Autophagy is a core cytoplasmic degradation process. It is established that KRas-mutant lung cancer cells require basal autophagy for survival. However, the mechanisms that govern this are poorly understood. It has recently been suggested that selective autophagic degradation of signalling complexes may regulate downstream cell signalling pathways. Primarily, this thesis aims to uncover molecular mechanisms through which selective autophagy can regulate signalling pathways that may impact upon cancer cell proliferation. Previous work in the lab identified a putative interaction between the signalling protein TRAF3 and the autophagy protein Ndp52 via mass spectrometric screening. In this thesis I have identified TRAF3 as a target of selective autophagy in both KRas-mutant lung cancer cells and in in vitro transformed MEFs. TRAF3 is a negative regulator of a gene expression regulation pathway called alternative NF-κB. As such, autophagy of TRAF3 promotes basal activation of the alternative NF-κB signalling pathway. This basal activity supports the proliferation of cancer cells. Investigation of TRAF2, a protein closely related to TRAF3, revealed that it too associates with the autophagy pathway, but is not degraded. This is promoted by the activity of TBK1, which itself can phosphorylate TRAF2. Both TBK1 and TRAF2 promote alternative NF-κB signalling, and I investigate possible mechanisms underlying this, including changes in TRAF3 mRNA and protein levels and binding to other alternative NF-κB regulators. This thesis therefore identifies mechanisms through which basal alternative NF-κB signalling is regulated in KRas-mutant lung cancer cells, with implications for cell proliferation. Ultimately, this work provides valuable mechanistic insight to inform the use of autophagy and/or TBK1 inhibition in future cancer therapies.

T cells are an essential component of the adaptive immune system, which evolved to facilitate development of long-term, effective protection against infectious diseases. Upon activation, T cells play an important role in clearing infections, and especially, in preventing establishment of subsequent infections with the same pathogen. Because this is such a powerful response, it must be tightly regulated. Our lab has long been interested in how signaling molecules regulate the function of T and B lymphocytes. Our prior studies stimulated an interest in the signaling adapter molecule, Tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3). Our group previously produced a T cell-conditional (CD4-Cre) TRAF3-/- mouse, which demonstrated that TRAF3 unexpectedly plays an important positive role in T cell functions, including providing help for B cell responses, protection from infectious pathogens, cytokine production and proliferation. After TCR engagement, TRAF3 associates with the T Cell Receptor (TCR)/CD28 complex. These data identified a new role for TRAF3 in T cell activation. There are three signals that are required for full T cell activation. The three types of receptors that deliver these signals are the TCR, co-stimulatory receptors and cytokine receptors. This dissertation explores the regulatory role of TRAF3 in the 3 signals required for T cellsactivation. In signal 1, TRAF3 enhances TCR signaling by regulating the localization of the TCR inhibitors, PTPase non-receptor type 22 (PTPN22) and the c-Src kinase (Csk). Our lab previously reported that recruitment of TRAF3 to the TCR complex requires co-stimulation of CD28, the primary receptor for signal 2. In this dissertation, we show that TRAF3 associates with the Linker of Activated T cells (LAT) complex, demonstrating preference for distinct LAT-associated proteins. For delivery of signal 3, T cells require stimulation of a cytokine receptor, such as IFNαR, for differentiation of a T cell to an effector cell. Upon IFN stimulation, TRAF3 inhibits IFNαR-induced early molecular events, which results in the regulation of both canonical and non-canonical IFNαR signaling pathways. The results presented in this dissertation highlight the dynamic roles of TRAF3 as a regulator of T cell activation, by regulating multiple T cell signaling pathways.

