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Yan P, Liu Y, Zhang M, Liu N, Zheng Y, Zhang H, Zhou H, Sun M. Reconstitution of peripheral blood T cell receptor β immune repertoire in immune checkpoint inhibitors associated myocarditis. CARDIO-ONCOLOGY (LONDON, ENGLAND) 2024; 10:35. [PMID: 38863010 PMCID: PMC11165862 DOI: 10.1186/s40959-024-00230-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/15/2024] [Indexed: 06/13/2024]
Abstract
PURPOSE Immune checkpoint inhibitors (ICIs)-associated myocarditis was a rare yet severe complication observed in individuals undergoing immunotherapy. This study investigated the immune status and characteristics of patients diagnosed with ICIs- associated myocarditis. METHODS A total of seven patients diagnosed with ICIs-associated myocarditis were included in the study, while five tumor patients without myocarditis were recruited as reference controls. Additionally, 30 healthy individuals were recruited as blank controls. Biochemical indices, electrocardiogram, and echocardiography measurements were obtained both prior to and following the occurrence of myocarditis. High-throughput sequencing of T cell receptor (TCR) was employed to assess the diversity and distribution characteristics of TCR CDR3 length, as well as the diversity of variable (V) and joining (J) genes of T lymphocytes in peripheral blood. RESULTS In the seven patients with ICIs-associated myocarditis, Troponin T (TNT) levels exhibited a significant increase following myocarditis, while other parameters such as brain natriuretic peptide (BNP), QTc interval, and left ventricular ejection fraction (LVEF) did not show any significant differences. Through sequencing, it was observed that the diversity and uniformity of CDR3 in the ICIs-associated myocarditis patients were significantly diminished. Additionally, the distribution of CDR3 nucleotides deviated from normality, and variations in the utilization of V and J gene segments. CONCLUSION The reconstitution of the TCR immune repertoire may play a pivotal role in the recognition of antigens in patients with ICIs-associated myocarditis.
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Affiliation(s)
- Peng Yan
- Department of Oncology, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Yanan Liu
- Department of Oncology, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Mingyan Zhang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ning Liu
- Department of Oncology, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Yawen Zheng
- Department of Oncology, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Haiqin Zhang
- Department of Oncology, Jinan Central Hospital, Shandong First Medical University, Jinan, China
| | - Hao Zhou
- Graduate School, Shandong First Medical University, Jinan, China
| | - Meili Sun
- Department of Oncology, Jinan Central Hospital, Shandong First Medical University, Jinan, China.
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Bardwell B, Bay J, Colburn Z. The clinical applications of immunosequencing. Curr Res Transl Med 2024; 72:103439. [PMID: 38447267 DOI: 10.1016/j.retram.2024.103439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/20/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Technological advances in high-throughput sequencing have opened the door for the interrogation of adaptive immune responses at unprecedented scale. It is now possible to determine the sequences of antibodies or T-cell receptors produced by individual B and T cells in a sample. This capability, termed immunosequencing, has transformed the study of both infectious and non-infectious diseases by allowing the tracking of dynamic changes in B and T cell clonal populations over time. This has improved our understanding of the pathology of cancers, autoimmune diseases, and infectious diseases. However, to date there has been only limited clinical adoption of the technology. Advances over the last decade and on the horizon that reduce costs and improve interpretability could enable widespread clinical use. Many clinical applications have been proposed and, while most are still undergoing research and development, some methods relying on immunosequencing data have been implemented, the most widespread of which is the detection of measurable residual disease. Here, we review the diagnostic, prognostic, and therapeutic applications of immunosequencing for both infectious and non-infectious diseases.
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Affiliation(s)
- B Bardwell
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - J Bay
- Department of Medicine, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - Z Colburn
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA.
