Le virus Nipah (NiV) est un Paramyxovirus zoonotique hautement pathogène, porté par les chauves-souris frugivores, qui a émergé en 1998 en Malaisie. Les épidémies liées à ce virus encéphalitogène continuent de se succéder en Inde et au Bangladesh avec une mortalité pouvant dépasser les 90%. Devant l’absence de traitement et de vaccin, le NiV a été placé parmi les pathogènes de classe 4 requérant le plus haut niveau de biosécurité pour sa manipulation. L’étude des interactions entre le virus et les cellules du sang nous a permis de montrer que le NiV utilise les héparanes sulfates présents sur les leucocytes pour s’accrocher et se disséminer dans l’organisme et atteindre les cellules endothéliales. L’héparine inhibe ce processus ainsi que l’infection in vitro et in vivo mettant en avant une perspective de traitement applicable dans les pays émergents. Par ailleurs, l’analyse transcriptomique des cellules endothéliales infectées par le NiV a révélé l’implication de chimiokines dans la pathogenèse. CXCL10 apparaît en effet comme un marqueur voir une cible dans le cadre du développement de l’encéphalite virale, et l’interféron type 1 comme l’un des facteurs essentiels de la résistance des souris au NiV. Enfin, j’ai montré que la protéine non structurale C du NiV joue un rôle essentiel dans sa virulence, en atténuant la réponse interféron, en perturbant la réponse chimiokine lors de l’infection et en intervenant dans le maintien de la balance génome / antigénome lors du cycle réplicatif viral. Ces résultats permettent une meilleure compréhension de la pathogenèse du NiV et ouvrent de nouvelles perspectives de traitement contre ce virus zoonotique très dangereux pour l’homme / Nipah virus (NiV) is a highly pathogenic zoonotic Paramyxovirus that emerged in 1998 in Malaysia from frugivorous bats. The outbreaks of this encephalitic virus still occur annually in India and Bangladesh with the mortality rate reaching up to 90%. The lack of an effective vaccine or treatment limits experimentation with live virus to specially equipped BioSafety Level 4 laboratories. Studies of the interaction between the virus and blood cells revealed that NiV uses Heparan sulfates to stick on the surface of leukocytes for its dissemination within the host and reach endothelial cells. Heparin provided de possibility to inhibit this mechanism of transinfection, such as the infection in vitro and in vivo, opening new perspectives of low cost treatment for emerging countries. Then, transcriptomic analysis of NiV infected endothelial cells revealed the importance of cytokine in the pathogenesis. While CXCL10 appears as a good marker of encephalitis, interferon type 1 explains why mice are resistant to the infection with NiV. Finally, we show the essential role of the non structural C protein of NiV in its virulence, by limiting the interferon response, unbalancing the chemokine response during the infection and through the regulation of the genomic/antigenomic balance during the viral replication cycle. These results shed new light on NiV related pathogenesis and open new perspectives of treatment against this highly lethal zoonotic virus

La voie JAK / STAT est une voie majeure de signalisation intracellulaire, activée par plusieurs cytokines, y compris par les interférons (IFNs). Mon laboratoire a précédemment établi que l'endocytose et le trafic du récepteur de l’IFN alpha/beta (IFNAR) jusqu’à l'endosome précoce, joue un rôle clé dans l’activation de la voie de signalisation JAK/STAT et dans les activités antivirales et antiprolifératives induites par les IFNs de type I. Le récepteur de l’IFN de type I se compose de deux sous-unités: IFNAR1 et IFNAR2. Durant le trafic du récepteur vers l'endosome précoce, les deux sous-unités prennent des itinéraires différents - IFNAR1 est ubiquitiné et dégradé au lysosome tandis que IFNAR2 est recyclé vers la membrane plasmique. Les mécanismes moléculaires permettant un trafic différent des IFNAR1 et IFNAR2 restent mal compris.J’ai tout d’abord étudié le trafic intracellulaire des sous-unités IFNAR1 et IFNAR2 et j’ai pu montrer que les protéines Rab4 et Rab11 sont nécessaires au recyclage d’IFNAR2 à la membrane plasmique. Par la suite, j’ai identifié le complexe rétromère endosomal - VPS26A/VPS29/VPS35 comme un partenaire d’interaction avec IFNAR2 nécessaire pour son recyclage. En outre, j’ai montré que le complexe rétromère contrôle la séparation spatiotemporelle des sous-unités IFNAR1 et IFNAR2 au niveau de l'endosome précoce. En effet, la déplétion du complexe rétromère entraine une prolongation de l’association endosomale de deux sous-unités et une prolongation de la signalisation JAK/STAT induite par l’IFN tant pour la réponse précoce (phosphorylation de STAT1) que la réponse à plus long terme (expression des gènes stimulés par l'IFN). Des résultats en cours de publication par l’équipe montrent un rôle d’ESCRT-0 dans l’initiation de la signalisation JAK/STAT. J’ai montré que le rôle de la machinerie ESCRT dans ce processus est limité au complexe ESCRT-0. Les sous-complexes en aval d’ESCRT-0, bien que nécessaires à la dégradation d’IFNAR1, ne sont pas impliqués dans l’activation de la voie JAK/STAT.En conclusion, ces résultats nous ont permis d’établir un modèle dans lequel le