Codirecteur de recherche: Dr Sylvain Meloche / Durant ces quatre dernières années, le champ de recherche concernant l’immunité innée a grandement été influencé par la découverte des IKK-related kinases, TBK1 et IKKi, deux kinases régulant l’activité des facteurs de transcription IRF-3/IRF-7 et NF-κB. Les kinases TBK1 and IKKi furent notamment démontrées comme étant responsables de la phosphorylation en C-terminal de IRF-3. Toutefois, l’identité des sites phosphoaccepteurs ciblés par ces kinases restait un sujet de controverse. En combinant la spectrométrie de masse aux essais de phosphorylation in vitro de His-IRF-3 par la kinase recombinante TBK1, nous démontrons que les sérines 396 et 402 sont directement phosphorylées par cette kinase. Nos analyses biochimiques révèlent également que la mutation S396A, localisée dans le cluster II, abolit l’homodimérisation, l’association à CBP et l’accumulation nucléaire de IRF-3. De façon intéressante, la mutation de la sérine 339, impliquée dans la stabilité de IRF-3, provoque également une perte d’association à CBP et de la dimérisation du facteur de transcription sans toutefois affecter la transactivation des gènes antiviraux en autant que la sérine 396 soit disponible pour accepter un événement de phosphorylation. Nos expériences de complémentation de MEFs IRF-3 KO révèlent la présence d’un mécanisme compensatoire impliquant la sérine 339 et la sérine 396 dans l’induction des IFN-stimulated genes (ISGs), ISG56 and ISG54. Globalement, les données présentées dans cette étude nous ont permis de reconsidérer le modèle d’activation du facteur de transcription IRF-3 actuellement proposé et d’y ajouter certaines subtilités. TRAF3 est également un médiateur central impliqué dans l’induction de la réponse interféron de type I. Cette fois, en couplant la spectrométrie de masse à la technique de purification protéique par affinité, nous avons identifié Sec16A et p115, deux protéines du système de transport vésiculaire ER-Golgi , comme étant des nouveaux partenaires protéiques de Flag-TRAF3. Nos expériences démontrent la localisation cellulaire de TRAF3 au niveau du système de transport vésiculaire. De plus, la diminution des niveaux d’expression de p115 ou Sec16A provoque une redistribution cellulaire de TRAF3 et affecte la réponse interféron suivant une stimulation par de l’ARN double brin. Nos résultats démontrent également une colocalisation de TRAF3 et TRADD au niveau du cis-Golgi ainsi qu’une interaction avec la protéine du translocon Sec61β médiée par l’intermédiaire de Sec5. De façon générale, nos données suggèrent que la localisation cellulaire de TRAF3 au niveau des compartiments de transport vésiculaire est requise afin d’obtenir une réponse antiviral optimale par la voie de signalisation cellulaire associée aux RIG-I-like RNA helicases, RIG-I et MDA5. Nos données appuient également le rôle potentiel précédemment suggéré de l’exocyste dans l’établissement d’une réponse antivirale. / Over the past four years, the field of the innate immune response has been highly influenced by the discovery of the IκB kinase (IKK)-related kinases, TBK1 and IKKi, which regulate the activity of IRF-3/IRF-7 and NF-κB transcription factors. The IKK-related kinases, TBK1 and IKKi, were recently shown to be responsible for the C-terminal phosphorylation of IRF-3. However, the identity of the phosphoacceptor site(s) targeted by these two kinases remains unclear. By combining mass spectrometry analysis to in vitro kinase assays using full length His-IRF3 as a substrate, we have demonstrated that serine 402 and serine 396 were directly targeted by TBK1. Analysis of Ser/Thr to Ala mutants revealed that S396A mutation, located in cluster II, abolished IRF-3 homodimerization, CBP association and nuclear accumulation. Interestingly, mutation of serine 339, which is involved in IRF-3 stability, also abrogated CBP association and dimerization without affecting gene transactivation as long as serine 396 remained available for phosphorylation. Complementation of MEFs IRF-3 KO also reveals a compensatory mechanism of serine 339 and serine 396 in the ability of IRF-3 to induce IFN-stimulated genes (ISGs) ISG56 and ISG54 expression. These data lead us to reconsider the current model of IRF-3 activation. TRAF3 is also a central mediator that is important for inducing type I interferon production in response to intracellular double-stranded RNA. By combining Flag-Affinity purification using Flag-TRAF3 as a bait to mass spectrometry, we have identified Sec16A and p115, two proteins of the ER-to-Golgi vesicular transport system, as novel TRAF3 interactors. We found that TRAF3 localizes to the ER-to-Golgi vesicular pathway and behaves like a cis-Golgi protein. Depletion of p115 or Sec16A disrupts the cis-Golgi cellular localization of TRAF3 and affects type I Interferon response following double-stranded RNA treatment. Furthermore, we demonstrate that TRAF3 colocalizes with TRADD at the cis-Golgi and also interacts with the translocon protein Sec61β in a Sec5 dependent manner. Together, our data suggest that the cellular localization of TRAF3 to the ER-to-Golgi transport compartments is required for an optimal RIG-I-like Helicases (RLH)-Cardif-dependent antiviral immune response. Our findings also highlight the potential role of the exocyst in the innate immune response.

