Over the past 30 years, transcription factor nuclear factor kappa B (NF-κB) has been extensively characterized in organisms ranging from flies to humans, where it is known to play key roles in developmental and immune-related processes. More recently, DNA sequencing approaches have identified homologs of NF-κB and many upstream signaling components in basal phyla, including Cnidaria (sea anemones, corals, hydras, and jellyfish), Porifera (sponges), and single-celled protists, including Capsaspora owczarzaki and some choanoflagellates. However, little is known about the activity and regulation of NF-κB proteins in these basal organisms. In this dissertation, the structure, activity, and biology of NF-κB in three basal phyla is examined and the extent of conservation with more derived organisms as well as phylum-specific properties are investigated. In the coral Orbicella faveolata (Of) a simplified but nearly complete Toll-like receptor (TLR)-to-NF-κB pathway exists, but basal to cnidarians, there are fewer upstream signaling molecules present. For example, in the poriferan Amphimedon queenslandica (Aq) and the protist Capsaspora owczarzaki (Co), singular NF-κBs and some upstream signaling proteins are encoded in their genomes, but no canonical TLRs exist. In contrast, the expanded family of choanoflagellates, including the choanoflagellate Acanthoeca spectabilis (As), contains TLR-like and up to three NF-κB-like homologs, although their domain structures differ from NF-κB pathway members of higher organisms. Of-NF-κB, Aq-NF-κB, and Co-NF-κB all resemble the mammalian NF-κB protein p100 in that they contain an N-terminal DNA-binding domain, a C-terminal Ankyrin (ANK) repeat domain, and similar DNA binding-site profiles. C-terminal truncation results in translocation of these basal NF-κBs to the nucleus and increases their DNA-binding and transcriptional activation activities. Nevertheless, unlike mammalian NF-κB p100, the C-terminal sequences of Aq-NF-κB do not inhibit its DNA-binding activity. The three As-NF-κB-like proteins all consist of primarily the N-terminal conserved Rel Homology domain sequences of NF-κB, but lack C-terminal ANK repeats. All three As-NF-κB proteins constitutively enter the nucleus of human and Co cells, but differ from one another in DNA-binding and transcriptional activation activities. Furthermore, all three As-NF-κB proteins can form heterodimers, indicating that NF-κB diversified into multi-subunit families at least two times during evolution. Expression of IKKs induce proteasome-dependent C-terminal processing of Of-NF-κB and Aq-NF-κB in human cells, and processing requires C-terminal serines. In contrast, C-terminal processing of Co-NF-κB is not induced by co-expression of IKK in human cells and no IKK homolog exists in the Co genome, suggesting that IKK-mediated processing of NF-κB is a mechanism that evolved solely in animals. Treatment of Of and sponge tissue with lipopolysaccharide (LPS), a ligand for mammalian innate immunity, results in gene expression changes consistent with NF-κB pathway mobilization in Of and increases both DNA-binding activity and processing of sponge NF-κB. Furthermore, sponge tissue contains constitutive NF-κB site DNA-binding activity, as well as nuclear and processed NF-κB. Moreover, exogenously expressed Co-NF-κB localizes to the nucleus in Co cells. Together, these data suggest that the mechanism as well as level of activation of NF-κB in basal organisms is different from what is observed in higher organisms. Additionally, NF-κB mRNA and DNA-binding levels differ across three life stages of Capsaspora, suggesting distinct roles for NF-κB in these life stages. RNA-seq and GO analyses identify possible gene targets and biological functions of Co-NF-κB. Overall, these data represent the first functional characterization of NF-κB signaling proteins in an endangered coral, in any organisms basal to cnidarians (i.e., an evolutionary important sponge), and outside the Kingdom Animalia (protists). These findings suggest that these seemingly simple organisms contain conserved innate immune-like pathways that may be regulated by NF-κB and provide information about the evolution and diversification of this biologically important transcription factor.

