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Tfh Cells in Health and Immunity: Potential Targets for Systems Biology Approaches to Vaccination. Int J Mol Sci 2020; 21:ijms21228524. [PMID: 33198297 PMCID: PMC7696930 DOI: 10.3390/ijms21228524] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
T follicular helper (Tfh) cells are a specialised subset of CD4+ T cells that play a significant role in the adaptive immune response, providing critical help to B cells within the germinal centres (GC) of secondary lymphoid organs. The B cell receptors of GC B cells undergo multiple rounds of somatic hypermutation and affinity maturation within the GC response, a process dependent on cognate interactions with Tfh cells. B cells that receive sufficient help from Tfh cells form antibody-producing long-lived plasma and memory B cells that provide the basis of decades of effective and efficient protection and are considered the gold standard in correlates of protection post-vaccination. However, the T cell response to vaccination has been understudied, and over the last 10 years, exponential improvements in the technological underpinnings of sampling techniques, experimental and analytical tools have allowed multidisciplinary characterisation of the role of T cells and the immune system as a whole. Of particular interest to the field of vaccinology are GCs and Tfh cells, representing a unique target for improving immunisation strategies. Here, we discuss recent insights into the unique journey of Tfh cells from thymus to lymph node during differentiation and their role in the production of high-quality antibody responses as well as their journey back to the periphery as a population of memory cells. Further, we explore their function in health and disease and the power of next-generation sequencing techniques to uncover their potential as modulators of vaccine-induced immunity.
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Dupic T, Marcou Q, Walczak AM, Mora T. Genesis of the αβ T-cell receptor. PLoS Comput Biol 2019; 15:e1006874. [PMID: 30830899 PMCID: PMC6417744 DOI: 10.1371/journal.pcbi.1006874] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 03/14/2019] [Accepted: 02/17/2019] [Indexed: 11/18/2022] Open
Abstract
The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called α and β, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human TCR repertoires, we quantitively characterize the αβ generation process. We estimate the probabilities of a rescue recombination of the β chain on the second chromosome upon failure or success on the first chromosome. Unlike β chains, α chains recombine simultaneously on both chromosomes, resulting in correlated statistics of the two genes which we predict using a mechanistic model. We find that ∼35% of cells express both α chains. Altogether, our statistical analysis gives a complete quantitative mechanistic picture that results in the observed correlations in the generative process. We learn that the probability to generate any TCRαβ is lower than 10(-12) and estimate the generation diversity and sharing properties of the αβ TCR repertoire.
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MESH Headings
- Chromosomes, Human
- Humans
- Probability
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
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Affiliation(s)
- Thomas Dupic
- Laboratoire de physique théorique et hautes énergies, CNRS and Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Quentin Marcou
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
| | - Thierry Mora
- Laboratoire de physique de l’ENS, CNRS, Sorbonne Université, and École normale supérieure (PSL), 24 rue Lhomond, 75005 Paris, France
- * E-mail: (AMW); (TM)
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Elhanati Y, Sethna Z, Callan CG, Mora T, Walczak AM. Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination. Immunol Rev 2018; 284:167-179. [PMID: 29944757 PMCID: PMC6033145 DOI: 10.1111/imr.12665] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the extreme diversity of T-cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely shared sequences, often referred to as "public," have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here, we show that even for large cohorts, the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations, we propose a public/private sequence classifier, "PUBLIC" (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes.
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Affiliation(s)
- Yuval Elhanati
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | - Zachary Sethna
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | | | - Thierry Mora
- Laboratoire de physique statistiqueCNRSSorbonne UniversitéUniversité Paris‐Diderot, and École Normale Supérieure (PSL University)ParisFrance
| | - Aleksandra M. Walczak
- Laboratoire de physique théoriqueCNRSSorbonne Université, and École Normale Supérieure (PSL University)ParisFrance
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Toor AA, Toor AA, Rahmani M, Manjili MH. On the organization of human T-cell receptor loci: log-periodic distribution of T-cell receptor gene segments. J R Soc Interface 2016; 13:20150911. [PMID: 26763333 DOI: 10.1098/rsif.2015.0911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The human T-cell repertoire is complex and is generated by the rearrangement of variable (V), diversity (D) and joining (J) segments on the T-cell receptor (TCR) loci. The T-cell repertoire demonstrates self-similarity in terms clonal frequencies when defined by V, D and J gene segment usage; therefore to determine whether the structural ordering of these gene segments on the TCR loci contributes to the observed clonal frequencies, the TCR loci were examined for self-similarity and periodicity in terms of gene segment organization. Logarithmic transformation of numeric sequence order demonstrated that the V and J gene segments for both T-cell receptor α (TRA) and β (TRB) loci are arranged in a self-similar manner when the spacing between the adjacent segments was considered as a function of the size of the neighbouring gene segment, with an average fractal dimension of approximately 1.5. Accounting for the gene segments occurring on helical DNA molecules with a logarithmic distribution, sine and cosine functions of the log-transformed angular coordinates of the start and stop nucleotides of successive TCR gene segments showed an ordered progression from the 5' to the 3' end of the locus, supporting a log-periodic organization. T-cell clonal frequency estimates, based on V and J segment usage, from normal stem cell donors were plotted against the V and J segment on TRB locus and demonstrated a periodic distribution. We hypothesize that this quasi-periodic variation in gene-segment representation in the T-cell clonal repertoire may be influenced by the location of the gene segments on the periodic-logarithmically scaled TCR loci. Interactions between the two strands of DNA in the double helix may influence the probability of gene segment usage by means of either constructive or destructive interference resulting from the superposition of the two helices.
