Os papilomavírus humanos são vírus de DNA que infectam epitélios em regiões anatômicas específicas. Alguns tipos de HPV, coletivamente denominados de alto risco oncogênico, têm associação etiológica com o câncer do colo do útero. Estes vírus expressam dois oncogenes, E6 e E7, que alteram o ciclo celular e o programa de diferenciação das células. Isto promove o acúmulo de defeitos mitóticos e instabilidade genômica, contribuindo à transformação maligna. Alterações nos sistemas de reparo de dano ao DNA associadas à presença de HPV têm sido descritas em diferentes modelos experimentais, no entanto, não tem sido analisadas de maneira sistemática. No presente estudo, avaliamos a expressão de 135 genes envolvidos nas vias de reparo de dano ao DNA em queratinócitos primários humanos e em linhagens derivadas de carcinomas do colo do útero positivas e negativas para HPV. Nossos resultados indicam a presença de alterações importantes na expressão de genes envolvidos nas vias de reparo de dano ao DNA em linhagens derivadas de tumores do colo do útero. / Human papillomaviruses are DNA viruses that infect epithelia in specific anatomical regions. Some HPV types, collectively known as high-risk types are etiologically associated with cervical cancer. These viruses express two oncogenes E6 and E7 that alter the cell cycle and cell differentiation. Besides, they promote genomic instability and the accumulation of mitotic defects contributing to malignant transformation. Alterations in the DNA damage repair systems associated with HPV presence have been described in various experimental model systems. However, they have not been systematically analyzed. In this study, we evaluated the expression of 135 genes involved in the DNA damage repair pathways in primary human keratinocytes and cervical cancer derived cell lines. Our results show the presence of important alterations in the expression of DNA damage repair genes in cervical cancer derived cell lines.

The error free repair of DNA double strand breaks through the homologous recombinational repair pathway is essential for organisms of all types to sustain life. A detailed structural and mechanistic understanding of this pathway has been the target of intense study since the identification of bacterial recA, the gene whose product is responsible for the catalysis of DNA strand exchange, in 1965. The work presented here began with defining residues that are important for the assembly and stability of the RecA filament, and progressed to the identification of residues critical for the transfer of ATP-mediated allosteric information between subunits in the protein's helical filament structure. My work then evolved to investigate similar mechanistic details concerning the role of ATP in the human RecA homolog, Rad51. Results from non-conservative mutagenesis studies of the N-terminal region of one subunit and the corresponding interacting surface on the neighboring subunit within the RecA protein, led to the identification of residues critical for the formation of the inactive RecA filament but not the active nucleoprotein filament. Through the use of specifically engineered cysteine substitutions we observed an ATP-induced change in the efficiency of cross subunit disulfide bond formation and concluded that the position of residues in this region as defined by the current crystal structure may not accurately reflect the active form of the protein. These ATP induced changes in positioning led to the further investigation of the allosteric mechanism resulting in the identification of residue Phe217 as the key mediator for ATP-induced information transfer from one subunit to the next. In transitioning to investigate homologous mechanisms in the human pathway I designed a system whereby we can now analyze mutant human proteins in human cells. This was accomplished through the use of RNA interference, fluorescent transgenes, confocal microscopy and measurements of DNA repair. In the process of establishing the system, I made the first reported observation of the cellular localization of one of the Rad51 paralogs, Xrcc3, before and after DNA damage. In addition we found that a damage induced reorganization of the protein does not require the presence of Rad51 and the localization to DNA breaks occurs within 10 minutes. In efforts to characterize the role of ATP in human Rad51 mediated homologous repair of double strand breaks we analyzed two mutations in Rad51 specifically affecting ATP hydrolysis, K133A and K133R. Data presented here suggests that, in the case of human cells, ATP hydrolysis and therefore binding, by Rad51 is essential for successful repair of induced damage.

No description available.