Protein-protein interactions (PPI) mediate numerous biological processes, but inhibiting these interactions with small molecules has been difficult to achieve in drug discovery. A small number of successes have shown that some PPIs are amenable to inhibition. Computational algorithms designed to measure the druggability of PPIs have been developed based on these successes. These algorithms have identified the interaction between the NF-κB essential modulator (NEMO) and I𝜅B kinase β (IKKβ) as a candidate for inhibition. Furthermore, in vivo peptide-based inhibition of the NEMO-IKKβ interface has shown benefits in attenuating the NF-𝜅B response in cellular and animal models. In addition to its intrinsic interest as a drug target, developing inhibitors against the NEMO/IKKβ interaction may help in the development of improved methods for PPI inhibition. In this thesis, the production of full-length, recombinant forms of soluble NEMO is described. This protein was used in a variety of biochemical assays to advance our understanding of NEMO structure and function. Furthermore, a fluorescence anisotropy (FA) assay was developed to screen for compounds inhibiting the NEMO/IKKβ PPI. Hits from the FA assay were tested by several methods to confirm true inhibition. Additionally, the FA assay was used to accurately measure the affinity of NEMO for IKKβ and to assess the degree of cooperativity in IKKβ binding. The oligomeric state of NEMO has been characterized through the development of a panel of NEMO cysteine to alanine mutants, using polyacrylamide gel electrophoresis analysis, analytical ultracentrifugation, and fluorescence anisotropy. These data represent the first comprehensive characterization of full-length human NEMO, and may provide a path toward development of drug-like inhibitors of the NEMO/IKKβ interaction.

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<p>Coronaviruses are the largest known RNA viruses and infect a wide range of hosts. Human coronaviruses traditionally have been known to be the cause of the common cold and have been vastly understudied due to low morbidity and mortality. The emergence of SARS-CoV and MERS-CoV has altered the landscape of coronavirus research and proven the deadly capabilities of human coronaviruses. With two recent zoonotic events, it is increasingly important to understand the molecular biology of human coronaviruses. The coronavirus nucleocapsid protein is an essential structural protein that complexes with the viral genome. Though nucleocapsid formation is the protein’s major role, it has also been found to have other functions and effects during infection. The following research aimed to examine how the human coronavirus nucleocapsid protein affects the innate immune response <em>in vitro</em>. Modulation of the type I interferon response by the nucleocapsid was first investigated and the nucleocapsids were shown to have the ability to block interferon signalling. Additionally, the nucleocapsid protein was found to cause a dysregulation of transcription factor NFKB1. We propose a novel mechanism of this NFKB1 negative regulation interference. Taken together, we have further characterized the significant role of the coronavirus nucleocapsid protein in innate immune evasion.</p> / Doctor of Philosophy (Medical Science)

La survie des êtres vivants repose sur leur capacité d'adaptation à leur environnement et au maintien de l'homéostasie cellulaire. Au cours de mon doctorat, je me suis intéressée à deux de ces aspects : d'abord à la réponse immunitaire innée et inflammatoire par l'étude des voies associées aux facteurs de transcription NF-kB et ensuite à l'autophagie, qui consiste en la capacité d'une cellule à dégrader certains composants cellulaires ou des pathogènes intracellulaires. La rapidité d'activation/inactivation de ces processus cellulaires est permise par des modifications post-traductionnelles de certains acteurs parmi lesquelles l'ubiquitination des protéines, qui consiste en la liaison covalente de mono- ou polymères d'ubiquitines sur des protéines, et qui apparaît désormais comme un mécanisme majeur. Dans ce contexte, mes travaux ont consisté d'une part, en la mise en évidence de la fonction de la déubiquitinase USP36 dans la régulation de la voie immunitaire NF-B associée au récepteur 1 au TNFa (TNF-R1) en cellules humaines en culture. J'ai montré par des approches de biologie cellulaire et de biochimie qu'USP36 est un régulateur négatif spécifique de cette voie et est constitutivement associée au récepteur, contribuant ainsi à la régulation de l'ubiquitination de RIP1, un composant essentiel de la voie du TNF-R1. De cette étude, nous avons conclu