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Affiliation(s)
- Amir A Toor
- Bone Marrow Transplant Program, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Abdullah A Toor
- School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohamed Rahmani
- Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
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Elhanati Y, Marcou Q, Mora T, Walczak AM. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. Bioinformatics 2016; 32:1943-51. [PMID: 27153709 PMCID: PMC4920122 DOI: 10.1093/bioinformatics/btw112] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/20/2016] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events-choices of gene templates, base pair deletions and insertions-described by probability distributions. Not all scenarios are equally likely, and the same receptor sequence may be obtained in several different ways. Quantifying the distribution of these rearrangements is an essential baseline for studying the immune system diversity. Inferring the properties of the distributions from receptor sequences is a computationally hard problem, requiring enumerating every possible scenario for every sampled receptor sequence. RESULTS We present a Hidden Markov model, which accounts for all plausible scenarios that can generate the receptor sequences. We developed and implemented a method based on the Baum-Welch algorithm that can efficiently infer the parameters for the different events of the rearrangement process. We tested our software tool on sequence data for both the alpha and beta chains of the T cell receptor. To test the validity of our algorithm, we also generated synthetic sequences produced by a known model, and confirmed that its parameters could be accurately inferred back from the sequences. The inferred model can be used to generate synthetic sequences, to calculate the probability of generation of any receptor sequence, as well as the theoretical diversity of the repertoire. We estimate this diversity to be [Formula: see text] for human T cells. The model gives a baseline to investigate the selection and dynamics of immune repertoires. AVAILABILITY AND IMPLEMENTATION Source code and sample sequence files are available at https://bitbucket.org/yuvalel/repgenhmm/downloads CONTACT elhanati@lpt.ens.fr or tmora@lps.ens.fr or awalczak@lpt.ens.fr.
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Affiliation(s)
- Yuval Elhanati
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Quentin Marcou
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Thierry Mora
- Laboratoire de physique statistique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
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Phetsouphanh C, Kelleher AD. The Role of PKC-θ in CD4+ T Cells and HIV Infection: To the Nucleus and Back Again. Front Immunol 2015; 6:391. [PMID: 26284074 PMCID: PMC4519685 DOI: 10.3389/fimmu.2015.00391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/17/2015] [Indexed: 11/13/2022] Open
Abstract
Protein kinase C (PKC)-θ is the only member of the PKC family that has the ability to translocate to the immunological synapse between T cells and antigen-presenting cells upon T cell receptor and MHC-II recognition. PKC-θ interacts functionally and physically with other downstream effector molecules to mediate T cell activation, differentiation, and migration. It plays a critical role in the generation of Th2 and Th17 responses and is less important in Th1 and CTL responses. PKC-θ has been recently shown to play a role in the nucleus, where it mediates inducible gene expression in the development of memory CD4+ T cells. This novel PKC (nPKC) can up-regulate HIV-1 transcription and PKC-θ activators such as Prostratin have been used in early HIV-1 reservoir eradication studies. The exact manner of the activation of virus by these compounds and the role of PKC-θ, particularly its nuclear form and its association with NF-κB in both the cytoplasmic and nuclear compartments, needs further precise elucidation especially given the very important role of NF-κB in regulating transcription from the integrated retrovirus. Continued studies of this nPKC isoform will give further insight into the complexity of T cell signaling kinases.
