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Les mutations dans les gènes codant pour les facteurs NER donnent lieu à des maladies autosomiques récessives telles que Xeroderma pigmentosum (XP), le syndrome de Cockayne (CS) et la trichothiodystrophie (TTD). Les phénotypes associés à ces syndromes génétiques se caractérisent par une sensibilité extrême à la lumière UV, avec prédisposition accrue à certains cancers (pour XP et XP / CS combiné, principalement), ainsi qu’un retard mental et des signes de progeria (pour CS et XP / CS combiné). Si on peut admettre une corrélation entre réparation de l'ADN endommagé et sensibilité aux UV / cancer, celle avec les symptômes neurologiques/progéroïdes est encore sujet à débat. Une explication pourrait provenir du rôle des facteurs NER dans la régulation de la transcription. Nous proposons une vue d’ensemble des roles de XPG et XPC dans la régulation de la transcription en absence des stress exogènes et comment CSA et CSB orchestrent l’arret de la transcription après une attaque génotoxique. XPC était capable d’interagir stablement avec la methyltransferase NSD3. Des mutations dans XPC altèrent le transcriptôme et la distribution des H3K36me3. Les mutations dans XPG dérégulent l’expression génique et XPG est capable d’etre recruté sur l’ensemble du genôme avec TFIIH. CSA et CSB faisant partie de la machinerie ubiquitin/proteasôme, régulent le recrutement de facteurs fixant l’ADN et contrôlant le programme transcriptionnel après irradiation aux UV. Nos donnés mettent en évidence le rôle des facteurs NER dans la transcription et leur défaut d’action provoque les maladies XP et XP/CS. En plus, nos données fournissent des explications sur le méchanisme d’arrêt de la transcription après un stress genotoxique et pose la question de l’origine du phenotype CS. / Mutations in genes coding for NER factors give rise to autosomal recessive diseases such as Xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The phenotypes associated with these genetic syndromes spans from extreme sensitivity to UV light, with increased predisposition to cancer (for XP and combined XP/CS, mostly), mental retardation and progeria (for CS and combined XP/CS). Whether the correlation between defective DNA repair reactions and UV-sensitivity/cancer may be more intuitive, a link with neurological/progeroid symptoms is still a matter of debate. As a possible explanation, it has been proposed a connection between NER and transcription regulation. We propose additional insights on XPG and XPC roles in transcription regulation in absence of exogenous stress and how CSA and CSB orchestrate transcription arrest due to genotoxic attack. XPC was able to stably interact with NSD3 methyltransferase. Mutations in XPC also disturbed the transcriptome and the H3K36me3 distribution. Mutations in XPG deregulate gene expression and XPG is able to be recruited genome wide together with TFIIH. CSA and CSB can, as part of the ubiquitin/proteasome machinery, regulate the recruitment timing of DNA binding factors and control transcriptional program after UV irradiation. Hence, our data shed more light in NER factors role in transcription and their defective action as a cause of XP and XP/CS disorders. Additionally, our data provide explanations on the mechanism of transcription arrest following genotoxic stress and pose questions about the origins of CS phenotype.

