Plasmodium falciparum (P. falciparum) infection modulates the response of innate immune cells. The aim of this work was to study the impact of P. falciparum infection and P. falciparum-derived molecules on the response of dendritic cells (DC) and monocytes. In paper I we investigated the effects of natural hemozoin (nHZ), a P. falciparum-derived molecule, on the phenotype and functionality of DC. We found that exposure to nHZ impaired the capacity of DC to mature. Paper II is a follow-up on paper I, where the underlying transcriptional events preceding the nHZ-induced impairment of DC maturation were investigated. More specifically, we examined the involvement of certain transcription factors, subunits of chromatin remodeling complexes and histone modifications in the regulation of DC maturation. Our findings suggest that nHZ-exposure of DC does not lead to recruitment or enrichment of molecules needed for transcriptional activation. In paper III we investigated P. falciparum effects in vivo in sympatric ethnic groups with differential susceptibility towards P. falciparum infection living in Burkina Faso. The aim of this study was to establish the transcriptional networks underlying the relatively better protection against P. falciparum infection observed in the Fulani ethnic group compared to other sympatric ethnic groups. Our findings reveal differential gene expression in monocytes of infected Fulani compared to uninfected Fulani and the difference concerned multiple classes of genes including signal transduction, immunological responses and chromatin remodelers. The results provide new aspects on molecules and regulatory mechanisms that are involved in the relatively more protective response against P. falciparum infection. Taken together, the work presented in this thesis leads to a deeper understanding of the P. falciparum-induced modulation of responses of innate immune cells and the underlying mechanisms possibly regulating those responses. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.</p>

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Les IgIV, une préparation thérapeutique d'IgG normales, sont utilisées dans le traitement de diverses maladies auto-immunes et inflammatoires. Les mécanismes par lesquels les IgIV exercent une activité anti-inflammatoire ne sont pas complètement compris. Elles interagissent avec de nombreux composants du système immunitaire et modulent leurs fonctions. Des études récentes ont rapporté que l'hème oxygénase-1 (HO-1) joue un rôle important dans la régulation de la réponse inflammatoire dans un certain nombre de pathologies. Plusieurs agents thérapeutiques exercent des effets anti-inflammatoires grâce à l'induction de l'HO-1. Etant donné le rôle commun anti-inflammatoire de l'HO-1 et des IgIV, j'ai étudié l'implication de l'HO-1 dans les mécanismes d'action des IgIV. J'ai montré que les effets des IgIV ne sont pas associés à l'induction de l'HO-1, que ce soit dans des cellules de l'immunité innée comme les monocytes, cellules dendritiques ou macrophages, ou dans les reins et foie de souris avec une encéphalomyélite auto-immune expérimentale traitées par les IgIV. Des données récentes dans des modèles expérimentaux suggèrent que les IgIV induisent la sécrétion d’IL-4 des basophiles en augmentant l’IL-33 des cellules innées SIGN-R1+. J’ai rapporté que les IgIV induisent directement l’activation de basophiles pré-stimulés avec l’IL-3 alors que contrairement au modèle murin, l’IL-33 n’est pas indispensable. L’activation des basophiles par les IgIV est associée à l’expression augmentée de CD69 et la sécrétion d’IL-4, d’IL-6 et d’IL-8. Ces fonctions sont médiées par les fragments F(ab’)2 qui se lient à des IgE membranaires et activent la voie Syk. / Intravenous immunoglobulin (IVIG), a therapeutic normal immunoglobulin G preparation, is used in the therapy of various autoimmune and inflammatory conditions. The mechanisms by which IVIG exerts anti-inflammatory effects are not completely understood. It interacts with numerous components of the immune system including dendritic cells, macrophages, T and B cells and modulates their functions. Recent studies have reported that heme oxygenase-1 (HO-1) pathway plays an important role in the regulation of inflammatory response in several pathologies. Several therapeutic agents exert anti-inflammatory effects via induction of HO-1. Therefore, in view of common anti-inflammatory role exerted by both HO-1 and IVIG, I investigated if mechanisms of IVIG implicate HO-1. I show that anti-inflammatory effects of IVIG were not associated with an induction of HO-1 either in innate cells such as monocytes, dendritic cells and macrophages or in the kidneys or liver of experimental autoimmune encephalomyelitis. Recent data in experimental models suggest that IVIG induces IL-4 in basophils by enhancing IL-33 in SIGN-R1+ innate cells. I reported that IVIG directly induces activation of IL-3-primed basophils while unlike mice IL-33 was dispensable. The activation of basophils by IVIG was associated with enhanced expression of CD69 and secretion of IL-4, IL-6 and IL-8. These functions of IVIG are mediated via F(ab’)2 fragments that bind to basophil surface IgE and activate Syk pathway.

