Indiana University-Purdue University Indianapolis (IUPUI) / Coxiella burnetii is the etiologic agent of Q fever, a zoonotic disease characterized by flu-like sickness in acute cases; endocarditis may occur and turn deadly if not treated correctly in chronic patients. Coxiella, an obligate intracellular bacterium, requires establishment of a replicative niche in the host cell. After being phagocytosed by the eukaryotic cell, the bacterium resides in a tight-fitting nascent phagosome which matures through the host canonical endocytic pathway, acquiring endosomal/lysosomal markers as well as acidic pH. Initial acidification of the Coxiella containing vacuole (CCV) is central to the bacterium’s pathogenesis because translocation of bacterial effector proteins into the host cell by the type 4B secretion system (T4BSS) initiates only after it senses the acidic environment. The effector proteins are required for subverting different host cell functions in favor of Coxiella growth, CCV maturation and are crucial for bacterial virulence. Contrary to the belief that since CCV matures through the host endocytic pathway, CCV is as acidic as lysosome, we found that CCV is significantly less acidic (pH~5.2) than lysosomes (pH~4.8) and inducing further CCV acidification causes Coxiella lysis. Furthermore, increasing lysosomal biogenesis in the host cell is detrimental for Coxiella growth. So, we hypothesized that Coxiella blocks lysosomal biogenesis in host cells to maintain the CCV pH just optimal for its growth. Lysosomal biogenesis is regulated by the master transcription factor EB (TFEB). Its ability to act as a transcription factor depends on its subcellular localization, which relies on its phosphorylation state. TFEB, when phosphorylated is cytosolic and inactive, whereas dephosphorylated TFEB translocates to the nucleus and is active, binding to promoter regions of lysosomal genes of the CLEAR network, thus controlling lysosome biogenesis. Therefore, we hypothesized that Coxiella blocks TFEB translocation to the nucleus, thus inhibiting lysosome biogenesis. We determined that Coxiella grows significantly better in TFEB-KO cells than they do in parentals. Also, using a torin-induced TFEB translocation model, we observed remarkably decreased TFEB activation in the Coxiella infected cells as was evident by less TFEB translocation to nucleus. Overall, data obtained from this work suggest that Coxiella inhibits lysosome biogenesis by blocking TFEB nuclear translocation.

Plusieurs études ont suggéré une implication des glycogène synthase kinases 3 (GSK3) dans la carcinogenèse, notamment du pancréas. Des études ont rapporté des résultats contradictoires quant à l’impact des GSK3 sur la survie cellulaire. Au niveau du pancréas, il a été observé que l’inhibition des GSK3 inhibe la croissance entre autres via la régulation de la voie JNK ou NFkB. Les inhibiteurs des GSK3 sont présentement à l’étude comme traitement de différentes pathologies, notamment pour le cancer pancréatique. Une meilleure compréhension des voies de signalisation régulées par les GSK3 sera donc nécessaire. Nous avons entrepris ces travaux afin de mieux comprendre les mécanismes impliqués dans la régulation de la survie des cellules pancréatiques tumorales par les GSK3. Nous avons démontré que l’inhibition des GSK3 induit l’apoptose et l’autophagie dans les cellules pancréatiques tumorales humaines. L’inhibition des GSK3 stimule l’autophagie autant dans les cellules pancréatiques tumorales que non tumorales, alors que l’apoptose est induite spécifiquement dans les cellules tumorales. Contrairement à l’apoptose, l’autophagie est induite indépendamment de la voie JNK-cJUN suite à l’inhibition des GSK3. Nos résultats démontrent que l’inhibition des GSK3 mène à l’inactivation de la voie mTORC1 qui pourrait contribuer à l’induction de l’autophagie. D’autre part, nos travaux ont démontré pour la première fois que les GSK3 régulent le facteur de transcription EB (TFEB) dans les cellules pancréatiques tumorales. En effet, l’inhibition des GSK3 entraîne la déphosphorylation de TFEB, notamment sur la Ser211, la dissociation des 14-3- 3 et sa translocation nucléaire. Nos résultats suggèrent que la régulation de TFEB par les GSK3 impliquerait des Ser/Thr phosphatases et pourrait être indépendante de l’activité mTORC1. L’inhibition de l’autophagie ou la déplétion de l’expression de TFEB sensibilise les cellules pancréatiques tumorales à l’apoptose induite suite à l’inhibition des GSK3 suggérant un rôle pro-survie de l’autophagie et de TFEB dans ces cellules. Enfin, l’inhibition des GSK3 semble mener à l’inhibition de la glycolyse qui contribuerait à l’induction de l’apoptose. En résumé, nos résultats démontrent que l’inhibition des GSK3 induit à la fois des signaux pro-apoptotiques et pro-survie suggérant que l’équilibre entre ces signaux dicterait l’impact des GSK3 sur la survie des cellules pancréatiques tumorales humaines.

