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Homologous Recombination (HR) is a major double-stranded break (DSB) DNA repair pathway. It utilizes the sister chromatid as a template, thus promoting error-free repair. The initial HR step is DNA end resection with the creation of RPA coated single-stranded DNA (ssDNA) overhangs. This is followed by RAD51 loading onto the resected DNA, triggering strand invasion, and homology search. The BRCA1 protein is fundamental for HR mediated DNA repair, and patients with germline BRCA1 mutations have a high risk of developing cancer. These BRCA1 mutant tumors are HR deficient, and as a result, sensitive to PARP inhibitors (PARPi). BRCA1 likely promotes DNA end resection by displacing 53BP1 from the DSBs and also promotes RAD51 loading by enabling the formation of the larger BRCA1-PALB2-BRCA2 complex trough its coiled-coil region. Although BRCA1 functions in both HR steps, its essential role in each step is unclear, with previous reports showing that RAD51 loading after DNA end resection occurred could be BRCA1 independent. Here, we demonstrated that full HR restoration after activation of end resection mediated by 53BP1 knockout (KO), requires the expression of a BRCA1 protein that retained the coiled-coil region and its protein interactions. We observed that although 53bp1 KO can restore the Mendelian frequencies of a Brca1 null mouse model, mice were still tumor prone, PARPi sensitive, and had low levels of RAD51 γ-irradiation-induced foci (IRIF), suggesting that HR levels were minimal. Moreover, in order to significantly increase PARPi resistance in human cancer cell lines, 53BP1 loss of function (LoF) needs to be associated with the expression of a hypomorphic BRCA1 protein that retained the PALB2 interaction. We also demonstrated that Brca1 compound heterozygosity could rescue the developmental defects observed in Brca1 mutant homozygous mice, as long as the alleles retained complementary HR-related functions. Additionally, these compound heterozygotes mice were not tumor prone and had a normal lifespan, suggesting that HR was restored. In contrast, when the allele combination did not exhibit complementary functions, the developmental defects persisted. Overall, we demonstrated that to fully function in mouse development, tumor suppression, and drug resistance, BRCA1 role is critical in both the DNA end resection and the RAD51 loading HR steps. / Biomedical Sciences

[pt] Em função da predominância das fontes hidráulicas no sistema elétrico brasileiro, há uma grande incerteza na oferta futura de energia. Para lidar com a incerteza hidrológica, a política ótima de operação do sistema elétrico brasileiro é fruto de um sofisticado modelo de otimização estocástica no qual são considerados um amplo conjunto de séries sintéticas (cenários) de Energia Natural Afluente (ENA). Tradicionalmente, as séries sintéticas de ENA têm sido geradas por modelos periódicos autorregressivos PAR(p). Recentemente, o advento da energia eólica e o crescimento da sua participação no sistema elétrico brasileiro apontam para a necessidade de métodos capazes de gerar séries sintéticas de velocidade do vento. Assim, nesta tese propõe-se uma metodologia para geração de séries sintéticas baseada no uso combinado da modelagem PAR(p) e da análise espectral singular. A metodologia proposta é geral e pode ser usada na geração de séries sintéticas da ENA e da velocidade de vento. A análise espectral singular ou Singular Spectrum Analysis (SSA) é uma metodologia recente em séries temporais. Através de SSA pode-se extrair tendências ou sazonalidades bem como suavizar a série através da remoção de componentes ruidosas. SSA vem sendo aplicado com sucesso em diversas áreas do conhecimento como em Hidrologia e Economia. A Multi-channel Singular Spectrum Analysis (MSSA) é uma extensão natural do SSA quando aplicada a múltiplas séries simultaneamente. A metodologia proposta foi aplicada às séries de ENA dos quatro subsistemas elétricos (Nordeste, Norte, Sudeste/Centro-Oeste e Sul) e comparada ao modelo PAR(p) já existente. Adicionalmente, a metodologia proposta foi aplicada na geração de séries sintéticas de velocidade do vento em duas localidades situadas no Nordeste brasileiro. Os bons resultados alcançados indicam que a metodologia proposta pode ser utilizada na geração de séries sintéticas de ENA e de energia eólica consideradas nos modelos de otimização estocástica que auxiliam o planejamento da operação energética do sistema elétrico brasileiro. / [en] Due