Durant ces quatre dernières années, le champ de recherche concernant l’immunité innée a grandement été influencé par la découverte des IKK-related kinases, TBK1 et IKKi, deux kinases régulant l’activité des facteurs de transcription IRF-3/IRF-7 et NF-κB. Les kinases TBK1 and IKKi furent notamment démontrées comme étant responsables de la phosphorylation en C-terminal de IRF-3. Toutefois, l’identité des sites phosphoaccepteurs ciblés par ces kinases restait un sujet de controverse. En combinant la spectrométrie de masse aux essais de phosphorylation in vitro de His-IRF-3 par la kinase recombinante TBK1, nous démontrons que les sérines 396 et 402 sont directement phosphorylées par cette kinase. Nos analyses biochimiques révèlent également que la mutation S396A, localisée dans le cluster II, abolit l’homodimérisation, l’association à CBP et l’accumulation nucléaire de IRF-3. De façon intéressante, la mutation de la sérine 339, impliquée dans la stabilité de IRF-3, provoque également une perte d’association à CBP et de la dimérisation du facteur de transcription sans toutefois affecter la transactivation des gènes antiviraux en autant que la sérine 396 soit disponible pour accepter un événement de phosphorylation. Nos expériences de complémentation de MEFs IRF-3 KO révèlent la présence d’un mécanisme compensatoire impliquant la sérine 339 et la sérine 396 dans l’induction des IFN-stimulated genes (ISGs), ISG56 and ISG54. Globalement, les données présentées dans cette étude nous ont permis de reconsidérer le modèle d’activation du facteur de transcription IRF-3 actuellement proposé et d’y ajouter certaines subtilités. TRAF3 est également un médiateur central impliqué dans l’induction de la réponse interféron de type I. Cette fois, en couplant la spectrométrie de masse à la technique de purification protéique par affinité, nous avons identifié Sec16A et p115, deux protéines du système de transport vésiculaire ER-Golgi , comme étant des nouveaux partenaires protéiques de Flag-TRAF3. Nos expériences démontrent la localisation cellulaire de TRAF3 au niveau du système de transport vésiculaire. De plus, la diminution des niveaux d’expression de p115 ou Sec16A provoque une redistribution cellulaire de TRAF3 et affecte la réponse interféron suivant une stimulation par de l’ARN double brin. Nos résultats démontrent également une colocalisation de TRAF3 et TRADD au niveau du cis-Golgi ainsi qu’une interaction avec la protéine du translocon Sec61β médiée par l’intermédiaire de Sec5. De façon générale, nos données suggèrent que la localisation cellulaire de TRAF3 au niveau des compartiments de transport vésiculaire est requise afin d’obtenir une réponse antiviral optimale par la voie de signalisation cellulaire associée aux RIG-I-like RNA helicases, RIG-I et MDA5. Nos données appuient également le rôle potentiel précédemment suggéré de l’exocyste dans l’établissement d’une réponse antivirale. / Over the past four years, the field of the innate immune response has been highly influenced by the discovery of the IκB kinase (IKK)-related kinases, TBK1 and IKKi, which regulate the activity of IRF-3/IRF-7 and NF-κB transcription factors. The IKK-related kinases, TBK1 and IKKi, were recently shown to be responsible for the C-terminal phosphorylation of IRF-3. However, the identity of the phosphoacceptor site(s) targeted by these two kinases remains unclear. By combining mass spectrometry analysis to in vitro kinase assays using full length His-IRF3 as a substrate, we have demonstrated that serine 402 and serine 396 were directly targeted by TBK1. Analysis of Ser/Thr to Ala mutants revealed that S396A mutation, located in cluster II, abolished IRF-3 homodimerization, CBP association and nuclear accumulation. Interestingly, mutation of serine 339, which is involved in IRF-3 stability, also abrogated CBP association and dimerization without affecting gene transactivation as long as serine 396 remained available for