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.

Le virus de la rage est un pathogène neurotrope qui, actuellement, fait toujours plus de 55000 morts par an et dont la pathogenèse présente toujours de nombreuses zones d’ombre. Le mécanisme par lequel le virus échappe au système immunitaire de même que l’implication d’autres types cellulaires, particulièrement au niveau de la phase de latence, n’est pas encore connu. Il en est de même pour le mécanisme par lequel le virus induit un dysfonctionnement neuronal. Dans le cadre de ce projet de thèse, nous avons donc décidé d’étudier l’implication du macrophage et des caspases dans l’infection induite par le virus rabique. <p>Nos résultats ont permis de démontrer que, malgré la faiblesse de la production virale in vitro, les macrophages infectés par une souche virulente de virus rabique étaient capables de transmettre l’infection et d’induire une encéphalite mortelle chez la souris. Ces résultats suggèrent que les macrophages sont susceptibles d’être des hôtes potentiels du virus.<p>Dans un deuxième temps, nous avons également mis en évidence des différences de caractéristiques d’infection entre les souches virulentes et atténuées du virus rabique. Nous avons en effet démontré qu’en comparaison avec la souche vaccinale ERA, l’infection par la souche virulente CVS-11 était moins productive dans les cellules d’origine périphérique, tels que les cellules musculaires ou les macrophages. En revanche, la souche virulente se réplique mieux dans le cerveau et dans les cellules d’origine neuronale. Chez le macrophage, nous avons pu observer que l’infection par la souche atténuée ERA induisait une plus forte mortalité que celle générée par la souche CVS-11. Nos analyses ont mis en évidence que cette mortalité était de type apoptotique et qu’elle impliquait l’activation des caspases-1, -3, -7, -8, -9, du facteur Bid et de l’IL-1β. Des analyses réalisées sur des macrophages knock-out pour les caspase-1, -3 et -7 ont démontré d’une part l’importance de la caspase-3 dans la mortalité cellulaire et d’autre part qu’une déficience en caspase-7 pouvait être associée à une charge virale plus élevée, particulièrement en cas d’infection avec la souche virulente. In vivo, nous avons observé que l’inoculation de la souche CVS-11 chez des souris déficientes en caspase-3 retardait l’apparition des symptômes et de la mortalité sans pour autant modifier l’issue inéluctable de la maladie. Chez les souris caspase-1 knock-out, l’inoculation d’une souche atténuée entrainait une morbidité plus élevée que celle observée chez les souris WT.<p>Ce travail de thèse nous a donc permis d’améliorer notre compréhension des mécanismes impliqués dans la pathogénèse du virus rabique et dans la réponse de l’hôte à l’infection et a souligné le rôle potentiel du macrophage comme vecteur de dissémination virale/<p><p>Rabies virus is a neurotropic pathogen which currently causes more than 55000 deaths a year and our knowledge on its pathogenesis still contains many gaps. The mechanism by which the virus escapes the immune system as well as the involvement of different cell types, particularly in the asymptomatic phase, is still unknown. The situation is similar for the mechanism by which the virus induces neuronal dysfunction. In this work, we decided to study the involvement of caspases and the macrophage in infection induced by rabies virus.<p>Our results demonstrated that, despite a weak virus production in vitro, macrophages infected with a virulent strain of rabies virus were able to transmit infection and induce fatal encephalitis in mice. These results suggest that macrophages may be potential cellular hosts of rabies virus.<p>In a second step, we demonstrated differences in infection characteristics between virulent and attenuated rabies virus strains. Indeed, we showed that, in comparison with the ERA vaccine strain, infection with the virulent strain CVS-11 strain was less productive in cells of peripheral origin, such as muscle cells or macrophages. In contrast, the virulent strain replicated best in the brain and in neuronal cells. In the macrophage, we observed that infection with the attenuated strain ERA strain induced a higher mortality than that induced by the CVS-11 strain. Our analyzes showed that mortality was apoptotic and involved the activation of caspases-1, -3, -7, -8, -9, IL-1β and cleavage of Bid. Analyzes performed on macrophages deficient for caspase-1, -3 or -7 indicated the importance of caspase-3 in cell death and demonstrated that a deficiency in caspase- 7 could be associated with a higher viral loadd, particularly in case of infection with the virulent strain. In vivo, we observed that the inoculation of the CVS-11 strain in mice deficient in caspase-3 delayed the onset of symptoms and mortality without changing the fatal outcome of the disease. Inoculation of caspase-1 knockout mice with the attenuated strain resulted in a higher morbidity than that observed in wild type mice.<p>This work allowed us to improve our understanding of the mechanisms involved in the pathogenesis of rabies virus and in the host response and highlighted a potential role for the macrophage as a vector of virus dissemination.<p><p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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?”