O funcionamento pleno e harmônico de uma célula está intimamente associado à sua capacidade de manter a integridade genômica. Diversos agentes químicos e físicos exógenos, bem como produtos do próprio metabolismo celular, podem interagir com o DNA, causando danos a esta molécula. Em respota a esses eventos, um intrincado mecanismo de resposta a danos ao DNA é ativado, podendo culminar tanto na correção das lesões, como na ativação de programas de morte celular, como a apoptose, sempre com o intuito de preservar a homeostase tecidual. Falhas neste mecanismo estão associadas a um aumento nas taxas de mutação, que apesar de constituírem a base da diversidade genética e evolução das espécies, está intimimamente associado à tumorigênese e ao envelhecimento. Neste trabalho, dividido em duas partes, utilizamos células de glioma humano como modelo de estudo para quimioterapia adjuvante, bem como também utilizamos neurônios humanos obtidos à partir de células-tronco pluripotente-induzidas como modelo de estudo para a neurodegeneração característica da síndrome de Cockayne, uma doença genética na qual os pacientes apresentam deficiências em mecanismos de reparo de DNA, bem como envelhecimento precoce. Na primeira etapa, avaliamos a resposta de células de glioma a cloroquina, um promissor adjuvante no tratamento desta enfermidade, e notamos que a resistência das células a esta droga estava intimamente relacionada ao seu potencial de membrana mitocondrial, o qual podia ser desfeito por meio da inibição da quinase ATR. Apesar da função canônica desta proteína se dar através da regência da resposta a danos ao DNA, notamos que a sua participação como agente promotor de resistência à cloroquina se dava independentemente deste mecanismo. Também notamos que a combinação da cloroquina com a inibição de ATR via silenciamento gênico exercia um potente efeito tóxico sobre as células tumorais tratadas com o quimioterápico Temozolomida. Já na etapa final desta tese, através do emprego da reprogramação celular, obtivemos, pela primeira vez, neurônios humanos de pacientes portadores da síndrome de Cockayne a partir de fibroblastos de pele. Com este modelo de estudo, foi possível observar que esses neurônios apresentavam uma reduzida densidade de puncta sináptica, bem como uma aparente deficiência na sincronia de suas atividades. Por fim, por meio do sequenciamento do RNA destes neurônios, identificamos uma desregulação na expressão de diversas vias relacionadas ao funcionamento e comunicação neural. As implicações para o uso da cloroquina como adjuvante no tratamento de gliomas, bem como as vantagens do uso de neurônios humanos de Cockayne em detrimento aos modelos atualmente disponíveis, também são discutidos. / Genome integrity is constantly threatened by chemical and physical exogenous agents, as well as products of cells own metabolism, and capability of cells to overcome these challenges is essential to achieve homeostasis. In response to DNA lesions, cells activate a dynamic and intricate DNA damage response that ultimately results either in lesion resolution, or in cell death through apoptosis. Regardless the fate chosen, tissue homeostasis is the ultimate goal. Flaws in this mechanism are associated to an increase in mutation rates. Although it constitutes the basis of genetic diversity and evolution, it is also strictly associated to tumorigenesis and aging. In this thesis, separated in two chapters, we used human glioma cells as a model to study adjuvant chemotherapy, and induced pluripotent stem cells-derived human neurons as a model to study neurodegeneration in Cockayne syndrome, a genetic disease in which patients display defects in DNA repair mechanisms, and also premature aging. In the first chapter, we investigated the response of cancer cells to chloroquine, a promising adjuvant drug in glioma therapy, and we noticed that cellsresistance to this drug was strictly associated to its mitochondrial membrane potential values, which could be dismantled through ATR inhibition. Interestingly, we noticed that the ability of ATR to promote resistance of glioma cells to chloroquine was independent of its canonical role in the DNA damage response. We also noticed that combined treatment of chloroquine to ATR inhibition through gene silencing exerted a powerful toxic effect on glioma cells treated with the chemotherapeutic Temozolomide. In the second chapter of this thesis, we employed cell reprogramming technique to obtain, for the first time, human neurons from Cockayen Syndrome patients from skin fibroblasts. With this model, we were able to identify a reduced density of synaptic puncta, as well as reduced synchrony in the activity of the patients neurons. Through RNA sequencing, we noticed several pathways related to synapses and neuronal function deregulated in Cockayne Sydrome patients neurons. Implications for the use of chloroquine as an adjuvant drug in glioma therapy, as well as the advantage of using iduced pluripotent stem cells-derived Cockayne syndrome human neurons (instead of currently available models) to study this disease, are also discussed.