qu'USP36 est un acteur clé de la voie du TNF-R1 permettant la répression de la voie en absence d'activation et favorisant un retour à l'état stationnaire en réponse à une stimulation au TNFa. D'autre part, mes travaux ont consisté en la réalisation d'un crible génétique in vivo chez la Drosophile pour l'identification de déubiquitinases impliquées dans la régulation de l'autophagie. J'ai identifié UBPY et USP12 dont la perte de fonction affecte à la fois la progression de l'autophagie et de l'endocytose. A partir de l'étude de ces enzymes, nous avons pu établir qu'une voie endocytaire intacte est requise pour le bon fonctionnement de l'autophagie. / The survival of living organisms is based on their ability to adapt to their environment and to maintain their cellular integrity. During my PhD, I was interested in two of these aspects: first, the innate immunity and inflammatory response through the study of the NF-kB-associated pathways, and then in autophagy, consisting in the ability of a cell to degrade some cellular components or intracellular pathogens. The rapid activation/inactivation of these cellular processes is permitted by the post-translational modifications of some components. Among these changes, protein ubiquitination, consisting in the covalent binding of ubiquitin mono- or polymers on target proteins, appears to be an essential mechanism. In this context, my work consisted on one hand, in showing the function of the deubiquitinating enzyme USP36 in the regulation of the immune pathway depending on the TNFa-associated receptor 1 (TNF -R1) pathway in cultured human cells. Using cellular and biochemical approaches, I showed that USP36 is a specific negative regulator of this pathway, constitutively associated with the receptor and which contributes to the regulation of the ubiquitination status of RIP1, which plays a major role in signal transduction. From this study, we conclude that USP36 is a key component of the TNF-R1 pathway, allowing for the repression of this pathway without stimulation and promoting the return to the steady-state after TNFa; treatment. On the other hand, I performed a genetic screen in vivo in Drosophila for the identification of deubiquitinating enzymes involved in regulating autophagy. I identified UBPY and USP12, whose loss-of-function affects both progression of autophagy and endocytosis. Further investigations allowed us to establish that an intact endocytic pathway is required for productive autophagy.

Zelluläre Seneszenz beschreibt einen terminalen Zellzyklus-Arrest. Nach zellulärem Stress u. a. durch aktivierte Onkogene oder DNA-schädigende Chemotherapie wird Seneszenz induziert und kann so zur Tumorsuppression bzw. zum Behandlungserfolg beitragen. Vor kurzem wurde gezeigt, dass der Transkriptionsfaktor NF-kappaB – welcher bisher vor allem durch seine onkogenen Funktionen mit Krebs in Verbindung gebracht wurde - bei der Seneszenz-assoziierten Zytokinausschüttung mitwirkt und den seneszenzten Phänotyp möglicherweise sogar verstärkt, wodurch NF-kappaB potentiell eine tumorsuppressive Rolle zukäme. Ziel dieser Arbeit ist die Untersuchung des NF-kappaB-Signalweges in Seneszenz und Therapie. In der vorliegenden Arbeit zeige ich die deutliche Aktivierung von NF-kappaB nach Therapie-induzierter Seneszenz (therapy-induced senescence, TIS) und erhöhte Expression NF-kappaB-regulierter Zytokine. TIS ist vor allem in vivo mit starker Aktivität des NF-kappaB-Signalweges assoziiert und von selbiger abhängig. Primäre Eµ-myc-transgene Mauslymphome wurden nach ihrer endogenen NF-kappaB-Aktivität klassifiziert bzw. mit inhibierenden und aktivierenden NF-kappaB-Konstrukten modifiziert, welche auch in diffusen großzelligen B-Zell Lymphomen (diffuse large B-cell lymphoma, DLBCL) als natürlich vorkommende Mutationen gefunden wurden. Über einen neuartigen „Cross-Species“-Vergleich wurden Bcl2-hochexprimierende Keimzentrums-B-Zell-DLBCL (germinal center B-cell type, GCB) als klinisch relevante Gruppe identifiziert, welche nach NF-kappaB-Hyperaktivierung signifikant besser auf Therapie ansprach. Diese Ergebnisse zeigen eine kontextspezifische, d. h. von „onkogenen Netzwerken“ abhängige Rolle des NF-kappaB Signalweges unter Chemotherapie. Diese Information könnte für künftige klinische Studien bedeutsam sein, da sie Bedingungen aufzeigt, unter denen NF-kappaB als Vermittler einer erwünschten Therapie-induzierten Seneszenzantwort eher nicht inhibiert werden sollte. / Cellular senescence is a terminal cell-cycle arrest program that is executed in response to cellular stresses, such as activated oncogenes or DNA-damaging anti-cancer chemotherapy, where it serves as a tumor-suppressive