O melanoma cutâneo maligno é uma lesão neoplásica originada nos melanócitos epidérmicos, sendo altamente invasiva e agressiva, com elevada taxa de mortalidade, cuja incidência vem aumentando nos últimos anos. O tratamento do melanoma é cirúrgico e os pacientes com metástase podem receber quimioterapia com cisplatina que ao formarem adutos com o DNA alteram o processo de replicação da célula cancerosa. Sugere-se que os sistemas de reparo do DNA tenham um papel importante na etiologia do melanoma (reparo deficiente) e no tratamento do mesmo (eficiente eliminação dos adutos). A identificação prévia da resposta dos pacientes com melanoma ao tratamento com cisplatina pode ser um indicador biológico importante na clínica oncológica. O presente trabalho teve como objetivo, a partir de linfócitos de sangue periférico de pacientes com melanoma e de controles, avaliar o dano no DNA antes e após a adição, in vitro, de cisplatina (10?M, 100?M e 250?M), além de estimar a capacidade de reparo do DNA, após a retirada da droga (1h, 2,5h e 5h). Foram utilizados os testes do micronúcleo (MN - dano basal) e do Cometa (dano basal, ação da cisplatina e reparo do DNA). A análise citogenética foi possível em 20 pacientes com melanoma (10 homens e 10 mulheres, média de 50,6 ± 5,9 anos) e 19 controles (9 homens e 10 mulheres, média de 49,9 ± 5,5 anos) que também responderam a um questionário sobre hábitos e tipos de exposição a fatores de risco ao melanoma. A frequência do dano basal pelo teste do MN e do Cometa em linfócitos de pacientes (MN = 1,2 ± 1,2 e Cometa = 59,3 ± 62,5) foi praticamente o dobro da observada nos controles (MN = 0,6 ± 1,0 e Cometa = 35,3 ± 18,6) embora a diferença entre os grupos, em ambos os testes, não tenha sido considerada estatisticamente significante (p=0,23 e p=0,85, respectivamente). O tratamento in vitro com cisplatina, em comparação com o dano basal, aumentou a frequência de Cometas nas três concentrações estudadas (10?M, 100?M e 250?M) tanto para os pacientes (65,50 ± 50,06, 72,74 ± 50,89 e 77,26 ± 44,16) quanto para os controles (66,53 ± 49,85, 66,53 ± 26,33 e 81,74 ± 43,12) diferença esta considerada significante somente para o grupo controle, nas três concentrações avaliadas (p=0,0175, p=0,0002, e p=0,0002, respectivamente). Quanto aos diferentes tempos de reparo (1h, 2,5h e 5h), após a retirada de cisplatina nas diferentes concentrações estudadas, verificou-se aumento na frequência média de Cometas tanto para os pacientes com melanoma (93,88 ± 33,7, 101,75 ± 35,7 e 99,31 ± 32,30) quanto para os controles (92,45 ± 38,4, 100,82± 38,8 e 100,81± 31,7), diferença que foi estatisticamente significante quando comparada ao dano basal observado nos pacientes (p<0,001) e nos controles (p<0,001). Resultados semelhantes foram observados quando comparados em conjunto os escores dos tempos de reparo com o escore obtido após tratamento com cisplatina nos pacientes (71,09 ± 48,2; p<=0,005) e nos controles (71,59 ± 40,5; p<=0,005). Os resultados obtidos parecem indicar um padrão de resposta semelhante em relação à cisplatina e ao reparo do DNA nos dois grupos de indivíduos avaliados. O período de incubação das células, após a retirada da cisplatina, bem como o número de indivíduos avaliados podem ter influenciado nos resultados obtidos. Por outro lado, a resposta observada nos linfócitos in vitro, pode não ser representativa do efeito in vivo da célula tumoral. Entretanto, a identificação de marcadores de resposta a tratamentos com quimioterápicos, a partir de linfócitos de sangue periférico pode ser uma estratégia de pesquisa importante na prática clínica, inclusive para o melanoma. / Cutaneous melanoma is a malignant tumor originated from epidermal melanocytes, highly invasive and aggressive, with high mortality, and incidence that has been increasing over the years. The treatment for melanoma is surgery and patients with metastasis may receive chemotherapy with cisplatin, that results in DNA adducts that alters the replication process in cancer cells. It is suggested that the DNA repair systems have an important role in the etiology of melanoma (risk due to deficient repair) and treatment efficiency (removal of DNA adducts can decrease the treatment results). The prior identification of the response of melanoma patients to treatment with cisplatin may be an important biological marker in clinical oncology. The aim of this study was to assess, in peripheral blood lymphocytes from melanoma patients and controls, the DNA damage before and after the addition of cisplatin (10?M, 100?M and 250?M), in vitro, and estimate the capacity of DNA repair after drug removal (1h, 2.5h and 5h). The micronucleus test (MN - basal DNA damage) and the Comet assay (basal DNA damage, action of cisplatin and DNA repair) were used for the evaluation. Cytogenetic analysis was performed in 20 melanoma patients (10 men and 10 women, average age 50.6 ± 5.9 years old) and 19 controls (9 men and 10 women, average age 49.9 ± 5.5 years old) who also answered a questionnaire on habits and types of exposure to risk factors for melanoma. The frequency of basal DNA damage by the MN test and the Comet assay in lymphocytes from patients (MN = 1.2 ± 1.2 and Comet = 59.3 ± 62.5) was nearly twice the observed in controls (MN = 0, 6 ± 1.0 and Comet = 35.3 ± 18.6), although the difference between the groups in both tests was not considered statistically significant (p = 0.23 and p = 0.85, respectively). The in vitro treatment with cisplatin, compared with the basal DNA damage, increased the frequency of Comets in the three studied concentrations (10?M, 100?M and 250?M) for patients (65.50 ± 50.06, 72.74 ± 50.89 and 77.26 ± 44.16) and for the controls (66.53 ± 49.85, 66.53 ± 26.33 and 81.74 ± 43.12) and the difference was statistically significant only for the control group, for all cisplatin concentrations (p = 0.0175, p = 0.0002 and p = 0.0002, respectively). Considering the different repair times (1h, 2.5h and 5h), after removal of cisplatin at different concentrations, there was an increase in the mean frequency of Comets for both melanoma patients (93.88 ± 33.7, 101.75 ± 35.7 and 99.31 ± 32.30) and for the controls (92.45 ± 38.4, 100.82 ± 38.8 and 100.81 ± 31.7), and the difference was statistically significant when the repair Comet score was compared to the basal DNA damage observed in patients (p <0.001) and controls (p <0.001). Similar results were observed when the Comet scores of repair times were compared to the Comet scores obtained after treatment with cisplatin in patients (71.09 ± 48.2, p <= 0.005) and controls (71.59 ± 40.5, p <= 0.005). The results seem to indicate a similar pattern of response to cisplatin and DNA repair in both groups of subjects evaluated. The period of incubation of the cells after cisplatin removal and the number of individuals studied may have influenced the results. The lymphocytes\' response, in vitro, to cisplatin may not be representative of the in vivo effect of tumor cell. However, the identification of markers of response to treatment with chemotherapy from peripheral blood lymphocytes may be an important research strategy in clinical practice, including melanoma.

In order to evaluate the suitability of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) as a potential drug target for an anti-parasite therapy, we are studying its role in the bloodstream form of Trypanosoma brucei brucei, the eukaryotic parasite that causes African Sleeping Sickness. Eukaryotic TDP1 removes covalently trapped topoisomerase IB and other adducts from the 3’ end of the DNA at DNA strand breaks. Covalent topoisomerase IB stalling is caused by endogenous DNA damage and by anti-cancer drugs such as camptothecin (CPT). A potential approach could be to use TDP1 inhibitors synergistically with CPT in a combined anti-parasite therapy. T. brucei TDP1 knock out cells are hypersensitive to CPT and accumulate in the late S phase of the cell cycle upon treatment with the drug. The CPT hypersensitivity of the TDP1-/- cells can be fully rescued through ectopic expression of wild type TDP1. The catalytic activity of TDP1 is required for complementation of the CPT sensitivity since overexpression of a catalytically inactive mutant form of TDP1 further sensitises TDP1-/- cells to CPT. In this context, expression of the mutant H358N, which shows reduced activity, also increases sensitivity of TDP1-/- cells to the drug. Surprisingly, expressing TDP1 carrying an analogous mutation to the one that causes SCAN1, a human neurodegenerative disease, does not sensitise TDP1-/- cells further. With this unique set of mutant TDP1 proteins in a TDP1-/- background we hope to answer questions concerning TDP1 function that have so far been elusive.

