Immunodepression and Immunosuppression During Aging

International audienc

Active regulatory T-cells contribute to broadened T-cell repertoire diversity in ivIg-treated SLE patients

Octapharma

Broadened T-cell Repertoire Diversity in ivIg-treated SLE Patients is Also Related to the Individual Status of Regulatory T-cells

Intravenous IgG (ivIg) is a therapeutic alternative for lupus erythematosus, the mechanism of which remains to be fully understood. Here we investigated whether ivIg affects two established sub-phenotypes of SLE, namely relative oligoclonality of circulating T-cells and reduced activity of CD4 + Foxp3+ regulatory T-cells (Tregs) reflected by lower CD25 surface density.Octapharma research funding; Fundação para a Ciência e a Tecnologia postdoctoral fellowships: (SFRH/BPD/20806/2004, SFRH/BPD/34648/2007); FCT Programa Pessoa travel grant

Caractérisation de la diversité du répertoire TCR par modélisation de données de séquençage haut-débit

T lymphocytes (LT) are key players in the immune system, a complex and dynamic system evolving over the organism’s life. The concept of "lymphocyte repertoire" designates a collection of lymphocytes sharing the same phenotype, the same function or any other criteria. Each LT is characterized by a unique membrane receptor, called TCR, allowing it to recognize specifically antigens. TCRs are characterized by variable regions produced by a series of somatic rearrangements that occur during the thymic differentiation; these regions engage LT recognition diversity. The “TCR repertoire” approach focuses the clonal characterisation of LT populations on the diversity of the TCR expressed on the scale of the population. The high-throughput sequencing of TCR chains (RepSeq) describes this diversity with unprecedented precision. However, this approach requires adapted tools to enable a relevant deciphering of the analysed TCR repertoire diversity. My thesis aimed to: i) deepen the concept of diversity of the lymphocyte repertoire, ii) develop an appropriate methodology to exploit optimally RepSeq data while taking into account the limits of this technology, and iii) develop a tool providing immunologists a thorough characterisation of their TCR repertoires of interest.Les lymphocytes T (LT) sont des acteurs-clés du système immunitaire, un système complexe et dynamique évoluant au cours de la vie de l'organisme. On appelle " répertoire lymphocytaire ", une collection de lymphocytes partageant un même phénotype, une même fonction ou tout autres critères, chacun caractérisé par un récepteur membranaire unique, appelé TCR, lui permettant de reconnaitre de manière spécifique les antigènes. Les TCR sont caractérisés par des régions variables, produites par une série de réarrangements somatiques ayant lieu pendant la différenciation thymique, et qui assurent la diversité de reconnaissance des LT. On parle de répertoire TCR lorsque l'on s'attache à définir les caractéristiques clonales des populations lymphocytaires T sur la base de la diversité des TCR exprimés à l'échelle de la population. Le séquençage à haut débit des chaînes TCR permet désormais de décrire cette diversité avec une précision sans précédent. Cette approche requiert néanmoins des outils adaptés pour permettre une caractérisation pertinente de la structure des répertoires analysés. Un axe de recherche de L'unité I3 est l'analyse du répertoire TR de plusieurs populations lymphocytaires T en situation d'auto-immunité ou d'inflammation. Dans ce contexte, les objectifs de ma thèse ont été de : i) approfondir le concept de diversité du répertoire lymphocytaire, ii) mettre au point une méthodologie adaptée permettant d'exploiter les données de séquençage de manière optimale en prenant en compte les limites de cette technologie, et iii) développer un outil permettant aux immunologistes une caractérisation approfondie et facilement interprétable des répertoires qu'ils étudient

Deciphering TCR repertoire diversity by RepSeq data modelinig

Les lymphocytes T (LT) sont des acteurs-clés du système immunitaire, un système complexe et dynamique évoluant au cours de la vie de l'organisme. On appelle " répertoire lymphocytaire ", une collection de lymphocytes partageant un même phénotype, une même fonction ou tout autres critères, chacun caractérisé par un récepteur membranaire unique, appelé TCR, lui permettant de reconnaitre de manière spécifique les antigènes. Les TCR sont caractérisés par des régions variables, produites par une série de réarrangements somatiques ayant lieu pendant la différenciation thymique, et qui assurent la diversité de reconnaissance des LT. On parle de répertoire TCR lorsque l'on s'attache à définir les caractéristiques clonales des populations lymphocytaires T sur la base de la diversité des TCR exprimés à l'échelle de la population. Le séquençage à haut débit des chaînes TCR permet désormais de décrire cette diversité avec une précision sans précédent. Cette approche requiert néanmoins des outils adaptés pour permettre une caractérisation pertinente de la structure des répertoires analysés. Un axe de recherche de L'unité I3 est l'analyse du répertoire TR de plusieurs populations lymphocytaires T en situation d'auto-immunité ou d'inflammation. Dans ce contexte, les objectifs de ma thèse ont été de : i) approfondir le concept de diversité du répertoire lymphocytaire, ii) mettre au point une méthodologie adaptée permettant d'exploiter les données de séquençage de manière optimale en prenant en compte les limites de cette technologie, et iii) développer un outil permettant aux immunologistes une caractérisation approfondie et facilement interprétable des répertoires qu'ils étudient.T lymphocytes (LT) are key players in the immune system, a complex and dynamic system evolving over the organism’s life. The concept of "lymphocyte repertoire" designates a collection of lymphocytes sharing the same phenotype, the same function or any other criteria. Each LT is characterized by a unique membrane receptor, called TCR, allowing it to recognize specifically antigens. TCRs are characterized by variable regions produced by a series of somatic rearrangements that occur during the thymic differentiation; these regions engage LT recognition diversity. The “TCR repertoire” approach focuses the clonal characterisation of LT populations on the diversity of the TCR expressed on the scale of the population. The high-throughput sequencing of TCR chains (RepSeq) describes this diversity with unprecedented precision. However, this approach requires adapted tools to enable a relevant deciphering of the analysed TCR repertoire diversity. My thesis aimed to: i) deepen the concept of diversity of the lymphocyte repertoire, ii) develop an appropriate methodology to exploit optimally RepSeq data while taking into account the limits of this technology, and iii) develop a tool providing immunologists a thorough characterisation of their TCR repertoires of interest

RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy

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

RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy

International audienceHigh-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

GeVaDSs – decision support system for novel Genetic Vaccine development process

<p>Abstract</p> <p>Background</p> <p>The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories.</p> <p>Results</p> <p>We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system) an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses.</p> <p>Conclusions</p> <p>GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: <url>http://gevads.cs.put.poznan.pl/preview/</url>(login: viewer, password: password).</p

Statistical and computer modelling of T lymphocyte population's dynamics in mice through aging

info:eu-repo/semantics/publishe