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3
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Potential of TCR sequencing in graft-versus-host disease. Bone Marrow Transplant 2023; 58:239-246. [PMID: 36477111 PMCID: PMC10005964 DOI: 10.1038/s41409-022-01885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Graft-versus-host disease (GvHD) remains one of the major complications following allogeneic haematopoietic stem cell transplantation (allo-HSCT). GvHD can occur in almost every tissue, with the skin, liver, and intestines being the mainly affected organs. T cells are implicated in initiating GvHD. T cells identify a broad range of antigens and mediate the immune response through receptors on their surfaces (T cell receptors, TCRs). The composition of TCRs within a T cell population defines the TCR repertoire of an individual, and this repertoire represents exposure to self and non-self proteins. Monitoring the changes in the TCR repertoire using TCR sequencing can provide an indication of the dynamics of a T cell population. Monitoring the frequency and specificities of specific TCR clonotypes longitudinally in different conditions and specimens (peripheral blood, GvHD-affected tissue samples) can provide insights into factors modulating immune reactions following allogeneic transplantation and will help to understand the underlying mechanisms mediating GvHD. This review provides insights into current studies of the TCR repertoire in GvHD and potential future clinical implications of TCR sequencing.
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AIRR Community Guide to Planning and Performing AIRR-Seq Experiments. Methods Mol Biol 2022; 2453:261-278. [PMID: 35622331 PMCID: PMC9761540 DOI: 10.1007/978-1-0716-2115-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
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High-throughput and single-cell T cell receptor sequencing technologies. Nat Methods 2021; 18:881-892. [PMID: 34282327 PMCID: PMC9345561 DOI: 10.1038/s41592-021-01201-8] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)-antigen complexes and drive the antigen-specific adaptive immune response to pathogens and cancer. The TCR repertoire in each individual is highly diverse, which allows for recognition of a wide array of foreign antigens, but also presents a challenge in analyzing this response using conventional methods. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences, analyze their antigen specificities using experimental and computational tools, and pair TCRs with transcriptional and epigenetic cell state phenotypes in single cells. In this Review, we highlight these technological advances and describe how they have been applied to discover fundamental insights into T cell-mediated immunity.
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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7
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Zhu C, Liang Q, Liu Y, Kong D, Zhang J, Wang H, Wang K, Guo Z. Kidney injury in response to crystallization of calcium oxalate leads to rearrangement of the intrarenal T cell receptor delta immune repertoire. J Transl Med 2019; 17:278. [PMID: 31438987 PMCID: PMC6704580 DOI: 10.1186/s12967-019-2022-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background Calcium oxalate (CaOx), the major constituent of most kidney stones, induces inflammatory infiltration and injures renal tubular cells. However, the role of γδT cells in CaOx-mediated kidney injury remains unclear. Therefore, this study investigated the distribution of intrarenal γδT cells and T cell receptor δ (TCRδ) immune repertoires in response to interactions with CaOx crystals. Methods CaOx crystal mouse model was established by glyoxylate injection. Flow cytometer was used to analyze the expression of CD69 and IL-17 from intrarenal γδT cells. Furthermore, TCR immune repertoire sequencing (IR-Seq) was used to monitor the profile of the TCRδ immune repertoire. Results Our results indicated that CaOx crystals lead to obvious increases in the expression and activation of intrarenal γδT cells. In TCRδ immune repertoire, the majority of V/J gene and V–J/V–D–J combination segments, barring individual exceptions, were similar between kidneys with CaOx formation and control kidneys. Impressively, high complementarity determining region 3 (CDR3) diversity was observed in response to CaOx crystal formation along with distinct CDR3 distribution and abundance. Conclusion Our work suggests the presence of aberrant γδT cell activation and reconstitution of the TCRδ immune repertoire in response to CaOx crystal deposition.