Une meilleure connaissance des déterminants viraux et cellulaires impliqués dans la régulation de l’expression lentivirale est essentielle pour (i) maitriser l’expression d’un transgène dans le cadre d’un transfert de gène et (ii) mieux comprendre l’absence/la perte de l’expression du virus de l’immunodéficience humaine de type 1 (VIH-1) observé en cas de latence virale après infection. Dans ce contexte, les facteurs cellulaires impliqués dans la reconnaissance et la réparation des cassures de l'ADN, activés dès les étapes précoces du cycle viral, pourraient participer au contrôle de l’expression rétrovirale. Dans la première partie de cette étude, nous avons généré une collection de vecteurs lentiviraux codant le transgène green fluorescent protein (gfp) avec des design variés : promoteur du VIH-1 [long terminal repeat (LTRs)] ou d’origine hétérologue [e.g., promoteur viral CMV (cytomegalovirus), ou humain PGK (phosphoglycerate kinase)], intégrase native ou mutée, LTRs natifs ou self inactivating (SIN). En particulier, nous avons caractérisé l’impact de l’insertion de différentes séquences hétérologues au sein des SIN-LTRs sur l’expression du transgène gfp au cours du temps dans un contexte compétent ou déficient pour l’intégration. Nous avons mis en évidence un phénomène de modulation du niveau d’expression du transgène (d’un facteur 0,3 à 1,8; comparé aux vecteurs sans insertion) qui est dépendant de la séquence insérée et de son orientation. L’expression transgénique résulterait donc d’une balance coûts/bénéfices associés à l’insertion d’éléments aux extrémités des vecteurs qui pourrait déterminer le niveau d’expression du transgène à partir de vecteurs modifiés. Dans la seconde partie, nous avons réalisé une analyse systématique et comparative de l’expression lentivirale au sein des cellules humaines de carcinome de côlon HCT 116 déplétées pour le complexe Ku. Ce complexe, qui est essentiel à la survie chez l’homme et est impliqué dans les processus de réparation de l’ADN, a été identifié comme une cible anti-VIH potentielle. Nous avons mis en évidence que la déplétion en Ku induit une diminution de l’expression précoce du VIH-1 de façon spécifique du LTR et indépendante de Tat. Même si l’action de Ku nécessite l’intégration du VIH-1, sa déplétion ne modifie pas l’efficacité d’intégration virale mais agit plutôt au niveau transcriptionnel. Da façon importante, la réactivation de l’expression du transgène après traitement par l’activateur de NF-κB (Nuclear Factor κB), le TNFα (tumor necrosis factor α) ou un inhibiteur des déacétylases d’histones, la trichostatine A est favorisée par la déplétion en Ku. A l’inverse, en présence d’un niveau normal en Ku, les cellules exprimant le VIH-1 seraient contre-sélectionnées dans le temps. Ainsi, la déplétion en Ku pourrait promouvoir l’établissement d’un état (reactivable) de latence transcriptionelle associé à une moindre contre-sélection des cellules transduites. Les résultats issus de ce travail de thèse démontrent que l’expression lentivirale varie en fonction de nombreux paramètres, dont (i) le design des vecteurs, (ii) le type cellulaire transduit et son fond génétique, et (iii) le temps écoulé depuis la transduction, reflétant ainsi des interactions différentielles entre le vecteur et son hôte. / An improved knowledge of the viral and cellular determinants implicated in the regulation of the lentiviral gene expression is crucial (i) for a better control of transgene expression in strategies designed for gene transfer and (ii) for uncovering the mechanisms of viral latency observed after infection with the human immunodeficiency virus type 1 (HIV-1) and accounting for the absence/loss of HIV-1 expression. Cellular factors involved in the mechanism of detecting/repairing DNA lesions are largely activated during the initial steps of viral cycle and, thus, may participate in the control of lentiviral expression. In the first part of this study, we generated a set of lentiviral vectors encoding for the transgene green fluorescent protein (gfp) with various design: the original promoter [long terminal repeat (LTRs)] or of heterologuous origins (e.g., the viral cytomegalovirus, CMV or the human phosphoglycerate kinase, PGK), wild-type or mutated integrase and wild-type or self inactivating (SIN) LTRs. By taking advantage of these constructs, we characterized the impact of the insertion of distinct heterologuous sequences within SIN-LTRs on the expression of gfp over the time in conditions of proficiency or deficiency for the integration. We put in evidence a phenomenon of modulation of the level of the transgene