Because of the severe toxicity and limiting side effects of traditional chemotherapy, there exists a critical need to develop better-tolerated, safer drugs to treat cancer. Recent advances in our understanding of the molecular mechanisms governing carcinogenesis have ushered in a new age in drug discovery and have enabled the design of much more sophisticated agents to treat cancer. This work describes two approaches to the development of novel, specifically targeted cancer therapeutics.The first approach involves the synthesis of a class of a new class of small molecules called epidithiodiketopiperazines (ETPs) designed to inhibit hypoxia-induced transcription. Specifically, these agents block the interaction of the transcription factor HIF-1α (hypoxia inducible factor-1α) and its required coactivator p300/CBP by inducing a structural change in p300 that renders it incapable of binding to HIF-1α. Preventing hypoxia-mediated transcription has the potential to stop the process of angiogenesis that is critical for sustained tumor growth and metastasis. Moreover, because HIF-1α also controls genes for energy production and matrix remodeling, ETPs may also halt metabolic adaptation and tumor progression. Our results show that ETPs prevent the association of HIF-1α and p300 and abrogate hypoxia signaling on both the transcriptional and translational levels in endogenous systems. In addition, they do not exhibit broad-spectrum cytotoxicity or global inhibition of the transcriptional response.The second approach addresses the validation of poly(ADP-ribose) glycohydrolase (PARG) as a new therapeutic target. This project describes studies aimed to further our understanding of the interaction between poly(ADP-ribose) polymerases (PARPs) and PARG with the ultimate goal of using this knowledge to design novel therapeutics. This portion of the dissertation involves a series of studies in mouse embryonic fibroblasts (MEFs) with genetic mutations in their PARP and PARG function. MEF cell lines containing a truncated form of PARG lacking the regulatory domain demonstrate over-activation of PARP-1, but not PARP-2. Additionally, deletion of the PARG regulatory domain impairs the DNA damage response to SSBs and DSBs and significantly increases cell death resulting from genotoxic stress. Taken together, these studies suggest a specific interaction between PARP-1 and the regulatory domain of PARG that is critical for proper PARP-1 function.

Poly(ADP)ribose (PAR) metabolism is essential to many cellular functions, including the maintenance of genomic integrity, the regulation of cell death mechanisms, as well as the regulation of gene expression. Recent work has uncovered many new players in the expanding effort to understand PAR metabolism and its cellular impact. PARP-1, the prototypical poly(ADP)ribose polymerase, was the first to be discovered, and has since been shown to be vital in the cellular response to DNA damage. Indeed, one report demonstrating that PARP-1 activation is required for apoptosis-inducing factor (AIF) release from mitochondria uncovered a novel link between DNA damage and signaling for cell death. The events following PARP activation, leading to signaling for AIF release, however, are still poorly understood. Based on our observations, we have developed a model to explain the nuclear/mitochondrial crosstalk that occurs following PARP activation. The work presented here answers several important questions regarding the relationship between ADP-ribose metabolism and mitochondria, including the role of PAR in signaling for the release of AIF, the presence of ADP-ribose metabolism protein members in mitochondria, and mitochondrial transcriptional effects following PARP activation. This work presents several novel findings, including the first report of a mitochondrial matrix isoform of poly(ADP-ribose) glycohydrolase (PARG) as well as direct evidence of mitochondria-associated PARP activity. Furthermore, it provides evidence for a novel effect of PARP-1 activation, in the specific transcriptional upregulation of the mitochondrial gene, NADH dehydrogenase, subunit 1 (ND1). Our data is consistent with the hypothesis that uncontrolled PARP activity results in energy metabolism dysfunction and cell death. Furthermore, it supports a model in which PARP activity is required for normal transcriptional responses in mitochondria following DNA damage. In total, this report adds to the body of work outlining the roles of PARP following DNA damage recognition and activation, demonstrating that ADP-ribose metabolism plays an important role in cell death regulation by both direct and indirect means.