La compréhension des mécanismes immunologiques précoces mis en place suite à l’administration de vaccins est encore de nos jours largement méconnue. Pourtant de plus en plus d’études démontrent l’importance de ces mécanismes très précoces faisant intervenir les acteurs de l’immunité innée dans la génération d’une réponse spécifique efficace après vaccination. La peau est un organe intéressant pour l'administration de vaccins du fait de sa richesse en cellules présentatrices d'antigènes (APC), qui sont des cellules essentielles dans la mise en place de la réponse immunitaire. L'administration par voie intradermique du vaccin ADN de type auxoGTU induit des réponses immunitaires fortes et persistantes, en particulier en association avec une électroporation (EP) locale chez le macaque cynomolgus. Le but de ce travail de thèse fut de caractériser les réponses immunitaires locales précocement mises en place suite à l’administration par voie intradermique du vaccin ADN auxo-GTU en association avec une EP. Dans un premier temps, nous avons décrit les populations de cellules immunitaires présentes dans la peau normale chez le macaque cynomolgus.L'épiderme contient des cellules de Langerhans (LC) qui sont : CD1a+ CD1c- et des lymphocytes T caractérisés par l’expression du CD3. Le derme contient des cellules CD1a+CD1c-, qui présentent des similitudes avec les LC et correspondent donc probablement à des LC en migration à travers le derme. Il contient également des cellules dendritiques dermales (DDC) CD1a+CD1c+, des macrophages résidants CD163highCD11b+ et les lymphocytes T CD3+. Chez certains animaux, nous avons mis en évidence la présence de granulocytes CD66+ dans le derme sain. Les populations de cellules immunitaires identifiées chez le macaque sont similaires à celles identifiées chez l’homme malgré de légères différences phénotypiques. Cette caractérisation nous a ensuite permis d'étudier l’impact de la vaccination sur les populations immunitaires de la peau.Nous avons démontré que la vaccination induit le recrutement de granulocytes et de monocytes/macrophages inflammatoires dans l'épiderme et dans le derme, ainsi qu’un recrutement plus tardif de cellules dendritiques inflammatoires épithéliales (IDEC) dans l'épiderme. Dans l'épiderme, 24h après immunisation, nous avons observé une augmentation transitoire des LC accompagnée d’une surexpression de HLA-DR, de CD86 et de CD83, ce qui démontre leur maturation. Entre 24h et 72h, le nombre de LC diminue, ce qui suggère que les LC matures quittent l’épiderme pour migrer vers les nœuds lymphatiques. Ces événements cellulaires sont majoritairement dus à l’EP, indépendamment de la présence du vaccin à ADN. L’analyse du microenvironnement mis en place dans la peau suite à la vaccination révèle une libération de facteurs solubles pro-inflammatoires, comme MCP-1, IL-18 , IL-15, IL-8 et de facteurs solubles anti- inflammatoires comme IL-1RA et sCD40L dès 24h, dont certains sont considérablement augmentés par la présence de l’ADN vaccinal. Nos résultats suggèrent que l’EP, indépendamment de la présence de l'ADN, est suffisante pour induire la mobilisation des cellules et la maturation des DC au niveau du site de vaccination, ce qui montre un important rôle adjuvant de l’EP. Cependant, il semble que l'ADN soit nécessaire pour générer un microenvironnement favorable à l'activation optimale des APC. Ce travail fournit des éléments importants sur les mécanismes de l'inflammation locale et ouvre de nouvelles possibilités pour les stratégies vaccinales. / Mechanisms involved in early vaccine response are poorly understood. However, more and more studies show the importance of innate immunity in the very early times following vaccine administration in the generation of an optimal specific immune response. Skin is an interesting target for vaccine delivery because of its richness in antigen presenting cells (APC) which are essential cells in immune responses. The intradermal delivery of auxoGTU DNA vaccine was shown to induce strong and persistent immune responses, especially in association with electroporation in cynomolgus macaque. The aim of this work was to characterize the early local immune responses followed intradermal auxoGTU DNA vaccination in association with EP in cynomolgus macaque. In a first step, we have described immune cell populations present in the normal skin in the cynomolgus macaques. The epidermis contains CD1a+CD1c- Langerhans cells (LCs), and CD3+ T cells. The dermis contains CD1a+CD1c- cells, which present similarities with LCs and probably correspond to LC in migration through dermis. It also contains CD1a+CD1c+ dermal dendritic cells (DDCs), CD163highCD11b+ resident macrophages, and CD3+ T cells. We found CD66+ polymorphonuclear cells in healthy dermis in some of