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Affiliation(s)
- Chansavath Phetsouphanh
- The Kirby Institute of Infectious Diseases in Society, University of New South Wales , Sydney, NSW , Australia
| | - Anthony D Kelleher
- The Kirby Institute of Infectious Diseases in Society, University of New South Wales , Sydney, NSW , Australia
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Carico Z, Krangel MS. Chromatin Dynamics and the Development of the TCRα and TCRδ Repertoires. Adv Immunol 2015; 128:307-61. [DOI: 10.1016/bs.ai.2015.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Numerical modelling of the V-J combinations of the T cell receptor TRA/TRD locus. PLoS Comput Biol 2010; 6:e1000682. [PMID: 20174554 PMCID: PMC2824756 DOI: 10.1371/journal.pcbi.1000682] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/21/2010] [Indexed: 01/07/2023] Open
Abstract
T-Cell antigen Receptor (TR) repertoire is generated through rearrangements of V and J genes encoding α and β chains. The quantification and frequency for every V-J combination during ontogeny and development of the immune system remain to be precisely established. We have addressed this issue by building a model able to account for Vα-Jα gene rearrangements during thymus development of mice. So we developed a numerical model on the whole TRA/TRD locus, based on experimental data, to estimate how Vα and Jα genes become accessible to rearrangements. The progressive opening of the locus to V-J gene recombinations is modeled through windows of accessibility of different sizes and with different speeds of progression. Furthermore, the possibility of successive secondary V-J rearrangements was included in the modelling. The model points out some unbalanced V-J associations resulting from a preferential access to gene rearrangements and from a non-uniform partition of the accessibility of the J genes, depending on their location in the locus. The model shows that 3 to 4 successive rearrangements are sufficient to explain the use of all the V and J genes of the locus. Finally, the model provides information on both the kinetics of rearrangements and frequencies of each V-J associations. The model accounts for the essential features of the observed rearrangements on the TRA/TRD locus and may provide a reference for the repertoire of the V-J combinatorial diversity. Lymphocytes of the immune system ensure the body defense by the expression of receptors which are specific of targets, termed antigens. Each lymphocyte, deriving from the same original clone, expresses the same unique receptor. To achieve the production of receptors covering the wide variety of antigens, lymphocytes use a specialized genetic mechanism consisting of gene rearrangements. For instance, the genes encoding the receptor of the alpha chain of the T lymphocyte receptor (TRA) spread over a 1500 Kb genetic region which includes around 100 V genes, 60 J genes, and a single C gene. To constitute a functional alpha chain, one of the V and one of the J genes rearrange together to form a single exon. The precise definition of these V-J combinations is essential to understand the repertoire of TRA. We have developed a numerical model simulating all of the V-J combinations of TRA, fitting the available experimental observations obtained from the analysis of TRA in T lymphocytes of the thymus and the blood. Our model gives new insights on the rules controlling the use of V and J genes in providing a dynamic estimation of the total V-J combinations.
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Krangel MS. Mechanics of T cell receptor gene rearrangement. Curr Opin Immunol 2009; 21:133-9. [PMID: 19362456 DOI: 10.1016/j.coi.2009.03.009] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 03/13/2009] [Indexed: 11/20/2022]
Abstract
The four T cell receptor genes (Tcra, Tcrb, Tcrg, Tcrd) are assembled by V(D)J recombination according to distinct programs during intrathymic T cell development. These programs depend on genetic factors, including gene segment order and recombination signal sequences. They also depend on epigenetic factors. Regulated changes in chromatin structure, directed by enhancers and promoter, can modify the availability of recombination signal sequences to the RAG recombinase. Regulated changes in locus conformation may control the synapsis of distant recombination signal sequences, and regulated changes in subnuclear positioning may influence locus recombination events by unknown mechanisms. Together these influences may explain the ordered activation and inactivation of T cell receptor locus recombination events and the phenomenon of Tcrb allelic exclusion.
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Affiliation(s)
- Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.
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Abstract
T lymphocyte development is directed by a gene-expression program that occurs in the complex nucleoprotein environment of chromatin. This review examines basic principles of chromatin regulation and evaluates ongoing progress toward understanding how the chromatin template is manipulated to control gene expression and gene recombination in developing thymocytes. Special attention is devoted to the loci encoding T cell receptors alpha and beta, T cell coreceptors CD4 and CD8, and the enzyme terminal deoxynucleotidyl transferase. The properties of SATB1, a notable organizer of thymocyte chromatin, are also addressed.
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Affiliation(s)
- Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, North Carolina 27710 USA.
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Huang CY, Sharma GG, Walker LM, Bassing CH, Pandita TK, Sleckman BP. Defects in coding joint formation in vivo in developing ATM-deficient B and T lymphocytes. ACTA ACUST UNITED AC 2007; 204:1371-81. [PMID: 17502661 PMCID: PMC2118620 DOI: 10.1084/jem.20061460] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ataxia-telangiectasia mutated (ATM)–deficient lymphocytes exhibit defects in coding joint formation during V(D)J recombination in vitro. Similar defects in vivo should affect both T and B cell development, yet the lymphoid phenotypes of ATM deficiency are more pronounced in the T cell compartment. In this regard, ATM-deficient mice exhibit a preferential T lymphopenia and have an increased incidence of nontransformed and transformed T cells with T cell receptor α/δ locus translocations. We demonstrate that there is an increase in the accumulation of unrepaired coding ends during different steps of antigen receptor gene assembly at both the immunoglobulin and T cell receptor loci in developing ATM-deficient B and T lymphocytes. Furthermore, we show that the frequency of ATM-deficient αβ T cells with translocations involving the T cell receptor α/δ locus is directly related to the number of T cell receptor α rearrangements that these cells can make during development. Collectively, these findings demonstrate that ATM deficiency leads to broad defects in coding joint formation in developing B and T lymphocytes in vivo, and they provide a potential molecular explanation as to why the developmental impact of these defects could be more pronounced in the T cell compartment.
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Affiliation(s)
- Ching-Yu Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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