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Affiliation(s)
- Chao Zhu
- Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Qing Liang
- Department of Basic Medical Sciences, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yaqun Liu
- Department of Rheumatology and Immunology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Deliang Kong
- Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Jie Zhang
- Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Hu Wang
- Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Kejia Wang
- Department of Basic Medical Sciences, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Zhiyong Guo
- Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
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Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction. J Transl Med 2019; 17:40. [PMID: 30728066 PMCID: PMC6366076 DOI: 10.1186/s12967-019-1788-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Acute myocardial infarction (AMI) is characterized by an inflammatory process in which T cell plays a key role. However, the profile of immune microenvironment in AMI is still uncertain. High-throughput sequencing of T cell receptor (TCR) provides deep insight into monitoring the immune microenvironment. METHODS 30 patients with AMI were enrolled and 30 healthy individuals were recruited as controls. Flow cytometer were used to analyze the distribution of αβ T cells and their CD69 expression from peripheral leukomonocytes. TCRβ repertoire library was amplified by two-round multiplex PCR and detected by next-generation sequencing (NGS). RESULTS The percentage of αβ T cells in AMI patients were significantly restricted than those in healthy controls, while the highly activated αβ T cells along with distinguishing usage of variable (V), diversity (D) and joining (J) gene segments were also found in AMI patients. In addition, AMI induced a significantly restricted CDR3 amino acid (AA) diversity and remarkably reconstituted TCR immune repertoires. Finally, we identified several AMI-associated tendency of CDR3 AAs expression after AMI. CONCLUSIONS Our work suggests that the aberrant αβ T cells distribution and activation may associated with the pathogenesis of AMI and demonstrates a reconstitution of TCRβ immune repertoire after AMI.
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Chaara W, Gonzalez-Tort A, Florez LM, Klatzmann D, Mariotti-Ferrandiz E, Six A. RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy. Front Immunol 2018; 9:1038. [PMID: 29868003 PMCID: PMC5962720 DOI: 10.3389/fimmu.2018.01038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/25/2018] [Indexed: 12/30/2022] Open
Abstract
High-throughput sequencing (HTS) has the potential to decipher the diversity of T cell repertoires and their dynamics during immune responses. Applied to T cell subsets such as T effector and T regulatory cells, it should help identify novel biomarkers of diseases. However, given the extreme diversity of TCR repertoires, understanding how the sequencing conditions, including cell numbers, biological and technical sampling and sequencing depth, impact the experimental outcome is critical to proper use of these data. Here, we assessed the representativeness and robustness of TCR repertoire diversity assessment according to experimental conditions. By comparative analyses of experimental datasets and computer simulations, we found that (i) for small samples, the number of clonotypes recovered is often higher than the number of cells per sample, even after removing the singletons; (ii) high-sequencing depth for small samples alters the clonotype distributions, which can be corrected by filtering the datasets using Shannon entropy as a threshold; and (iii) a single sequencing run at high depth does not ensure a good coverage of the clonotype richness in highly polyclonal populations, which can be better covered using multiple sequencing. Altogether, our results warrant better understanding and awareness of the limitation of TCR diversity analyses by HTS and justify the development of novel computational tools for improved modeling of the highly complex nature of TCR repertoires.
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Affiliation(s)
- Wahiba Chaara
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Ariadna Gonzalez-Tort
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Laura-Maria Florez
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
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Castro R, Navelsaker S, Krasnov A, Du Pasquier L, Boudinot P. Describing the diversity of Ag specific receptors in vertebrates: Contribution of repertoire deep sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:28-37. [PMID: 28259700 DOI: 10.1016/j.dci.2017.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
During the last decades, gene and cDNA cloning identified TCR and Ig genes across vertebrates; genome sequencing of TCR and Ig loci in many species revealed the different organizations selected during evolution under the pressure of generating diverse repertoires of Ag receptors. By detecting clonotypes over a wide range of frequency, deep sequencing of Ig and TCR transcripts provides a new way to compare the structure of expressed repertoires in species of various sizes, at different stages of development, with different physiologies, and displaying multiple adaptations to the environment. In this review, we provide a short overview of the technologies currently used to produce global description of immune repertoires, describe how they have already been used in comparative immunology, and we discuss the future potential of such approaches. The development of these methodologies in new species holds promise for new discoveries concerning particular adaptations. As an example, understanding the development of adaptive immunity across metamorphosis in frogs has been made possible by such approaches. Repertoire sequencing is now widely used, not only in basic research but also in the context of immunotherapy and vaccination. Analysis of fish responses to pathogens and vaccines has already benefited from these methods. Finally, we also discuss potential advances based on repertoire sequencing of multigene families of immune sensors and effectors in invertebrates.