As our body's guardian, the immune system maintains systemic health through removal of pathogens, damage and cancer. Ageing of the immune system is associated with compromised immune responses as well as decreased tumour surveillance and is therefore a key risk factor for major diseases in the elderly. Adaptive immune responses are mediated by T and B lymphocytes, and failure in adaptive immunity is a particular hallmark of the ageing organism. Here we show that autophagy is impaired in aged murine B lymphocytes, and loss of autophagy causes severely reduced B cell responses. Our data demonstrate that B cell senescence can be reversed in an autophagy-dependent manner by spermidine, a naturally occurring polyamine metabolite. Mechanistically, our study reveals that the translation factor eIF5A, that requires spermidine for its activation, regulates the expression of the master autophagy/lysosomal transcription factor TFEB. Importantly, we show in humans that spermidine, eIF5A and TFEB levels decrease with age and may serve as ageing biomarkers. Taken together our results indicate that the translational control of autophagy by eIF5A is dysregulated with ageing, and identify a novel pathway with therapeutic implications.

Obesity is a rapidly growing epidemic in the USA and worldwide. While the molecular and cellular mechanism of obesity is incompletely understood, studies have shown that excess adiposity may arise from increased adipogenesis (hyperplasia) and adipocyte size (hypertrophy) . Emerging evidence underscores autophagy as an important mediator of adipogenesis and adiposity. We are interested in the upstream regulator of adipocyte autophagy and how it impacts adipocyte biology. Given that metabolic stress activates transcription factor FoxO1 in obesity, my dissertation project is designed to depict the role of FoxO1 in adipocyte autophagy and biology. We found that FoxO1 upregulation was concomitant with elevation of autophagy activity during adipogenesis. Inhibition of FoxO1 suppressed autophagy flux and almost completely prevented adipocyte differentiation. For the first time, we found that the kinetics of FoxO1 activation followed a series of sigmoid curves that showed multiple activation-inactivation transitions during adipogenesis. Our study provides critical evidence casting light on the controversy in the literature that either persistent inhibition or activation of FoxO1 suppresses adipogenesis. In addition, we identified two central pathways that FoxO1-mediated autophagy regulated adipocyte biology: (1) to control lipid droplet growth via fat specific protein 27 (FSP27) in adipocytes; and (2) to differentially regulate mitochondrial uncoupling proteins (UCP) that have been implicated in browning of white adipose tissue and redox homeostasis. Mechanistically, FoxO1 appears to induce autophagy through the transcription factor EB (Tfeb), which was previously shown to regulate both autophagosome and lysosome. Chromatin immunoprecipitation assay demonstrated that FoxO1 directly bound to the promoter of Tfeb, and inhibition of FoxO1 attenuated the binding, which resulted in reduced Tfeb expression. To investigate the role of FoxO1 in vivo, we have developed mouse models to modulate FoxO1 in adipose tissue using an inducible Cre-loxP system. Tamoxifen is widely used to activate the inducible Cre recombinase that spatiotemporally control target gene expression in animal models, but it was unclear whether tamoxifen itself may affect adiposity and confounds phenotyping. Part of my dissertation work was to address this important question. We found that tamoxifen led to reduced fat mass independent of Cre, which lasted for 4-5 weeks. Mechanistically, Tamoxifen induced reactive oxygen species (ROS) and augmented apoptosis. Our data reveals a critical period of recovery following tamoxifen treatment in the study of inducible knockout mice. Together, my dissertation work demonstrates FoxO1 as a critical regulator of adipocyte autophagy via Tfeb during adipogenesis. FoxO1-mediated autophagy controls FSP27, lipid droplet growth, and mitochondrial uncoupling proteins. Further study of FoxO1-autophagy axis in obese subjects is of physiological significance, and the investigation is under way. / Ph. D.

