH. We characterized the TCR V-J pairing profile of naïve and memory CD4+ T cells in healthy donors, HIV-infected antiretroviral therapy (ART)-naïve patients and long-term (over 5 years) ART-experienced patients by performing TCR sequencing. We developed a V-J index with 18 parameters which were subdivided into five categories (expression coverage, cumulative percentage of the top tenth percentile, diversity, intra-individual similarity and inter-individual similarity). In ART-naïve patients, 14 of the 18 parameters were significantly altered. Long-term ART recovered ten parameters. The four unrecovered parameters were related to inter-individual similarity. Therefore, these findings indicate that long-term ART could only partially recover TCR V-J pairs and introduce newly impacted V-J pairs. Moreover, these results provide new insights into the V-J pairing of the TCR and into the disturbance of TCR repertoire in HIV infection.
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MESH Headings
- Adult
- Anti-Retroviral Agents/therapeutic use
- CD4 Lymphocyte Count
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Female
- HIV Infections/drug therapy
- HIV Infections/genetics
- HIV Infections/immunology
- Humans
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Joining Region/immunology
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/immunology
- Immunologic Memory/immunology
- Male
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Time Factors
- Young Adult
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Affiliation(s)
- Guoli Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Jiarui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Henghui Zhang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Yu Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Virus Resources and Application, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yu Hao
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Junyan Han
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Juan Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Liuluan Zhu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Yongqin Zeng
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Bei Li
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Rui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Chuan Song
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China
| | - Fujie Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Chen Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
| | - Hongxin Zhao
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
| | - Hui Zeng
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China.
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
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2
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Yao WQ, Wu F, Zhang W, Chuang SS, Thompson JS, Chen Z, Zhang SW, Clipson A, Wang M, Liu H, Bibawi H, Huang Y, Campos L, Grant JW, Wright P, Ei-Daly H, Rásó-Barnett L, Farkas L, Follows GA, Gao Z, Attygalle AD, Ashton-Key M, Liu W, Du MQ. Angioimmunoblastic T-cell lymphoma contains multiple clonal T-cell populations derived from a common TET2 mutant progenitor cell. J Pathol 2020; 250:346-357. [PMID: 31859368 PMCID: PMC7064999 DOI: 10.1002/path.5376] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/28/2019] [Accepted: 12/12/2019] [Indexed: 02/05/2023]
Abstract
Angioimmunoblastic T‐cell lymphoma (AITL) is a neoplastic proliferation of T follicular helper cells with clinical and histological presentations suggesting a role of antigenic drive in its development. Genetically, it is characterized by a stepwise acquisition of somatic mutations, with early mutations involving epigenetic regulators (TET2, DNMT3A) and occurring in haematopoietic stem cells, with subsequent changes involving signaling molecules (RHOA, VAV1, PLCG1, CD28) critical for T‐cell biology. To search for evidence of potential oncogenic cooperation between genetic changes and intrinsic T cell receptor (TCR) signaling, we investigated somatic mutations and T‐cell receptor β (TRB) rearrangement in 119 AITL, 11 peripheral T‐cell lymphomas with T follicular helper phenotype (PTCL‐TFH), and 25 PTCL‐NOS using Fluidigm polymerase chain reaction (PCR) and Illumina MiSeq sequencing. We confirmed frequent TET2, DNMT3A, and RHOA mutations in AITL (72%, 34%, 61%) and PTCL‐TFH (73%, 36%, 45%) and showed multiple TET2 mutations (2 or 3) in 57% of the involved AITL and PTCL‐TFH. Clonal TRB rearrangement was seen in 76 cases with multiple functional rearrangements (2–4) in 18 cases (24%). In selected cases, we confirmed bi‐clonal T‐cell populations and further demonstrated that these independent T‐cell populations harboured identical TET2 mutations by using BaseScope in situ hybridization, suggesting their derivation from a common TET2 mutant progenitor cell population. Furthermore, both T‐cell populations expressed CD4. Finally, in comparison with tonsillar TFH cells, both AITL and PTCL‐TFH showed a significant overrepresentation of several TRB variable family members, particularly TRBV19*01. Our findings suggest the presence of parallel neoplastic evolutions from a common TET2 mutant haematopoietic progenitor pool in AITL and PTCL‐TFH, albeit to be confirmed in a large series of cases. The biased TRBV usage in these lymphomas suggests that antigenic stimulation may play an important role in predilection of T cells to clonal expansion and malignant transformation. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Wen-Qing Yao
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Fangtian Wu
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Haematology, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, PR China
| | - Wenyan Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | | | - Joe S Thompson
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shao-Wei Zhang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Alexandra Clipson
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ming Wang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Hongxiang Liu
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hani Bibawi
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yuanxue Huang
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Luis Campos
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - John W Grant
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Penny Wright
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hesham Ei-Daly
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lívia Rásó-Barnett
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lorant Farkas
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - George A Follows
- Department of Haematology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zifen Gao
- Department of Pathology, Health Science Centre, Peking University, Beijing, PR China
| | | | - Margaret Ashton-Key
- Department of Cellular Pathology, Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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3
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Lu S, White JV, Judy RI, Merritt LL, Lin WL, Zhang X, Solomides C, Nwaneshiudu I, Gaughan J, Monos DS, Oleszak EL, Platsoucas CD. Clonally expanded alpha-chain T-cell receptor (TCR) transcripts are present in aneurysmal lesions of patients with Abdominal Aortic Aneurysm (AAA). PLoS One 2019; 14:e0218990. [PMID: 31310631 PMCID: PMC6634378 DOI: 10.1371/journal.pone.0218990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/14/2019] [Indexed: 01/25/2023] Open
Abstract
Abdominal aortic aneurysm (AAA) is a life-threatening immunological disease responsible for 1 to 2% of all deaths in 65 year old or older individuals. Although mononuclear cell infiltrates have been demonstrated in AAA lesions and autoimmunity may be responsible for the initiation and account for the propagation of the disease, the information available about the pathogenesis of AAA is limited. To examine whether AAA lesions from patients with AAA contain clonally expanded α-chain TCR transcripts, we amplified by the non-palindromic adaptor-PCR (NPA-PCR)/Vα-specific PCR and/or the Vα-specific PCR these α-chain TCR transcripts. The amplified transcripts were cloned and sequenced. Substantial proportions of identical α-chain TCR transcripts were identified in AAA lesions of 4 of 5 patients, demonstrating that clonally expanded T cells are present in these AAA lesions. These results were statistically significant by the bimodal distribution. Three of 5 of these patients were typed by DNA-based HLA-typing and all three expressed DRB1 alleles containing the DRβGln70 amino acid residue that has been demonstrated to be associated with AAA. All three patients exhibited clonally expanded T cells in AAA lesions. Four of the 5 patients with AAA who exhibited clonal expansions of α-chain TCR transcripts, also exhibited clonal expansions of β-chain TCR transcripts in AAA lesions, as we have demonstrated previously (J Immunol 192:4897, 2014). αβ TCR-expressing T cells infiltrating AAA lesions contain T-cell clones which have undergone proliferation and clonal expansion in vivo in response to as yet unidentified specific antigens that may be self or nonself. These results provide additional evidence supporting the hypothesis that AAA is a specific antigen-driven T-cell autoimmune disease.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence/genetics