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Affiliation(s)
- Rosario Castro
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - Sofie Navelsaker
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, Adamstuen Campus, Oslo 0454, Norway; Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain. Genome Med 2015; 7:124. [PMID: 26608341 PMCID: PMC4658769 DOI: 10.1186/s13073-015-0239-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/06/2015] [Indexed: 01/12/2023] Open
Abstract
Background Despite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against the utilized viral strains (homotypic response). Identification of structural patterns of the B cell repertoire associated to heterotypic neutralization may contribute to identify relevant epitopes for a universal vaccine against influenza. Methods Blood samples were collected from volunteers immunized with 2008/2009 trivalent inactivated vaccine (TIV), pandemic H1N1 (pdmH1N1) monovalent inactivated vaccine (MIV) and the 2014/2015 TIV. Neutralization was assessed by hemagglutination and microneutralization test. IgG VH amplicons derived from peripheral blood RNA from pre-immune and 7 days post vaccination were subjected to 454-Roche sequencing. Full reconstruction of the sampled repertoires was done with ImmunediveRsity. Results The TIV induced a predominantly homotypic neutralizing serologic response, while the 09 MIV induced a heterotypic neutralizing seroconversion in 17 % of the individuals. Both the 08/09 and the 14/15 TIV were associated with a reduction in clonotypic diversity, whereas 09 MIV was the opposite. Moreover, TIV and MIV induced distinctive patterns of IGHV segment use that are consistent with B cell selection by conserved antigenic determinants shared by the pre-pandemic and the pandemic strains. However, low somatic hypermutation rates in IgG after 09 MIV immunization, but not after 08/09 and 14/15 TIV immunization were observed. Furthermore, no evidence of the original antigenic sin was found in the same individuals after vaccination with the three vaccines. Conclusions Immunization with a new influenza virus strain (2009 pdmH1N1) induced unique effects in the peripheral B cell repertoire clonal structure, a stereotyped response involving distinctive IGHV segment use and low somatic hypermutation levels. These parameters were contrastingly different to those observed in response to pre-pandemic and post-pandemic vaccination, and may be the result of clonal selection of common antigenic determinants, as well as germinal center-independent responses that wane as the pandemic strain becomes seasonal. Our findings may contribute in the understanding of the structural and cellular basis required to develop a universal influenza vaccine. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0239-y) contains supplementary material, which is available to authorized users.
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Herzig CTA, Mailloux VL, Baldwin CL. Spectratype analysis of the T cell receptor δ CDR3 region of bovine γδ T cells responding to leptospira. Immunogenetics 2014; 67:95-109. [PMID: 25502871 DOI: 10.1007/s00251-014-0817-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 11/16/2014] [Indexed: 01/13/2023]
Abstract
Gamma delta T cells comprise the majority of blood T cells in ruminants at birth and remain at high levels for several years with most expressing the WC1 co-receptor. A subpopulation of Bos taurus WC1(+) cells expressing a restricted set of WC1 molecules respond immediately by proliferation and interferon-γ production to leptospira following vaccination, preceding the response by CD4 T cells. Our goal is to define the γδ T cell recognition elements involved. Previously, we showed that the responding cells employed a variety of TRDV genes indicating that the CDR1 and CDR2 of TCRδ could vary and may not be principally involved in antigen specificity. Murine and human γδ T cells bind T22 and self lipids through their CDR3δ. Like mice, cattle use up to five TRDD genes in a single CDR3δ adding flexibility to length and configuration for antigen binding. Here, we used spectratyping to evaluate the CDR3δ of leptospira-responsive cells. Little or no compartmentalization of CDR3δ was found for antigen-responsive cells that incorporated TRDV1, TRDV2, or TRDV3 even though they comprise the majority of the leptospira-responding population. Compartmentalization occurred for TRDV4-containing transcripts and was maintained over time and among cattle. However, no common amino acid motif was apparent in those CDR3δ sequences, although a bias in D gene usage occurred. We hypothesize that the restricted set of WC1 co-receptors expressed by the responding cells may lend specificity to the response through their ability to bind bacteria facilitating interaction of various TCRs with bacterial components resulting in cross-linking and activation.
