The Wnt pathway is a fundamental signalling pathway conserved in all animals, regulating growth, differentiation, embryonic development, and tissue homeostasis in adults. Wnt signalling is kept quiescent by ubiquitin-mediated degradation of the transcription factor β-catenin, orchestrated by a group of proteins called the Destruction Complex. Aberrant Destruction Complex activity is a common theme in many cancers, and is the primary cause of colon cancer. Through mass spectrometry analysis of Axin protein complexes (a key Destruction Complex component) we identified the deubiquitinating enzyme USP34 as an Axin-interacting protein. Functional studies showed USP34 functions to positively regulate Wnt signalling, acting downstream of β-catenin stabilization. While characterizing USP34 we also discovered a new positive regulatory role for Axin in promoting signalling that is dependent on its nuclear localization. Our results suggest that USP34 stabilizes the nuclear pool of Axin through regulating its ubiquitination and offers a potential strategy to target pathological Wnt signalling.

The Wnt pathway is a fundamental signalling pathway conserved in all animals, regulating growth, differentiation, embryonic development, and tissue homeostasis in adults. Wnt signalling is kept quiescent by ubiquitin-mediated degradation of the transcription factor β-catenin, orchestrated by a group of proteins called the Destruction Complex. Aberrant Destruction Complex activity is a common theme in many cancers, and is the primary cause of colon cancer. Through mass spectrometry analysis of Axin protein complexes (a key Destruction Complex component) we identified the deubiquitinating enzyme USP34 as an Axin-interacting protein. Functional studies showed USP34 functions to positively regulate Wnt signalling, acting downstream of β-catenin stabilization. While characterizing USP34 we also discovered a new positive regulatory role for Axin in promoting signalling that is dependent on its nuclear localization. Our results suggest that USP34 stabilizes the nuclear pool of Axin through regulating its ubiquitination and offers a potential strategy to target pathological Wnt signalling.

Le mélanome cutané est un cancer très agressif, responsable de 80% des décès liés aux cancers de la peau. Le mélanome métastatique (MM) est souvent résistant à la radiothérapie et aux chimiothérapies. Sa progression est majoritairement initiée par des mutations oncogéniques des gènes BRAF et NRAS activant la voie de prolifération MEK/ERK. Le MM est difficile à traiter malgré le succès de nouveaux traitements (thérapies ciblant l’oncogène BRAFV600E et immunothérapies), qui sont cependant limités à certains patients. De plus l'émergence de résistances ne permet pas d’obtenir une réponse durable, ce qui incite à rechercher de nouvelles cibles tumorales. Dans les cellules cancéreuses, l’accumulation d’altérations génétiques et le fort index prolifératif accroissent leur addiction aux mécanismes de contrôle de la qualité du protéome, comme le système ubiquitine-protéasome (UPS). L’UPS comprend une machinerie protéolytique (le protéasome 26S) et un réseau d’enzymes régulant l’ubiquitination de protéines cibles. La réaction enzymatique de retrait de l’ubiquitine est la déubiquitination, réalisés par de protéases spécifiques appelées DéUBiquitinases (DUBs). Malgré l’importance des DUBs dans de nombreuses situations pathologiques comme le cancer, leur implication dans la physiopathologie du mélanome est mal connue. Afin d’identifier des DUBs dont l’activité est modulée dans le mélanome, nous avons utilisé une méthode d’étiquettage biochimique in vitro des DUBs actives (‘’DUB trap assay’’) qui nous a permis d’identifier USP14 (Ubiquitin Specific Protease 14) dont l’activité est augmentée dans nos lignées de mélanome par rapport aux mélanocytes. USP14 est associée physiquement au protéasome, avec un rôle important sur la protéostasie cellulaire en général. L’analyse de données bioinformatiques publiques confirme l’importance de USP14 dans le mélanome en associant l’expression du gène USP14 à la progression du mélanome et à un mauvais pronostic. Nous avons ensuite montré que cibler USP14 par des approches génétique (siRNA) ou pharmacologique (inhibiteurs de l’activité) a un effet anti-mélanome in vitro et in vivo, associé à une accumulation de protéines polyubiquitinées, générant un stress du réticulum endoplasmique, la dépolarisation de la mitochondrie et une production de ROS, aboutissant à une mort indépendante des caspases. Cet effet cytotoxique est obtenu indépendamment du statut mutationnel des protéines oncogéniques (BRAFV600E, NRAS, NF1), des suppresseurs de tumeurs (TP53, PTEN), du niveau de résistance aux thérapies ciblées ou du statut phénotypique des mélanomes. Ces résultats indiquent que USP14 représente une nouvelle cible thérapeutique pertinente dans le mélanome. Dans la continuité de ces travaux, j’ai cherché à identifier d'autres DUBs pouvant jouer un rôle dans la prolifération et la survie des cellules de mélanome en réalisant le criblage d'une banque de siRNA ciblant 90 DUBs sur une lignée de cellules de mélanome. Outre le fait de confirmer l’implication de USP14 dans la prolifération du mélanome, ce criblage génétique révèle que la déplétion d’une autre DUB associée au protéasome a un puissant effet antiprolifératif sur les cellules de mélanome. Nos travaux préliminaires montrent que le ciblage de cette nouvelle DUB se traduit par un arrêt de prolifération suivi d’une mort cellulaire associée à des dommages à l’ADN in vitro et in vivo. Dans l’ensemble, mes travaux de thèse révèlent un rôle essentiel des DUBs associées au protéasome dans la prolifération et la survie du mélanome, et ouvrent la piste à de nouvelles stratégies thérapeutiques ciblant les mécanismes aberrants de la protéostasie tumorale de ce cancer. / Non communiqué