O funcionamento pleno e harmônico de uma célula está intimamente associado à sua capacidade de manter a integridade genômica. Diversos agentes químicos e físicos exógenos, bem como produtos do próprio metabolismo celular, podem interagir com o DNA, causando danos a esta molécula. Em respota a esses eventos, um intrincado mecanismo de resposta a danos ao DNA é ativado, podendo culminar tanto na correção das lesões, como na ativação de programas de morte celular, como a apoptose, sempre com o intuito de preservar a homeostase tecidual. Falhas neste mecanismo estão associadas a um aumento nas taxas de mutação, que apesar de constituírem a base da diversidade genética e evolução das espécies, está intimimamente associado à tumorigênese e ao envelhecimento. Neste trabalho, dividido em duas partes, utilizamos células de glioma humano como modelo de estudo para quimioterapia adjuvante, bem como também utilizamos neurônios humanos obtidos à partir de células-tronco pluripotente-induzidas como modelo de estudo para a neurodegeneração característica da síndrome de Cockayne, uma doença genética na qual os pacientes apresentam deficiências em mecanismos de reparo de DNA, bem como envelhecimento precoce. Na primeira etapa, avaliamos a resposta de células de glioma a cloroquina, um promissor adjuvante no tratamento desta enfermidade, e notamos que a resistência das células a esta droga estava intimamente relacionada ao seu potencial de membrana mitocondrial, o qual podia ser desfeito por meio da inibição da quinase ATR. Apesar da função canônica desta proteína se dar através da regência da resposta a danos ao DNA, notamos que a sua participação como agente promotor de resistência à cloroquina se dava independentemente deste mecanismo. Também notamos que a combinação da cloroquina com a inibição de ATR via silenciamento gênico exercia um potente efeito tóxico sobre as células tumorais tratadas com o quimioterápico Temozolomida. Já na etapa final desta tese, através do emprego da reprogramação celular, obtivemos, pela primeira vez, neurônios humanos de pacientes portadores da síndrome de Cockayne a partir de fibroblastos de pele. Com este modelo de estudo, foi possível observar que esses neurônios apresentavam uma reduzida densidade de puncta sináptica, bem como uma aparente deficiência na sincronia de suas atividades. Por fim, por meio do sequenciamento do RNA destes neurônios, identificamos uma desregulação na expressão de diversas vias relacionadas ao funcionamento e comunicação neural. As implicações para o uso da cloroquina como adjuvante no tratamento de gliomas, bem como as vantagens do uso de neurônios humanos de Cockayne em detrimento aos modelos atualmente disponíveis, também são discutidos. / Genome integrity is constantly threatened by chemical and physical exogenous agents, as well as products of cells own metabolism, and capability of cells to overcome these challenges is essential to achieve homeostasis. In response to DNA lesions, cells activate a dynamic and intricate DNA damage response that ultimately results either in lesion resolution, or in cell death through apoptosis. Regardless the fate chosen, tissue homeostasis is the ultimate goal. Flaws in this mechanism are associated to an increase in mutation rates. Although it constitutes the basis of genetic diversity and evolution, it is also strictly associated to tumorigenesis and aging. In this thesis, separated in two chapters, we used human glioma cells as a model to study adjuvant chemotherapy, and induced pluripotent stem cells-derived human neurons as a model to study neurodegeneration in Cockayne syndrome, a genetic disease in which patients display defects in DNA repair mechanisms, and also premature aging. In the first chapter, we investigated the response of cancer cells to chloroquine, a promising adjuvant drug in glioma therapy, and we noticed that cellsresistance to this drug was strictly associated to its mitochondrial membrane potential values, which could be dismantled through ATR inhibition. Interestingly, we noticed that the ability of ATR to promote resistance of glioma cells to chloroquine was independent of its canonical role in the DNA damage response. We also noticed that combined treatment of chloroquine to ATR inhibition through gene silencing exerted a powerful toxic effect on glioma cells treated with the chemotherapeutic Temozolomide. In the second chapter of this thesis, we employed cell reprogramming technique to obtain, for the first time, human neurons from Cockayen Syndrome patients from skin fibroblasts. With this model, we were able to identify a reduced density of synaptic puncta, as well as reduced synchrony in the activity of the patients neurons. Through RNA sequencing, we noticed several pathways related to synapses and neuronal function deregulated in Cockayne Sydrome patients neurons. Implications for the use of chloroquine as an adjuvant drug in glioma therapy, as well as the advantage of using iduced pluripotent stem cells-derived Cockayne syndrome human neurons (instead of currently available models) to study this disease, are also discussed.