to the predominance of hydraulic sources in the Brazilian electrical system, there is a large uncertainty in future energy supply. To deal with hydrologic uncertainty, the optimal operation policy of the Brazilian electric system is the result of a sophisticated stochastic optimization where are considered a large set of synthetic series (scenarios) of Affluent Natural Energy (ENA). Traditionally, synthetic ENA series have been generated by periodic autoregressive models PAR (p). Recently, the advent of wind energy and its growth of participation in Brazilian electrical system indicate to the need for methods to generate synthetic series of wind speed. Thus, this thesis proposes a methodology for generating synthetic series based on the combined use of PAR (p) models and the Singular Spectrum Analysis (SSA). The proposed methodology is general and can be used to generate synthetic series of ENA and wind speed. SSA is a recent methodology in time series. Through SSA it can extract trends or seasonality and smoothing by removing the series of noisy components. SSA has been successfully applied in various fields of knowledge as in Hydrology and Economics. Multi-channel Singular Spectrum Analysis (MSSA) is a natural extension of the SSA when applied to multiple series simultaneously. The proposed methodology was applied to the ENA series of four electric subsystems (Northeast, North, Southeast / Midwest and South) and compared to the PAR (p) existing model. Additionally, the proposed methodology was applied to the generation of synthetic series of wind speed at two sites located in the Brazilian Northeast. The good results achieved demonstrate that the proposed methodology can be used to generate synthetic series of ENA and wind energy considered in stochastic optimization models that assist planning the operation of the Brazilian electric energy system.

Introduction Le cancer bronchique est un problème de santé publique en étant la première cause de décès par cancer dans le monde. Il reste de mauvais pronostic avec une résistance au Cisplatine qui est inéluctable dans l’histoire naturelle de la maladie. Nous nous sommes intéressés à l’association du CDDP aux inhibiteurs de la Poly(ADP-ribose) polymérase. Les inhibiteurs pharmacologiques de PARP sont source d’optimisme en oncologie clinique en monothérapie pour des tumeurs déficientes pour une voie de réparation de l’ADN et en association aux cytotoxiques classiques.Matériel et méthodes Nous avons généré 9 clones résistants au CDDP après culture de la lignée A549 dans des faibles doses de CDDP. Deux inhibiteurs pharmacologiques de PARP, CEP8983 (CEP) et PJ34 (PJ), ainsi que des siRNA spécifiques de PARP1 sont utilisés pour l’inhibition de PARP. L’apoptose est mesurée en cytométrie de flux par l’intermédiaire du potentiel membranaire de la mitochondrie DiOC6(3) et la perméabilisation de la membrane plasmique est évaluée par l’iodide de propidium. Le test de clonogénicité permet d’évaluer la capacité des cellules à échapper à la mort et à former une colonie. L’activité métabolique des cellules est mesurée par la mesure de clivage du sel de tetrazolium WST-1. L’immunofluorescence sur cellules fixées a permis d’étudier les dommages de l’ADN (γH2AX), la voie intrinsèque de l’apoptose (l’activation de la caspase 3 et la libération du cytochrome c) et la recombinaison homologue (BRCA1, RAD51). En Western Blot nous avons mesuré l’expression et l’activité de PARP (PAR) ainsi que l’expression d’acteurs de la réparation par excision de base (BER) (XRCC1 and polymérase β). Nous avons développé une méthode de détection de PAR en immunohistochimie sur des tissus inclus en paraffine. Résultats Nous avons trouvé un effet synergique pour l’association du CDDP aux inhibiteurs de PARP in vitro. De façon inattendue nous avons observé que les clones résistants au CDDP développent une addiction à PARP et sont spécifiquement tués par l’inhibition de PARP contrairement à la lignée parentale. Ces clones exhibent une hyperexpression et une hyperactivité de PARP. La réponse aux inhibiteurs de PARP corrèle plus précisément avec l’activation plutôt qu’avec l’expression de PARP, pointant que PAR est un biomarqueur plus précis que PARP. Nous avons observé que l’hyperactivation de PARP accompagne une résistance induite au CDDP et prédispose à une sensibilité aux inhibiteurs de PARP dans d’autres lignées de cancer bronchique (H460 et H1650), de mésothéliome (P31), de cancer de l’ovaire (TOV112D) et de col (HeLa). Dans des expériences