Major diseases such as cardiovascular diseases, diabetes, obesity and tumor growth are known to involve inflammatory angiogenesis. MCP-induced protein 1 (MCPIP1) encoded by ZC3H12A gene, was reported to promote angiogenesis and is addressed in my dissertation as MCPIP. The mechanism/s involved in the angiogenic differentiation induced by MCPIP was however unknown. The aim of this study was to bridge this gap in our knowledge and delineate the molecular mechanisms and sequential processes involved in angiogenesis mediated via MCPIP. To determine if angiogenesis induced by inflammatory cytokines, TNF-, IL-1 and IL-8 is mediated via induction of MCPIP, knockdown of MCPIP by its specific siRNA, in human umbilical vein endothelial cells was performed. Oxidative stress, ER stress and autophagy are known to be involved in mediating inflammation. We hypothesized that MCPIP-induced angiogenic differentiation is mediated via induction of oxidative stress, ER stress and autophagy. Chemical inhibitors and specific gene knockdown approach were used to inhibit each process postulated. Oxidative stress was inhibited by apocynin or cerium oxide nanoparticles or knockdown of NADPH oxidase subunit, phox47. Endoplasmic reticulum (ER) stress was blocked by tauroursodeoxycholate or knockdown of ER stress signaling protein IRE-1 and autophagy was inhibited by the use of 3methyl adenine, or LY 294002 or by specific knockdown of beclin1. Matrigel assay was used as an in vitro tool to assay angiogenic differentiation. Inhibition of each step inhibited the subsequent steps postulated. The results reveal that angiogenesis induced by inflammatory agents is mediated via sequential induction of MCPIP that causes v oxidative and nitrosative stress resulting in ER stress leading to autophagy required for angiogenesis. MCPIP has deubiquitinase and anti-dicer RNase activities. If and how the dual enzymatic activities of MCPIP mediate angiogenesis was unknown. Our results showed that hypoxia-induced angiogenesis is mediated via MCPIP. MCPIP deubiquitinated ubiquitinated hypoxia-inducible factor (HIF-1) and the stabilized HIF-1 entered the nucleus to promote the transcription of its target genes, cyclooxygenase-2 and vascular endothelial growth factor causing the activation of p38 MAP kinase involved in angiogenesis. MCPIP expression promoted angiogenesis by inhibition of thrombospondin-1 synthesis via induction of silent information regulator (SIRT)-1 and/or via suppression of VEG-inhibitor levels caused by inhibition of NF-B activation. MCPIP inhibited the production of the anti-angiogenic microRNAs (miR)-20b and miR-34a that repress the translation of HIF-1 and SIRT-1, respectively. Cells expressing the RNasedead mutant of MCPIP, D141N, that had lost the ability to induce angiogenesis had deubiquitinase activity but did not inhibit the production of miR-20b and miR-34a. Mimetics of miR-20b and miR-34a inhibited MCPIP-induced angiogenesis. These results show for the first time that both deubiquitinase and anti-dicer RNase activities of MCPIP are involved in inflammatory angiogenesis. Results from our study delineate key processes that could be potential targets for therapeutic intervention against inflammatory angiogenesis.