- Antigens/genetics
- Antigens/immunology
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/pathology
- Cells, Cultured
- Clone Cells/immunology
- Humans
- Male
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Sequence Analysis, RNA
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
- Transcription, Genetic
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Affiliation(s)
- Song Lu
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - John V. White
- Department of Surgery, Advocate Lutheran General Hospital and University of Illinois School of Medicine, Park Ridge, IL, United States of America
| | - Raquel I. Judy
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
| | - Lisa L. Merritt
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
| | - Wan Lu Lin
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Xiaoying Zhang
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Charalambos Solomides
- Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Ifeyinwa Nwaneshiudu
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - John Gaughan
- Biostatistics Consulting Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
| | - Dimitri S. Monos
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Emilia L. Oleszak
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
- Department of Anatomy and Cell Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
- Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States of America
| | - Chris D. Platsoucas
- Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States of America
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, United States of America
- Center for Molecular Medicine, Old Dominion University, Norfolk, VA, United States of America
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4
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Rizzetto S, Eltahla AA, Lin P, Bull R, Lloyd AR, Ho JWK, Venturi V, Luciani F. Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. Sci Rep 2017; 7:12781. [PMID: 28986563 PMCID: PMC5630586 DOI: 10.1038/s41598-017-12989-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/14/2017] [Indexed: 11/12/2022] Open
Abstract
Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% − 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.
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Affiliation(s)
- Simone Rizzetto
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Auda A Eltahla
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Peijie Lin
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, UNSW, Sydney, Australia
| | - Rowena Bull
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Andrew R Lloyd
- School of Medical Sciences, UNSW, Sydney, Australia.,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.,St. Vincent's Clinical School, UNSW, Sydney, Australia
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia
| | - Fabio Luciani
- School of Medical Sciences, UNSW, Sydney, Australia. .,Viral Immunology Systems Program, Kirby Institute for Infection and Immunity, UNSW, Sydney, Australia.
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5
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Shahsavarian MA, Chaaya N, Costa N, Boquet D, Atkinson A, Offmann B, Kaveri SV, Lacroix-Desmazes S, Friboulet A, Avalle B, Padiolleau-Lefèvre S. Multitarget selection of catalytic antibodies with β-lactamase activity using phage display. FEBS J 2017; 284:634-653. [PMID: 28075071 DOI: 10.1111/febs.14012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 10/29/2016] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
Abstract
β-lactamase enzymes responsible for bacterial resistance to antibiotics are among the most important health threats to the human population today. Understanding the increasingly vast structural motifs responsible for the catalytic mechanism of β-lactamases will help improve the future design of new generation antibiotics and mechanism-based inhibitors of these enzymes. Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 109 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R-TEM β-lactamase as targets for selection of catalytic antibodies with β-lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β-lactam ring. Structural modeling of the selected scFv has revealed the presence of different motifs in each of the antibody fragments potentially responsible for their catalytic activity. Our results confirm (a) the validity of using our two target inhibitors for the in vitro selection of catalytic antibodies endowed with β-lactamase activity, and (b) the plasticity of the β-lactamase active site responsible for the wide resistance of these enzymes to clinically available inhibitors and antibiotics.
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Affiliation(s)
- Melody A Shahsavarian
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Nancy Chaaya
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Narciso Costa
- Service de Pharmacologie et d'Immuno-analyse (SPI), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Boquet
- Service de Pharmacologie et d'Immuno-analyse (SPI), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexandre Atkinson
- Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, Université de Nantes, France
| | - Bernard Offmann
- Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, Université de Nantes, France
| | - Srini V Kaveri
- UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U 1138, Paris, France.,Equipe Immunopathology and Therapeutic Immunointervention, Centre de Recherche des Cordeliers, Paris, France.,International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Sébastien Lacroix-Desmazes
- UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U 1138, Paris, France.,Equipe Immunopathology and Therapeutic Immunointervention, Centre de Recherche des Cordeliers, Paris, France.,International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Alain Friboulet
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Bérangère Avalle
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Séverine Padiolleau-Lefèvre
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
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6
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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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7
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Falta MT, Tinega AN, Mack DG, Bowerman NA, Crawford F, Kappler JW, Pinilla C, Fontenot AP. Metal-specific CD4+ T-cell responses induced by beryllium exposure in HLA-DP2 transgenic mice. Mucosal Immunol 2016; 9:218-28. [PMID: 26129650 PMCID: PMC4698108 DOI: 10.1038/mi.2015.54] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/16/2015] [Indexed: 02/04/2023]
Abstract
Chronic beryllium disease (CBD) is a granulomatous lung disorder that is associated with the accumulation of beryllium (Be)-specific CD4(+) T cells into the lung. Genetic susceptibility is linked to HLA-DPB1 alleles that possess a glutamic acid at position 69 (βGlu69), and HLA-DPB1*02:01 is the most prevalent βGlu69-containing allele. Using HLA-DP2 transgenic (Tg) mice, we developed a model of CBD that replicates the major features of the human disease. Here we characterized the T-cell receptor (TCR) repertoire of Be-responsive CD4(+) T cells derived from the lungs of Be oxide-exposed HLA-DP2 Tg mice. The majority of Be-specific T-cell hybridomas expressed TCR Vβ6, and a subset of these hybridomas expressed identical or nearly identical β-chains that were paired with different α-chains. We delineated mimotopes that bind to HLA-DP2 and form a complex recognized by Be-specific CD4(+) T cells in the absence of Be. These Be-independent peptides possess an arginine at p5 and a tryptophan at p7 that surround the Be-binding site within the HLA-DP2 acidic pocket and likely induce charge and conformational changes that mimic those induced by the Be(2+) cation. Collectively, these data highlight the interplay between peptides and Be in the generation of an adaptive immune response in metal-induced hypersensitivity.
