Étude systématique de la fonction contexte-dépendante d'OX40 Ligand sur la polarisation des lymphocytes T CD4 auxiliaires chez l’Homme

Adaptive immunity is mainly orchestrated by CD4 T helper cells. They have the ability to polarize in several subsets, each associated to a suitable phenotype for the encounter pathogen. T helper cell activation can be regulated by co-stimulator, such as OX40 Ligand, or co-inhibitor immune checkpoint molecules. These molecules have been studied individually, in specific conditions. However, context-dependency may explain large parts of the functional variability of biological molecules on a given output. Currently, there is no framework to analyze and quantify context-dependency of a molecule over multiple contexts and response outputs. My PhD project focused on OX40L function on T helper cell polarization, in 4 molecular and 11 cellular contexts. We measured 17 T helper cytokines and developed a statistical modeling strategy to quantify OX40L context-dependency on these cytokines. This revealed highly variable qualitative and quantitative context-dependency scores, depending on the output cytokine and context type. Among molecular contexts, Th2 was the most influential on OX40L function. Among cellular contexts, dendritic cell type rather than activating stimulus was dominant in controlling OX40L contextdependency. My thesis work unveils the complex determinants of OX40L function, provides a unique framework to quantify the context-dependent functional variability of any biomolecule, and supports that context-dependency should be more taken into consideration in future studies.L'immunité adaptative est principalement orchestrée par des lymphocytes T CD4 auxiliaires. Ils ont la capacité de se polariser en plusieurs sous-populations, chacune associée à un phénotype approprié au pathogène rencontré. L'activation des lymphocytes T auxiliaires peut être régulée par des checkpoints immunitaires co-stimulateurs, tel que OX40 Ligand, ou co-inhibiteurs. Ces molécules ont été étudiées individuellement, dans des conditions spécifiques. Cependant, la contexte-dépendance pourrait expliquer une grande partie de la variabilité fonctionnelle des biomolécules. Il n'y a actuellement aucune méthode permettant d’analyser et de quantifier la contexte-dépendance d’une molécule dans plusieurs contextes et sur une réponse donnée.Mon projet de thèse a porté sur la fonction de OX40L sur la polarisation des cellules T auxiliaires, dans 4 contextes moléculaires et 11 cellulaires. Nous avons mesuré 17 cytokines T auxiliaires et développé une stratégie de modélisation statistique pour quantifier la contexte-dépendance deOX40L. Les scores de contexte-dépendance se sont révélés très variables qualitativement et quantitativement, en fonction de la cytokine et du type de contexte. Parmi les contextes Th, Th2 était le plus influent sur la fonction OX40L. Parmi les contextes DC, le type de cellules dendritique était dominant dans le contrôle de la contexte-dépendance de OX40L plutôt que le stimuli d’activation. Mon travail de thèse dévoile les complexes déterminants de la fonction de OX40L, fournit une méthode unique pour quantifier la variabilité fonctionnelle contexte-dépendante de n’importe quelle biomolécule et appuie sur le fait que la contexte-dépendance devrait être davantage prise en considération dans les études futures

Étude systématique de la fonction contexte-dépendante d'OX40 Ligand sur la polarisation des lymphocytes T CD4 auxiliaires chez l’Homme

Adaptive immunity is mainly orchestrated by CD4 T helper cells. They have the ability to polarize in several subsets, each associated to a suitable phenotype for the encounter pathogen. T helper cell activation can be regulated by co-stimulator, such as OX40 Ligand, or co-inhibitor immune checkpoint molecules. These molecules have been studied individually, in specific conditions. However, context-dependency may explain large parts of the functional variability of biological molecules on a given output. Currently, there is no framework to analyze and quantify context-dependency of a molecule over multiple contexts and response outputs. My PhD project focused on OX40L function on T helper cell polarization, in 4 molecular and 11 cellular contexts. We measured 17 T helper cytokines and developed a statistical modeling strategy to quantify OX40L context-dependency on these cytokines. This revealed highly variable qualitative and quantitative context-dependency scores, depending on the output cytokine and context type. Among molecular contexts, Th2 was the most influential on OX40L function. Among cellular contexts, dendritic cell type rather than activating stimulus was dominant in controlling OX40L contextdependency. My thesis work unveils the complex determinants of OX40L function, provides a unique framework to quantify the context-dependent functional variability of any biomolecule, and supports that context-dependency should be more taken into consideration in future studies.L'immunité adaptative est principalement orchestrée par des lymphocytes T CD4 auxiliaires. Ils ont la capacité de se polariser en plusieurs sous-populations, chacune associée à un phénotype approprié au pathogène rencontré. L'activation des lymphocytes T auxiliaires peut être régulée par des checkpoints immunitaires co-stimulateurs, tel que OX40 Ligand, ou co-inhibiteurs. Ces molécules ont été étudiées individuellement, dans des conditions spécifiques. Cependant, la contexte-dépendance pourrait expliquer une grande partie de la variabilité fonctionnelle des biomolécules. Il n'y a actuellement aucune méthode permettant d’analyser et de quantifier la contexte-dépendance d’une molécule dans plusieurs contextes et sur une réponse donnée.Mon projet de thèse a porté sur la fonction de OX40L sur la polarisation des cellules T auxiliaires, dans 4 contextes moléculaires et 11 cellulaires. Nous avons mesuré 17 cytokines T auxiliaires et développé une stratégie de modélisation statistique pour quantifier la contexte-dépendance deOX40L. Les scores de contexte-dépendance se sont révélés très variables qualitativement et quantitativement, en fonction de la cytokine et du type de contexte. Parmi les contextes Th, Th2 était le plus influent sur la fonction OX40L. Parmi les contextes DC, le type de cellules dendritique était dominant dans le contrôle de la contexte-dépendance de OX40L plutôt que le stimuli d’activation. Mon travail de thèse dévoile les complexes déterminants de la fonction de OX40L, fournit une méthode unique pour quantifier la variabilité fonctionnelle contexte-dépendante de n’importe quelle biomolécule et appuie sur le fait que la contexte-dépendance devrait être davantage prise en considération dans les études futures