Cockayne syndrome (CS) is a rare, segmental premature aging disorder in which the majority of cases are caused by mutations in the Cockayne syndrome group B protein (CSB). CSB is a multifunctional protein implicated in DNA repair, transcription and chromatin remodeling. The results presented here demonstrate that CSB plays an important role in telomere maintenance and DSB repair. We find that CS cells accumulate telomere doublets, have increased telomere-bound TRF1, decreased TERRA levels and a defect in telomerase-dependent telomere lengthening. These results imply that CS patients may be defective in telomere maintenance. We also uncover a novel and important role of CSB in DNA DSB repair. We show that CSB facilitates HR and supresses NHEJ during S and G2 phase. We find that CSB interacts with RIF1 and is recruited by RIF1 to DSBs in S phase. At DSBs, CSB remodels the chromatin extensively, which in turn limits RIF1 recruitment and promotes BRCA1 accumulation. The chromatin remodeling activity of CSB requires not only damage-induced phosphorylation on S10 by ATM but also cell cycle-dependent phosphorylation of S158 by cyclin A-CDK2. Both modifications are needed for the intramolecular interaction of CSB N-terminal domain with its ATPase domain. This intramolecular interaction has previously been reported to regulate the ATPase activity of CSB. Taken together, these results suggest that ATM and CDK2 control of CSB to promote chromatin remodeling, which in turn inhibits RIF1 in DNA DSB repair pathway choice. / Thesis / Doctor of Philosophy (PhD)

L’imagerie en tenseur de diffusion, ou DTI, est une application de l’imagerie de diffusion qui permet de quantifier en chaque direction de l’espace la diffusion des molécules d’eau. Cette technique permet d’obtenir la direction de fibres cérébrales en chaque voxel, et de reconstruire indirectement les faisceaux de substance blanche du cerveau en 3D par tractographie. Les paramètres scalaires du tenseur, la FA ou fraction d’anisotropie, et l’ADC ou coefficient apparent de diffusion, permettent d’analyser la microstructure cérébrale de manière quantifiée. Les applications du DTI sont nombreuses, comme l’étude du développement cérébral normal et des pathologies de la substance blanche.Nous avons tout d’abord étudié le DTI chez le fœtus. Pour ce faire, une chaîne de traitement d’images DTI fœtales, compilée dans un logiciel, Baby Brain Toolkit (BTK) (https://github.com/rousseau/fbrain), a été implémentée. Ce logiciel permet notamment de corriger les artéfacts de mouvements qui dégradent la qualité du DTI fœtal. BTK a été validé sur des cas normaux, puis a été appliqué à un modèle de malformation cérébrale. Nous avons aussi étudié un cas d’infection à cytomégalovirus en DTI.Nous avons ensuite analysé l’intérêt des paramètres scalaires DTI dans l’étude d’une leucodystrophie rare, le syndrome de Cockayne. Le DTI permet de diagnostiquer le syndrome de Cockayne, de distinguer ses sous-types cliniques, et d’approcher sa physiopathologie. Nous avons ainsi montré qu’il s’agit d’une pathologie hypomyélinisante primitive, suivie d’une démyélinisation secondaire de bas grade. / Diffusion tensor imaging (DTI) is a diffusion-weighted imaging application that allows water motion quantification in any direction. This technique determines brain fiber direction in each voxel, and reconstructs indirectly white matter fibers tracts in 3D with tractography. Scalar DTI parameters, such as fractional anisotropy (FA) and apparent diffusion coefficient (ADC), provide a quantitative analysis of brain microstructure. DTI applications are numerous, especially in the study of brain development and white matter pathologies.First, we studied DTI in the fetus. For this, we implemented a processing method for fetal DTI images, and compiled it in a software, Baby brain Toolkit (BTK) (https://github.com/rousseau/fbrain). BTK was validated on normal cases, and then applied to a brain malformation model. We also studied a case of cytomegalovirus infection with DTI.We then investigated the utility of scalar DTI parameters in a rare leukodystrophy, Cockayne syndrome. DTI allows to diagnose Cockayne syndrome, to distinguish between clinical subtypes, and to understand its pathophysiology. We showed that Cockayne syndrome was a primitive hypomyelinating disorder, followed by a low grade secondary demyelination.