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Affiliation(s)
- Michael T. Falta
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Alex N. Tinega
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Douglas G. Mack
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Natalie A. Bowerman
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Frances Crawford
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
,Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206 USA
| | - John W. Kappler
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
,Howard Hughes Medical Institute, National Jewish Health, Denver, CO 80206 USA
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121 USA
| | - Andrew P. Fontenot
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
,Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
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8
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Cukalac T, Kan WT, Dash P, Guan J, Quinn KM, Gras S, Thomas PG, La Gruta NL. Paired TCRαβ analysis of virus-specific CD8(+) T cells exposes diversity in a previously defined 'narrow' repertoire. Immunol Cell Biol 2015; 93:804-14. [PMID: 25804828 DOI: 10.1038/icb.2015.44] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023]
Abstract
T-cell receptor (TCR) usage has an important role in determining the outcome of CD8(+) cytotoxic T-lymphocyte responses to viruses and other pathogens. However, the characterization of TCR usage from which such conclusions are drawn is based on exclusive analysis of either the TCRα chain or, more commonly, the TCRβ chain. Here, we have used a multiplexed reverse transcription-PCR protocol to analyse the CDR3 regions of both TCRα and β chains from single naive or immune epitope-specific cells to provide a comprehensive picture of epitope-specific TCR usage and selection into the immune response. Analysis of TCR repertoires specific for three influenza-derived epitopes (D(b)NP(366), D(b)PA(224) and D(b)PB1-F2(62)) showed preferential usage of particular TCRαβ proteins in the immune repertoire relative to the naive repertoire, in some cases, resulting in a complete shift in TRBV preference or CDR3 length, and restricted repertoire diversity. The NP(366)-specific TCRαβ repertoire, previously defined as clonally restricted based on TCRβ analysis, was similarly diverse as the PA(224)- and PB1-F2(62)-specific repertoires. Intriguingly, preferred TCR characteristics (variable gene usage, CDR3 length and junctional gene usage) appeared to be able to confer specificity either independently or in concert with one another, depending on the epitope specificity. These data have implications for established correlations between the nature of the TCR repertoire and response outcomes after infection, and suggest that analysis of a subset of cells or a single TCR chain does not accurately depict the nature of the antigen-specific TCRαβ repertoire.
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Affiliation(s)
- Tania Cukalac
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Wan-Ting Kan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Guan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Kylie M Quinn
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
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9
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Simon P, Omokoko TA, Breitkreuz A, Hebich L, Kreiter S, Attig S, Konur A, Britten CM, Paret C, Dhaene K, Türeci Ö, Sahin U. Functional TCR retrieval from single antigen-specific human T cells reveals multiple novel epitopes. Cancer Immunol Res 2014; 2:1230-44. [PMID: 25245536 DOI: 10.1158/2326-6066.cir-14-0108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The determination of the epitope specificity of disease-associated T-cell responses is relevant for the development of biomarkers and targeted immunotherapies against cancer, autoimmune, and infectious diseases. The lack of known T-cell epitopes and corresponding T-cell receptors (TCR) for novel antigens hinders the efficient development and monitoring of new therapies. We developed an integrated approach for the systematic retrieval and functional characterization of TCRs from single antigen-reactive T cells that includes the identification of epitope specificity. This is accomplished through the rapid cloning of full-length TCR-α and TCR-β chains directly from single antigen-specific CD8(+) or CD4(+) T lymphocytes. The functional validation of cloned TCRs is conducted using in vitro-transcribed RNA transfer for expression of TCRs in T cells and HLA molecules in antigen-presenting cells. This method avoids the work and bias associated with repetitive cycles of in vitro T-cell stimulation, and enables fast characterization of antigen-specific T-cell responses. We applied this strategy to viral and tumor-associated antigens (TAA), resulting in the retrieval of 56 unique functional antigen-specific TCRs from human CD8(+) and CD4(+) T cells (13 specific for CMV-pp65, 16 specific for the well-known TAA NY-ESO-1, and 27 for the novel TAA TPTE), which are directed against 39 different epitopes. The proof-of-concept studies with TAAs NY-ESO-1 and TPTE revealed multiple novel TCR specificities. Our approach enables the rational development of immunotherapy strategies by providing antigen-specific TCRs and immunogenic epitopes.
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Affiliation(s)
- Petra Simon
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Tana A Omokoko
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Andrea Breitkreuz
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Lisa Hebich
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Sebastian Kreiter
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Sebastian Attig
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Abdo Konur
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany
| | - Cedrik M Britten
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany
| | - Claudia Paret
- Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany
| | - Karl Dhaene
- Department of Pathology, Algemeen Stedelijk Ziekenhuis Aalst, Aalst, Belgium
| | - Özlem Türeci
- Ganymed Pharmaceuticals AG, An der Goldgrube 12, Mainz, Germany
| | - Ugur Sahin
- Division of Translational and Experimental Oncology, Department of Medicine III, Johannes Gutenberg University, Mainz, Germany. Translational Oncology at the University Medical Center, Johannes Gutenberg University, Mainz gGmbH, Germany.
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10
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Mayans S, Stepniak D, Palida S, Larange A, Dreux J, Arlian B, Shinnakasu R, Kronenberg M, Cheroutre H, Lambolez F. αβT cell receptors expressed by CD4(-)CD8αβ(-) intraepithelial T cells drive their fate into a unique lineage with unusual MHC reactivities. Immunity 2014; 41:207-218. [PMID: 25131531 PMCID: PMC4142827 DOI: 10.1016/j.immuni.2014.07.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 07/12/2014] [Indexed: 11/25/2022]
Abstract
Coreceptor CD4 and CD8αβ double-negative (DN) TCRαβ(+) intraepithelial T cells, although numerous, have been greatly overlooked and their contribution to the immune response is not known. Here we used T cell receptor (TCR) sequencing of single cells combined with retrogenic expression of TCRs to study the fate and the major histocompatibility complex (MHC) restriction of DN TCRαβ(+) intraepithelial T cells. The data show that commitment of thymic precursors to the DN TCRαβ(+) lineage is imprinted by their TCR specificity. Moreover, the TCRs they express display a diverse and unusual pattern of MHC restriction that is nonoverlapping with that of CD4(+) or CD8αβ(+) T cells, indicating that they sense antigens that are not recognized by the conventional T cell subsets. The new insights indicate that DN TCRαβ(+) T cells form a third lineage of TCRαβ T lymphocytes expressing a variable TCR repertoire, which serve nonredundant immune functions.