Inflammation is the response of the body to injury or threats. Immune cells such as macrophages have a crucial role in controlling and regulating this process. The potent pro-inflammatory cytokines interleukin (IL)-1beta and IL-18 are synthesized by macrophages as inactive precursors which activation follows a unique mechanism involving the activation of caspase-1 by assembly of a macromolecular complex called the inflammasome. However, the assembly of the inflammasome is a double-edged sword. Although inflammasome activation is necessary for a normal inflammatory response, its malfunction can trigger and contribute to inflammatory disorders such as gout, arthritis or cryopirin-associated periodic syndromes (CAPS). The fine regulation of this mechanism and the cell death associated with it is key for the outcome of the inflammatory process. In this thesis we tackle three aspects of the mechanisms and consequences of inflammasome activation. First we studied the role of the deubiquitinases USP7 and USP47 in inflammasome activation. We showed how USP7 and USP47 activity is increased upon danger signals and how that is necessary for the assembly of the inflammasome. We also pointed how their inhibition dampens the deubiquitination of ASC using a BRET2 assay. Second we examined how the activity of IL-18 is controlled by the release of IL-18BP during inflammasome activation. We showed how IL-18BP release increased upon membrane permeabilization and pyroptosis. This release happens in other types of lytic cell (necrosis and necroptosis) death but not in apoptosis. Finally, we showed that this IL-18BP acute release dampens IL-18 signalling and IFN gamma production by PBMCs. These results demonstrate a novel mechanism by which lytic cell death could dampen IL-18-driven inflammation and highlights a key role for IL-18BP in inflammasome related diseases. Finally we studied the role of inflammasome in lung epithelial cells as a model to investigate lung infections. We found that lung epithelial cells lack NLRP3 inflammasome activity and components, but express caspase-4 and caspase-8 which could have a role in the release of IL-1 family of cytokines. To conclude we showed how lung epithelial release IL-18 upon Aspergillus fumigatus infection. Overall, this thesis enhances our understanding of the mechanisms that control IL-1beta and IL-18 activity by regulating inflammasome activation and by understanding the consequences of its activation.

BAP1 est un suppresseur de tumeurs dont le nombre de partenaires protéiques rend complexe l'appréhension de son rôle dans la cellule. Chez la Drosophile, BAP1 et ASX forment le complexe Polycomb PR-DUB, qui déubiquitine l'histone H2A sur la lysine 119 afin de maintenir une répression transcriptionnelle sur ses gènes cibles. Comprendre les mécanismes de régulation de BAP1 et définir son implication au sein de la machinerie Polycomb s'avèrent donc des enjeux cruciaux pour mieux appréhender son rôle au cours de la tumorigenèse. Par des approches biochimiques, nous avons montré l'existence de plusieurs complexes fonctionnellement distincts associés à BAP1. ASXL1 semble ainsi nécessaire à l'activité H2A deubiquitinase de BAP1, tandis qu'ASXL2 forme un complexe ternaire avec BAP1 et la déméthylase d'histones KDM1B. Par ailleurs, nous avons démontré le potentiel de répresseur transcriptionnel de BAP1, qui semble posséder différents domaines répresseurs. Afin d'étudier ces aspects à l'échelle du génome, des analyses du transcriptome et de différentes marques d'histone sont en cours, dans des cellules sauvages ou mutées pour différents membres de la famille Polycomb. Dans un deuxième temps, nous avons entrepris une recherche exhaustive des substrats de BAP1. Nos résultats préliminaires suggèrent que non seulement H2A mais également H2B sont des cibles de BAP1, de même qu'un complexe protéique responsable du contrôle de la prolifération cellulaire via la régulation post-transcriptionnelle de plusieurs cyclines. Ces observations ouvrent la voie à plusieurs projets qui pourraient contribuer à expliquer les conséquences des mutations de BAP1 dans le processus tumoral. / BAP1 is as a tumor suppressor that associates to a variety of protein partners, thereby limiting the comprehension of its cellular functions. In Drosophila, BAP1 binds ASX to form the Polycomb PR-DUB complex, which deubiquitinates histone H2A on lysine 119 in order to maintain transcriptional repression on its target genes. Describing BAP1 mechanisms of action and defining how BAP1 cooperates with the Polycomb machinery are prerequisites to understand its role during tumorigenesis. Using a biochemical approach, we described the existence of several distinct subcomplexes associated with BAP1. Therefore, ASXL1 seems required for H2A deubiquitination, while ASXL2 forms a ternary complex of unknown function with BAP1 and the histone demethylase KDM1B. In addition, we demonstrated the transcriptional repressor function of BAP1, which possess several repressive domains. In addition, we are currently performing transcriptomic analysis combined with genome-wide mapping of different histone marks. These last analyses are performed in wild type cells or deficient in PR-DUB or other Polycomb components, which will help us to understand how BAP1 fits within the Polycomb machinery. In parallel, we engaged a comprehensive study aiming at the identification of new BAP1 substrates. Our preliminary results suggest that not only H2A but also H2B may be direct substrates of BAP1. In addition, we identified as a potential substrate the HNRNPM-IMP3 complex, which controls cell proliferation via post-transcriptional regulation of several cyclins. These observations pave the way for new projects that may contribute to explain the consequences of BAP1 mutations in cancer development.

The pathological changes of ubiquitination and deubiquitination following myocardial infarction (MI) and chronic heart failure (CHF) have been sparsely examined. We investigated the expression of muscle-specific E3 ubiquitin ligases and deubiquitinases in MI and CHF. Therefore, mice were assigned to coronary artery ligation for 3 days or 10 weeks as well as for sham operation (each n = 10). Expression of E3 ligases (MAFBX, MURF1, CHIP, ITCH, MDM2) and deubiquitinases (A20, CYLD, UCH-L1, USP14, USP19) was determined. After MI and in CHF, the mRNA expression of MURF1, CHIP and MDM2 (all p < 0.05) was decreased. Protein expression analyses revealed that ITCH expression decreased in CHF (p = 0.01), whereas MDM2 expression increased in MI (p = 0.02) and decreased in CHF (p = 0.02). Except for USP19 mRNA expression that decreased at 3 days and 10 weeks (both p < 0.01), the expression of other deubiquitinases remained unaffected after MI and CHF. The expression of myocardial E3 ligases is differentially regulated following MI, raising the question of whether an upstream regulation exists that is activated by MI for tissue protection or whether the downregulation of E3 ligases enables myocardial hypertrophy following MI.

No description available.

(ENGLISH) Ubiquitin signaling is a key regulatory mechanism for many important cellular processes such as transcription, differentiation and cell division. Cell division requires duplication of all genetic material during S-phase followed by its precise partitioning between two daughter cells during mitosis. Misregulation of the complex mitotic machinery may lead to aneuploidy and genomic instability, known drivers of tumorigenesis. Indeed, systematic genetic analysis of many cancer tissues over the last decades, indicates the presence of severe chromosome abnormalities in thousands of cancer tissue samples. In this work, I investigated the function of two components of ubiquitin signaling, the deubiquitinating enzyme UCHL3 and the E3 ubiquitin ligase TRIM15. The hypothesized role of E3 ligase TRIM15 in the cell cycle regulation could not be confirmed by our experiments, but I observed an effect on cell adhesion and motility instead. UCHL3 was identified using high-content visual siRNA screen, as a critical factor controlling genome segregation and integrity. Interestingly, it has been previously reported that UCHL3 levels are altered in various cancer types, especially colon cancer. My data demonstrate that UCHL3 drives proper alignment of chromosomes at the metaphase plate by facilitating...