in vivo nous avons noté que dans les xénogreffes obtenues à partir de clones résistants au CDDP, l’expression de PAR est stablement retrouvée en immunohistochimie. Ces tumeurs répondaient à l’inhibition de PARP par le PJ en diminuant l’expression de PAR. Les clones résistants au CDDP sensibilisés aux I PARP ont une recombinaison homologue conservée, cependant ont un déficit dans les étapes terminales du BER.Conclusion Nous avons identifié un effet synergique pour l’association des inhibiteurs de PARP au CDDP de des lignées de cancer bronchique. Nous avons observé une dépendance à PARP dans des lignées de cancer bronchique résistantes au CDDP et déficientes pour l’élongation du BER. Nous postulant que PAR est un biomarqueur spécifique de la réponse aux inhibiteurs de PARP. / Introduction Driven by the facts that non small cell lung cancer (NSCLC) is the leading cause of cancer-related morbidity and mortality worldwide and that NSCLC patients often develop resistance against Cisplatin (CDDP)-based therapies, we addressed the question of the combination therapy of CDDP with poly(ADP-ribose) polymerases (PARP) inhibitors. Inhibitors of PARP have raised great expectations for the treatment of a variety of cancers, either as monotherapeutic agent against DNA repair-deficient tumours or combined to DNA-damaging compounds.Material and methods We generated nine CDDP-resistant clones by prolonged exposure to low dose CDDP of the A549 NSCLC parental cell line. Two distinct PARP inhibitors, CEP8983 (CEP) and PJ34 (PJ) as well as PARP1 knockdown with small interfering RNAs (siRNAs) were used for PARP inhibition. Apoptosis was measured by the simultaneous assessment for the loss of the mitochondrial transmembrane potential (m) and the breakdown of the plasma membrane using the m-sensitive fluorochrome DiOC6(3) and the vital dye propidium iodide, respectively. Moreover clonogenic survival was assessed. In vitro assessments of the enzymatic activity of cells were based on the reduction of the colorless tetrazolium salt. Immunofluorescence microscopy determinations were performed with antibodies specific for DNA damage (γH2AX), intrinsic apoptosis (cleaved Caspase-3 and cytochrome c), and homologous recombination (RAD51 and BRCA1). Immunoblotting was assed for PARP1 expression and activity (PAR) and base excision repair (BER) effectors (XRCC1 and polymerase β). We developed an immunohistochemical staining method that specifically detects PAR on paraffin-embedded cell pellets and tissue sections.Results We found that PARP inhibitors and PARP1 siRNAs synergized with CDDP in the killing of NSCLC cells in vitro. Unexpectedly, CDDP-resistant NSCLC cell clones developed addiction to PARP hyperactivation, thereby becoming susceptible to apoptosis induction by PARP inhibition. We showed that these cisplatin-resistant clones, exhibited high PARP protein levels and increased PARP activity, leading to an increased poly-ADP ribosylation of cellular proteins, as compared to their parental, cisplatin-sensitive counterparts. These cisplatin-resistant cells become susceptible to cell death as induced by PARP inhibition, correlating with the hyperactivity of PARP (elevated PAR levels) more accuratly than with the overexpression of PARP. Suggesting that PAR levels may constitute a more accurate biomarker than PARP to predict the sensitivity of cells to PARP inhibition. We expanded the observation that cisplatin resistance causes PARP upregulation and hyperactivation and subsequent sensitization to PARP inhibition to additional five human cancer cell lines including two NSCLC (H1650 and H460), one mesothelioma (P31), one ovarian (TOV112D) and one cervical cancer (HeLa) cell line. To get further insight into this issue, we generated in vivo experiments. Tumors derived from CDDP-resistant cells were characterized by elevated levels of PAR suggesting that PAR levels are preserved during tumor formation. Those PAR-overexpressing tumors responded to the administration of PJ in vivo with a consistent reduction in PAR immunoreactivity. CDDP resistant clones that are specifically killed by PARP inhibitors assessed efficient homologous recombination repair however deficient BER elongation.Conclusion We showed a beneficial effect for the association therapy of PARP inhibitors with CDDP in several NSCLC cell lines. We have identified an addiction to PARP in CDDP resistant cell lines with deficient BER elongation. We postulate that PAR is a specific predictive biomarker for the response to PARP inhibitors.