Alzheimers sjukdom är den vanligaste orsaken till demens och i samband med att befolkningen blir större och allt äldre ökar även antalet patienter. Vid sjukdomen sker en hjärnatrofi och de mikroskopiska fynd man ser är extracellulära plack av β-amyloid, intracellulära neurofibriller av fosforylerat tau och förlust av nervcellsutskott, axoner, synapser och dendriter. Några av de tidiga patologiska förändringarna man kan se är störningar i nervcellernas lysosomala system som fyller en viktig roll vid nedbrytning av makromolekyler. I en tidigare studie har man påvisat förhöjda nivåer av proteiner från det lysosomala systemet i cerebrospinalvätska. Syftet med den här studien var att mäta nivåer av det lysosomala systemets proteiner i human hjärnvävnad från patienter med Alzheimer och jämföra dessa med kontrollprover. De sex proteiner som analyserades med Western blot var EEA1, PICALM, LAMP-1, LAMP-2, LC3 och TFEB. Resultaten visar på signifikant ökning i temporala cortex av LAMP-1 och LAMP-2 och en signifikant minskning av LC3 och EEA1 hos patienter med Alzheimers sjukdom. För att kunna dra riktiga slutsatser kring hur de ökade nivåerna i cerebrospinalvätska speglar de olika sjukdomsmekanismerna i hjärnan krävs vidare analyser av fler patientprover samt prover från andra områden i hjärnan. / Alzheimer's disease is the most common cause of dementia, and when the population becomes larger and older also the number of patients increase. A cerebral atrophy and microscopic findings of extracellular plaques of β-amyloid, intracellular neurofibrillary of phosphorylated tau and loss of nerve cell protrusions, axons, synapses and dendrites are seen during the disease. One of the early pathological changes is the disruption of the neuronal lysosomal network that plays an important role in the degradation of macromolecules. In a previous study elevated levels of proteins of the lysosomal network in cerebrospinal fluid from Alzheimer’s disease patients was demonstrated. The purpose of this study was to measure levels of the lysosomal network system in the brain. The six proteins EEA1, PICALM, LAMP-1, LAMP -2, LC3 and TFEB were analyzed in human brain tissue from five Alzheimer's disease cases and five control cases by Western blot. The results show a significant increase in the temporal cortex of LAMP-1 and LAMP -2 and a significant decrease of LC3 and EEA1 in patients with Alzheimer's disease. In order to draw proper conclusions about how the increased levels in cerebrospinal fluid reflect the different disease mechanisms in the brain it requires further analysis of more patient samples and from other areas of the brain.