retromère joue un rôle clef dans la régulation spatio-temporelle du tri endosomal d’IFNAR et de la signalisation JAK/STAT au niveau de l’endosome précoce. Après la séparation rétromère-dépendante des sous-unités du récepteur et la terminaison de la signalisation JAK/STAT, la dégradation lysosomale d’IFNAR1 est assurée par la machinerie ESCRT en aval d’ESCRT-0. / The JAK/STAT pathway is a major intracellular signaling pathway that is activated by several cytokines including interferons (IFNs). My laboratory has previously established that endocytosis and trafficking of the IFN alpha/beta receptor (IFNAR) to the early endosome is key for the activation of JAK/STAT signaling and for the antiviral and antiproliferative activities induced by type I IFNs. The functional type I IFN receptor - IFNAR - consists of two subunits: IFNAR1 and IFNAR2. Upon endocytosis to the early endosome, both subunits take different trafficking routes – IFNAR1 is ubiquitinated and degraded in the lysosome, whereas IFNAR2 recycles back to the plasma membrane. The molecular mechanisms behind the separation of IFNAR1 and IFNAR2, as well as their distinct trafficking routes remain poorly understood.First, I studied the intracellular trafficking of IFNAR1 and IFNAR2 subunits and showed the requirement for Rab4 and Rab11 in IFNAR2 recycling to the plasma membrane. Next, I identified the endosomal retromer complex – VPS26A/VPS29/VPS35 as an IFNAR2 interacting partner, required for IFNAR2 recycling. Additionally, I was able to show that retromer controls the spatiotemporal separation of IFNAR1 and IFNAR2 subunits at the early endosome. Indeed, retromer depletion resulted in prolonged endosomal association of both subunits and prolonged activation of IFN-induced JAK/STAT signaling, at both early (STAT1 phosphorylation) and longer time response (IFN-stimulated gene expression). Unpublished results of our team indicate the role of ESCRT-0 in initiation of the IFN-mediated JAK/STAT signaling. I found that role of the ESCRT machinery in this process is limited to the ESCRT-0. ESCRT subcomplexes downstream of ESCRT-0, although required for IFNAR1 degradation, are not involved in activation of the JAK/STAT pathway.In conclusion, these results permit us to draw a model in which the retromer is a key spatiotemporal regulator of IFNAR endosomal sorting and the JAK/STAT signaling at level of the early endosome. Once retromer-mediated subunits separation is accomplished and JAK/STAT signaling is terminated, ESRCT machinery downstream to ESCRT-0 mediates IFNAR1 lysosomal degradation.

Toxoplasma gondii est un parasite répandu, ayant un impact médical et vétérinaire. Chez les hôtes intermédiaires, les tachyzoïtes et les bradyzoïtes sont responsables de la toxoplasmose aiguë (TA) et chronique (TC), respectivement. Sous la réponse immunitaire, la TA évolue en TC, se manifestant par des kystes latents dans le cerveau et les muscles squelettiques. De plus, une forte corrélation existe entre la TC et plusieurs neuropathologies et cancers. Chez les patients immunodéprimés, la TC peut être réactivée et conduire à une maladie potentiellement fatale. Les traitements actuels ciblent principalement les TA, et présentent plusieurs effets secondaires. Nous nous sommes concentrés sur la TC et la compréhension de ses mécanismes moléculaires. Nous avons d’abord étudié l’efficacité de l’imiquimod contre la TA et la TC. Au cours de la TA, l'imiquimod a entraîné le recrutement de cellules T dans le péritoine et la rate de souris traitées et a considérablement diminué le nombre de kystes cérébraux lors de l'établissement de la TC. Remarquablement, le gavage de souris avec les kystes cérébraux restants chez des souris traitées à l'imiquimod n'a pas pu induire de TC. Après l'établissement de la TC, nous avons démontré que l'imiquimod réduisait considérablement le nombre de kystes cérébraux chez les souris chroniquement infectées et augmentait les récepteurs Toll-Like 11 et 12, qui se lient à une protéine du tachyzoïte, la profiline. Parallèlement, l’expression de TLR-7 augmentait, probablement par son agoniste, l'imiquimod. L'imiquimod induit une interconversion, comme l'indiquent la diminution du taux de protéine P21 et l'augmentation du taux de protéine P30, exprimées exclusivement et respectivement chez les bradyzoïtes et les tachyzoïtes. Les voies en aval de TLR-11/12 ont été activées via la voie MyD88 de signalisation, entraînant une induction ultérieure de la réponse immunitaire. In vitro, l'imiquimod n’affecte pas la souche Toxoplasma dépourvue de profiline, suggérant un rôle via le complexe Profilin/TLR-11/12. Enfin, le traitement par l'imiquimod a régulé positivement les transcrits des ligands 9 (CXCL9) et 10 (CXCL10), connus pour induire le recrutement de lymphocytes T dans des foyers réactivés du Toxoplasme afin d'éliminer l'infection.Ensuite, nous nous sommes concentrés sur les mécanismes moléculaires impliqués dans la TA et particulièrement dans la TC. Nous avons caractérisé P18, un membre de la superfamille SRS. Lorsque nous avons supprimé P18, la virulence était atténuée au cours de la TA, dû à un échappement plus rapide des tachyzoïtes du péritoine de souris, parallèle à un recrutement significatif de cellules dendritiques. De manière concomitante, moins de tachyzoïtes étaient détectés dans la rate, tandis que plus de parasites ont atteint le cerveau de souris infectées. L’élimination de P18 a augmenté le nombre de kystes de bradyzoïtes in vitro et dans le cerveau de souris infectées. Une expression induite de cytokines, notamment CXCL9 et 10, a également été observée. L’immunosuppression de souris KO P18 infectées a retardé la réactivation. L’infection orale de souris immunodéficientes ayant des macrophages fonctionnels a montré un prolongement de survie, contrairement aux souris n’ayant pas de macrophage, soulignant un rôle de l'IFN-g dans l’interconversion. Collectivement, ces données confirment le rôle de P18 dans la modulation de la réponse immunitaire, facilitant le passage des tachyzoïtes dans le cerveau et favorisant la formation de kystes. P18 joue également un rôle central dans la réactivation et la dissémination de parasites de manière dépendante de l'IFN-g. Dans l'ensemble, nous avons montré le potentiel thérapeutique prometteur de l'imiquimod contre la toxoplasmose et caractérisé le rôle de P18 dans l'immunomodulation afin de contrôler la dissémination et l'interconversion. Notre étude ouvre la voie à de nouvelles approches thérapeutiques contre la toxoplasmose, sa persistance et sa réactivation. / Toxoplasma gondii is a prevalent parasite of medical and veterinary impact. In intermediate hosts, tachyzoïtes and bradyzoïtes are responsible for acute and chronic toxoplasmosis (AT and CT), respectively. In immunocompetent patients, AT evolves, due to the host immunity, into a persistent CT, which manifests as latent tissue cysts in the brain and skeletal muscles. CT correlates with several neuro-pathologies and cancers. In immunocompromised patients, CT may reactivate and poses a life threatening condition. Current treatments primarily target AT, are limited to general anti-parasitic/anti-bacterial drugs, and associate with several limitations. Here, we focused on targeting CT and understanding its molecular mechanisms. First, we explored the efficacy of Imiquimod against AT and CT. During AT, Imiquimod led to recruitment of T cells to peritoneum and spleen of treated mice and significantly decreased the number of brain cysts upon establishment of CT. Remarkably, gavage of mice with the remaining brain cysts from Imiquimod treated mice, failed to induce CT. Post-establishment of CT, we demonstrated that Imiquimod sharply reduced the number of brain cysts in chronically infected mice, and significantly increased Toll-Like Receptors 11 and 12. These TLRs are usually expressed by dendritic cells and monocytes, and bind a tachyzoïte actin-binding protein, profilin. Concomitantly, TLR-7 was upregulated, likely by its agonist Imiquimod. Imiquimod induced interconversion as documented by the decreased protein levels of P21, and increased protein levels of P30, exclusively expressed in bradyzoïtes and tachyzoïtes respectively. Pathways downstream from TLR-11/12 were activated, through MyD88 dependent TLR signaling, which resulted in subsequent immune response induction. In vitro, Toxoplasma strain lacking profilin, does not respond to Imiquimod, suggesting a role through Profilin/TLR-11/12. Finally, Imiquimod treatment upregulated the transcript expression levels of Chemokine (C-X-C motif) ligand 9 (CXCL9) and 10 (CXCL10), known to induce T cell recruitment to reactivated Toxoplasma foci to clear the infection.Then, we focused on molecular mechanisms involved in AT and notably CT. We characterized P18, a Surface-Antigen 1 (SAG-1) Related Sequence (SRS) superfamily member. When we deleted P18, the virulence was attenuated during AT. Indeed, P18 depletion led to a faster clearance of the parasites from the peritoneum of mice, paralleled by a substantial recruitment of dendritic cells, presumably a vehicle for tachyzoïte dissemination. Concomitantly, a lower number of tachyzoïtes was detected in the spleens while a higher number of parasites reached the brains of infected mice. P18 depletion increased the number of bradyzoïte cysts, in vitro and in the brains of infected mice. An induced expression of cytokines/chemokines, including CXCL9 and 10 was also observed. Immunosuppression of infected mice with KO P18, delayed reactivation. Oral infection of Severe Combined Immunodeficiency (SCID) (with IFN-g secreting macrophages), and NOD/Shi-scid/IL-2Rgnull (NSG) mice (lacking IFN-g), showed a significant prolonged survival in infected SCID but not NSG mice. This underlines a role for IFN-g in the conversion from bradyzoïtes to tachyzoïtes. Collectively, these data support a role of P18 in orchestrating the immune response, which ultimately facilitates tachyzoïte trafficking to the brain and favors cyst formation. P18 plays also a central role in parasite reactivation and dissemination in an IFN-g dependent fashion.Altogether, we showed the promising therapeutic potential of Imiquimod against toxoplasmosis and characterized P18 role in immunomodulation to control dissemination and interconversion. Our study paves the path towards new therapeutic approaches against toxoplasmosis. It tackled key questions pertaining to establishment, maintenance and reactivation of CT and should result in a comprehensive solution to this endemic disease.