Neuroinflammation in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia and the Interest of Induced Pluripotent Stem Cells to Study Immune Cells Interactions With Neurons

International audienceInflammation is a shared hallmark between amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). For long, studies were conducted on tissues of post-mortem patients and neuroinflammation was thought to be only bystander result of the disease with the immune system reacting to dying neurons. In the last two decades, thanks to improving technologies, the identification of causal genes and the development of new tools and models, the involvement of inflammation has emerged as a potential driver of the diseases and evolved as a new area of intense research. In this review, we present the current knowledge about neuroinflammation in ALS, ALS-FTD, and FTD patients and animal models and we discuss reasons of failures linked to therapeutic trials with immunomodulator drugs. Then we present the induced pluripotent stem cell (iPSC) technology and its interest as a new tool to have a better immunopathological comprehension of both diseases in a human context. The iPSC technology giving the unique opportunity to study cells across differentiation and maturation times, brings the hope to shed light on the different mechanisms linking neurodegeneration and activation of the immune system. Protocols available to differentiate iPSC into different immune cell types are presented. Finally, we discuss the interest in studying monocultures of iPS-derived immune cells, co-cultures with neurons and 3D cultures with different cell types, as more integrated cellular approaches. The hope is that the future work with human iPS-derived cells helps not only to identify disease-specific defects in the different cell types but also to decipher the synergistic effects between neurons and immune cells. These new cellular tools could help to find new therapeutic approaches for all patients with ALS, ALS-FTD, and FTD

A Quantitative Multivariate Model of Human Dendritic Cell-T Helper Cell Communication

International audienceCell-cell communication involves a large number of molecular signals that function as words of a complex language whose grammar remains mostly unknown. Here, we describe an integrative approach involving (1) protein-level measurement of multiple communication signals coupled to output responses in receiving cells and (2) mathematical modeling to uncover input-output relationships and interactions between signals. Using human dendritic cell (DC)-T helper (Th) cell communication as a model, we measured 36 DC-derived signals and 17 Th cytokines broadly covering Th diversity in 428 observations. We developed a data-driven, computationally validated model capturing 56 already described and 290 potentially novel mechanisms of Th cell specification. By predicting context-dependent behaviors, we demonstrate a new function for IL-12p70 as an inducer of Th17 in an IL-1 signaling context. This work provides a unique resource to decipher the complex combinatorial rules governing DC-Th cell communication and guide their manipulation for vaccine design and immunotherapies

Spatial Positioning and Matrix Programs of Cancer-Associated Fibroblasts Promote T-cell Exclusion in Human Lung Tumors

International audienceIt is currently accepted that cancer-associated fibroblasts (CAF) participate in T-cell exclusion from tumor nests. To unbiasedly test this, we used single-cell RNA sequencing coupled with multiplex imaging on a large cohort of lung tumors. We identified four main CAF populations, two of which are associated with T-cell exclusion: (i) MYH11+αSMA+ CAF, which are present in early-stage tumors and form a single cell layer lining cancer aggregates, and (ii) FAP+αSMA+ CAF, which appear in more advanced tumors and organize in patches within the stroma or in multiple layers around tumor nests. Both populations orchestrate a particular structural tissue organization through dense and aligned fiber deposition compared with T cell–permissive CAF. Yet they produce distinct matrix molecules, including collagen IV (MYH11+αSMA+ CAF) and collagen XI/XII (FAP+αSMA+ CAF). Hereby, we uncovered unique molecular programs of CAF driving T-cell marginalization, whose targeting should increase immunotherapy efficacy in patients bearing T cell–excluded tumors. SIGNIFICANCE: The cellular and molecular programs driving T-cell marginalization in solid tumors remain unclear. Here, we describe two CAF populations associated with T-cell exclusion in human lung tumors. We demonstrate the importance of pairing molecular and spatial analysis of the tumor micro-environment, a prerequisite to developing new strategies targeting T cell–excluding CAF

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.

Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern Toll-like receptor 3 (TLR3)- and interferon regulatory factor 7 (IRF7)-dependent type I interferon (IFN) immunity to influenza virus in 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally defined LOF variants underlying autosomal-recessive or autosomal-dominant deficiencies in 23 patients (3.5%) 17 to 77 years of age. We show that human fibroblasts with mutations affecting this circuit are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection