The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their early replication arrest. Treatment of patient cells with a protein farnesyltransferase inhibitor (FTI) did not result in reduction of DNA double-strand breaks and damage checkpoint signaling, although the treatment significantly reversed the aberrant shape of their nuclei. This suggests that DNA damage accumulation and aberrant nuclear morphology are independent phenotypes arising from prelamin A accumulation in these progeroid syndromes. Since DNA damage accumulation is an important contributor to the symptoms of HGPS, our results call into question the possibility of treatment of HGPS with FTIs alone.

No description available.

The teratogenic effects of valproic acid (VPA) are well known, though its teratogenic mechanism remains unknown. VPA induces oxidative stress, which may lead to double strand breaks (DSBs) in DNA. Though the cell may repair this damage via homologous recombination (HR) and non-homologous end joining (NHEJ), repair is not always error-free; genomic instability may arise from gene deletions, amplifications, rearrangements, and loss of heterozygosity. Such alterations may underpin VPAʼs teratogenicity. The present study evaluated VPAʼs ability to induce NHEJ and HR and characterized the changes in expression of two proteins key to HR (RAD51) and NHEJ (XRCC4). Using pKZ1 transgenic mice (C57BL/6 genetic background), we sought to measure NHEJ events via X-gal staining. Although consistent staining was observed in adult male brain (positive control), no staining was observed in embryos 12 or 24 hours after in utero exposure to a teratogenic dose of VPA (500 mg/kg, maternal subcutaneous dose) on gestational day 9 (GD9). To determine whether the lack of staining observed in embryos was due to low/absent expression of key DSB-repair proteins, we measured mRNA/protein expression of RAD51 and XRCC4 in C57BL/6, GD9-exposed embryos and maternal brain. One hour after treatment, XRCC4 was increased at the protein level in brain and embryo. RAD51 was not increased in embryos and not detected in adult brain. These data suggest that embryos do possess the protein mediators of NHEJ and HR and that VPA-induced changes in expression of XRCC4 may influence the type of repair pursued, potentially affecting DSB repair fidelity (accuracy). Determination of fidelity of VPA-induced HR was attempted with the Chinese hamster ovary cell line (CHO33) using DNA sequencing; low template concentration and purity precluded successful sequencing of DNA from recombinant colonies and the assessment of fidelity. Overall, these data demonstrate that the lack of X-gal staining observed in pKZ1 embryos is not due to an underexpression of at least one key protein in the NHEJ pathway. Furthermore, a VPA-induced change in the the type of repair pathway pursued by the embryo may have teratological implications. / Thesis (Master, Pharmacology & Toxicology) -- Queen's University, 2012-10-15 11:06:30.613

Chromosomal replication is a source of spontaneous DNA double-strand breaks (DSBs). In E. coli, DSBs are repaired by homologous recombination using an undamaged sister template. During repair, the RecA protein polymerizes on single-stranded DNA generated at the site of the DSB and catalyses the search for sequence homologies on the undamaged sister template. This study utilized fluorescence microscopy to investigate the spatial and temporal dynamics of the RecA protein at the site of a replication-dependent DSB generated at the lacZ locus of the E. coli chromosome. The DSB was generated by SbcCD-mediated cleavage of a hairpin DNA structure formed on the lagging strand template of the replication fork by a long palindromic sequence. The tandem insertion of a recA-mCherry gene with the endogenous recA gene at the natural chromosomal locus produced no detectable effect on cell viability in the presence of DSB formation. During repair, the fluorescently-labelled RecA protein formed a transient focus, which was inferred to be the RecA nucleoprotein filament at the site of the replication-dependent DSB. The duration of the RecA focus at the site of the DSB was modestly reduced in a ΔdinI mutant and modestly increased in a ΔuvrD or ΔrecX mutant. Most cells underwent a period of extended cohesion of the sister lacZ loci after disappearance of the RecA focus. Segregation of the sister lacZ loci was followed by cell division, with each daughter cell obtaining a copy of the fluorescently-labelled lacZ locus. The RecA focus at the site of the DSB was observed predominantly between the mid-cell and the 1⁄4 position. In the absence of DSB formation, the lacZ locus exhibited dynamic movement between the mid-cell and the 1⁄4 position until the onset of segregation. Formation of the DSB and initiation of repair occurred at the spatial localization for replication of the lacZ locus while the downstream repair events occurred very close to the mid-cell. Genomic analysis of RecA-DNA interactions by ChIP-seq was used to demonstrate that the RecA focus at the lacZ locus was generated by the repair of the palindrome-induced DSB and not the repair of one-ended DSBs emanating from stalled replication forks at the repressor-bound operator arrays. This study has shown that the repair of a replication-dependent DSB occurs exclusively during the period of cohesion of the sister loci and the repair is efficiently completed prior to segregation of the two sister loci.