BRCA1 est un suppresseur de tumeur majeur jouant un rôle dans la transcription, la réparation de l’ADN et le maintien de la stabilité génomique. En effet, des mutations dans le gène BRCA1 augmentent considerablement le risque de cancers du sein et de l’ovaire. BRCA1 a été en majorité caractérisé pour son rôle dans la réparation de l’ADN par la voie de recombinaison homologue (HR) en présence de bris double brins, par example, induits par l’irradiation gamma (IR). Cependant, la fonction de BRCA1 dans d’autres voies de réparation de l’ADN, comme la réparation par excision de nucléotides (NER) ou par excision de base (BER), demeurent toutefois obscures. Il est donc important de comprendre la régulation de BRCA1 en présence d’agents génotoxiques comme le méthyle méthanesulfonate (MMS) ou l’UV, qui promouvoient le BER et le NER respectivement. Nos observations suggèrent que BRCA1 est dégradée par le protéasome après traitement avec le MMS ou les UV, et non avec l’IR. Par ailleurs, cette dégradation semble compromettre le recrutement de Rad51, suggérant que la voie de HR est inhibée. Nos résultats suggèrent que la HR est inhibée afin d’éviter l’activation simultanée de multiples voies de réparation. Nous avons aussi observé que la dégradation BRCA1 est réversible et que la restauration des niveaux de BRCA1 coïncide avec le recrutement de Rad51 aux sites de dommages. Cela suggère que la HR est réactivée tardivement par les bris double brins générés suite à l’effondrement des fourches de réplication. Ayant observé que BRCA1 est hautement régulé par l’ubiquitination et est ciblé par le protéasome pour dégradation, nous avons émis une hypothèse que BRCA1 est régulé par des déubiquitinases. Cela amène à caractériser plus en profondeur par un criblage en déplétant les déubiquitinases individuellement par RNAi et en observant leur effet sur le recrutement de BRCA1 et des protéines reliées à cette voie. Un criblage préliminaire nous a permi d’identifié candidats potentiels tel que BAP1, CXORF53, DUB3, OTUB1 et USP36. / BRCA1 is a tumour suppressor involved in transcription, DNA repair and maintenance of genomic stability. Indeed, BRCA1 mutation carriers have an exceptionally higher risk of breast and ovarian cancers. BRCA1 is mainly known for its role in homologous recombination repair (HR) by recruiting HR proteins to chromatin upon double strand break (DSBs) formation, e.g., following treatment with ionizing irradiation (IR). However, the function of BRCA1 in other DNA repair pathways such as nucleotide excision repair (NER) or base excision repair (BER) is still obscure. It is thus of fundamental and clinical importance to investigate BRCA1 function following exposure to diverse genotoxic agents. Using human cultured cell, we observed that BRCA1 is downregulated by the proteasome upon treatment with MMS or UV, but not with IR. Moreover, this downregulation prevents Rad51 recruitment to chromatin following exposure to MMS. Given that DNA damage induced by UV and MMS trigger NER and BER pathways respectively, this implies that HR could be inhibited in order to prevent competition between independent DNA repair pathways. We also found that BRCA1 downregulation is reversible and the recovery of BRCA1 levels correlates with the reappearance of BRCA1 and Rad51 on chromatin. This implies that the HR has been reactivated at the late stage of DNA damage for the repair of double strand breaks generated by replication fork collapse. Since BRCA1 stability is highly regulated by ubiquitination and is downregulated following MMS treatment, one would expect that a deubiquitinase is responsible for relieving this downregulation to promote the reactivation of the HR pathway. To characterize this aspect further, we conducted DUB RNAi screens in which a particular DUB is depleted and the localization of BRCA1 and other related proteins were observed. According to a preliminary screen, a few DUBs (BAP1, CXORF53, DUB3, OTUB1, and USP36) were identified as potential regulators of the stability and localization of BRCA1 and proteins involved in homologous recombination.