L’existence d’un partage des tâches a été démontrée au sein de nombreux systèmes biologiques et ce notamment en immunologie où il a été décrit dans le contexte de différentes sous-populations d’un même type cellulaire. Les cellules dendritiques plasmacytoïdes (pDC) jouent un rôle clé lors des infections virales. Les pDCs ont la capacité de sécréter de grandes quantités d’interférons de type I et de se différencier en cellules dendritiques matures capables d’activer une réponse immunitaire adaptative. Il a été proposé que ces fonctions innées et adaptatives soient séquentiellement induites après activation virale. Au cours de ma thèse, je me suis intéressée à ces deux fonctions principales des pDC et je suis arrivée à la description de différentes sous-populations de pDC activées : PD-L1+CD80- (P1), PD-L1+CD80+ (P2) and PD-L1-CD80+ (P3), démontrant qu’il existe un partage des tâches entre ces sous-types. P1 produit spécifiquement de l’IFN-α, indiquant une spécialisation en immunité innée, et promeut une réponse tolérogénique des cellules T CD4. Inversement, P3 induit une forte activation des cellules T CD4 naïves et une polarisation de type Th2, démontrant une spécialisation fonctionnelle dans l’immunité adaptative. P2 possède un profil fonctionnel intermédiaire. Plutôt qu’un lien séquentiel, nos résultats indiquent une exclusion réciproque des fonctions innées et adaptatives entre ces différents sous-types de pDC / Under microbial stimulation plasmacytoid pre-dendritic cells (pDC) secrete large amounts of type I interferon (IFN) and differentiate into mature dendritic cells capable of activating T cells. These innate and adaptive functions are thought to be induced sequentially in pDC through triggering of the IRF-7 and NFkB pathways, respectively. We found that viral activation of pDC induced their differentiation into three phenotypically distinct subsets: PD-L1+CD80- (P1), PD-L1+CD80+ (P2) and PD-L1-CD80+ (P3). P1 specifically produced IFN-α, indicating a specialization in innate immunity, while promoting weak activation and high IL-10 expression in CD4 T cells. Conversely, P3 showed increased expression of surface costimulatory molecules, improved migratory capacity, strong naïve CD4 T cell activation, and induction of Th2 differentiation. P2 had an intermediate functional profile. No conversion could be induced between subsets. We identified P1 in psoriatic skin, and blood from active lupus patients. Our results indicate reciprocal exclusion, rather than sequential link, of innate and adaptive pDC functions, with important implications in immune regulation and immunopathology.

Aicardi-Goutières syndrome (AGS) is an autosomal recessive encephalopathy with low incidence. The disease is caused by mutations in the genes encoding for TREX1, SAMHD1, ADAR, IFIH1 and the three genes encoding for the heterotrimeric RNase H2 enzyme. Biallelic mutations in any of the genes cause elevated type I interferon levels in the cerebrospinal fluid (CSF), the hallmark of AGS. In AGS patients, increased type I interferon levels cause massive inflammation in the brain that leads to mental and physical retardation that likely cause death in early childhood. AGS shows significant overlap with the prototypic autoimmune disease systemic lupus erythematosus (SLE). Like AGS patients, SLE patients are also characterized by increased type I interferon levels, anti-nuclear autoantibodies (ANAs) and arthritis. Moreover, heterozygous mutations in TREX1, SAMHD1 and RNase H2 are also found in a small fraction of SLE patients. Due to the genetic, molecular and clinical overlap, AGS is regarded as a monogenic variant of SLE. This overlap allows for the investigation of SLE pathomechanisms using genetically engineered mouse models with AGS-related mutations. In order to generate a mouse model that allows for the identification of pathomechanisms in AGS patients with mutations in the genes encoding for the RNase H2 enzyme, we generated mice with deficiency for the RNase H2 enzyme. Mice with complete deficiency for the RNase H2 enzyme (Rnaseh2c-/- or Rnaseh2bKOF/KOF) died perinatally or were stillborn. Mouse embryonic fibroblasts (MEFs) from E14.5 Rnaseh2bKOF/KOF embryos displayed impaired proliferation that was caused by the accumulation of MEF cells in G2/M of the cell cycle which increased with cultivation time or if MEF cells were isolated from E18.5 Rnaseh2bKOF/KOF embryos. Gene expression analysis of E14.5 fetal liver cells revealed a robust p53-mediated DNA damage response with the cell cycle inhibitor cyclin- dependent kinase inhibitor 1a (Cdkn1a, p21) being the most up-regulated gene. We found increased numbers of phosphorylated histone H2AX (γH2AX) in fetal liver and thymus cells from E18.5 Rnaseh2bKOF/KOF embryos, indicative of DNA double-strand breaks. Finally, we could show increased ribonucleotide loads in genomic DNA from embryos that were completely deficient for the RNase H2 enzyme. Collectively, we have demonstrated that complete RNase H2 deficiency causes persistent genomic ribonucleotide loads that render the DNA instable and prone to DNA strand breaks. DNA damage leads to the activation of p53 that in turn activates the cell cycle inhibitor p21 that inhibits cell cycle progression and likely causes accumulation of RNase H2-deficient cells in G2/M. To bypass early lethality we also generated bone marrow chimera and cell type-specific knockouts of the Rnaseh2b gene. While fetal liver cells of E14.5 Rnaseh2bKOF/KOF embryos could maintain hematopoiesis of irradiated recipient mice for almost one year, bone marrow cells from these primary recipients failed to reconstitute lethally irradiated mice in a secondary transfer. In line with this observation, VavCre-mediated deletion of the Rnaseh2b gene caused a more than hundred fold reduction of peripheral blood B cells, while B cell numbers remained unaltered upon CD19Cre-mediated deletion that occurs much later in B cell development. These data suggested that RNase H2 deficiency leads to the accumulation of genomic ribonucleotides that might cause the accumulation of a so far uncharacterized DNA damage species with increasing cell cycle passages. The data further supported our hypothesis that the impact of RNase H2 deficiency is determined by the number of cell proliferation. Finally, an epidermis-specific knockout of the Rnaseh2b gene displayed the most dramatic phenotype. Knockout mice were characterized by hyperpigmentation, hair loss and spontaneous ulcerations of the skin. Microscopically, these mice displayed moderate thickening of the epidermis and dermal fibrosis as indicated by increased collagen deposition. Macroscopic skin phenotypes were completely dependent on p53 expression, since concomitant deletion of the p53 gene rescued mice from hyperpigmentation, hair loss and ulcerations. This data demonstrated that Rnaseh2b deficiency in the epidermis may also lead to DNA damage and subsequent p53 activation as shown for fetal liver from E14.5 RNase H2-deficient embryos. Preliminary data also indicate an increased incidence of cancer formation in RNase H2/p53 double knockouts, identifying the RNase H2 enzyme as an important tumor suppressor.

HINTERGRUND: Eine inadäquate Aktivierung von Typ-1-IFN kann in der Entstehung von Autoimmunität und Autoinflammation resultieren. Die einer solchen dysregulierten Typ-1-IFN-Achse zu Grunde liegenden Störungen werden primär über das angeborene Immunsystem vermittelt. Krankheitsbilder, die durch eine chronische Typ-1-IFN-Aktivierung bedingt sind, werden daher unter dem Begriff Typ-1-Interferonopathien zusammengefasst. Diese Gruppe seltener, genetisch bedingter Erkrankungen zeichnet sich durch eine große symptomatische Bandbreite aus, wobei vor allem neurologische und kutane Manifestationen im Vordergrund stehen. Bisher aufgeklärte Pathomechanismen dieser systemisch-entzündlichen Erkrankungen haben einen Einblick in neue zellintrinsische Mechanismen gegeben, die zu einer Typ-1-IFN-Aktivierung führen und auf Störungen im Metabolismus und der immunologischen Erkennung intrazellulärer Nukleinsäuren beruhen. Daraus ergeben sich auch Erkenntnisse hinsichtlich des Einsatzes einer immunmodulatorischen Therapie zur kausalen Behandlung von Typ-1-Interferonopathien. FRAGESTELLUNG: Typ-1-Interferonopathien gehören zu den genetisch bedingten, seltenen Erkrankungen. Eine Diagnosestellung ist jedoch aufgrund mangelnder Kenntnisse über die Krankheitsursache häufig nicht möglich, sodass kausale Therapieansätze für viele Patienten nicht existieren. Die Aufklärung der genetischen Ursache solcher Erkrankungen ist demnach von essentieller Bedeutung. Auch die hier untersuchten Familien leiden an bisher nicht molekulargenetisch diagnostizierten Krankheiten, deren Phänotyp jedoch eine Typ-1-Interferonopathie vermuten lässt. Vor diesem Hintergrund war es das Ziel dieser Arbeit, bisher unbekannte Gene zu identifizieren und zu charakterisieren, welche Krankheitsbilder mit chronischer Typ-1-IFN-Aktivierung verursachen. MATERIAL UND METHODEN: Anhand klinischer Daten wurden zunächst die Krankheitsbilder der zwei betroffenen Familien charakterisiert und hinsichtlich der Gemeinsamkeiten mit bekannten Typ-1-Interferonopathien untersucht. Zudem wurde das Vorliegen einer chronischen Typ-1-IFN-Aktivierung bei den erkrankten Familienmitgliedern untersucht. Mit Hilfe von Exomanalysen und anschließenden bioinformatischen Analysen wurde nach dem ursächlichen Krankheitsgen gesucht. Die in diesem Rahmen in der Familie 1 nachgewiesene STING-Mutation wurde unter Verwendung von molekularbiologischen sowie zellbiologischen Analysen eingehend untersucht und zudem ihre Konsequenzen auf die IFN-Achse und die Stabilität des STING-Dimers mittels Strukturmodellierungen charakterisiert. Hinsichtlich der Aufklärung der genetischen Ursache der Erkrankung der Familie 2 wurde ebenfalls eine Exomanalyse durchgeführt. Da dabei jedoch keine Mutation identifiziert werden konnte, erfolgte eine Analyse differentiell exprimierter Transkripte mit Hilfe von Transkriptomdaten von Fibroblasten gesunder Kontrollen im Vergleich zu erkrankten Familienmitgliedern der Familie 2. ERGEBNISSE: Im Verlauf dieser Arbeit konnte in der Familie 1 mit einem familiären Chilblain Lupus eine kausale heterozygote Mutation im STING-Gen identifiziert werden. Diese bisher nicht beschriebene Mutation bedingt den Aminosäureaustausch Gly166Glu (G166E) im hochkonservierten Dimerinterface des STING-Proteins. Strukturmodelle ergaben Hinweise auf strukturverändernde Eigenschaften der Mutation G166E, die das STING-Dimer konstitutiv aktivieren. Dies konnte experimentell bestätigt werden, da in den peripheren Blutzellen der Patienten eine erhöhte IFN-Signatur nachgewiesen werden konnte und Patientenfibroblasten eine erhöhte Produktion von IFN-β sowie eine vermehrte Phosphorylierung von IRF3 zeigten. Um den Einfluss einer therapeutischen Immunmodulation über eine JAK-Inhibition zu untersuchen, wurden zwei Erkrankte der Familie 1 mit dem JAK-Inhibitor Tofacitinib über einen Zeitraum von 17 Tagen behandelt. Es konnte dabei in vivo eine signifikant reduzierte IFN-Signatur nachgewiesen werden. Mit Hilfe der Exomanalyse konnte in der konsanguinen Familie 2 mit einem AGS-ähnlichen Phänotyp keine kausale Mutation identifiziert werden. Es zeigte sich zudem, dass in den Patientenzellen keine erhöhte IFN-Signatur sowie keine erhöhte IFN-β Produktion nachweisbar waren. Die vergleichende Transkriptomanalyse ergab keine auffällige differentielle Expression von Genen des Aminosäure-Metabolismus, der Seneszenz, des Zellzyklus, der DNA-Schadensantwort und DNA-Reparatur sowie von Genen immunologischer Prozesse. Allerdings wurde die vollständig fehlende Expression der Gene COL6A1 und COL6A2 in den Patientenzellen nachgewiesen. SCHLUSSFOLGERUNG: Die identifizierte STING-Mutation der Familie 1 führt zu einer chronischen Aktivierung der Typ-1-IFN-Achse und ist folglich als Gain-of-function Mutation anzusehen. Die Behandlung mit dem immunmodulierenden JAK-Inhibitor Tofacitinib führt zu einer Verminderung der IFN-Signatur und bietet somit einen vielversprechenden Ansatz für eine kausale Therapie. Weiterführende Untersuchungen, vor allem bezüglich der Langzeiteffekte, sind hier jedoch noch erforderlich. Die Erkrankung der Familie 2 ist dagegen vermutlich nicht den Typ-1-Interferonopathien zuzuordnen. Vielmehr scheint es zum jetzigen Zeitpunkt wahrscheinlich, dass eine Mutation innerhalb eines regulatorischen Elements, das die Expression der Gene COL6A1 und COL6A2 reguliert, für den Phänotyp der Erkrankten verantwortlich ist. Weiterführende Untersuchungen sind hier zukünftig von großem Interesse.