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Affiliation(s)
- Carolyn T A Herzig
- Department of Veterinary and Animal Sciences, University of Massachusetts, Integrated Sciences Building, 661 N. Pleasant St, Amherst, MA, 01003, USA
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Valdés-Alemán J, Téllez-Sosa J, Ovilla-Muñoz M, Godoy-Lozano E, Velázquez-Ramírez D, Valdovinos-Torres H, Gómez-Barreto RE, Martinez-Barnetche J. Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing. MAbs 2013; 6:493-501. [PMID: 24492293 DOI: 10.4161/mabs.27435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.
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Affiliation(s)
- Javier Valdés-Alemán
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México; Programa de Ingeniería en Biotecnología; Universidad Politécnica del Estado de Morelos; Jiutepec, México
| | - Juan Téllez-Sosa
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Marbella Ovilla-Muñoz
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Elizabeth Godoy-Lozano
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Daniel Velázquez-Ramírez
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Humberto Valdovinos-Torres
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Rosa E Gómez-Barreto
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Jesús Martinez-Barnetche
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
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Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol 2013; 4:413. [PMID: 24348479 PMCID: PMC3841818 DOI: 10.3389/fimmu.2013.00413] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023] Open
Abstract
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.
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Affiliation(s)
- Adrien Six
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Maria Encarnita Mariotti-Ferrandiz
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Wahiba Chaara
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Susana Magadan
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
| | - Hang-Phuong Pham
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2 , Montpellier , France
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS and Ecole Normale Supérieure , Paris , France
| | - Véronique Thomas-Vaslin
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure , Paris , France
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
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Zoete V, Irving M, Ferber M, Cuendet MA, Michielin O. Structure-Based, Rational Design of T Cell Receptors. Front Immunol 2013; 4:268. [PMID: 24062738 PMCID: PMC3770923 DOI: 10.3389/fimmu.2013.00268] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157–165 cancer-testis epitope. Fifty-four percent of the designed sequence replacements exhibited improved pMHC binding as compared to the native TCR, with up to 150-fold increase in affinity, while preserving specificity. Genetically engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity, KD = ∼1 − 5 μM. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function, in line with the “half-life” model of T cell activation. Our computer-aided protein-engineering approach requires the 3D-structure of the TCR-pMHC complex of interest, which can be obtained from X-ray crystallography. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes when experimental data is not available. Since the accuracy of the models depends on the prediction of the TCR orientation over pMHC, we have complemented the approach with a simplified rigid method to predict this orientation and successfully assessed it using all non-redundant TCR-pMHC crystal structures available. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of stage IV melanoma.
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Affiliation(s)
- V Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics , Lausanne , Switzerland
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16
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Limited T cell receptor beta variable repertoire responses to ESAT-6 and CFP-10 in subjects infected with Mycobacterium tuberculosis. Tuberculosis (Edinb) 2013; 93:529-37. [PMID: 23845455 DOI: 10.1016/j.tube.2013.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 02/08/2023]
Abstract
Mycobacterium tuberculosis (MTB)-specific antigens, ESAT-6 or CFP-10 play a key role in diagnosis and control MTB infection. T cell receptor (TCR) reflects the status and function of T cells. However, the features of the TCR beta variable (TCRBV) repertoire used against ESAT-6 and CFP-10 from MTB subjects have not been well described. The molecular profiles of TCRBV complementarity-determining region 3 (CDR3) in PBMCs with or without ESAT-6 or CFP-10 stimulation were assayed using a gene melting spectral pattern (GMSP) assay developed in our previous study. The average number of skewed TCRBV family in PBMCs stimulated with ESAT-6 or CFP-10 was significantly higher than that in unstimulated PBMCs. TCRBV3, BV5.1, BV12, BV13.1, BV13.2, BV20 and BV24 were used more frequently than other TCRBV members in PBMCs from MTB subjects, and TCRBV3, BV5.1 in stimulated PBMCs have a preference in the usage of variable (V) and joining (J) segments and CDR3. The results indicate that the T cell immune response in MTB subjects involves a few of specific T cells. The preferred usage of certain V and J segments and CDR3s of TCRBV3 or BV5.1 may be related to ESAT-6 or CFP-10 respectively, which would help clinical differential diagnosis and treatment of MTB-infected subjects.