The genome of each cell is under constant threat from various forms of DNA damage. In order to protect themselves from this danger, cells possess a number of pathways able to resolve DNA lesions. The addition of poly(ADPribose) is a post-translational modification produced by attaching successive ADP-ribose moieties to a protein acceptor, forming long chains. Enzymes called poly(ADP-ribose) polymerases (PARPs) catalyse the production of these modifications, and a number of different PARPs have been linked to the process of DNA repair, including PARP1, PARP2 and PARP3. How these enzymes might function together to facilitate the repair of different lesions is unclear. Furthermore, inhibitors that target these enzymes are in clinical use for their ability to kill homologous recombination deficient tumour cells, through a mechanism of synthetic lethality. Which subset of PARPs is necessary to inhibit to achieve maximum efficacy of these agents has not been assessed. I use genome editing to generate cells disrupted for these PARPs in different combinations. Whilst loss of PARP1 compromises cellular tolerance to homologous recombination deficiency, this is independent of the status of PARP2 and PARP3, indicating the development of PARP1-specific inhibitors may hold therapeutic potential. In contrast to these observations, I uncover strong redundancy between PARP1 and PARP2 in the repair of damaged DNA bases through the base excision repair (BER) pathway. I also identify BER independent roles of both PARP1 and PARP2 in resolving replication forks that have collided with BER-intermediates, through promoting the stability of Rad51 nucleofilaments via an Fbh1-dependent mechanism. Thus PARP1 and PARP2 perform two closely-linked functions in response to cellular base damage promoting resolution of these lesions directly through BER, and stabilising replication forks which have encountered BER intermediates.

Clinical trials are currently exploring the combinations of P ARP inhibitors and immunotherapies in the treatment of ovarian cancer, but their effects on the ovarian tumour microenvironment (TME) remain unclear. Here, we investigate how olaparib, PD-L1 monoclonal antibodies and their combination can influence TME composition and survival of tumour-bearing mice. We further explored how BRCA mutations can influence the response to therapy. Olaparib and combination therapies similarly improved the median survival of Brca1- and Brca2-deficient tumour-bearing mice. Anti-PD-L1 monotherapy improved the survival of mice with Brca1-null tumours, but not Brca2-null tumours. A detailed analysis of the TME revealed that the olaparib monotherapy resulted in a large number of immunosuppressive and immunomodulatory effects in the more inflamed Brca1-deficient TME but not Brca2-deficient tumours. Anti-PD-L1 treatment was mostly immunosuppressive, resulting in a systemic reduction of cytokines and a compensatory increase of PD-L1. The results of the combination therapy generally resembled the effects of one or both of the monotherapies, along with unique changes observed in certain immune populations. In-silico analysis of RNA-seq also revealed numerous differences between Brca-mutated tumour models. In summary, these findings shed light on the influence of novel therapeutics and BRCA mutations on the ovarian TME.

O reconhecimento da flagelina é compartilhado pelo receptor transmembrânico TLR5 e citosólico NAIP5/NLRC4. Entretanto, pouco se sabe sobre os mecanismos efetores individuais induzidos a partir do reconhecimento extra e intracelular da flagelina. Aqui, nós demonstramos que macrófagos estimulados com a flagelina citosólica (FLA-BSDot) induziu a expressão de iNOS, enzima responsável pela produção do óxido nítrico (NO). A expressão de iNOS foi dependente do eixo NAIP5/NLRC4/caspase-1 e independente de IL-1β, IL-18 e MyD88, descartando a via de ativação dos TLRs. Ainda, esta via não requer a ativação do fator de transcrição IRF-1, mas envolve a ativação do NF-kB, assim como a clivagem da enzima PARP-1 (poly(ADP-ribose)polymerase-1). Por fim, avaliamos a relevância biológica desta via no controle das infecções por L. pneumophila e S. Typhimurium, dados que definem um mecanismo efetor adicional no controle de patógenos. / Recognition of flagellin is shared by transmembranic TLR5 and cytosolic NAIP5/NLRC4. However, little is known about the individual effector mechanisms induced by extra and intracellular flagellin. Here, we have demonstrated that cytosolic flagellin-stimulated macrophages (FLA-BSDot) induced iNOS expression, an enzyme responsible for the production of nitric oxide (NO). iNOS expression was dependent of the NAIP5/NLRC4/caspase-1 axis and independent of IL-1β, IL-18 and MyD88, discarding TLRs signaling pathway. Still, this pathway do not require the activation of IRF-1 transcriptional factor, but involves NF-kB activation as well as the cleavage of the enzyme, PARP-1 (poly(ADP-ribose)polymerase-1). Finally, we have evaluated the biological relevance of this pathway in the control of the infections by L. pneumophila e S. Typhimurium, which define an additional effector mechanism to the control of pathogens.

La kinase dépendante des cyclines 5 (Cdk5) est un facteur de sensibilité aux inhibiteurs de PARP et aux rayonnements ionisants (RI), elle est nécessaire pour le point de contrôle du cycle cellulaire en phase S. Cependant, elle n’est pas directement impliquée dans la réparation des cassures de brin d’ADN, suggérant un rôle dans les étapes plus précoces de la signalisation des dommages. Nous rapportons ici que des cellules HeLa déplétées pour Cdk5 (Cdk5 KD) montrent une grande sensibilité aux RI surtout lorsqu'elles sont irradiées en phase S, au 5-Fluoro-Uracile, à la 6-Thioguanine et à une exposition chronique à l'hydroxyurée (HU). Les cellules Cdk5 KD montrent une altération de la dynamique de la phase S causée par une vitesse de réplication plus lente et une réduction des origines actives par mégabase d'ADN. En revanche, après un traitement au HU, ces cellules sortent plus rapidement du blocage en phase S. Ceci s’accompagne d’une déficience de la phosphorylation de RPA-32 sur les sérines 29 et 33 et de SMC1 sur la sérine 966 ainsi que d’une réduction du niveau de dommages de l'ADN évalués par le test des comètes alcalines, de l’intensité du signal gamma-H2AX, des foyers RPA, Rad51 et RPA sur les sérines 4 et 8 ainsi que du niveau d'échanges de chromatides sœurs. Des essais kinase in vitro couplés à la spectrométrie de masse ont montré que Cdk5 peut phosphoryler RPA-32 sur ses sérines 23, 29, et 33. De plus, des niveaux inférieurs d’expression de Cdk5 ont été associés à une meilleure survie sans métastases chez des patientes atteintes d’un cancer du sein et à une réduction de la survie des cellules de tumeurs du sein déplétées pour Cdk5 après un traitement aux RI et en présence d’un inhibiteur de PARP. Globalement, ces résultats montrent que Cdk5 est nécessaire pour la réplication basale et l'activation du point de contrôle en phase S en réponse à un stress réplicatif, ouvrant des perspectives cliniques intéressantes pour améliorer la destruction des cellules tumorales dans certaines populations de patientes atteintes de cancer du sein grâce à des agents qui génèrent un stress réplicatif. / Cyclin dependent kinase 5 (Cdk5) is a determinant of sensitivity to PARP inhibitors and ionizing radiation (IR) and is required for the intra-S DNA damage checkpoint. It is not however directly implicated in strand break repair suggesting a role in the earlier steps of checkpoint activation. We report here that Cdk5-Depleted (Cdk5-KD) HeLa cells show higher sensitivity to IR when irradiated in S-Phase, and to chronic hydroxyurea (HU) exposure, 5-Fluorouracil and 6-Thioguanine. Cdk5-KD cells show altered basal S-Phase dynamics caused by a slower replication velocity and fewer active origins per megabase of DNA, however they show a faster recovery from an HU block. This was accompanied by impaired RPA-32 priming serine 29 and serine 33 phosphorylations and SMC1-Serine 966 phosphorylation as well as lower levels of DNA damage assessed by the alkaline Comet assay, gamma-H2AX signal intensity, RPA and Rad51 foci and RPA-32 serine 4 and serine 8 phosphorylation and levels of sister chromatid exchanges. In vitro kinase assays coupled with mass spectrometry showed that Cdk5 can phosphorylate RPA-32 on serines 23, 29, and 33. In addition lower Cdk5 levels were associated with longer metastasis free survival in breast cancer patients and lower cell survival in Cdk5 depleted breast tumor cells after treatment with IR and a PARP inhibitor. Taken together, these results show that Cdk5 is necessary for basal replication and replication stress checkpoint activation and opens up interesting clinical opportunities to enhance tumor cell killing in certain populations of breast cancer patients through agents that generate replication stress.

Les modifications post-traductionnelles des protéines de réparation de l'ADN et des facteurs chromatiniens par poly(ADP-ribose)ylation et par phosphorylation sont essentielles pour le maintien de l'intégrité de l'ADN et de la chromatine, en particulier dans la réponse cellulaire aux dommages de l'ADN induits par radiation ionisantes (RI). Parmi les protéines impliquées dans ces deux processus nous trouvons, respectivement, la poly(ADP-ribose) polymérase-1 (PARP-1) et PARP-2, et la kinase dépendante des cyclines Cdk5 : PARP-1 et PARP-2 sont impliqué dans le mécanisme de réparationdes cassures simples brin (CSBs) de l'ADN (Single Strand Break Repair : SSBR ) et la déplétion de Cdk5 a été liée à l'augmentation de la sensibilité des cellules aux inhibiteurs de PARPs. Nous avons montré, en utilisant des cellules HeLa stablement déplété pour Cdk5 ou PARP-2, que ces deux protéines sont impliquées dans les deux sous-voies du SSBR, le short- (SPR) et le long-patch repair (LPR). L'absence de Cdk5 ou PARP-2 entraîne des modifications du fonctionnement du SSBR, notamment en termes de recrutement des protéines de réparation PARP-1 et XRCC1, impliquées dans le SPR, et PCNA, protéine clé du LPR, au site du photo-dommage. PARP-2 et Cdk5 agissent aussi sur la balance du niveau des poly(ADP-ribose) car en absence de Cdk5 une hyper-activation de PARP-1 a été montrée, et en absence de PARP-2 une diminution de l'activité de la protéine poly(ADP-ribose) glycohydrolase (PARG) a été aussi observée. Cependant, malgré ces changements les deux lignées cellulaires dépourvues de Cdk5 (Cdk5KD) ou de PARP-2 (PARP-2KD) réparent de façon normale les CSBs radio-induites, mais, intéressement et contrairement aux cellules PARP-2KD, les cellules Cdk5KDsont sensibles à l'effet létal des RI. De plus nous avons montré que Cdk5, PARP-2 et PARG sont toutes les trois impliquées dans la régulation du recrutement et de dissociation du facteur chromatinien ALC1 suggérant leur implication dans la régulation de la dynamique de la chromatine en réponse aux photo-dommages de l'ADN. Ces résultats avec l'observation de la diminution du recrutement de PARP-1 dans les cellules Cdk5KD et PARP-2KD, montrent l'apparition d'un réseau complexe de phosphorylation et de poly(ADP-ribose)ylation en réponse aux RI qui implique Cdk5 , PARP-1,PARP-2 and PARG et qui est fort probablement initié par l'activité kinase de Cdk5.

O reconhecimento da flagelina é compartilhado pelo receptor transmembrânico TLR5 e citosólico NAIP5/NLRC4. Entretanto, pouco se sabe sobre os mecanismos efetores individuais induzidos a partir do reconhecimento extra e intracelular da flagelina. Aqui, nós demonstramos que macrófagos estimulados com a flagelina citosólica (FLA-BSDot) induziu a expressão de iNOS, enzima responsável pela produção do óxido nítrico (NO). A expressão de iNOS foi dependente do eixo NAIP5/NLRC4/caspase-1 e independente de IL-1β, IL-18 e MyD88, descartando a via de ativação dos TLRs. Ainda, esta via não requer a ativação do fator de transcrição IRF-1, mas envolve a ativação do NF-kB, assim como a clivagem da enzima PARP-1 (poly(ADP-ribose)polymerase-1). Por fim, avaliamos a relevância biológica desta via no controle das infecções por L. pneumophila e S. Typhimurium, dados que definem um mecanismo efetor adicional no controle de patógenos. / Recognition of flagellin is shared by transmembranic TLR5 and cytosolic NAIP5/NLRC4. However, little is known about the individual effector mechanisms induced by extra and intracellular flagellin. Here, we have demonstrated that cytosolic flagellin-stimulated macrophages (FLA-BSDot) induced iNOS expression, an enzyme responsible for the production of nitric oxide (NO). iNOS expression was dependent of the NAIP5/NLRC4/caspase-1 axis and independent of IL-1β, IL-18 and MyD88, discarding TLRs signaling pathway. Still, this pathway do not require the activation of IRF-1 transcriptional factor, but involves NF-kB activation as well as the cleavage of the enzyme, PARP-1 (poly(ADP-ribose)polymerase-1). Finally, we have evaluated the biological relevance of this pathway in the control of the infections by L. pneumophila e S. Typhimurium, which define an additional effector mechanism to the control of pathogens.

La Poly(ADP-ribosyl)ation est une modification post-traductionnelle des protéines catalysée par les poly(ADP-ribose) polymérases (PARPs), une famille de 17 membres. Nous avons débuté la caractérisation fonctionnelle d’un nouveau membre de cette famille : la Poly(ADP-Ribose) Polymérase-3 (PARP-3). Cette protéine était très peu étudiée. Le gène humain Parp3 permet l’expression de deux isoformes. Tandis que l’isoforme longue a été identifiée comme un composant centrosomal, l’isoforme courte est accumulée dans le noyau. En outre, seule l’isoforme courte est exprimée chez la souris. Pour étudier les conséquences fonctionnelles de l’absence de PARP-3 dans les cellules humaines, nous avons généré un modèle cellulaire de fibroblastes de poumons humains (MRC5) déplété en PARP-3 par la méthode de l’interférence ARN. Nos travaux ont permis d’identifier PARP-3 comme un nouvel acteur spécifique de la réponse cellulaire aux cassures double brin de l’ADN (DSB). Nous avons également entrepris une recherche de partenaires de PARP-3 par spectrométrie de masse. Nous avons identifié une interaction de PARP-3 avec la protéine NuMA, un régulateur essentiel de la division mitotique. Nos travaux ont mis en évidence l’existence d’un complexe protéique composé de PARP-3, NuMA et Tankyrase 1 (PARP-5a), impliquée dans les mécanismes mitotiques. PARP-3 a un rôle charnière dans la régulation de ce complexe qui joue un rôle fondamental dans la progression mitotique au travers de la maintenance du fuseau mitotique et de la résolution des télomères. Les rôles de PARP-3 dans les mécanismes de réparation des DSB ainsi que dans la progression mitotique en font une cible prometteuse en thérapie du cancer. / Poly(ADP-ribosyl)ation is a post-translational modification of proteins mediated by poly(ADP-ribose) polymerases (PARPs), a family of 17 members. We started the functional characterization of a new member of this family : the Poly(ADP-Ribose) Polymerase-3 (PARP-3). This protein was poorly studied. The human Parp3 gene displays two splicing variants giving rise to two proteins. Whereas the full length hPARP-3 has been identified as a core component of the centrosome throughout the cell cycle, the shorter splice variant accumulates within the nucleus. Of note, only the shorter nuclear variant is found in mice. We generated PARP-3 depletion in human lung cell line (MRC5) using RNA interference to analyse functional consequences of PARP-3 absence. We identified PARP-3 as a new specific actor of Double-Strand Breaks (DSB) repair mechanism. We also identified a new protein partner of PARP-3, NuMA, which is an essential regulator of mitotic division. These cells also showed problems in mitosis entry, in mitotic spindle formation, an increased mitosis duration and chromosomes aberrations. Performing protein interaction studies and using biochemical approaches, we highlighted a protein complex composed of PARP-3, NuMA and Tankyrase 1 (PARP-5a), involved in mitotic mechanisms. PARP-3 has a key role in the regulation of this complex. It plays essential role in mitotic progression and in mitotic spindle integrity maintenance and in telomere stability. The roles of PARP-3 in both DSB repair mechanisms and in mitotic progression indicate PARP-3 as a possible promising therapeutic target in cancer therapy.

PARP-1 has been identified as a major player in apoptotic pathways. Its excessive activation causes mitochondrial dysfunction, permeability, and AIF mitochondrion-to-nucleus translocation. It has been suggested that PARP-1 interacts indirectly with Bnip3, a mitochondrial pro-apoptotic factor. However, the mechanistic linkage is still not well understood. Our lab has shown that cytosolic/nuclear NAD+ depletion is a hallmark for PARP-1 over activation and inhibition of sirtuin activity. Specifically in my project, we think that PARP-1 induced- NAD+ depletion and sirtuin inhibition causes hyperacetylation of the α subunit of the transcription factor HIF-1 allowing increased HIF-1 binding to Bnip3 upstream promoter, and increased Bnip3 expression. Indeed, our PARP-1 Knock out neurons, MNNG and PJ34 treatment, chromatin immunoprecipitation, and HIF-1α loss of function studies strongly confirmed the necessity of HIF-1 to increase Bnip3 expression in hypoxia. Overall, our research suggests a role for HIF-1 in increasing PARP-1 dependent Bnip3 expression in hypoxic models. / May 2016