Celiaki (glutenintolerans) är en kronisk, autoimmun sjukdom med diffusa symtom. Vid förtäring av glutenhaltig mat uppstår en allergisk reaktion hos glutenintoleranta individer. Gluten kan inte fullständigt brytas ned av kroppens enzymer, vilket betyder att icke nedbrutna peptidfragment (såsom glutamin) absorberas i tarmslemhinnan. Enzymet transglutaminas katalyserar omvandlingen av glutamin till glutamat. Glutenkänsliga T-celler aktiveras av glutamat att utsöndra proinflammatoriska cytokiner såsom interferon-gamma (IFN-γ) och tumörnekrosfaktor-alfa (TNF-⍺). Syftet med studien var att undersöka om gluten- och gliadinstimulering av celler i helsaliv in vitro kan inducera produktion av IFN-γ och TNF-⍺. Pilotstudier med 2 försökspersoner utfördes, där celler i salivprover stimulerades med enzymatiskt nedbrutet gliadin (<40 mg gliadin), samt PHA (5 µg/mL), PMA (50 ng/mL) och LPS (1 µg/mL) 20 timmar vid 37 ˚C. Cytokinproduktionen i salivproverna kvantifierades med ELISA och uppreglering av IFN-γ och TNF-⍺ undersöktes med RT-qPCR. Efter metodutveckling upprepades stimulering och ELISA med salivprov från 12 försökspersoner (6 individer med och utan celiaki). Immunreaktionen som uppstår hos glutenintoleranta individer in vivo kunde inte återskapas i saliv in vitro med den framtagna metoden. Hos övervägande delen av salivproverna var cytokinproduktionen under detektionsgränsen, 4 pg/mL för IFN-γ och 15,6 pg/mL för TNF-⍺. Det finns risk för att outforskade detaljer eller agens saknades från reaktionskedjan och därmed kunde den förväntade immunreaktionen inte återskapas. En annan felkälla kan vara för låg koncentration av immunceller i saliven. / Celiac disease is a chronic, autoimmune disease that has diffuse symptoms. Upon consuming gluten containing food, an allergic reaction occurs in gluten-sensitive individuals. Gluten cannot be fully digested by human enzymes, which leads to non-digested peptide fragments (such as glutamine) to be absorbed in the gastrointestinal wall. The transglutaminase enzyme catalyzes the conversion of glutamine to glutamate. Glutamate activates gluten-specific T-lymphocytes to produce proinflammatory cytokines e.g., interferon-gamma (IFN-γ) and tumor necrosis factor alpha (TNF-⍺). The aim of this study was to investigate whether stimulation of cells in whole saliva in vitro with gluten and gliadin can induce production of IFN-γ and TNF-⍺. Pilot studies were conducted, where cells in saliva from 2 subjects was stimulated with enzymatically digested gliadin (<40 mg gliadin) together with PHA (5 µg/mL), PMA (50 ng/mL) and LPS (1 µg/mL) for 20 hours at 37 ˚C. The production of cytokines was quantified by ELISA, and the upregulation of IFN-γ and TNF-⍺ was analyzed by RT-qPCR. After method development, the stimulations and ELISA quantifications of the proinflammatory cytokines were repeated in saliva samples from 12 subjects (6 individuals with and without celiac disease). The immune reaction that occurs in people with celiac disease could not be recreated in saliva in vitro with the developed method. In most of the samples the production of cytokines was under the detection range, 4 pg/mL for IFN-γ and 15,6 pg/mL for TNF-⍺. There is risk of unstudied details or agents missing from the reaction chain, and therefore the expected immune reaction could not be recreated. Another source of error could be low concentration of immune cells in saliva.

Host immune responses must be tightly regulated by an intricate balance between positive and negative signals while fighting pathogens; persistent pathogens may usurp these regulatory mechanisms to dampen host immunity to facilitate survival in vivo. Here we report that Tim-3, a negative signalling molecule expressed on monocytes and T cells, is up-regulated on natural killer (NK) cells in individuals chronically infected with hepatitis C virus (HCV). Additionally, the transcription factor T-bet was also found to be up-regulated and associated with Tim-3 expression in NK cells during chronic HCV infection. MicroRNA-155 (miR-155), an miRNA that inhibits signalling proteins involved in immune responses, was down-regulated in NK cells by HCV infection. This Tim-3/T-bet over-expression and miR-155 inhibition were recapitulated in vitro by incubating primary NK cells or NK92 cell line with Huh-7 hepatocytes expressing HCV. Reconstitution of miR-155 in NK cells from HCV-infected patients led to a decrease in T-bet/Tim-3 expression and an increase in interferon-γ production. Blocking Tim-3 signalling also enhanced interferon-γ production in NK cells by improving signal transducer and activator of transcription-5 phosphorylation. These data indicate that HCV-induced, miR-155-regulated Tim-3 expression regulates NK cell function, suggesting a novel mechanism for balancing immune clearance and immune injury during chronic viral infection.