the animals. Immune cell populations in the macaque are similar to those in humans despite moderate differences in phenotype. This characterization has allowed us to study the impact of vaccination on immune populations of the skin. We have demonstrated a recruitment of granulocytes and inflammatory monocytes/macrophages in epidermis and dermis, as well as a population of inflammatory dendritic epithelial cell (IDEC) in epidermis after vaccination. In epidermis, 24h after treatment, we have observed an initial increase of LC with an up-regulation of HLA-DR, CD86 and CD83, demonstrating their maturation. Between 24h and 72h, LC number decreased, suggesting that mature LC has leaved epidermis to migrate to skin draining lymph node. All these cellular events were almost due to EP process, independently of DNA vaccine presence. The skin microenvironment reveals a release of pro-inflammatory soluble factors, as MCP-1, IL-18, IL-15, IL-8 and anti-inflammatory mediators as IL-1RA and sCD40L by 24h, all considerably enhanced in the presence of DNA.Our results suggest that EP, independently of the presence of DNA, is sufficient to induce cells mobilization and DC maturation at the vaccinated site, suggesting an important adjuvant effect of EP. However, it seems that DNA is required to generate a favorable microenvironment essential for correct APC activation. This work provides important clues to local inflammation mechanisms and opens up new possibilities for vaccine strategies.

Microglia and brain-resident macrophages are the sentinel immune cells of the central nervous system (CNS), and are ideally situated to respond to any damage to the brain parenchyma or vasculature. Circulating leukocytes are generally excluded from the CNS environment under homeostatic conditions but can gain access to this region in diseases that disrupt immune system function and blood-brain barrier integrity. Although these diverse immune cells exhibit properties that may engender them to be well-suited to resolve microcirculatory insults, their relative contributions to the recanalization of capillary rupture in the cortex, known as cerebral microbleeds (CMBs), has yet to be described. CMBs are particularly concerning in conditions, such as diabetes mellitus (DM), in which these insults occur more frequently and potentially underlie the onset and progression of cognitive decline. Using in vivo 2-photon microscopy and confocal imaging, here I highlight the compromised repair of CMBs in a mouse model of type 1 DM and characterize the robust, heterogeneous macrophage response to these insults. Specifically, 20% of damaged capillaries were eliminated from the circulation in the diabetic cortex and chronic insulin treatment failed to prevent this microvascular loss. Administration of interferon-α or interferon-γ neutralizing antibodies to dampen inflammatory signalling, or dexamethasone to reduce global inflammation, also failed to improve repair rates of damaged microvessels in diabetic mice. In contrast, CMBs in nondiabetic mice repaired without exception. Interestingly, depletion of CNS macrophages using the colony stimulating factor-1 receptor antagonist PLX5622 resulted in microvascular elimination in nondiabetic mice. Given the robust depletion of brain macrophage populations with this treatment, at first these data suggested that these cells were necessary for microvascular repair since their elimination produced vessel loss. However, by parsing the data I identified that microvessels repaired in all cases where macrophages were not identified at the CMB; when CX3CR1+ aggregate was localized to the injury, ~20% of microvessels were eliminated. These findings show that CNS macrophages are not required for microvascular repair following CMB. Immunofluorescent co-labelling of various microglial and macrophage markers within the diabetic CMB milieu revealed a novel population of Mac2+/TMEM119- cells, distinct from homeostatic TMEM119+ microglia. These cells reliably localized to CMBs that failed to repair and rarely associated with vessels that recanalized; Mac2+/TMEM119- cells were not found within nondiabetic CMBs. Treatment of diabetic mice with clodronate liposomes (CLR) to deplete circulating phagocytic leukocytes prevented aggregation of Mac2+/TMEM119- cells to CMBs and improved capillary repair rates. The efficacy of CLR in excluding these cells from the CMB aggregate, coincident with eradication of monocytes from circulation, indicated that these cells likely arose from the periphery. In vivo 2-photon imaging revealed significant increases in lipofuscin at the site of diabetic CMBs relative to the nondiabetic context; other phagocytic markers including CD68 and TREM2 were also upregulated. Mac2+/TMEM119- cells showed elevated lipofuscin content