Die Komposition der Skelettmuskulatur resultiert aus der fein abgestimmten Balance von Proteinauf- und Abbaumechanismen. Die Skelettmuskelatrophie kann in verschiedenen Situationen entstehen bzw. von diversen Krankheiten ausgelöst werden (Altern, Hunger, Krebs, Nervenschädigung, Kachexie) und ist meist die Folge von gesteigertem Proteinabbau, der die Proteinsynthese überwiegt. Der Muskelabbau ist physiologisch teilweise sinnvoll und dient der Notversorgung von lebenswichtigen Organen mit Lipiden, Aminosäuren und Glukose. Insgesamt ist eine funktionsfähige Muskulatur sehr wichtig, sowohl für Gesunde als auch Erkrankte, da bei Muskelatrophie auslösenden Erkrankungen das Gesamtüberleben wesentlich verringert ist und die Lebensqualität der Patienten enorm reduziert ist. Der Abbau von strukturellen Muskelproteinen wurde hauptsächlich dem Ubiquitin-Proteasom System zugeschrieben, dessen Regulation und von seinen einzelnen Enzymen muss genauestens verstanden sein, um in der Zukunft zielgerichtete Therapien entwickeln zu können. Eines der zentralen Enzyme in der Skelett- und Herzmuskelatrophie ist die E3 Ubiquitin Ligase MuRF1. In nahezu allen Modellen für Muskelatrophie wurde eine starke Zunahme der Expression von MuRF1 beschrieben. Betrachtet man die sehr zentrale Rolle von MuRF1 im UPS, dort vermittelt MuRF1 den Abbau von strukturellen Proteinen des Sarkomers, und der beobachteten starken Regulation bei diversen Atrophie-Modellen, wird klar, wie wichtig das Verständnis der transkriptionellen Regulation von MuRF1 selbst ist. In den letzten Jahren wurden bereits einige Transkriptionsfaktoren identifiziert, die an der Regulation von MuRF1 bei verschiedenen Atrophie-Modellen beteiligt sind, die Studien zeigten aber auch, dass noch nicht alle Modelle erklärt werden konnten. Um die verbleibenden Wissenslücken zu füllen, wurde in dieser Studie nach neuen transkriptionellen Regulatoren von MuRF1 gesucht und deren Beteiligung an bereits bekannten Signalwegen analysiert. / Skeletal muscle mass is permanently balanced as a result of fine tuned protein synthesis and degradation mechanisms. Skeletal muscle atrophy occurs when protein degradation exceeds protein synthesis, which happens in a variety of conditions, such as aging, starvation, cancer, cachexia or denervation. Degradation of muscle mass can sometimes be useful, e.g. as source for lipids, amino acids and glucose in case of critical malnutrition as well as several other physiological conditions. But a solid composition and thereby functional maintenance of muscles is necessary for healthy individuals as well as individuals suffering from atrophy releasing diseases as to retain their mobility and to preserve full heart functions. Since degradation of structural proteins in muscle tissue has been addressed mainly to the ubiquitin-proteasome-system, the regulation of the participating components needs to be understood in detail to develop constructive treatments and therapies for atrophy prevention. One of the key enzymes in skeletal and heart muscle atrophy is the E3 ubiquitin ligase MuRF1. Its expression levels and protein content was found to be elevated in almost every know atrophy model. MuRF1 is very critical for the muscles composition and thus their functional integrity, as it marks and initiates degradation of structural and contractile proteins via the UPS. Since MuRF1 plays a prominent role in muscle atrophy, its transcriptional regulation needs to be well understood to develop effective therapies for all the different atrophy models MuRF1 has been linked to. Several transcription factors have been identified to regulate MuRF1 at different ratios and in diverse atrophy models. Importantly, they do not explain all MuRF1 inducing events observed. To fill some of the remaining knowledge gaps, the studies aims were to find new transcriptional regulators for MuRF1 and to analyze potential involvements of the obtained candidates in pathways affecting skeletal muscle atrophy.

L’ataxie spinocérébelleuse de type 3, aussi connue en tant que la maladie de Machado-Joseph (MMJ), est une maladie qui se développe lorsqu’il y a une expansion des trinucléotides CAG dans la région codante du gène ATXN3. Ce dernier code pour la protéine ATXN3, une enzyme désubiquitinante avec des fonctions essentielles dans le maintien et la stabilisation de l’homéostasie protéique, la résistance au stress, la régulation de la transcription, la réparation de l’ADN, l’organisation du cytosquelette et la régulation de la myogenèse. Les principaux symptômes associés à cette maladie sont l’ataxie (le symptôme clé), une détérioration motrice progressive, la dystonie, la spasticité et la rigidité. Du fait de l’absence de thérapie spécifique et efficace pour traiter les individus atteints de la MMJ, l’approfondissement des connaissances liées à cette maladie