Durant ma thèse, nous avons identifier PlpA comme une cytotoxine conservée dans des isolats cliniques d'origines diverses, contrairement à son homologue, le facteur de virulence ExoU de Pseudomonas aeruginosa. Un rôle dans la cytotoxicité envers des cellules phagocytaires de l'immunité innée a été attribué à PlpA, et celui-ci dépend de l'intégrité de la dyade catalytique Ser/Asp, caractéristique des protéines de la famille des patatines. Un interactome réalisé in vivo dans des cellules hôtes nous a permis d'identifier des transporteurs de la mitochondrie comme partenaires de PlpA. L'interaction de PlpA avec ses partenaires mitochondriaux, aurait de manière inattendue un effet anti-apoptotique sur les macrophages, mais conduit cependant, à la mort de ceux-ci vraisemblablement par un phénomène de nécrose induite.PlpD a précédemment été caractérisée par Salacha et ses collaborateurs comme étant l'archétype du Système de Sécrétion de Type Vd (2010). Bien que le mécanisme précis de sécrétion de cette protéine reste à ce jour mal connu, nos travaux ont permis de lui attribuer un rôle dans la compétition bactérienne, conférant ainsi un avantage compétitif aux souches qui la possède. D'ailleurs, l'analyse phylogénétique de PlpD (Salacha et al., 2010 ; Heinz & Lithgow 2014) révèle la conservation de cette protéine au sein de nombreuses espèces vivants dans un environnement hostile, suggérant ainsi la nécessité de cette protéine dans l'implantation et la conservation de niches écologiques, que se soit dans l'environnement ou au cours d'infections polymicrobiennes chez un organisme hôte. / During my PhD, in the PAO1 strain of Pseudomonas aeruginosa, we identified PlpA as a cytotoxin conserved in clinical isolates of various origins, contrary to its virulence factor ExoU homologues. A cytotoxic role of PlpA has been highlighted against phagocytic cells, and showed to depend on the integrity of its Ser/Asp catalytic dyad. An in vivo interactome allowed us to identify mitochondrial transporters as partners of PlpA. Interestingly, PlpA interaction with these partners has an anti-apoptotic effect on macrophages but ultimely allows macrophages death probably by a necroptosis phenomenon. PlpD was previously described by Salacha and collaborators as the SST5d archetype (Salacha et al., 2010). While its exact secretion mechanism remains poorly understood, our work allowed showing that it played a role in bacterial competition. PlpD phylogenetic analysis (Salacha et al., 2010 ; Heinz & Lithgow 2014) revealed its conservation in many species living in hostile environments, suggesting its necessity in the implantation and conservation of ecological niches in the environment or during polymicrobial infections into host organism.

Transcriptional regulation is the principal mechanism in establishing cell-type specific gene activity by exploring an almost infinite space of different combinations of regulatory elements, transcription factors with high precision. Recent efforts have mapped thousands of candidate regulatory elements, of which a great portion is cell-type specific yet it is still unclear as to what fraction of these elements is functional, what genes these elements regulate, or how they are established in a cell-type specific manner. In this dissertation, I will discuss methods and approaches I developed to better understand the role of regulatory elements and transcription factors in gene expression regulation. First, by comparing the transcriptome and chromatin landscape between mouse and human innate immune cells I showed specific gene expression programs are regulated by highly conserved regulatory elements that contain a set of constrained sequence motifs, which can successfully classify gene-induction in both species. Next, using chromatin interactions I accurately defined functional enhancers and their target genes. This fine mapping dramatically improved the prediction of transcriptional changes. Finally, we built a supervised learning approach to detect the short DNA sequences motifs that regulate the activation of regulatory elements following LPS stimulation. This approach detected several transcription factors to be critical in remodeling the epigenetic landscape both across time and individuals. Overall this thesis addresses several important aspects of cis-regulatory elements in transcriptional regulation and started to derive principles and models of gene-expression regulation that address the fundamental question: “How do cis-regulatory elements drive cell-type-specific transcription?”