relative to homeostatic microglia; their association with CMBs may thus signal an increase in phagocytosis that contributes to capillary pruning. Taken together, these data identify a novel Mac2+/TMEM119- macrophage associated with pathological microvascular elimination following CMB in the diabetic neocortex. These findings highlight the diversity of immune cell responses to CNS injury and provide insights into the cellular mechanisms of capillary pruning. Furthermore, these advances in our understanding of the regulation of microvascular elimination in the diabetic brain may have clinical implications for patients with DM as they provide evidence for putative adjuvant anti-inflammatory treatments, such as CLR, in mitigating cerebrovascular pathology. / Graduate / 2022-05-06

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Glioblastoma (GBM) is the most common primary brain tumor in adults and represents one of the most aggressive tumor types. Despite treatment GBM remains incurable and when treated the tumor recurs more aggressive and treatment resistant than before. The understanding of the underlying pathophysiology of GBM has increased in recent years, yet the high mortality with a 5-year survival rate of less than 10% remains. Previous studies from the research group, have shown that complement protein C3 is upregulated in stromal and glioma cells in lower oxygen tensions, and this indicates that C3 might play a role in certain GBM tumor microenvironment (TME) niches. For this reason, it is of great interest to investigate how glioma cells are affected when stimulated with C3. With cell proliferation-, migration assays and gene expression analysis with real time quantitative polymerase chain reaction (qPCR) it was possible to investigate how glioma cells respond to treatment with C3 and C3a-receptor antagonist. By optimizing an antibody panel for detection of macrophages/microglia, astrocytes and tumor cells we made it possible to study the modulation of immune parameters during treatment with C3A-receptor antagonist in mice. / Glioblastom (GBM) är den vanligaste primära hjärntumören hos vuxna och representerar en av de mest aggressiva tumörtyperna. Trots behandling förblir GBM obotlig och efter behandling återkommer tumören mer aggressiv och behandlingsresistent än tidigare. Förståelsen för den underliggande patofysiologin för GBM har ökat de senaste åren, trots detta kvarstår den höga dödligheten med en 5-årig överlevnadsprognos under 10%. Tidigare studier från forskningsgruppen har också visat att komplementprotein C3 är uppreglerat i gliomceller under lågt syretryck, vilket indikerar att C3 kan spela en roll i olika miljöer som finns i GBM. Av denna anledning är det av stort intresse att undersöka hur gliomceller påverkas när de stimuleras med C3. Med cellproliferation-, migrerings analyser och genuttrycksanalys med real time quantitative polymerase chain reaction (qPCR) var det möjligt att undersöka hur gliomceller, men även andra komponenter av tumor microenvironment (TME) svarar på behandling av C3 och C3A-receptor antagonist. Genom att optimera en antikroppspanel, med detektion av makrofager/ mikroglia, astrocyter och tumörceller har vi nu gjort det möjligt att studera moduleringen av immun parametrar vid behandling av C3A-receptor antagonist i möss.

In humans, various dietary and social factors led to the development of increased brain sizes alongside large adipose tissue stores. Complex reciprocal signaling mechanisms allow for a fine-tuned interaction between the two organs to regulate energy homeostasis of the organism. As an endocrine organ, adipose tissue secretes various hormones, cytokines, and metabolites that signal energy availability to the central nervous system (CNS). Vice versa, the CNS is a critical regulator of adipose tissue function through neural networks that integrate information from the periphery and regulate sympathetic nerve outflow. This review discusses the various reciprocal signaling mechanisms in the CNS and adipose tissue to maintain organismal energy homeostasis. We are focusing on the integration of afferent signals from the periphery in neuronal populations of the mediobasal hypothalamus as well as the efferent signals from the CNS to adipose tissue and its implications for adipose tissue function. Furthermore, we are discussing central mechanisms that fine-tune the immune system in adipose tissue depots and contribute to organ homeostasis. Elucidating this complex signaling network that integrates peripheral signals to generate physiological outputs to maintain the optimal energy balance of the organism is crucial for understanding the pathophysiology of obesity and metabolic diseases such as type 2 diabetes.

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