The innate immune system provides the first line of defense against infection. Pathogens are detected though a variety of Pattern Recognition Receptors (PRRs), which activate downstream signaling cascades. Effector molecules such as cytokines and chemokines are released upon activation and aid in cell recruitment, control of pathogen replication, and coordination of the adaptive immune response. Nucleic acids that are released into the cytosol during viral and bacterial infection are recognized through a special class of PRRs, coined cytosolic nucleic acid sensors. Upon recognition, these receptors induce the production of type I interferons and other cytokines to aid in pathogen clearance. Although many cytosolic nucleic acid sensors have been discovered, it is unclear how they work in concert to mediate these responses. The Interferon Gamma Inducible protein (IFI)16 and its proposed mouse orthologue IFI204 are cytosolic DNA sensors that have been linked to the detection of cytosolic DNA during infection with Herpes Simplex Virus (HSV-1). IFI16 binds dsDNA that has been released into the cytosol during viral infection and engages the adaptor molecule Stimulator of Interferon Genes (STING) leading to TANK binding kinase-1 (TBK1) dependent phosphorylation of interferon regulatory factor 3 (IRF3) and transcription of type I interferons and interferon stimulated genes. In addition to its role as a sensor, in chapter two of this thesis we describe a broader role for IFI16 in the regulation of the type I IFN response to RNA and DNA viruses in anti-viral immunity. In an effort to better understand the role of IFI16 in coordinating type I IFN gene regulation, we generated cell lines with stable knockdown of IFI16 and examined responses to DNA and RNA viruses as well as other inducers of IFN such as cyclic-dinucleotides. As expected, stable knockdown of IFI16 led to a severely attenuated type I IFN response to cytosolic DNA ligands and DNA viruses. In contrast, expression of the NF-κB regulated cytokines such as IL-6 and IL-1β were unaffected in IFI16 knockdown cells, suggesting that the role of IFI16 in sensing these triggers was unique to the type I IFN pathway. Surprisingly, we also found that knockdown of IFI16 led to a severe attenuation of expression of IFN-α and IFN stimulated genes such as RIG-I in response to cyclic GMP-AMP (cGAMP), a second messenger produced in response to cGAS, as well as RNA ligands and viruses. Analysis of IFI16 knockdown cells revealed compromised occupancy of RNA polymerase II on the IFN-α promoter in IFI16 knockdown cells suggesting that transcription of ISGs is dependent on IFI16. Since IFI16 knockdown compromised not only DNA virus driven pathways, we propose additional regulatory roles outside of DNA sensing. Collectively, these results indicate that IFI16 plays a role in the regulation of type I IFN gene transcription and production in response to both RNA and DNA viruses. The role of IFI16/IFI204 has been studied extensively in vitro, however the role of the receptors in vivo has yet to be determined. In chapter three of this thesis, we developed a mouse deficient in IFI204 to explore the role of IFI204 in in vivo immune responses to viruses. We investigated the ability of IFI204 deficient cells to induce type I interferons and other cytokines in response to a panel of DNA and RNA ligands in vitro. IFI204 deficient BMDMs displayed a partial defect in type I interferon induction in response to both DNA and RNA ligands and viruses as compared to WT mice. We also observed that this phenotype is time dependent, since there was no change in type I interferon induction after 12 hours post infection as compared to earlier time points. In contrast to these results, expression of the NF-κB regulated cytokines IL-6 and IL-1β were unaffected in IFI16 knockdown cells. These results suggest that IFI204 plays a partial role in the induction of type I interferons in response to both DNA and RNA ligands. Additionally, IFI204 may work in tandem with other receptors in a sequential manner to amplify the type I interferon response. We also studied the involvement of IFI204 in an in vivo model of HSV-1 infection. IFI204 knockout mice produce less brain and serum IFN-β, IL-6, and IL-1β 72 hours post intraperitoneal infection with HSV-1. Furthermore, IFI204 -/- mice are more susceptible to HSV-1 infection as compared to WT mice. These data indicate that IFI204 mediates the response to HSV-1 in vivo by inducing the production of cytokines that are necessary for the control of viral infection.

Transcriptional regulatory complexes control gene expression patterns and permit cellular responses to stimuli. Deregulation of complex components upsets target gene expression and can lead to disease. This dissertation examines proteins involved in two distinct regulatory complexes: C-terminal binding protein (CtBP) 1 and 2, and Interferon Regulatory Factors (IRF) 3 and 5. Although critical in developmental processes and injury response, CtBP transcriptional repression of cell adhesion proteins, pro-apoptotic factors, and tumor suppressors has been linked to the pathogenesis of multiple forms of cancer. IRFs function in the immune system and have been implicated in autoimmune disorders. Understanding IRF activation is critical to treating pathogens that target IRF function or for future autoimmune disease therapies. We attempted to determine crystal structures that would provide the details of IRF activation, allowing insight into mechanisms of pathogen immune evasion and autoimmune disorders. Although no new structures were solved, we have optimized expression of C-terminal IRF-3 / co-activator complexes, as well as full-length IRF3 and IRF5 constructs. Modifying the constructs coupled with new crystal screening will soon result in structures which detail IRF activation, advancing understanding of the roles of IRF family members in disease. Through structural and biochemical characterization we sought to identify and develop inhibitors of CtBP transcriptional regulatory functions. High concentrations of CtBP substrate, 4-Methylthio 2-oxobutyric acid (MTOB), have been shown in different cancer models to interfere with CtBP transcriptional regulation. We began the process of structure based drug design by solving crystal structures of both CtBP family members bound to MTOB. The resulting models identified critical ligand contacts and unique active site features, which were utilized in inhibitor design. Potential CtBP inhibitors were identified and co-crystallized with CtBP1. One such compound binds to CtBP more than 1000 times more tightly than does MTOB, as a result of our structure-based inclusion of a phenyl ring and a novel pattern of hydrogen bonding. This molecule provides a starting point for the development of compounds that will both bind more tightly and interfere with transcriptional signaling as we progress towards pharmacologically targeting CtBP as a therapy for specific cancers.