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17
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Castro R, Jouneau L, Pham HP, Bouchez O, Giudicelli V, Lefranc MP, Quillet E, Benmansour A, Cazals F, Six A, Fillatreau S, Sunyer O, Boudinot P. Teleost fish mount complex clonal IgM and IgT responses in spleen upon systemic viral infection. PLoS Pathog 2013; 9:e1003098. [PMID: 23326228 PMCID: PMC3542120 DOI: 10.1371/journal.ppat.1003098] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 11/09/2012] [Indexed: 01/12/2023] Open
Abstract
Upon infection, B-lymphocytes expressing antibodies specific for the intruding pathogen develop clonal responses triggered by pathogen recognition via the B-cell receptor. The constant region of antibodies produced by such responding clones dictates their functional properties. In teleost fish, the clonal structure of B-cell responses and the respective contribution of the three isotypes IgM, IgD and IgT remain unknown. The expression of IgM and IgT are mutually exclusive, leading to the existence of two B-cell subsets expressing either both IgM and IgD or only IgT. Here, we undertook a comprehensive analysis of the variable heavy chain (VH) domain repertoires of the IgM, IgD and IgT in spleen of homozygous isogenic rainbow trout (Onchorhynchus mykiss) before, and after challenge with a rhabdovirus, the Viral Hemorrhagic Septicemia Virus (VHSV), using CDR3-length spectratyping and pyrosequencing of immunoglobulin (Ig) transcripts. In healthy fish, we observed distinct repertoires for IgM, IgD and IgT, respectively, with a few amplified μ and τ junctions, suggesting the presence of IgM- and IgT-secreting cells in the spleen. In infected animals, we detected complex and highly diverse IgM responses involving all VH subgroups, and dominated by a few large public and private clones. A lower number of robust clonal responses involving only a few VH were detected for the mucosal IgT, indicating that both IgM(+) and IgT(+) spleen B cells responded to systemic infection but at different degrees. In contrast, the IgD response to the infection was faint. Although fish IgD and IgT present different structural features and evolutionary origin compared to mammalian IgD and IgA, respectively, their implication in the B-cell response evokes these mouse and human counterparts. Thus, it appears that the general properties of antibody responses were already in place in common ancestors of fish and mammals, and were globally conserved during evolution with possible functional convergences.
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Affiliation(s)
- Rosario Castro
- Virologie et Immunologie Moléculaires, INRA, Jouy-en-Josas, France
| | - Luc Jouneau
- Virologie et Immunologie Moléculaires, INRA, Jouy-en-Josas, France
| | - Hang-Phuong Pham
- UPMC Univ Paris 06, UMR 7211, “Integrative Immunology” Team, Paris, France; CNRS, UMR 7211, “Immunology, Immunopathology, Immunotherapy,” Paris, France
| | - Olivier Bouchez
- UMR INRA 0444 Laboratoire de Génétique Cellulaire, GeT-PlaGe Core Facility, Castanet Tolosan, France
| | - Véronique Giudicelli
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d'ImmunoGénétique Moléculaire LIGM, IGH, UPR CNRS 1142 and Université Montpellier 2, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d'ImmunoGénétique Moléculaire LIGM, IGH, UPR CNRS 1142 and Université Montpellier 2, Montpellier, France
| | - Edwige Quillet
- Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
| | | | - Frédéric Cazals
- INRIA Sophia-Antipolis - Méditerranée, Algorithms-Biology-Structure, Sophia-Antipolis, France
| | - Adrien Six
- UPMC Univ Paris 06, UMR 7211, “Integrative Immunology” Team, Paris, France; CNRS, UMR 7211, “Immunology, Immunopathology, Immunotherapy,” Paris, France
| | - Simon Fillatreau
- Deutsches RheumaForschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Jouy-en-Josas, France
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18
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Abstract