est nécessaire. Le but de cette thèse est de comprendre davantage les mécanismes et voies de signalisations impliqués dans la pathologie de la MMJ. Pour atteindre cet objectif, à partir de notre modèle transgénique C. elegans MMJ, deux différents criblages ont été effectués : un criblage non biaisé de 3942 composés, et un criblage de modificateurs génétiques à base d’ARN interférent (ARNi) de 387 clones de facteurs de transcription. Le premier criblage nous a permis d’identifier cinq molécules prometteuses : l’alfacalcidol, le chenodiol, le cyclophosphamide, le fenbufen et le sulfaphenazole. Elles ont permis la restauration du défaut de la motilité, la protection contre la neurodégénérescence, et une augmentation de la durée de vie réduite chez les vers mutants. Trois parmi ces molécules, le chenodiol, le fenbufen et le sulfaphenazole ont démontré une nécessité de la présence de HLH-30/TFEB, un régulateur clé de l’autophagie et de la biogenèse lysosomale, pour leurs propriétés neuroprotectrices. Concernant le deuxième criblage, il nous a permis d’identifier un nouveau gène candidat impliqué dans la MMJ, fkh-2/FOXG1. L’inactivation de ce gène a entraîné une aggravation du défaut de la motilité, de la neurodégénérescence, et de la longévité réduite. À l’inverse, sa surexpression a restauré tous ces phénotypes, suggérant ainsi un rôle neuroprotecteur pour FKH-2/FOXG1 dans la MMJ. Le modèle C. elegans de MMJ et les criblages sont des outils puissants permettant un approfondissement des connaissances quant à la pathologie de la MMJ. Pour cette thèse, par l’identification des molécules neuroprotectrices et les facteurs de transcription HLH-30/TFEB et FKH-2/FOXG1, ayant des activités neuroprotectrices dans notre modèle lorsqu’ils sont surexprimés, il a été possible à mieux comprendre la pathologie de la MMJ, ainsi que les mécanismes et les voies de signalisation qui y sont impliqués. Ces découvertes sont prometteuses à investiguer dans des organismes modèles plus avancés, des applications précliniques et également, pour le développement de nouvelles interventions thérapeutiques pour la MMJ. / Spinocerebellar ataxia type 3, also known as Machado-Joseph disease (MJD), is a polyglutamine expansion disease arising from a trinucleotide CAG repeat expansion in the coding region of ATXN3. This gene encodes ATXN3 protein, a deubiquitinating enzyme, which is involved in protein homeostasis maintenance and stabilization, stress resistance, transcription regulation, DNA repair, cytoskeleton organisation and myogenesis regulation. The main symptoms associated with this disease are ataxia (the key symptom), progressive motor deterioration, dystonia, spasticity and stiffness. Due to our incomplete understanding of mechanisms and molecular pathways related to this disease, there are no therapies that successfully treat core MJD patients. Therefore, the identification of new candidate targets related to this disease is needed. The aim of this thesis is to gain insights into the pathways and mechanisms leading to MJD. In order to achieve this goal, we performed two different screens, a blind drug screen of 3942 compounds to identify protective small molecules, and a large-scale RNA interference (RNAi) screen of 387 transcription factor genes leading to identification of modifiers involved in our transgenic C. elegans MJD model. The first screen allowed us to identify five lead compounds restoring motility, protecting against neurodegeneration, and increasing the lifespan in mutant worms. These compounds were alfacalcidol, chenodiol, cyclophosphamide, fenbufen and sulfaphenazole. We then found that three of these compounds, chenodiol, fenbufen and sulfaphenazole required HLH-30/TFEB, a key transcriptional regulator of the autophagy and the lysosomal biogenesis, to complete their neuroprotective activities. The second screen brought us to identify a news hit gene candidate involved in MJD, fkh-2/FOXG1. We showed that inactivation of this gene enhanced the motility defect, neurodegeneration and reduced longevity in our MJD model. However, in opposite, its overexpression rescued all these phenotypes, suggesting a neuroprotective role for FKH-2/FOXG1 in MJD when overexpressed. C. elegans models for MJD and the screenings are promising tools to understand the mechanisms and pathways causing neurodegeneration, leading to MJD. In this study, we identified positively acting compounds that may be promising candidates for investigation in mammalian models of MJD and preclinical applications in the treatment of this disease. Also, we gained insights into the pathways of MJD and found that HLH-30/TFEB and FKH-2/FOXG1 are both implicated in MJD and have neuroprotective activities when they are overexpressed. These promising findings may aid the development of novel therapeutic interventions for MJD.