Prostatacancer är den sjätte mest förekommande cancertypen i världen, och den tredje vanligaste cancertypen bland män. De olika typer av behandlingar som finns idag botar oftast inte sjukdomen. Det är därför viktigt att utveckla bättre behandlingsmetoder. Det är sedan tidigare känt att mangan kan orsaka apoptos i olika celltyper. Det ger en möjlighet att använda mangan för att hämma cancer och det är därför viktigt att veta vilka apoptotiska markörer som är involverade. Syftet med projektet var att undersöka om de sker en ökning av de apoptotiska markörerna kluven Kaspas-3 och kluven PARP efter manganbehandling av prostatacancerceller. Därefter kunna avgöra om manganbehandlingen har orsakat celldöd genom att inducera apoptos. Under projektet odlades prostatacancerceller (PC3) som sedan behandlades med 200 µM mangan under 6, 24 och 48 timmar. Därefter mättes mängden av proteinerna kluven Kaspas-3 och kluven PARP med hjälp av ett sandwich-ELISA kit. En tydlig stegvis ökning av apoptosmarkörerna med inkuberingstid hade förväntats. Det förväntade resultatet erhölls inte, för kluven Kaspase-3 ledde manganbehandlingen t.o.m. till en sänkning av koncentrationen. Det kan ha uppstått problem vid analysen som t.ex dålig lysering av cellerna eller ojämn tillväxt av dem. Det behövs fler studier för att utreda detta och för att undersöka andar potentiella apoptosmarkörer. / Prostate cancer is the sixth most common cancer type in the world, and the third most common cancer type among men. The different types of treatments that are available today do not usually cure the disease. It is therefore important to develop better treatment methods. It has previously been stated that manganese can cause apoptosis in different cell types. It provides an opportunity to use manganese to inhibit cancer and it is therefore important to know which apoptotic markers that are involved. The purpose of the project was to investigate whether an increase in the apoptotic markers cleaved Kaspas-3 and cleaved PARP after manganese treatment of prostate cancer cells. Thereafter, it can determine whether manganese treatment has caused cell death by inducing apoptosis. During the project prostate cancer cells (PC3-cells) were cultivated, then treated with 200 µM manganese for 6, 24 and 48 hours. The amount of the proteins cleaved Kaspas-3 and cleaved PARP was measured by using a sandwich ELISA kit. A clear gradual increase of apoptotic markers with incubation time was expected. The expected result was not obtained, for cleaved Kaspase-3 manganese treatment even decreased the concentrations. There may have been problems with the performance of the analysis such as poor lysis of the cells or uneven growth of the cells. More studies are required to investigate this and other potential apoptotic markers.

Le seul traitement actuellement disponible pour les accidents vasculaires cérébraux d’origine ischémique est la thrombolyse par l’activateur tissulaire du plasminogène recombinant (rt-PA). Cependant, l’efficacité du rt-PA est souvent partielle ou absente, et des phénomènes de réocclusion du vaisseau peuvent être observés. Par ailleurs, l’administration de rt-PA est associée à un risque hémorragique. Il apparaît donc indispensable de rechercher les mécanismes à l’origine de la toxicité vasculaire du rt-PA, afin de pouvoir développer des stratégies capables de protéger le lit vasculaire. Parmi ces stratégies, notre équipe a montré dans des modèles expérimentaux que l’inhibition d’une enzyme nucléaire, la poly(ADP-ribose) polymérase ou PARP, permet de protéger la barrière hémato-encéphalique, de réduire les hémorragies et d’améliorer la reperfusion cérébrale suite à l’administration post-ischémique de rt-PA. Dans ce contexte, mon travail a consisté à étudier les mécanismes impliqués dans les altérations vasculaires associées à l’administration de rt-PA à la suite de l’ischémie. Mes travaux de recherche ont comporté un volet in vivo et un volet in vitro. Les études réalisées in vivo ont été menées dans un modèle murin d’ischémie cérébrale thrombo-embolique. Nos résultats indiquent que ni l’ischémie, ni le rt-PA, ni l’association au rt-PA d’un puissant inhibiteur de PARP, le PJ34, ne modifient à 24 heures la présence de dépôts de fibrine, marqueur d’hypoperfusion et de réocclusion. Nous nous sommes ensuite intéressés à deux marqueurs endothéliaux d’inflammation : VCAM-1 et ICAM-1, et avons montré que leur expression, qui augmente 24 heures après l’ischémie, n’est pas modifiée par le rt-PA. Enfin, l’association du PJ34 au rt-PA réduit significativement l’expression post-ischémique de VCAM-1, ce qui suggère le rôle de la PARP dans l’expression de cette molécule d’adhésion. La seconde partie de mon travail a été réalisée in vitro sur une lignée de cellules endothéliales cérébrales murines (bEnd.3). Le rt-PA est à l’origine de changements caractéristiques au niveau de l’organisation et de la morphologie de ces cellules. Ces changements ne sont pourtant associés ni à une dégradation de l’expression des molécules de jonctions inter-endothéliales (occludine, VE-cadhérine), ni à une augmentation de l’expression des marqueurs endothéliaux pro-inflammatoires (VCAM-1, ICAM-1). Nous nous sommes également intéressés à d’autres marqueurs de dysfonction endothéliale, les microparticules endothéliales (MPE). Nos résultats montrent que le rt-PA est à l’origine d’une augmentation importante de la libération des MPE. L’utilisation d’un inhibiteur de la protéine p38, le SB203580, et d’un inhibiteur de PARP, le PJ34, permet de réduire cette augmentation, ce qui suggère que p38 et la PARP pourraient être impliquées dans la production de MPE induite par le rt-PA. En conclusion, l’ensemble de ce travail contribue à préciser les effets vasculaires du rt-PA. Parmi ces effets, la mise en évidence de la production de MPE, via la PARP, est particulièrement novatrice. / Thrombolysis with recombinant tissue plasminogen activator (rt-PA) is currently the only approved pharmacological strategy for acute ischemic stroke. However, the efficacy of rt-PA is rarely complete, and arterial reocclusion can be observed. Furthermore, administration of rt-PA increases the risk of hemorrhagic transformations. Therefore, it is essential to seek mechanisms underlying the vascular toxicity of rt-PA in order to develop strategies protecting the vascular bed. Among these strategies, our laboratory has previously shown that inhibition of poly (ADP-ribose) polymerase (PARP), a nuclear enzyme, protects the blood-brain barrier, reduces hemorrhagic transformations and improves cerebral reperfusion following the post-ischemic administration of rt-PA. In this context, the aim of the present work was to establish the post-ischemic mechanisms of rt-PA-induced vascular alterations. The research was divided into (1) in vivo experiments and (2) in vitro studies to examine the effect of rt-PA on the endothelium. The in vivo studies were performed in a mouse model of thrombo-embolic stroke induced by thrombin injection in the middle cerebral artery. Our results showed that neither ischemia, nor rt-PA, nor the association to rt-PA of the potent inhibitor of PARP PJ34 alter cerebral fibrin deposits, a marker of hypoperfusion and reocclusion, at 24 hours after ischemia. We then evaluated the expression of two endothelial markers of inflammation : VCAM-1 (vascular cell adhesion molecule-1) and ICAM-1 (intercellular adhesion molecule-1). Our results showed that their expressions increase 24 hours after ischemia and are not modified by rt-PA. Finally, the association of PJ34 to rt-PA significantly reduced the post-ischemic expression of VCAM-1, suggesting a role for PARP in the expression of this adhesion molecule. The second part of my work was carried out in vitro in cultures of mouse brain-derived endothelial cells bEnd.3. In the presence of rt-PA, the organization and the morphology of the endothelial cells radically changed. However, these changes were associated neither to a degradation of endothelial junction proteins (occludin, VE-cadherin (vascular endothelial-cadherin)), nor to an increase in the expression of pro-inflammatory endothelial markers (VCAM-1, ICAM-1). We were also interested in a recently identified marker of endothelial dysfunction : endothelial microparticles (EMP). Our results showed that rt-PA induces a significant increase in the EMP released by bEnd.3 cells. The use of a p38 inhibitor, SB203580, and the PARP inhibitor, PJ34, reduced this increase, suggesting that p38 and PARP could be involved in the EMP production induced by rt-PA. In conclusion, this work helps to clarify the vascular effects of rt-PA. Among these effects, the highlight of EMP production, through PARP pathway, is particularly original.