phosphorylation. Complementation of MEFs IRF-3 KO also reveals a compensatory mechanism of serine 339 and serine 396 in the ability of IRF-3 to induce IFN-stimulated genes (ISGs) ISG56 and ISG54 expression. These data lead us to reconsider the current model of IRF-3 activation. TRAF3 is also a central mediator that is important for inducing type I interferon production in response to intracellular double-stranded RNA. By combining Flag-Affinity purification using Flag-TRAF3 as a bait to mass spectrometry, we have identified Sec16A and p115, two proteins of the ER-to-Golgi vesicular transport system, as novel TRAF3 interactors. We found that TRAF3 localizes to the ER-to-Golgi vesicular pathway and behaves like a cis-Golgi protein. Depletion of p115 or Sec16A disrupts the cis-Golgi cellular localization of TRAF3 and affects type I Interferon response following double-stranded RNA treatment. Furthermore, we demonstrate that TRAF3 colocalizes with TRADD at the cis-Golgi and also interacts with the translocon protein Sec61β in a Sec5 dependent manner. Together, our data suggest that the cellular localization of TRAF3 to the ER-to-Golgi transport compartments is required for an optimal RIG-I-like Helicases (RLH)-Cardif-dependent antiviral immune response. Our findings also highlight the potential role of the exocyst in the innate immune response. / Codirecteur de recherche: Dr Sylvain Meloche

Tumor-necrosis factor (TNF)-receptor (R) associated factor 3 (TRAF3) is an important adaptor protein that plays a variety of context-dependent regulatory roles in all types of immune cells. In B cells, TRAF3 mediates signaling downstream of CD40, B cell activating factor (BAFF)-R, and toll-like receptors (TLR)s to restrain B cell survival and function. Downstream of CD40 and BAFF-R, TRAF3 negatively regulates NF-κB2 activation through NF-κB inducing kinase (NIK) stabilization. NF-κB2 activation is important for B cell-homeostatic survival. However, the constitutively active NF-κB2 in other TRAF3 deficient immune cell types does not lead to increased cell survival. More importantly, loss-of-function mutations of the TRAF3 gene are found at relatively high frequencies in B cell malignancies such as multiple myeloma and B cell lymphoma. Therefore, TRAF3 plays a critical and unique role in B cells to restrain cell survival and differentiation that contributes to B cell malignancies. In this study, we aim to identify TRAF3 modulated survival pathways that contribute to homeostatic B-cell survival and B-cell differentiation. We found that TRAF3 degradation was not sufficient or necessary to induce NF-κB2 activation. We also showed that TRAF3 degradation is dependent on association with TRAF2 and cytoplasmic tail of CD40 or BAFF-R. TRAF3 regulation of NIK is important for mature B cell development; however, NIK only partially contributes to TRAF3-mediated B cell survival. TRAF3 also regulates the protein level of proviral integrations of Moloney virus (Pim2), a pro-survival serine/threonine protein kinase encoded by the Pim2 gene, to restrain B cell survival; this regulation can operate independently of the NF-κB2 pathway. Furthermore, we showed that TRAF3 negatively regulates IL-6R signaling, a pathway that contributes to expansion of the plasma cell compartment and to the pathogenesis of multiple myeloma, a plasma cell malignancy. We found that TRAF3 facilitates recruitment of PTPN22, a tyrosine phosphatase, to associate with Jak1 following IL-6 binding to the IL-6R complex. This regulation by TRAF3 restrains plasma cell differentiation, and also provides the first demonstration that PTPN22 regulates cytokine receptor signaling. Collectively, these findings highlight the importance of TRAF3 in the regulation of B cell-specific survival and differentiation pathways. This information could be exploited for more precise and effective therapeutic choices in treatment of B cell malignancies with TRAF3 deficiencies.