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Affiliation(s)
- Sofia Mayans
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Clinical Microbiology-Immunology, NUS Building 6C, 901 85 Umeå, Sweden
| | - Dariusz Stepniak
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- eBioscience, 10255 Science center drive, San Diego, CA, 92121, USA
| | - Sakina Palida
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- HHMI – UCSD, 9500 Gilman Dr, George Palade 310 La Jolla, CA 92093-0647, USA
| | - Alexandre Larange
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Joanna Dreux
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Britni Arlian
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- The Scripps Research Institute, 10550 North Torrey Pines Road, MB-209, La Jolla, CA, 92037, USA
| | - Ryo Shinnakasu
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Riken, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Mitchell Kronenberg
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Hilde Cheroutre
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Florence Lambolez
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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11
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Bowerman NA, Falta MT, Mack DG, Wehrmann F, Crawford F, Mroz MM, Maier LA, Kappler JW, Fontenot AP. Identification of multiple public TCR repertoires in chronic beryllium disease. THE JOURNAL OF IMMUNOLOGY 2014; 192:4571-80. [PMID: 24719461 DOI: 10.4049/jimmunol.1400007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chronic beryllium disease (CBD) is a granulomatous lung disease characterized by the accumulation of beryllium (Be)-specific CD4(+) T cells in bronchoalveolar lavage. These expanded CD4(+) T cells are composed of oligoclonal T cell subsets, suggesting their recruitment to the lung in response to conventional Ag. In the current study, we noted that all bronchoalveolar lavage-derived T cell lines from HLA-DP2-expressing CBD patients contained an expansion of Be-responsive Vβ5.1(+) CD4(+) T cells. Using Be-loaded HLA-DP2-peptide tetramers, the majority of tetramer-binding T cells also expressed Vβ5.1 with a highly conserved CDR3β motif. Interestingly, Be-specific, Vβ5.1-expressing CD4(+) T cells displayed differential HLA-DP2-peptide tetramer staining intensity, and sequence analysis of the distinct tetramer-binding subsets showed that the two populations differed by a single conserved amino acid in the CDR3β motif. TCR Vα-chain analysis of purified Vβ5.1(+) CD4(+) T cells based on differential tetramer-binding intensity showed differing TCR Vα-chain pairing requirements, with the high-affinity population having promiscuous Vα-chain pairing and the low-affinity subset requiring restricted Vα-chain usage. Importantly, disease severity, as measured by loss of lung function, was inversely correlated with the frequency of tetramer-binding CD4(+) T cells in the lung. Our findings suggest the presence of a dominant Be-specific, Vβ5.1-expressing public T cell repertoire in the lungs of HLA-DP2-expressing CBD patients using promiscuous Vα-chain pairing to recognize an identical HLA-DP2-peptide/Be complex. Importantly, the inverse relationship between expansion of CD4(+) T cells expressing these public TCRs and disease severity suggests a pathogenic role for these T cells in CBD.
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Affiliation(s)
- Natalie A Bowerman
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
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12
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Kobayashi E, Kishi H, Ozawa T, Horii M, Hamana H, Nagai T, Muraguchi A. Retroviral vectors for homologous recombination provide efficient cloning and expression in mammalian cells. Biochem Biophys Res Commun 2014; 444:319-24. [PMID: 24462869 DOI: 10.1016/j.bbrc.2014.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 01/14/2014] [Indexed: 11/19/2022]
Abstract
Homologous recombination technologies enable high-throughput cloning and the seamless insertion of any DNA fragment into expression vectors. Additionally, retroviral vectors offer a fast and efficient method for transducing and expressing genes in mammalian cells, including lymphocytes. However, homologous recombination cannot be used to insert DNA fragments into retroviral vectors; retroviral vectors contain two homologous regions, the 5'- and 3'-long terminal repeats, between which homologous recombination occurs preferentially. In this study, we have modified a retroviral vector to enable the cloning of DNA fragments through homologous recombination. To this end, we inserted a bacterial selection marker in a region adjacent to the gene insertion site. We used the modified retroviral vector and homologous recombination to clone T-cell receptors (TCRs) from single Epstein Barr virus-specific human T cells in a high-throughput and comprehensive manner and to efficiently evaluate their function by transducing the TCRs into a murine T-cell line through retroviral infection. In conclusion, the modified retroviral vectors, in combination with the homologous recombination method, are powerful tools for the high-throughput cloning of cDNAs and their efficient functional analysis.
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Affiliation(s)
- Eiji Kobayashi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
| | - Tatsuhiko Ozawa
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Masae Horii
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Terumi Nagai
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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13
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Kobayashi E, Kishi H, Muraguchi A. A novel system for cloning human TCRs: Cutting short the way to TCR-based anticancer therapy. Oncoimmunology 2014; 3:e27258. [PMID: 24653962 PMCID: PMC3960297 DOI: 10.4161/onci.27258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 11/19/2022] Open
Abstract
T-cell receptor (TCR)-based gene immunotherapy has emerged as a promising approach for the treatment of multiple malignancies. We have recently reported an efficient system for the cloning and functional evaluation of TCR-coding cDNAs. This system, which we named hTEC10, allows for the determination of TCR antigen specificity in less than 10 days, and may therefore constitute a fast and powerful platform for the development of new TCR-based anticancer therapies.
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Affiliation(s)
- Eiji Kobayashi
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama, Japan
| | - Atsushi Muraguchi
- Department of Immunology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Toyama, Japan
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14
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Eugster A, Lindner A, Heninger AK, Wilhelm C, Dietz S, Catani M, Ziegler AG, Bonifacio E. Measuring T cell receptor and T cell gene expression diversity in antigen-responsive human CD4+ T cells. J Immunol Methods 2013; 400-401:13-22. [PMID: 24239865 DOI: 10.1016/j.jim.2013.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/11/2013] [Indexed: 12/25/2022]
Abstract
T cells have diversity in TCR, epitope recognition, and cytokine production, and can be used for immune monitoring. Furthermore, clonal expansion of TCR families in disease may provide opportunities for TCR-directed therapies. We developed methodology for sequencing expressed genes of TCR alpha and beta chains from single cells and applied this to vaccine (tetanus-toxoid)-responsive CD4(+) T cells. TCR alpha and beta chains were both successfully sequenced in 1309 (43%) of 3038 CD4(+) T cells yielding 677 different receptors. TRAV and TRBV gene usage differed between tetanus-toxoid-responsive and non-responsive cells (p=0.004 and 0.0002), and there was extensive TCR diversity in tetanus-toxoid-responsive cells within individuals. Identical TCRs could be recovered in different samples from the same subject: TCRs identified after booster vaccination were frequent in pre-booster memory T cells (31% of pre-booster TCR), and also identified in pre-booster vaccination naïve cells (6.5%). No TCR was shared between subjects, but tetanus toxoid-responsive cells sharing one of their TCR chains were observed within and between subjects. Coupling single-cell gene expression profiling to TCR sequencing revealed examples of distinct cytokine profiles in cells bearing identical TCR. Novel molecular methodology demonstrates extensive diversity of Ag-responsive CD4(+) T cells within and between individuals.
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Affiliation(s)
- Anne Eugster
- DFG Research Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD).
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15
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Kobayashi E, Mizukoshi E, Kishi H, Ozawa T, Hamana H, Nagai T, Nakagawa H, Jin A, Kaneko S, Muraguchi A. A new cloning and expression system yields and validates TCRs from blood lymphocytes of patients with cancer within 10 days. Nat Med 2013; 19:1542-6. [PMID: 24121927 DOI: 10.1038/nm.3358] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 04/08/2013] [Indexed: 12/19/2022]
Abstract
Antigen-specific T cell therapy, or T cell receptor (TCR) gene therapy, is a promising immunotherapy for infectious diseases and cancers. However, a suitable rapid and direct screening system for antigen-specific TCRs is not available. Here, we report an efficient cloning and functional evaluation system to determine the antigen specificity of TCR cDNAs derived from single antigen-specific human T cells within 10 d. Using this system, we cloned and analyzed 380 Epstein-Barr virus-specific TCRs from ten healthy donors with latent Epstein-Barr virus infection and assessed the activity of cytotoxic T lymphocytes (CTLs) carrying these TCRs against antigenic peptide-bearing target cells. We also used this system to clone tumor antigen-specific TCRs from peptide-vaccinated patients with cancer. We obtained 210 tumor-associated antigen-specific TCRs and demonstrated the cytotoxic activity of CTLs carrying these TCRs against peptide-bearing cells. This system may provide a fast and powerful approach for TCR gene therapy for infectious diseases and cancers.
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Affiliation(s)
- Eiji Kobayashi
- 1] Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan. [2]
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16
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Weissbrich B, Nauerth M, Busch DH. Adoptive immunotherapy: New assay for the identification of T cells with optimal avidity. Oncoimmunology 2013; 2:e26199. [PMID: 24244903 PMCID: PMC3825721 DOI: 10.4161/onci.26199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 08/17/2013] [Indexed: 12/15/2022] Open
Abstract
T cells expressing high avidity T-cell receptors (TCRs) have been shown to mediate superior therapeutic effects. A novel koff-rate assay allows for the quantitative and reproducible assessment of the avidity of TCRs for their ligands directly on living T cells, ex vivo. This assay might facilitate the selection of T cells with an optimal avidity for their target, hence favoring the development of adoptive immunotherapeutic regimens.
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Affiliation(s)
- Bianca Weissbrich
- Institute for Medical Microbiology; Immunology and Hygiene; Technische Universität München; Munich, Germany
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17
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La Gruta NL, Thomas PG. Interrogating the relationship between naïve and immune antiviral T cell repertoires. Curr Opin Virol 2013; 3:447-51. [PMID: 23849601 DOI: 10.1016/j.coviro.2013.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/22/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022]
Abstract
Understanding how naïve virus-specific CD8+ T cells influence the type of immune response generated after virus infection is critical for the development of enhanced therapeutic and vaccination strategies to exploit CD8+ T cell-mediated immunity. Recent technological advances in T cell isolation and T receptor sequencing have allowed for greater understanding of the basic structure of immune T cell repertoires, the diversity of responses within and between individuals, and changes in repertoires over time and in response to infection conditions. In this review, we discuss the current understanding of how T cell repertoires contribute to potent antiviral responses. Additionally we compare the state of the art in receptor sequencing, highlighting the advantages and disadvantages of the three most common approaches: next-generation sequencing, template-switch anchored RT-PCR, and multiplex single cell PCR. Finally, we describe how TCR sequencing has delineated the relationship between naïve and immune T cell repertoires.
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Affiliation(s)
- Nicole L La Gruta
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC 3010, Australia.
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18
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Howland SW, Poh CM, Gun SY, Claser C, Malleret B, Shastri N, Ginhoux F, Grotenbreg GM, Rénia L. Brain microvessel cross-presentation is a hallmark of experimental cerebral malaria. EMBO Mol Med 2013; 5:984-99. [PMID: 23681698 PMCID: PMC3721469 DOI: 10.1002/emmm.201202273] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/02/2023] Open
Abstract
Cerebral malaria is a devastating complication of Plasmodium falciparum infection. Its pathogenesis is complex, involving both parasite- and immune-mediated events. CD8+ T cells play an effector role in murine experimental cerebral malaria (ECM) induced by Plasmodium berghei ANKA (PbA) infection. We have identified a highly immunogenic CD8 epitope in glideosome-associated protein 50 that is conserved across rodent malaria species. Epitope-specific CD8+ T cells are induced during PbA infection, migrating to the brain just before neurological signs manifest. They are functional, cytotoxic and can damage the blood–brain barrier in vivo. Such CD8+ T cells are also found in the brain during infection with parasite strains/species that do not induce neuropathology. We demonstrate here that PbA infection causes brain microvessels to cross-present parasite antigen, while non-ECM-causing parasites do not. Further, treatment with fast-acting anti-malarial drugs before the onset of ECM reduces parasite load and thus antigen presentation in the brain, preventing ECM death. Thus our data suggest that combined therapies targeting both the parasite and host antigen-presenting cells may improve the outcome of CM patients.