mechanism or contributes to treatment outcome, respectively. Recently, transcription factor NF-kappaB which has long been linked to cancer development primarily through its oncogenic functions, has been postulated to participate in a senescence-associated and possibly senescence-reinforcing cytokine response, thereby suggesting a tumor-restraining role for NF-kappaB. The aim of my PhD project was to understand the role of the NF-kappaB pathway in senescence and cancer treatment outcome. In this thesis, I show markedly elevated NF-kappaB activity upon therapy-induced senescence (TIS), associated with strong upregulation of NF-kappaB-controlled cytokines. TIS is associated with and depends on hyper-activated NF-kappaB signaling. By characterization and genetic engineering of primary mouse lymphomas according to distinct NF-kappaB-related oncogenic networks reminiscent of diffuse large B-cell lymphoma (DLBCL) subtypes, Bcl2-overexpressing germinal center B-cell-like (GCB) DLBCL were identified as a clinically relevant subgroup with significantly superior outcome when NF-kappaB is hyperactive. These results demonstrate the context-dependent role of NF-kappaB signaling in cancer therapy and unveil oncogenic scenarios in which NF-kappaB hyperactivity unexpectedly accounts for superior long-term outcome to therapy. This finding has significant ramifications for future clinical trials that aim at inhibiting NF-kappaB activity based on the assumption of its detrimental impact on treatment outcome.

Bisher wurde davon ausgegangen, dass der IKK-komplex durch Regulation des Transkriptionsfaktors NF-kappaB die stressinduzierte Expression von Zielgenen steuert. Im Rahmen der hier vorgelegten Dissertation konnte jedoch gezeigt werden, dass der IKK-Komplex unabhängig von seiner Rolle in der NF-kappaB-Aktivierung die Stabilität einer Vielzahl von mRNAs kontrolliert. Mittels der Kombination von Ko-Immunopräzipitationsstudien und SILAC-MS konnte die induzierte Interaktion der regulatorischen Untereinheit des IKK-Komplexes IKKgamma mit dem Gerüstprotein EDC4 (Enhancer of Decapping 4) nachgewiesen werden. EDC4 ist eine essentielle Komponente sogenannter zytoplasmatischer „Processing Bodies“ (P-Bodies). Diese fungieren als Depots für die Speicherung von mRNAs, aber auch als Orte der mRNA-Degradation und der miRNA-vermittelten Repression spezifischer Zielgene. Die Interaktion von IKKgamma mit EDC4 konnte durch verschiedene Stimuli induziert werden. Dazu zählen DNA-Schäden durch Doppelstrangbrüche, aber auch die Aktivierung von Oberflächenrezeptoren durch TNFalpha und IL-1beta. EDC4 dient darüber hinaus als Substrat der Kinase IKKbeta. Mittels Massenspektrometrie und Kinaseassays konnten vier IKK-abhängige Phosphorylierungsstellen identifiziert werden. Die IKK-vermittelte Phosphorylierung von EDC4 ist essentiell für die Regulation von mRNAs und die damit verbundene Bildung der zytoplasmatischen P-Bodies. Diese Befunde konnten sowohl in stabilen induzierbaren Zelllinien, mittels transienter Transfektion und durch den Gebrauch von Kinaseinhibitoren in primären als auch in Krebszelllinien bestätigt werden. mRNA-Stabilitätsassays und eine RNA-Seq Analyse bestätigten die stressinduzierten Änderungen in den Halbwertszeiten spezifischer Transkripte und offenbarten einen gemeinsamen Regulationsmechanismus des IKK-Komplexes mit EDC4. / The IKK complex is deemed to regulate gene expression through the activation of the transcription factor NF-kappaB. Here I describe an NF-kappaB-independent function of the IKK complex in regulating mRNA stability across different cell types and stimuli. A SILAC-MS screen for interaction partners of the regulatory subunit IKKgamma revealed an inducible interaction with Enhancer of mRNA Decapping 4 (EDC4). EDC4 is an essential component of cytoplasmic processing bodies (P-bodies). P-bodies function as sites of mRNA storage, degradation and miRNA-mediated silencing. Interaction between IKKgamma and EDC4 can be induced by various stimuli, including DNA damage, TNFalpha and IL-1beta. EDC4 was identified as a novel IKK substrate and four IKKbeta phosphorylation sites were determined by mass spectrometry and in kinase assays. Stable inducible cell lines, transient transfection and kinase inhibitors were used in different human cancer and in primary cell lines and demonstrated that phosphorylation of EDC4 by IKK is essential for formation of P-Bodies in response to numerous stimuli. mRNA stability assays confirmed stress-induced changes in the half-life of target mRNAs and revealed common regulation of mRNA stability by IKK and EDC4. The transcriptome-wide reach of this joint regulation was assessed via RNA-Seq analysis.