DNA double-strand breaks (DSBs), where both strands of the DNA duplex are simultaneously fractured, are considered the most lethal type of DNA damage. The conserved Mre11-Rad50 DNA repair complex enables the catalytic activities of the Mre11 nuclease and the Rad50 ATPase to function together to coordinate the recognition and processing of DSBs prior to the recruitment of long-range end-resection machinery required to trigger the DSB repair by the homologous recombination (HR) pathway. Fast-scan atomic force microscopy (AFM) in fluid conditions was primarily used to explore the architectural arrangement, DNA binding and processing machinery of the Mre11-Rad50 complex from the thermophilic crenarchaeote Sulfolobus acidocaldarius. The structural analysis identified four distinct architectural arrangements and demonstrates the key role of the Rad50 zinc hooks in the oligomerisation of the complex. AFM imaging showed a dynamic and Velcro-like interplay between Mre11-Rad50 protein complexes and the DNA double-helix using the Rad50 coiled-coils in a novel mode of DNA binding. The complex appears to use the Rad50 zinc hook region to bind to and track along dsDNA for broken DNA-terminals. Furthermore, the present study shows that this archaeal complex can drive extensive ATP-dependent unwinding of DNA templates. It is the first time that such unwinding has been observed in a single molecule study. These observations reveal novel activities leading to the proposal of a new model for Mre11-Rad50 action during DSB repair. AFM was also used to visualise the structure and activity of the HerA-NurA protein complex, which has been predicted to combine the activity of the NurA nuclease and hexameric HerA-translocase to generate long single-stranded DNA overhangs essential for DSB repair by HR in archaea. The present data verify and clarify the presumed biological role of this complex. Overall, the present study provides new insights into the initial steps of DNA DSB repair by the HR pathway and, most importantly, the detection of the broken ends.

B cells play crucial roles in the development of the two human autoimmune diseases, type 1 diabetes (T1D) and systemic lupus erythematosus (SLE). In the past decade, numerous studies showed positive responses of B cell depletion therapies in these two diseases. However, the beneficial effects are temporary and accompanied with adverse events. In this dissertation, we aimed to identify novel targets for a better modulation of disease development using mouse models. These diseases have circulating autoantibodies that are mostly mutated with an IgG isotype, indicating B cells that are producing them have been through the process of affinity maturation. Activation-induced cytidine deaminase (AID) is a core enzyme that regulates somatic hypermutation (SHM) and class switch recombination (CSR), the two key mechanisms in affinity maturation. We showed that genetic ablation of AID significantly inhibited the development of TID in NOD mice. Homologous recombination (HR) pathway is important for the repair of AID-induced DNA double strand breaks during CSR. 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid, also known as DIDS, is a small molecule that inhibits HR pathway and subsequently leads to apoptosis of class switching cells. DIDS treatment remarkably retarded the progression of TID, even when started at a relatively late stage, indicating the potential of this treatment for disease reversal. In both approaches, we observed a notable expansion of CD73+ B cells, which exerted an immunosuppressive role and could be responsible for T1D resistance. Next we examined the effect of targeting affinity maturation through these two approaches in lupus-prone mice. The genetic abrogation of AID in BXSB mice significantly ameliorated lupus nephritis and prolonged their lifespan. AID-deficient mice also exhibited improvement on disease hallmarks with increased marginal zone B cells and more normal splenic architecture. DIDS treatment notably reduced class switching when B cells were stimulated in vitro. However, the administration of DIDS did not strikingly alter the course of SLE in either BXSB mice or MRL/lpr mice. These findings demonstrated that affinity maturation could be a potential target for T1D and SLE, while further explorations into targeting other components in the repair pathway are warranted for SLE. Lastly, we assessed the effect of maternal AID modulation on the SLE development in the offspring using BXSB mouse model. Interestingly, the absence of maternal AID resulted in offspring that developed significantly more severe lupus nephritis compared to control. The offspring born to AID-deficient dams also exhibited elevated levels of pathogenic autoantibodies and exacerbated disease features. Therefore, the modulation of maternal AID could influence the SLE development in the offspring, and future investigations are needed to determine the underlying mechanisms responsible for the disease acceleration. / Doctor of Philosophy / The failure of the immune system to differentiate self from non-self leads to the development of autoimmune diseases. Type 1 diabetes (T1D) and systemic lupus erythematosus (SLE) are complex autoimmune diseases affecting millions of people in the world. Despite intensive research regarding these two diseases, no known cure is available indicating an imperative need for the development of novel therapies. With the importance of B cells in the pathogenesis of these two diseases, intensive research focused on whole B cell depletion therapies. However, these therapies exhibited high risks of infections as a result of depleting all the B cells. In this dissertation, we sought to selectively target specific B lymphocyte subsets that are crucial contributing factors in the development of T1D and SLE. While the effect of therapeutic treatment varied among different mouse models, the genetic manipulation of specific B cells successfully retarded the progression of both T1D and SLE and extended the lifespan of the mice. Further studies shed light on the possible mechanisms that are responsible for the disease inhibition. These data proved that targeting specific B cell compartment could be a potential disease management in T1D and SLE patients. In addition, using the established mouse model, we demonstrated the modulation of maternal factors significantly impact the SLE development in the offspring. Future experiments to identify the underlying mechanisms could provide more targets for the therapeutic development.

Résumé: Les cellules germinales mâles remodèlent leur chromatine pour compacter leur noyau afin de protéger leur matériel génétique et assurer un transit optimal vers le gamète femelle. Il a été démontré que tous les spermatides de plusieurs mammifères, incluant l’homme et la souris, présentaient ce mécanisme de remodelage de la chromatine. Celui-ci est caractérisé par une augmentation transitoire de cassures d’ADN dont une quantité importante sont bicaténaires. Ce remodelage chromatinien a été étudié et semble être conservé chez plusieurs espèces, allant de l’algue à l’humain. Dans le contexte de la recherche fondamentale sur le phénomène de la spermiogenèse, il devient parfois très difficile d’investiguer certains aspects importants en vertu de l’impossibilité de réaliser des manipulations génétiques simples. Il est donc impératif de développer un nouveau modèle d’étude plus permissif afin de palier à ces difficultés encourues. Comme le processus de maturation des spores chez la levure à fission présente de grandes similitudes avec la spermiogenèse des mammifères, l’utilisation d’un modèle d’étude basé sur la sporulation de la levure à fission Schizosaccharomyces pombe a été proposée comme modèle comparatif de la spermatogenèse murine. À la suite de la synchronisation de la méiose de la souche S. pombe pat1-114, des analyses d’électrophorèse en champ pulsé (PFGE) et de qTUNEL ont permis de déterminer la présence de cassures bicaténaires transitoires de l’ADN lors de la maturation post-méiotique des ascospores nouvellement formés (t>7h). Des analyses par immunobuvardages dirigés contre le variant d’histones H2AS129p suggère la présence d’un remodelage chromatinien postméiotique dix heures suivant l’induction de la méiose, corroborant le modèle murin. Enfin, des analyses protéomiques couplées à l’analyse par spectrométrie de masse ont permis de proposer l’endonucléase Pnu1 comme candidat potentiellement responsable des cassures bicaténaires transitoires dans l’ADN des ascospores en maturation. En somme, bien que le processus de maturation des spores soit encore bien méconnu, quelques parallèles peuvent être tracés entre la maturation des ascospores de la levure à fission et la spermiogenèse des eucaryotes supérieurs. En identifiant un modèle simple du remodelage chromatinien au niveau de la spermiogenèse animale, on s’assurerait ainsi d’un outil beaucoup plus malléable et versatile pour l’étude fondamentale des événements survenant lors de la spermiogenèse humaine. / Abstract : The male germ cells undergo a major chromatin remodeling process in order to protect their genetic material and ensure optimal transit to the female gamete. It has been demonstrated that all spermatids from several mammals, including humans and mice, require this structural transition in order to reach their full maturity and fertilizing potential. This mechanism is characterized by a transient surge in DNA breaks, including a significant number of double-stranded breaks. This feature has been studied and seems conserved in many species, ranging from algae to humans. In the context of basic research on the phenomenon of spermiogenesis, it is sometimes very difficult to investigate important aspects due to the impossibility of carrying out simple genetic manipulations. A more flexible model to overcome the incurred difficulties is therefore needed. Since the process of ascospore maturation of the fission yeast presents great similarities with mammal spermiogenesis, the use of a model based on the sporulation of the fission yeast Schizosaccharomyces pombe has been proposed as a comparative model to the murine spermatogenesis. Following synchronization of meiosis in the S. pombe diploid strain pat1-114, pulsed field gel electrophoresis and qTUNEL assay were used to determine the presence of transient double-stranded breaks in DNA during the post-meiotic maturation of newly formed ascospores (t> 7h). Analyses by immunoblotting directed against the histone variant H2AS129p suggests the presence of a post-meiotic chromatin remodeling to t=10h, that may share similarities with higher eu karyotes. Finally, proteomic analyzes coupled with mass spectrometry allowed us to propose the Pnu1 endonuclease as a potential candidate responsible for the transient DNA double-stranded breaks during ascospore morphogenesis. In sum mary, although the spore maturation process is still under investigation, some parallels can be drawn between the maturation of ascospores of fission yeast s and higher eukaryotic spermio genesis. Thus, identifying a simple eukaryotic model for chromatin remodeling in animal spermiogenesis would ensure a flexible genetic tool to decipher the molecular events occurring during human spermiogenesis.

O Glioblastoma Multiforme (GBM) é o tipo de tumor cerebral maligno com maior incidência na população. A perda do gene PTEN (fosfatase e tensina homóloga) é uma alteração comum associada ao GBM (até 60%) e esse gene codifica uma enzima que antagoniza a ação de PI3K, inibindo a fosforilação de AKT e, desse modo, regulando vias de sinalização relativas à sobrevivência celular e proliferação. Mutações em PTEN têm sido associadas à instabilidade genômica e ao aumento no número de quebras de fita dupla, além de serem relacionadas também à redução da expressão de RAD51, a qual é uma proteína-chave da via de reparo por recombinação homóloga (HR). Diante disso, o objetivo deste estudo foi avaliar se o status de PTEN interfere na expressão de RAD51 e proteínas parálogas (RAD51C e RAD51B) e, consequentemente, se PTEN é capaz de influenciar a eficiência de HR. Com o objetivo de induzir a formação de quebras de fita duplas (DSBs) no DNA, as células foram tratadas com a droga antitumoral etoposídeo, que produz quebras no DNA, principalmente duplas (DSBs). Duas linhagens de GBM com status diferentes de PTEN foram utilizadas: T98G (PTEN mutado) e LN18 (PTEN tipo selvagem). As células de GBM foram tratadas com etoposídeo em diferentes experimentos ou ensaios: proliferação celular, quantificação da necrose e apoptose, cinética do ciclo celular, imunofluorescência da proteína ?- H2AX, quantificação dos níveis de expressão de RAD51 e parálogas e o silenciamento de PTEN na linhagem LN18. Os resultados mostraram que a linhagem LN18 foi mais sensível à droga nos tempos iniciais (24 e 72 h) (até 61,2% de redução), em comparação com a T98G (até 12,3% de redução); no tempo mais tardio de análise (120 h), ambas as linhagens sofreram redução acentuadana proliferação. Adicionalmente, a LN18 exibiu maior porcentagem de células apoptóticas e necróticas, em comparação com a linhagem T98G, nos tempos de24, 72 e 120 horas após o tratamento. O ensaio de imunofluorescência revelou maior indução de células positivas para ?-H2AX na linhagem LN18 em relação à T98G (p =<0,001), após tratamento com etoposídeo (50 e 75 ?M). Nessas concentrações, a análise da cinética do ciclo celular mostrou um bloqueio na fase G2 em ambas as linhagens (p<0,01) nos tempos analisados (24, 48 e 72h), mas apenas a linhagem LN18 revelou bloqueio na fase S. A expressão de RAD51, RAD51B e C foi mais elevada em LN18 em comparação com a T98G e U87MG, nas células tratados (75?M) e controles. PTEN foi silenciado (siRNA-PTEN) na linhagem LN18 para verificar se a redução da expressão desse gene reduziria também a expressão de RAD51 e parálogas. Após 72 horas de silenciamento, com 69,9% de inibição de PTEN, a expressão de RAD51 e RAD51C também se mostrou reduzida em relação ao grupo controle. Em conjunto, os resultados obtidos no presente estudo indicam que o status de PTEN é crucial para as vias de sobrevivência, controle do ciclo celular e indução de apoptose nas células de GBM, indicando a relação entre PTEN e RAD51 e parálogas nas células de GBM tratadas com um indutor de quebras no DNA. Adicionalmente, outras ferramentas de estudo são requeridas para investigar as vias moleculares e possíveis interações e complexos proteicos envolvendo a participação de PTEN e RAD51 e suas proteínas parálogas / Glioblastoma multiforme (GBM) is the most common malignant brain tumor. Loss of PTEN (Phosphatase and tensin homolog deleted on chromosome 10) gene is the most frequent alteration associated with GBM and encodes a phosphatase enzyme that antagonizes the PI3K, by inhibiting AKT phosphorylation thereby regulating signaling pathways related to cell survival and proliferation. PTEN deficiency has been associated with genomic instability and increased endogenous DSBs, as well as reduced expression of RAD51, which is a key gene with crucial role in HR. In this study, we aimed to evaluate whether the PTEN status in GBM cell lines can affect RAD51 expression and HR efficiency under conditions of treatment with the antineoplastic drug etoposide, which targets the DNA topoisomerase II enzyme, thus leading to the production of DNA breaks. T98G (PTEN mutated) and LN18 (PTEN wild-type) cells were treated with etoposide, and several assays were carried out: cell proliferation, detection and quantification of necrosis and apoptosis, cell cycle kinetics, immunofluorescence staining, RAD51 (and paralogs) protein expression, and PTEN silencing in LN18 cell line, by using the siRNA method. LN18 cells showed a greater reduction in cell proliferation, compared to T98G after treatments (25, 50, 75 e 100 µM) at 24, 72 and 120h. Both cell lines showed a significant increase (p=<0.001) in cell death induction, but LN18 presented a greater percentage of apoptotic and necrotic cells than T98G (24, 72 and 120h). The induction of DSB was analyzed by immunostaining (with ?-H2AX antibody), and for the concentrations (50 and 75 µM) tested, LN18 showed higher levels of ?-H2AX positive cells than that observed for T98G (p=<0.001). The analysis of cell cycle kinetics performed for cells treated with etoposide (50 and 75 µM) and collected at 24, 48 and 72h, LN18 presented a greater G2-blockage, as compared to T98G; only LN18 showed a blockage at the S-phase. The expression of RAD51, RAD51B and C was higher in LN18 compared to T98G and U87MG cells treated with etoposide (75 µM) and controls. When we silenced PTEN in LN18 linage, to check if PTEN silencing may reduce the expression of RAD51 and its paralogs, we found a 69.9% reduction in PTEN protein expressions, and the expression of RAD51 and RAD51C was also found reduced, compared to the control group. Taken together, the results obtained in this study indicate that the status of PTEN is critical for survival pathways, cell cycle control and induction of apoptosis in GBM cells, confirming the relationship between PTEN and RAD51 and its paralogs in GBM cells treated with an inducer of DNA breaks. These results contribute with relevant information for further studies on molecular pathways underlying the interaction between PTEN and RAD51 and its paralogs

Butylated Hydroxyanisole, BHA, and Butylated Hydroxytoluene, BHT, are commonly used as preservatives for our food as well as additives in many products such as cosmetics, petroleum, and medicine. Although their use has been approved by the Food and Drug Administration (FDA), there have been controversies and debates on whether these phenol derivatives or antioxidants are safe to use. Their accumulative toxicology and side effects need to be thoroughly investigated as we continue to consume them on a daily basis. Data obtained by genomic analysis in Tang lab suggested the involvement of DNA damage checkpoint/repair pathways in the response network to these phenol stress factors. The aims of this thesis are to examine the morphological changes and potential DNA damage induced by exposing cells to BHA and BHT using fission yeast Schizosaccharomyces pombe as a model organism. Fluorescence microscopy was used to assess DNA double-strain breaks (DSBs) by monitoring the nuclear foci formation of Rad22, a DNA repair protein, in the presence of BHA and BHT. Changes in cell morphology were also studied under microscope. Preliminary data showed that cells treated with BHA and BHT exhibited morphological changes. In addition, for the first time in S. pombe cells, Rad22 foci in the nucleus of BHA and BHT treated cells were observed. Further investigation is needed to optimal the experimental condition to continue the study. These results will not only help us to better understand the effect of these phenol derivatives in the cells, but can also establish an experimental system for future studies on the interaction of the cells with stress factors and therapeutic drugs for human-related diseases such as cancer.

Les cassures double brin de l'ADN altèrent l'intégrité physique du chromosome et constituent l'un des types les plus sévères de dommages à l'ADN. Pour préserver l'intégrité du génome contre les effets potentiellement néfastes des cassures double brin de l'ADN, les cellules humaines ont développé plusieurs mécanismes de réparation, dont la réparation par recombinaison de l'ADN et la jonction d'extrémités non-homologues (NHEJ), catalysés par des enzymes spécifiques. Pendant ma thèse, nous avons caractérisé la dynamique de certaines des interactions protéines/ADN impliquées dans ces mécanismes au niveau de la molécule unique. Dans ce but, nous avons combiné des pinces optiques et de la micro-fluidique avec de la microscopie de fluorescence à champ large afin de manipuler une ou deux molécules d'ADN individuelles et d'observer directement les protéines de la réparation marquées par fluorescence agissant sur l'ADN. Nous avons concentré notre analyse sur trois protéines/complexes essentiels impliqués dans la réparation de l'ADN: (i) la protéine humaine d’appariement de brin RAD52, (ii) les protéines humaines XRCC4, XLF et le complexe XRCC4/Ligase IV de la NHEJ et (iii) le complexe humain MRE11/RAD50/NBS1. / DNA double-strand breaks disrupt the physical continuity of the chromosome and are one of the most severe types of DNA damage. To preserve genome integrity against the potentially deleterious effects of DNA double-strand breaks, human cells have evolved several repair mechanisms including DNA recombinational repair and Non-Homologous End Joining (NHEJ), each catalyzed by specific enzymes. In this thesis we aimed at unraveling the dynamics of protein/DNA transactions involved in DNA double-strand break repair mechanisms at single molecule level. To do this, we combined optical tweezers and microfluidics with wide-field fluorescence microscopy, which allowed us to manipulate individual DNA molecules while directly visualize fluorescently-labeled DNA repair proteins acting on them. We focused the study on three crucial proteins/complexes involved in DNA repair: (i) the human DNA annealing protein RAD52, (ii) the non-homologous end joining human proteins XRCC4 and XLF and the complex XRCC4/Ligase IV, and (iii) the human MRE11/RAD50/NBS1 complex.