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Affiliation(s)
- Shanshan W Howland
- Singapore Immunology Network, Agency for Science, Technology and Research A*STAR, Singapore, Singapore
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19
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Dössinger G, Bunse M, Bet J, Albrecht J, Paszkiewicz PJ, Weißbrich B, Schiedewitz I, Henkel L, Schiemann M, Neuenhahn M, Uckert W, Busch DH. MHC multimer-guided and cell culture-independent isolation of functional T cell receptors from single cells facilitates TCR identification for immunotherapy. PLoS One 2013; 8:e61384. [PMID: 23637823 PMCID: PMC3637308 DOI: 10.1371/journal.pone.0061384] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 03/07/2013] [Indexed: 02/05/2023] Open
Abstract
Adoptive therapy using T cells redirected to target tumor- or infection-associated antigens is a promising strategy that has curative potential and broad applicability. In order to accelerate the screening process for suitable antigen-specific T cell receptors (TCRs), we developed a new approach circumventing conventional in vitro expansion-based strategies. Direct isolation of paired full-length TCR sequences from non-expanded antigen-specific T cells was achieved by the establishment of a highly sensitive PCR-based T cell receptor single cell analysis method (TCR-SCAN). Using MHC multimer-labeled and single cell-sorted HCMV-specific T cells we demonstrate a high efficacy (approximately 25%) and target specificity of TCR-SCAN receptor identification. In combination with MHC-multimer based pre-enrichment steps, we were able to isolate TCRs specific for the oncogenes Her2/neu and WT1 even from very small populations (original precursor frequencies of down to 0.00005% of CD3(+) T cells) without any cell culture step involved. Genetic re-expression of isolated receptors demonstrates their functionality and target specificity. We believe that this new strategy of TCR identification may provide broad access to specific TCRs for therapeutically relevant T cell epitopes.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Neoplasm/immunology
- Cell Culture Techniques
- Cytomegalovirus/immunology
- Epitopes
- Gene Transfer Techniques
- HEK293 Cells
- Histocompatibility Antigens/chemistry
- Histocompatibility Antigens/metabolism
- Humans
- Immunotherapy
- Jurkat Cells
- Mice
- Molecular Sequence Data
- Polymerase Chain Reaction
- Protein Multimerization
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/isolation & purification
- Receptors, Antigen, T-Cell/therapeutic use
- Receptors, Antigen, T-Cell, alpha-beta
- Sequence Analysis, Protein
- Single-Cell Analysis
- Species Specificity
- Transgenes
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Affiliation(s)
- Georg Dössinger
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Mario Bunse
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Jeannette Bet
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Focus Group “Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München, Munich, Germany
| | - Julia Albrecht
- Clinical Cooperation Groups ‘‘Antigen-specific Immunotherapy’’ and “Immune Monitoring”, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
| | - Paulina J. Paszkiewicz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Focus Group “Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München, Munich, Germany
| | - Bianca Weißbrich
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Focus Group “Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München, Munich, Germany
| | - Isabell Schiedewitz
- Clinical Cooperation Groups ‘‘Antigen-specific Immunotherapy’’ and “Immune Monitoring”, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
| | - Lynette Henkel
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Clinical Cooperation Groups ‘‘Antigen-specific Immunotherapy’’ and “Immune Monitoring”, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
| | - Michael Neuenhahn
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Clinical Cooperation Groups ‘‘Antigen-specific Immunotherapy’’ and “Immune Monitoring”, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
| | - Wolfgang Uckert
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Humboldt-Universität, Berlin, Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Focus Group “Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München, Munich, Germany
- Clinical Cooperation Groups ‘‘Antigen-specific Immunotherapy’’ and “Immune Monitoring”, Helmholtz Center Munich (Neuherberg) and Technische Universität München, Munich, Germany
- DZIF - National Centre for Infection Research, Munich, Germany
- * E-mail:
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20
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Ozawa T, Piao X, Kobayashi E, Zhou Y, Sakurai H, Andoh T, Jin A, Kishi H, Muraguchi A. A novel rabbit immunospot array assay on a chip allows for the rapid generation of rabbit monoclonal antibodies with high affinity. PLoS One 2012; 7:e52383. [PMID: 23300658 PMCID: PMC3530603 DOI: 10.1371/journal.pone.0052383] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/12/2012] [Indexed: 12/25/2022] Open
Abstract
Antigen-specific rabbit monoclonal antibodies (RaMoAbs) are useful due to their high specificity and high affinity, and the establishment of a comprehensive and rapid RaMoAb generation system has been highly anticipated. Here, we present a novel system using immunospot array assay on a chip (ISAAC) technology in which we detect and retrieve antigen-specific antibody-secreting cells from the peripheral blood lymphocytes of antigen-immunized rabbits and produce antigen-specific RaMoAbs with 10–12 M affinity within a time period of only 7 days. We have used this system to efficiently generate RaMoAbs that are specific to a phosphorylated signal-transducing molecule. Our system provides a new method for the comprehensive and rapid production of RaMoAbs, which may contribute to laboratory research and clinical applications.