Die Zellen des Hodgkin-Lymphoms sind, neben einer permanenten Aktivierung des NF-kB Signalweges, durch eine konstitutive AP-1 Aktivität gekennzeichnet. Die vorliegende Arbeit beschäftigte sich mit der Analyse der aberranten AP-1 Aktivität in Zellen des Hodgkin-Lymphoms. Von besonderem Interesse ist in diesem Zusammenhang der JUN Promotor, da c-Jun unter anderem die Fähigkeit besitzt seinen eigenen Promotor positiv zu regulieren (Autoregulation). Im Rahmen dieser Arbeit wurden Faktoren, die mit dem JUN Promotor in Zellen des Hodgkin-Lymphoms assoziiert sind, über verschiedene chromatographische Reinigungsschritte angereichert, mittels Massenspektrometrie identifiziert und hinsichtlich ihres Einflusses auf die c-Jun Expression analysiert. Dabei wurden die zwei Faktoren ATF-3, aus der Familie der AP-1 Proteine, und p52, aus der NF-kB Familie, hinsichtlich ihres Einflusses auf die Überexpression von c-Jun in Hodgkinzellen genauer untersucht. Die hier aufgeführten Ergebnisse tragen zu einem besseren Verständnis der Regulation der konstitutiven AP-1 Aktivität in den Hodgkinzellen bei. Im Rahmen dieser Arbeit konnten zwei Faktoren identifiziert werden, die maßgeblich an der Regulation der Expression von c-Jun in Hodgkinzellen beteiligt sind. Eine besondere Rolle kommt dabei dem Transkriptionsfaktor p52 zu, da dieser unter anderem auch die Expression anderer Mitglieder der AP-1 Familie reguliert. Ein weiterer Befund dieser Arbeit, dass p50 und p52 die zentralen Komponenten der konstitutiven NF-kB Aktivität sind, rückt p52 in das Zentrum zukünftiger Forschung. Die Befunde dieser Arbeit belegen, dass die aberrante Aktivierung von AP-1 im Hodgkin-Lymphom nicht auf ein einzelnes Ereignis in der Zelle zurückzuführen ist, sondern das Ergebnis eines komplexen Zusammenspiels vieler Faktoren ist. / The cells of Hodgkin''s lymphoma are characterized by a permanent activation of the NF-kB signaling pathway and a constitutive AP-1 activation. The present study focused on the analysis of aberrant AP-1 activity in cells of Hodgkin''s lymphoma. Of particular interest in this context is the JUN promoter, since c-Jun has the ability to regulate its own promoter (autoregulation). In this work different JUN promoter associated factors were enriched through various chromatographic purification steps, identified by Mass spectrometry and analyzed in terms of its influence on the expression of c-Jun. The focus was on specific factors in cells of Hodgkin''s lymphoma. The two factors ATF-3 and p52, were analyzed in terms of their influence on the overexpression of c-Jun in cells of Hodgkin''s lymphoma. Another interesting finding of this study is, p50 and p52 are central components of the constitutive NF-kB activity. This puts p52 in the center of future research. The results presented here contribute to a better understanding of the regulation of the constitutive AP-1 activity in the Hodgkin cells. In this work two Factors (ATF3 and p52) could be identified, which are are involved in the regulation of the expression of c-Jun in Hodgkin cells. A special role is played by the transcription factor p52, which also regulates the expression of other members of the AP-1 family. The findings of this study also show that the aberrant activation of AP-1 in Hodgkin''s lymphoma is not due to a single event in the cell. It is rather a result of a complex interplay of many factors.