No description available.

The tumor necrosis factor (TNF) receptor-associated factors (TRAFs) were initially discovered as proteins that inducibly interact with the intracellular region of TNF receptors (TNFRs). Because the TNFRs lack intrinsic catalytic activity, the TRAFs are hypothesized to orchestrate signaling activation downstream of the TNFR superfamily, however their mechanism of activation remains unclear (Inoue et al., 2000; Bishop, 2004). Originally, the TRAFs were compared to the signal transducers and activators of transcription (STAT) protein family, due to their sequence homology, and the presence of multiple RING- and zinc-finger domains, suggesting that their function may be to regulate transcriptional activity (Rothe et al., 1994; Hu et al., 1994; Sato et al. 1995; Cheng et al., 1995). However, subsequent research focused predominantly on their cytoplasmic functions, and more recently on their function as E3 ubiquitin ligases (Pineda et al., 2007). In my research, I analyzed the subcellular localizations of the TRAFs following CD40 ligand (CD40L)-stimulation, and found that TRAF2 and 3 rapidly translocate into the nucleus of primary neurons and Neuro2a cells. Interestingly, similar analysis conducted in pre-B lymphocytes (Daudi cells) revealed a different response to CD40L-stimulation, with TRAF2 and 3 being rapidly degraded within 5-minutes of stimulation. These findings are significant because they demonstrate for the first time that the TRAFs translocate into the nucleus and suggest that they may function within the nucleus in a cell-specific manner. I next analyzed the ability of TRAF2 and 3 to bind to DNA, and found that they both bind to chromatin and the NF-kappaB consensus element in Neuro2a cells, following CD40L-stimulation. Similar analyses of the chromatin binding of TRAF2 and 3 in Daudi cells revealed that they were rapidly degraded, similar to the results from my analysis of their subcellular localization. These findings show for the first time that the TRAFs interact with DNA, and therefore support the hypothesis that the TRAFs may function within the nucleus as transcriptional regulators. Finally, I analyzed the ability of the TRAFs to regulate transcriptional activity by luciferase assay. Previous studies showed that overexpression of TRAF2 and 6 could induce NF-kappaB transcriptional activity; however researchers have not been able to determine the mechanism by which they do so. In my studies, I found that every TRAF can directly regulate transcriptional activity either as co-activators or co-repressors of transcription, in a cell- and target protein-specific manner. Additionally, I found that TRAF2 can act as a transcriptional activator, and that its ability to regulate transcription is largely dependent upon the presence of its RING-finger domain. In conclusion, these studies have revealed an entirely novel function for the TRAFs as immediate-early transcriptional regulators. Future research into the genes that are regulated by the specific TRAF complexes will further elucidate how the TRAFs regulate TNFR signaling, as well as whether dysfunctions in TRAF signaling may be associated with known disorders. If specific TRAF complexes are found to regulate specific genes, then pharmacological targeting of the individual TRAF complexes may allow for the highly specific inhibition of signaling events downstream of the TNFRs, without compromising overall receptor signaling, transcription factor pathways, or cellular systems.