Deux phénomènes liés au TFIIH ont été étudiés : l'influence des mutations spécifiques dans la sous-unité XPD de TFIIH sur la réponse transcriptionnelle de certains gènes après l'irradiation UV, et l'interaction entre le TFIIH et la transcription des gènes de classe III. Une analyse détaillée de la dynamique du transcriptome a été effectuée pour la réponse des cellules humaines mutantes XP-D/CS à l'UV. Il a été démontré que la dysrégulation sélective observée de l'expression des gènes était liée à l'incapacité pour la ré-initiation transcriptionnelle et à l'hétérochromatinisation suivante, où l'histonedésacétylase SIRT1 a été identifiée comme le principal facteur. Son inhibition a permis de recouvrer l'expression normale d'un nombre substantiel des gènes affectés. Une étude de la participation pangénomique du coeur de TFIIH dans latranscription a découvert son association avec les gènes actifs de classe III. Cette association a été démontrée être indépendante de Pol II. Le coeur de TFIIH a été montré participer directement à la transcription effectuée in vitro par Pol III.

Mutações em genes da via de reparo de DNA por excisão de nucleotídeo estão associados a doenças genéticas raras, como Xeroderma pigmentosum, Síndrome de Cockayne e Tricotiodistrofia. Este trabalho teve como objetivo identificar mutações responsáveis por essas Síndromes em pacientes brasileiros. Inicialmente o projeto teve como foco o estudo da comunidade de Araras, no interior de Goiás, onde existe uma das maiores incidências de pacientes XP no mundo. Duas mutações foram identificadas no gene POLH, associadas a dois efeitos fundadores independentes na região. Os dezessete pacientes, entre 10 e 80 anos, caracterizados geneticamente apresentam uma grande heterogeneidade das manifestações clínicas, com fenótipos brandos à extremamente agressivos. Esse estudo se estendeu a mais dezessete pacientes de todo o Brasil, incluindo outros grupos de complementação de XP, CS e TTD. Na segunda parte deste trabalho avaliamos a resposta das linhagens XP-V ao tratamento com cisplatina. Foi possível observar que essas linhagens são mais sensíveis aos danos induzidos pela cisplatina, encontram problemas na fase G1/S de replicação e possuem um aumento da marcação high-level para histona gH2AX. / Mutations at DNA repair genes are associated with rare genetic diseases such as Xeroderma pigmentosum, Cockayne syndrome and Trichothiodystrophy. This study aimed to identify mutations responsible for these syndromes in Brazilian patients. Initially the project focused on the study of Araras community in the state of Goiás, where there is one of the densest known areas of XP patients. Two mutations were identified at POLH gene, associated with two independent founders effects in the region. The seventeen patients between 10 and 80, characterized genetically a wide range of heterogeneity of clinical symptoms with mild to extremely aggressive phenotypes. Brazilian patients from other places were studied, including seventeen other patients with XP, CS and TTD phenotypes. In the second part of this work, we evaluated the response of XP-V cell lines treated with cisplatin. It was observed that Pol eta deficient cells are more sensitive to damage induced by cisplatin, as well as encounter problems in the S phase replication after 24 hours of treatment, and have increased high-level fluorescence for gH2AX.

Many steps go into developing a clinical viral gene therapy. The course starts with appropriate disease selection and moves through the many hurdles of in-vitro testing, animal model validation and proof-of-concept studies, all the way through pre-clinical large animal studies. In this thesis, I propose to outline the process of developing a translation pathway for a gene therapy using recombinant adeno-associated virus (rAAV). I will expand on this outline using data that I have generated during the course of my Ph.D. that ranges from animal model validation all the way through pre-clinical vector stability studies. Two disease models will be discussed throughout this thesis, Cockayne Syndrome (CS) and Alpha-1 Antitrypsin Deficiency (AATD). Cockayne Syndrome is a rare autosomal recessive genetic disorder involving mutations in either the CSA or CSB gene, leading to defects in DNA repair. Clinically this presents as progressive degeneration of the central nervous system, retina, cardiovascular system, and cochlea, which leads to mental retardation, post-natal growth defects, ocular abnormalities, and shortened life expectancy. Alpha-1 antitrypsin is a serine protease inhibitor largely produced in the liver that mainly functions to inhibit neutrophil elastase within the lung. AATD leads to an increased risk of emphysema, with shortened life expectancy, and also results in accumulations of mutant AAT polymers in the liver, sometimes leading to liver failure. Using these two disease models I will outline the upstream and downstream pre-clinical work as well as the transition to clinical trials of a rAAV based gene therapy.

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