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Affiliation(s)
- Tatsuhiko Ozawa
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Xiuhong Piao
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Eiji Kobayashi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yue Zhou
- Department of Cancer Cell Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroaki Sakurai
- Department of Cancer Cell Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Tsugunobu Andoh
- Department of Applied Pharmacology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Aishun Jin
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
- Department of Immunology, College of Basic Medical Sciences, Harbin Medical University, Nangang District, Harbin, China
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
- * E-mail:
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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21
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Sun X, Saito M, Sato Y, Chikata T, Naruto T, Ozawa T, Kobayashi E, Kishi H, Muraguchi A, Takiguchi M. Unbiased analysis of TCRα/β chains at the single-cell level in human CD8+ T-cell subsets. PLoS One 2012; 7:e40386. [PMID: 22792299 PMCID: PMC3391256 DOI: 10.1371/journal.pone.0040386] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/06/2012] [Indexed: 01/12/2023] Open
Abstract
T-cell receptor (TCR) α/β chains are expressed on the surface of CD8+ T-cells and have been implicated in antigen recognition, activation, and proliferation. However, the methods for characterization of human TCRα/β chains have not been well established largely because of the complexity of their structures owing to the extensive genetic rearrangements that they undergo. Here we report the development of an integrated 5′-RACE and multiplex PCR method to amplify the full-length transcripts of TCRα/β at the single-cell level in human CD8+ subsets, including naive, central memory, early effector memory, late effector memory, and effector phenotypic cells. Using this method, with an approximately 47% and 62% of PCR success rate for TCRα and for TCRβ chains, respectively, we were able to analyze more than 1,000 reads of transcripts of each TCR chain. Our comprehensive analysis revealed the following: (1) chimeric rearrangements of TCRδ-α, (2) control of TCRα/β transcription with multiple transcriptional initiation sites, (3) altered utilization of TCRα/β chains in CD8+ subsets, and (4) strong association between the clonal size of TCRα/β chains and the effector phenotype of CD8+ T-cells. Based on these findings, we conclude that our method is a useful tool to identify the dynamics of the TCRα/β repertoire, and provides new insights into the study of human TCRα/β chains.
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MESH Headings
- Adult
- CD8-Positive T-Lymphocytes/metabolism
- Cells, Cultured
- Gene Expression
- Humans
- Male
- Polymerase Chain Reaction
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Single-Cell Analysis/methods
- Transcription Initiation Site
- V(D)J Recombination
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Affiliation(s)
- Xiaoming Sun
- Center for AIDS Research, Kumamoto University, Honjo, Kumamoto, Japan
| | - Masumichi Saito
- Center for AIDS Research, Kumamoto University, Honjo, Kumamoto, Japan
| | - Yoshinori Sato
- Center for AIDS Research, Kumamoto University, Honjo, Kumamoto, Japan
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Honjo, Kumamoto, Japan
| | - Takuya Naruto
- Center for AIDS Research, Kumamoto University, Honjo, Kumamoto, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Eiji Kobayashi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Honjo, Kumamoto, Japan
- * E-mail:
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22
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Wälchli S, Løset GÅ, Kumari S, Nergård Johansen J, Yang W, Sandlie I, Olweus J. A practical approach to T-cell receptor cloning and expression. PLoS One 2011; 6:e27930. [PMID: 22132171 PMCID: PMC3221687 DOI: 10.1371/journal.pone.0027930] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/27/2011] [Indexed: 11/25/2022] Open
Abstract
Although cloning and expression of T-cell Receptors (TcRs) has been performed for almost two decades, these procedures are still challenging. For example, the use of T-cell clones that have undergone limited expansion as starting material to limit the loss of interesting TcRs, must be weighed against the introduction of mutations by excess PCR cycles. The recent interest in using specific TcRs for cancer immunotherapy has, however, increased the demand for practical and robust methods to rapidly clone and express TcRs. Two main technologies for TcR cloning have emerged; the use of a set of primers specifically annealing to all known TcR variable domains, and 5′-RACE amplification. We here present an improved 5′-RACE protocol that represents a fast and reliable way to identify a TcR from 105 cells only, making TcR cloning feasible without a priori knowledge of the variable domain sequence. We further present a detailed procedure for the subcloning of TcRα and β chains into an expression system. We show that a recombination-based cloning protocol facilitates simple and rapid transfer of the TcR transgene into different expression systems. The presented comprehensive method can be performed in any laboratory with standard equipment and with a limited amount of starting material. We finally exemplify the straightforwardness and reliability of our procedure by cloning and expressing several MART-1-specific TcRs and demonstrating their functionality.
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MESH Headings
- Cloning, Molecular/methods
- Electroporation
- Genetic Vectors/genetics
- Humans
- Jurkat Cells
- MART-1 Antigen/genetics
- MART-1 Antigen/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Recombination, Genetic/genetics
- Reproducibility of Results
- Retroviridae/genetics
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Affiliation(s)
- Sébastien Wälchli
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- * E-mail: (SW); (JO)
| | - Geir Åge Løset
- Department of Molecular Biosciences and Centre for Immune Regulation, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Shraddha Kumari
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Jorunn Nergård Johansen
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Weiwen Yang
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Inger Sandlie
- Department of Molecular Biosciences and Centre for Immune Regulation, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Johanna Olweus
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- * E-mail: (SW); (JO)
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23
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Warren RL, Freeman JD, Zeng T, Choe G, Munro S, Moore R, Webb JR, Holt RA. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res 2011; 21:790-7. [PMID: 21349924 DOI: 10.1101/gr.115428.110] [Citation(s) in RCA: 252] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Massively parallel sequencing is a useful approach for characterizing T-cell receptor diversity. However, immune receptors are extraordinarily difficult sequencing targets because any given receptor variant may be present in very low abundance and may differ legitimately by only a single nucleotide. We show that the sensitivity of sequence-based repertoire profiling is limited by both sequencing depth and sequencing accuracy. At two timepoints, 1 wk apart, we isolated bulk PBMC plus naïve (CD45RA+/CD45RO-) and memory (CD45RA-/CD45RO+) T-cell subsets from a healthy donor. From T-cell receptor beta chain (TCRB) mRNA we constructed and sequenced multiple libraries to obtain a total of 1.7 billion paired sequence reads. The sequencing error rate was determined empirically and used to inform a high stringency data filtering procedure. The error filtered data yielded 1,061,522 distinct TCRB nucleotide sequences from this subject which establishes a new, directly measured, lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis. TCRB nucleotide sequences obtained from two additional donors were compared to those from the first donor and revealed limited sharing (up to 1.1%) of nucleotide sequences among donors, but substantially higher sharing (up to 14.2%) of inferred amino acid sequences. For each donor, shared amino acid sequences were encoded by a much larger diversity of nucleotide sequences than were unshared amino acid sequences. We also observed a highly statistically significant association between numbers of shared sequences and shared HLA class I alleles.