Vaccines are the most effective tools to prevent infectious diseases and to minimize their impact on humans or animals. Despite the successful development of vaccines that are able to elicit potent and protective immune responses, the majority of vaccines have been so far developed empirically and mechanistic events leading to protective immune responses are often poorly understood. This hampers the development of new prophylactic as well as therapeutic vaccines for infectious diseases and cancer. Biological correlates of immune‐mediated protection are currently based on standard readout such as antibody titres and ELISPOT assays. The development of successful vaccines for difficult settings, such as infectious agents leading to chronic infection (HIV, HCV. . .) or cancer, calls for novel ‘readout systems’ or ‘correlates’ of immune‐mediated protection that would reliably predict immune responses to novel vaccines in vivo. Systems biology offers a new approach to vaccine design that is based upon understanding the molecular network mobilized by vaccination. Systems vaccinology approaches investigate more global correlates of successful vaccination, beyond the specific immune response to the antigens administered, providing new methods for measuring early vaccine efficacy and ultimately generating hypotheses for understanding the mechanisms that underlie successful immunogenicity. Using functional genomics, specific molecular signatures of individual vaccine can be identified and used as predictors of vaccination efficiency. The immune response to vaccination involves the coordinated induction of master transcription factors that leads to the development of a broad, polyfunctional and persistent immune response integrating all effector cells of the immune systems.
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Affiliation(s)
- Adrien Six
- UPMC Univ Paris 06, UMR 7211, F-75013 Paris, France.
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19
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Pham HP, Manuel M, Petit N, Klatzmann D, Cohen-Kaminsky S, Six A, Marodon G. Half of the T-cell repertoire combinatorial diversity is genetically determined in humans and humanized mice. Eur J Immunol 2011; 42:760-70. [PMID: 22105329 DOI: 10.1002/eji.201141798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 10/26/2011] [Accepted: 11/17/2011] [Indexed: 01/04/2023]
Abstract
In humanized mice, the T-cell repertoire is derived from genetically identical human progenitors in distinct animals. Thus, careful comparison of the T-cell repertoires of humanized mice with those of humans may reveal the contribution of genetic determinism on T-cell repertoire formation. Here, we performed a comprehensive assessment of the distribution of V-J combinations of the human β chain of the T-cell receptor (hTRBV) in NOD.SCID.γc(-/-) (NSG) humanized mice. We observed that numerous V-J combinations were equally distributed in the thymus and in the periphery of humanized mice compared with human references. A global analysis of the data, comparing repertoire perturbation indices in humanized NSG mice and unrelated human PBMCs, reveals that 50% of the hTRBV families significantly overlapped. Using multivariate ranking and bootstrap analyses, we found that 18% of all possible V-J combinations contributed close to 50% of the expressed diversity, with significant over-representation of BV5-J1.1+1.2 and BV6-J1.1+1.2 rearrangements. Finally, comparison of CD3(-) and CD3(+) thymocyte repertoires indicated that the observed V-J combination overlap was already present before TCR-MHC selection in the thymus. Altogether, our results show that half of the T-cell repertoire combinatorial diversity in humans is genetically determined.
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Affiliation(s)
- Hang-Phuong Pham
- Hôpital La Pitié-Salpêtrière, UPMC Univ Paris 06, UMR 7211, Paris, France
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20
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Harnessing immune responses against Plasmodium for rational vaccine design. Trends Parasitol 2011; 27:274-83. [PMID: 21531627 DOI: 10.1016/j.pt.2011.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 01/06/2023]
Abstract
In recent years, groundbreaking advances have been made in understanding the biology of and immune mechanisms against the Plasmodium spp. parasite, the causative agent of malaria. Novel features of the Plasmodium life cycle have been unravelled and immune mechanisms, which take place during both infection and immunization, have been dissected. We have undoubtedly enhanced our knowledge, but the question now is how to use this information to manipulate immune responses against Plasmodium and to develop an efficacious malaria vaccine. In this review, we discuss the latest developments in the field and speculate on how immune responses against Plasmodium could be harnessed for rational vaccine design and application.