expression due to the insertion (by a factor of 0.3 to 1.8, as compared to vectors without insert) that was dependant from the nature and/or the orientation of the insert. We speculate that a balance between the costs and the benefits associated to insertion at the extremities of lentiviral vectors may dictates the level expression of transgene from this engineered construct.In the second part, we performed a systematic and comparative analysis of the lentiviral expression on human HCT 116 colon carcinoma cells depleted from the complex Ku. This complex, which is essential for the survival in humans and has a described role in DNA repair process, has been previously identified as a potential target against HIV-1. Here, we showed that Ku depletion induced a decrease of the HIV-1 early expression in a fashion that was specific for LTR and independent from Tat. Although Ku action needed HIV-1 integration to host genome, its depletion did not modify the viral integration efficiency but rather acted at transcriptional level. Importantly, the reactivation of transgene expression by administering either the NF-κB (Nuclear Factor κB) activator, tumor necrosis factor α (TNFα) or the histone deacetylase inhibitor named trichostatin A was favored in a condition of Ku depletion. On the contrary, in presence of normal level of Ku, cells expressing HIV-1 displayed a high level of counter-selection over the time. Thus, our observations pleased to favor the hypothesis that Ku depletion promotes the establishment of a state of (reactivable) transcriptional latency associated to a lesser counter-selection of transduced cells. Altogether, the results obtained during this thesis demonstrate that lentiviral expression vary depending on (i) specific vector design, (ii) the transduced cell line and its genetic backbone, and (iii) the time elapse from transduction, as a consequence of modified interactions between the vector and its host.

L’édition du génome repose sur la création de cassures double brin à un endroit précis du génome à l’aide de nucléases artificielles (ZFN, TALEN, CRISPR/Cas9) et sur les différents systèmes de réparation que la cellule va mettre en place pour réparer ces dommages. Les deux systèmes de réparation principaux sont le NHEJ (Non Homologous End Joining) et la RH (Recombinaison Homologue). Le NHEJ consiste en une ligation directe des extrémités de la coupure pouvant induire de petites insertions ou délétions avant la ligation. Ces mutations, si elles sont introduites dans un exon, vont modifier le cadre de lecture et pouvoir inactiver le gène cible (Knock Out). La RH permet la réparation de la cassure en recopiant les informations présentes sur la chromatide soeur. Si un ADN exogène comportant des homologies avec la séquence à réparer est inséré avec les nucléases artificielles, la cellule peut le prendre comme matrice de réparation, il est ainsi possible d’insérer n’importe quelle mutation ou transgène de manière précise (Knock In). Ici, différentes stratégies ont été développées pour optimiser ces approches d’édition du génome. Le couplage du domaine Nter de la protéine CtIP à la nucléase Cas9 permet d’augmenter le taux d’insertion par homologie d’un transgène au site de coupure. Le couplage de l’exonucléase Trex2 à la nucléase Cas9 nickase permet quant à lui d’augmenter le taux de mutation après coupure. Ces nouvelles approches peuvent être largement utilisées et permettent de faciliter l’édition du génome. / Genome editing relies on the ability of artificial nucleases (TALEN or CRISPR/Cas9 system) to induce double strand break into a precise and unique sequence in a whole genome and on the different DNA repair system. The two major DNA repair systems are NHEJ (Non Homologous End Joining) and HR (Homologous Recombination). NHEJ consists on DNA end direct ligation. This system can lead to deletion or insertion at the cut site. These mutations, when induced in an exon, can induce reading frame change and gene inactivation (Knock out). HR consists on the use of sister chromatid to copy lost information in order to complete the double strand break. If an exogenous DNA with homologies with the targeted DNA is inserted with artificial nucleases, it can be used as a template and can permit to introduce any transgene at the cut site (Knock In). In this work, different strategies were used to optimize genome editing. By fusing Nter part of CtIP to Cas9, the KI rate of an exogenous DNA is increased and by fusing Trex2 exonuclease to Cas9, the mutation rate induced is also increased. These two approaches can be widely used to improve genome editing strategies.

Le génome humain est constamment la cible d'agents qui endommagent l'ADN. Ces dommages sont multiples et variés tels que les cassures simple et double brin (DSB). Les DSBs sont des lésions très toxiques dont l'origine peut être multiple. Les cellules de mammifères réparent les DSBs en utilisant deux mécanismes principaux, la recombinaison homologue (RH) qui est dépendante du cycle cellulaire et utilise la chromatide sœur comme matrice de réparation et la jonction des extrémités non homologues (NHEJ) qui est indépendante du cycle cellulaire et consiste en la ligation des extrémités d'ADN endommagées. Cette réparation a lieu dans un contexte chromatinien qui nécessite un dynamisme pour rendre accessible les sites lésés aux différentes machineries de réparation. Lors de mes travaux, j'ai étudié le remodeleur de la chromatine p400 ainsi que le variant d'histone H2A.Z qui sont deux protéines impliquées dans la dynamique de la chromatine, afin de comprendre leur rôle dans les mécanismes de réparation des DSBs et la stabilité du génome. p400, une ATPase de la famille SWI2/SNF2 participe à l'incorporation du variant d'histone H2A.Z dans la chromatine. Au cours de ma thèse, j'ai montré que la déplétion par siRNA du variant d'histone H2A.Z, dans la lignée d'ostéosarcome humain (U2OS) et dans des fibroblastes humains immortalisées, n'a pas d'effets sur la réparation des DSBs. Ces résultats sont corrélés avec une absence de recrutement de H2A.Z au niveau des cassures après étude par micro irradiation laser ou par immunoprécipitation de chromatine. Cependant, la déplétion de H2A.Z affecte la prolifération cellulaire en influençant l'efficacité de clonage et le cycle cellulaire. L'autre partie de mes travaux a mis en évidence que l'ATPase p400 est un frein à l'utilisation de la voie alternative de jonction des extrémités (alt-EJ) qui est un processus de réparation des DSBs très mutagène. L'augmentation des événements du NHEJ-Alternatif et la génération d'instabilité génétique observés lors de la déplétion de p400 par siRNA semblent tributaires de la résection des DSBs par CtIP. Ces résultats indiquent que p400 joue un rôle post-résection dans les étapes plus tardives de la RH. De plus, la déplétion de p400 conduit au recrutement de la polyADP ribose polymérase (PARP) et de l'ADN ligase 3 à la DSB, ce qui provoque la mort sélective de ces cellules lors d'un traitement par des inhibiteurs de PARP. Ces résultats montrent que P400 agit comme un frein pour empêcher l'utilisation du NHEJ-Alternatif et donc l'instabilité génétique. / The human genome is constantly targeted by DNA damaging agents. These damages are many and varied, such as single and double strand breaks (DSBs). The DSB are highly toxic lesions whose origin can be multiple. Mammalian cells mainly use two DNA repair pathways to repair DSB, homologous recombination (RH), which is dependent on the presence of the intact homologous copy (the sister chromatid) and on the cell cycle stage and the non-homologous end joining (NHEJ) pathway, which is cell cycle independent and performs direct ligation of the two DNA ends. The repair of DNA damage takes place in a chromatin context that needs to be remodeled to give access to damaged sites. During my work, I studied the chromatin remodeler p400 and the histone variant H2A.Z both involved in chromatin remodeling, to understand their role in DSB repair and genome stability. p400, an ATPase of the SWI2/SNF2 family is involved in the incorporation of H2A.Z in chromatin. I have shown that H2A.Z depletion in the osteosarcoma cell line U2OS and in immortalized human fibroblasts did not alter DSB repair. These results are correlated with the lack of H2A.Z recruitment at DSB observed after local laser irradiation or Chromatin Immunoprecipitation. However, H2A.Z depletion affects cell proliferation and the cell cycle distribution. In addition, I have shown that the chromatin remodeler p400 is a brake to the use of alternative End Joining (alt-EJ) which is a highly mutagenic repair process. The increase in alt-EJ events observed in p400-depleted cells is dependent on CtIP- mediated resection of DNA ends. Moreover, p400 depletion leads to the recruitment of poly(ADP) ribose polymerase (PARP) and DNA ligase 3 at DSB, leading to selective cell killing by PARP inhibitors. Altogether these results show that p400 acts as a brake to prevent alt-EJ dependent genetic instability and underline its potential value as a clinical marker.

Mammalian cells possess a variety of different DNA repair pathways, which work together to safeguard genomic integrity upon encountering different types of DNA damage. Among all lesions, DNA double-strand breaks (DSBs) are most toxic and, if left unrepaired, results in loss of genetic information and genomic instability- a hallmark of tumorigenesis. Ataxia Telangiectasia Mutated (ATM) is a protein kinase, a master regulator of the DNA damage response, and is activated upon the formation of DSBs. ATM senses DNA DSBs through its accessory proteins and functions as a transducer of the DNA damage response (DDR), which entails the activation of genes involved in DNA repair, cell cycle checkpoint, and apoptosis. Consequently, loss of ATM results in increased genomic instability and compromised checkpoint regulation. Moreover, loss of ATM has been reported in various human cancers, and Atm-deficient mice uniformly develop thymic lymphomas, highlighting its role as a tumor suppressor. Although ATM has been extensively studied, much of its known functions to date pertained to its kinase activity, and the structural function of ATM remains elusive. To investigate whether ATM possesses structural functions beyond its kinase activity, we generated a mouse model expressing kinase-dead (KD) ATM protein. Intriguingly, while Atm-/- are viable, AtmKD/KD and AtmKD/- mice were embryonic lethal and AtmKD/KD and AtmKD/- cells displayed greater genomic instability compared to ATM-null cells, suggesting that the presence of the ATM KD protein blocks additional DNA repair pathways that are not affected in ATM-null cells. In this context, we identified defects in homologous recombination, resolution of Camptothecin (CPT)-induced Topoisomerase-I lesions, and replication progression specifically in AtmKD/- cells beyond those observed in Atm-/-. Mouse model expressing KD ATM (AtmKD/-) in hematopoietic stem cells (HSCs) developed thymic lymphomas faster and more frequently than the corresponding model with the ATM-null HSCs, which was associated with increased genomic instability and loss of tumor-suppressor Pten. In collaboration with others, we showed that the majority of tumor-associated ATM mutations reported in TCGA are missense mutations and are highly enriched in the kinase domain, while Ataxia-Telangiectasia (A-T) associated germline ATM mutations are almost always truncating mutations leading to complete loss of ATM protein. This result suggests that ATM KD protein might be expressed in a significant fraction of human cancer. These results, for the first time, identified a previously unknown phosphorylation-dependent, structural function of ATM in the maintenance of genomic integrity and tumor suppression. Furthermore, the tumorigenicity and vulnerability to particular DNA damaging agents caused by the expression of the ATM KD protein relative to the loss of ATM highlight the importance of distinguishing the types of ATM mutations in tumors, and provide novel insights into the clinical use of specific ATM kinase inhibitors, as well as the prognosis and treatments of ATM-mutated cancers. ATM has been reported to be frequently inactivated in human B-cell lymphomas, including up to 50% Mantle Cell Lymphoma (MCL), which represents around 6% of all Non-Hodgkins Lymphomas (NHLs). MCL is characterized by the recurrent t(11;14)(q13;q32) translocation, which juxtaposes CCND1/BCL-1 to the IGH enhancer, leading to deregulated expression of CyclinD1 (CCND1). However, CyclinD1 overexpression in B cells alone is not sufficient to induce MCL in mouse models, and the role of ATM in the suppression of B-cell lymphomas is not well understood, in part due to the lack of ATM-deficient mature B-cell lymphoma models. To address this, we generated a mouse model that combines conditional deletion of ATM specifically in early progenitor B-cells via Mb1cre, and overexpressing CyclinD1 in lymphoid cells via EµCyclinD1 transgene. While ATM loss alone resulted in the development of indolent, clonal, mature B-cell lymphoma, combined ATM-loss and CyclinD1 overexpression accelerated and increased the incidence of B-cell lymphoma. Furthermore, ATM-loss combined with CyclinD1 overexpression led to greater genomic instability and the expansion of naïve ATM-deficient B-cells in the spleen. This study, for the first time, developed an ATM-deficient B-cell lymphoma model and demonstrated a synergistic function of ATM and CyclinD1 in pre-GC B-cell proliferation and lymphomagenesis. Furthermore, the mice described here provide a prototypic animal model to study the pathogenesis of human MCL, for which there are no suitable mouse models.

Timely completion of DNA replication in each cell cycle is crucial for maintaining genomic integrity. This is often challenged by the presence of various replication fork barriers (RFBs). On collision with a RFB, the fate of the replication fork remains uncertain. In some cases, the integrity of the fork is maintained until the barrier is removed or the fork is rescued by merging with the incoming fork. However, fork stalling can cause dissociation of all of the associated replication proteins (fork collapse). If this occurs, the cell's recombination machinery can intervene to help restart replication in a process called recombination-dependent replication (RDR). Programmed protein-DNA barriers like the Replication Terminator Sequence-1 (RTS1) have been used to demonstrate that replication fork blockage can induce recombination. However, it remains unclear how efficiently this recombination gives rise to replication restart and whether the restarted replication fork exhibits the same fidelity as an origin-derived fork. It is also unknown whether accidental replication barriers induce recombination in the same manner as programmed barriers. In this study, I introduce recombination reporters at various sites downstream of RTS1 to obtain information on both the fidelity and efficiency of replication restart. I find that unlike break induced replication (BIR), the restarted fork gives rise to hyper-recombination at least 75 kb downstream of the barrier. Surprisingly, fork convergence, rather than inducing recombination, acts to prevent or curtail genetic instability associated with RDR. I also investigate a number of genetic factors that have a role in either preventing or promoting genome instability associated with the progression of the restarted fork. To compare RTS1 with an accidental protein-DNA barrier, a novel site-specific barrier system (called MarBl) was established based on the human mariner transposase, Hsmar1, binding to its transposon end. Replication fork blockage at MarBl strongly induces recombination, more so than at RTS1. This appears to be a general feature of accidental barriers as introduction of the E. coli TusB-TerB site-specific barrier in S. pombe gives rise to a similar effect. Here, I compare and contrast accidental barriers with programmed barriers. I observe that there is very little replication restart, if any, at MarBl measured by direct repeat recombination downstream. This points to the fact that accidental barriers do not trigger fork collapse in the same way as programmed RFBs and that the increased recombination that they cause may be a consequence of the inability of replication forks to terminate correctly, owing to the bi-directional nature of the barrier. Several genetic factors are assessed for their impact on MarBl-induced recombination, which further highlights both similarities and differences with RTS1-induced recombination.