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Affiliation(s)
- René L Warren
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
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24
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The structure of superantigen complexed with TCR and MHC reveals novel insights into superantigenic T cell activation. Nat Commun 2010; 1:119. [PMID: 21081917 DOI: 10.1038/ncomms1117] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/18/2010] [Indexed: 11/09/2022] Open
Abstract
Superantigens (SAgs) are bacterial toxins that interact with immunoreceptors, T cell receptor (TCR) and major histocompatibility complex (MHC) class II, conventionally through the variable β-domain of TCR (TCRVβ). They induce a massive release of cytokines, which can lead to diseases such as food poisoning and toxic shock syndrome. In this study, we report the X-ray structure of the ternary complex between staphylococcal enterotoxin H (SEH) and its human receptors, MHC class II and TCR. The structure demonstrates that SEH predominantly interacts with the variable α-domain of TCR (TCRVα), which is supported by nuclear magnetic resonance (NMR) analyses. Furthermore, there is no contact between MHC and TCR upon complex formation. Structural analyses suggest that the major contact points to TCRVα are conserved among other bacterial SAgs. Consequently, a new dimension of SAg biology emerges, suggesting that in addition to the conventional interactions with the TCRVβ domain, SAgs can also activate T cells through the TCRVα domain.
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25
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Arakaki A, Ooya K, Akiyama Y, Hosokawa M, Komiyama M, Iizuka A, Yamaguchi K, Matsunaga T. TCR-beta repertoire analysis of antigen-specific single T cells using a high-density microcavity array. Biotechnol Bioeng 2010; 106:311-8. [PMID: 20073087 DOI: 10.1002/bit.22663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The antigen specificity of cytotoxic T cells, provided by T-cell receptors (TCRs), plays a central role in human autoimmune diseases, infection, and cancer. As the TCR repertoire is unique in individual cytotoxic T cells, a strategy to analyze its gene rearrangement at the single-cell level is required. In this study, we applied a high-density microcavity array enabling target cell screening of several thousands of single cells for identification of functional TCR-beta gene repertoires specific to melanoma (gp100) and cytomegalovirus (CMV) antigens. T cells expressing TCRs with the ability to recognize fluorescent-labeled antigen peptide tetramers were isolated by using a micromanipulator under microscopy. Regularly arranged cells on the microcavity array eased detection and isolation of target single cells from a polyclonal T-cell population. The isolated single cells were then directly utilized for RT-PCR. By sequencing the amplified PCR products, antigen-specific TCR-beta repertoires for gp100 and human cytomegalovirus antigens were successfully identified at the single-cell level. This simple, accurate, and cost-effective technique for single-cell analysis has further potential as a valuable and widely applicable tool for studies on gene screening and expression analyses of various kinds of cells.
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Affiliation(s)
- Atsushi Arakaki
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho Koganei, Tokyo 184-8588, Japan
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26
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Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res 2009; 19:1817-24. [PMID: 19541912 DOI: 10.1101/gr.092924.109] [Citation(s) in RCA: 287] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
T-cell receptor (TCR) genomic loci undergo somatic V(D)J recombination, plus the addition/subtraction of nontemplated bases at recombination junctions, in order to generate the repertoire of structurally diverse T cells necessary for antigen recognition. TCR beta subunits can be unambiguously identified by their hypervariable CDR3 (Complement Determining Region 3) sequence. This is the site of V(D)J recombination encoding the principal site of antigen contact. The complexity and dynamics of the T-cell repertoire remain unknown because the potential repertoire size has made conventional sequence analysis intractable. Here, we use 5'-RACE, Illumina sequencing, and a novel short read assembly strategy to sample CDR3(beta) diversity in human T lymphocytes from peripheral blood. Assembly of 40.5 million short reads identified 33,664 distinct TCR(beta) clonotypes and provides precise measurements of CDR3(beta) length diversity, usage of nontemplated bases, sequence convergence, and preferences for TRBV (T-cell receptor beta variable gene) and TRBJ (T-cell receptor beta joining gene) gene usage and pairing. CDR3 length between conserved residues of TRBV and TRBJ ranged from 21 to 81 nucleotides (nt). TRBV gene usage ranged from 0.01% for TRBV17 to 24.6% for TRBV20-1. TRBJ gene usage ranged from 1.6% for TRBJ2-6 to 17.2% for TRBJ2-1. We identified 1573 examples of convergence where the same amino acid translation was specified by distinct CDR3(beta) nucleotide sequences. Direct sequence-based immunoprofiling will likely prove to be a useful tool for understanding repertoire dynamics in response to immune challenge, without a priori knowledge of antigen.
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Affiliation(s)
- J Douglas Freeman
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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27
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Warren RL, Nelson BH, Holt RA. Profiling model T-cell metagenomes with short reads. ACTA ACUST UNITED AC 2009; 25:458-64. [PMID: 19136549 DOI: 10.1093/bioinformatics/btp010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION T-cell receptor (TCR) diversity in peripheral blood has not yet been fully profiled with sequence level resolution. Each T-cell clonotype expresses a unique receptor, generated by somatic recombination of TCR genes and the enormous potential for T-cell diversity makes repertoire analysis challenging. We developed a sequencing approach and assembly software (immuno-SSAKE or iSSAKE) for profiling T-cell metagenomes using short reads from the massively parallel sequencing platforms. RESULTS Models of sequence diversity for the TCR beta-chain CDR3 region were built using empirical data and used to simulate, at random, distinct TCR clonotypes at 1-20 p.p.m. Using simulated TCRbeta (sTCRbeta) sequences, we randomly created 20 million 36 nt reads having 1-2% random error, 20 million 42 or 50 nt reads having 1% random error and 20 million 36 nt reads with 1% error modeled on real short read data. Reads aligning to the end of known TCR variable (V) genes and having consecutive unmatched bases in the adjacent CDR3 were used to seed iSSAKE de novo assemblies of CDR3. With assembled 36 nt reads, we detect over 51% and 63% of rare (1 p.p.m.) clonotypes using a random or modeled error distribution, respectively. We detect over 99% of more abundant clonotypes (6 p.p.m. or higher) using either error distribution. Longer reads improve sensitivity, with assembled 42 and 50 nt reads identifying 82.0% and 94.7% of rare 1 p.p.m. clonotypes, respectively. Our approach illustrates the feasibility of complete profiling of the TCR repertoire using new massively parallel short read sequencing technology. AVAILABILITY ftp://ftp.bcgsc.ca/supplementary/iSSAKE.
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Affiliation(s)
- René L Warren
- BC Cancer Agency, Michael Smith Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada.
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