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21
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Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics 2011; 12:106. [PMID: 21310087 PMCID: PMC3045962 DOI: 10.1186/1471-2164-12-106] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/11/2011] [Indexed: 12/22/2022] Open
Abstract
Background Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR) repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited. Results We analyzed 3 monoclonal TCR from TCR transgenic, Rag-/- mice using Illumina® sequencing. A total of 27 sequencing reactions were performed for each TCR using a trifurcating design in which samples were divided into 3 at significant processing junctures. More than 20 million complementarity determining region (CDR) 3 sequences were analyzed. Filtering for lower quality sequences diminished but did not eliminate sequence errors, which occurred within 1-6% of sequences. Erroneous sequences were pre-dominantly of correct length and contained single nucleotide substitutions. Rates of specific substitutions varied dramatically in a position-dependent manner. Four substitutions, all purine-pyrimidine transversions, predominated. Solid phase amplification and sequencing rather than liquid sample amplification and preparation appeared to be the primary sources of error. Analysis of polyclonal repertoires demonstrated the impact of error accumulation on data parameters. Conclusions Caution is needed in interpreting repertoire data due to potential contamination with mis-sequence reads. However, a high association of errors with phred score, high relatedness of erroneous sequences with the parental sequence, dominance of specific nt substitutions, and skewed ratio of forward to reverse reads among erroneous sequences indicate approaches to filter erroneous sequences from repertoire data sets.
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Affiliation(s)
- Phuong Nguyen
- Department of Pathology, St, Jude Children's Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105, USA
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22
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Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR. High-throughput sequencing of the zebrafish antibody repertoire. Science 2009; 324:807-10. [PMID: 19423829 DOI: 10.1126/science.1170020] [Citation(s) in RCA: 358] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Despite tremendous progress in understanding the nature of the immune system, the full diversity of an organism's antibody repertoire is unknown. We used high-throughput sequencing of the variable domain of the antibody heavy chain from 14 zebrafish to analyze VDJ usage and antibody sequence. Zebrafish were found to use between 50 and 86% of all possible VDJ combinations and shared a similar frequency distribution, with some correlation of VDJ patterns between individuals. Zebrafish antibodies retained a few thousand unique heavy chains that also exhibited a shared frequency distribution. We found evidence of convergence, in which different individuals made the same antibody. This approach provides insight into the breadth of the expressed antibody repertoire and immunological diversity at the level of an individual organism.
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23
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Fairlie-Clarke KJ, Shuker DM, Graham AL. Why do adaptive immune responses cross-react? Evol Appl 2008; 2:122-31. [PMID: 25567852 PMCID: PMC3352416 DOI: 10.1111/j.1752-4571.2008.00052.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 11/06/2008] [Indexed: 11/29/2022] Open
Abstract
Antigen specificity of adaptive immune responses is often in the host's best interests, but with important and as yet unpredictable exceptions. For example, antibodies that bind to multiple flaviviral or malarial species can provide hosts with simultaneous protection against many parasite genotypes. Vaccinology often aims to harness such imprecision, because cross-reactive antibodies might provide broad-spectrum protection in the face of antigenic variation by parasites. However, the causes of cross-reactivity among immune responses are not always known, and here, we explore potential proximate and evolutionary explanations for cross-reactivity. We particularly consider whether cross-reactivity is the result of constraints on the ability of the immune system to process information about the world of antigens, or whether an intermediate level of cross-reactivity may instead represent an evolutionary optimum. We conclude with a series of open questions for future interdisciplinary research, including the suggestion that the evolutionary ecology of information processing might benefit from close examination of immunological data.
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Affiliation(s)
- Karen J Fairlie-Clarke
- Institutes of Evolution, Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories King's Buildings, Edinburgh, UK
| | - David M Shuker
- Institutes of Evolution, Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories King's Buildings, Edinburgh, UK
| | - Andrea L Graham
- Institutes of Evolution, Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories King's Buildings, Edinburgh, UK
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