Les cancers du poumon non à petites cellules (CPNPC) restent une cause majeure de mortalité par cancer, malgré l’apport de thérapies moléculaires ciblées et des immunothérapies. La survie des patients aux stades avancés reste limitée et la mise au point de biomarqueurs pronostiques permettant de stratifier les patients ou prédictifs de réponse à différents types de traitement constitue un enjeu important pour la prise en charge des patients.La mise au point de biomarqueurs obéit à des enjeux spécifiques tenant à la connaissance de la biologie tumorale dans des domaines complexes tels que celui de la réparation de l’ADN, aux caractéristiques des outils disponibles pour créer ces biomarqueurs et à leur applicabilité dans le contexte clinique.Dans le cadre de cette thèse, il a été étudié la manière dont l’expression de la protéine PARP1 peut s’intégrer aux biomarqueurs pronostiques de réparation de l’ADN dans les CPNPC. Il a par ailleurs été étudié le rôle de la protéine MMS19, identifiée à partir d’études d’expression génique, comme biomarqueur prédictif potentiel de réponse au cisplatine dans les CPNPC. Enfin, l’utilisation des cellules tumorales circulantes pour le développement de biomarqueurs a été étudiée dans le cadre de la détection des remaniements du gène ALK, une altération oncogénique constituant une cible thérapeutique dans les CPNPC. / Non-small cell lung cancers (NSCLC) remain a leading cause of cancer-related death despite the advent of targeted therapies and immunotherapies. At advanced stages, patient survival remains limited and establishment of new biomarkers, either prognostic for patient stratification or predictive of response to various therapies, is an important goal for patient’s treatment.Development of biomarkers is dependent on many components among which: knowledge of cancer cell biology in complex cellular processes such as DNA repair, characteristics of tools available to create biomarkers and applicability in daily medical practice.In this thesis, expression of PARP1 has been evaluated as a prognostic biomarker in NSCLC, in the broader context of DNA repair biomarkers. The biological and clinical relevance of MMS19 protein, identified in gene expression analysis , as a biomarker for cisplatin sensitivity in NSCLC has also been studied. Finally, the use of circulating tumor cells for biomarker development has been studied through the detection of ALK gene rearrangment, an oncogenic targetable alteration in NSCLC.

Chromosomes are very dynamic structures that are constantly undergoing physical changes necessary for cell survival. Studies in yeast and metazoans have shown that chromosomal loci exhibit large-scale changes in mobility in response to DNA double-strand breaks (DSBs). If left unrepaired, DSBs can lead to disease and even cell death. One of the predominant cellular pathways utilized to repair DSBs is homologous recombination (HR). DSB repair via HR requires a homologous DNA template to recover the missing genetic information lost at the break site. Our lab proposes that increased chromosome mobility (ICM) facilitates recombination by helping a broken chromosome successfully find its homolog. In support of this view, ICM is under the genetic control of the HR machinery and requires activation of the DNA damage checkpoint response. However, there is currently no consensus on the precise functional role of ICM in HR. In Chapter 1, I describe in detail the known steps of DSB repair via the HR pathway, and discuss some of the important advancements made in the field of cell biology that has helped shape our understanding of HR. I highlight the use of in vivo cell imaging and fluorescently labeled DNA repair proteins during the study of HR. Additionally, I discuss some of the first studies that examined chromosome dynamics within the nucleus in live cells. Lastly, I describe the phenomenon of increased chromosome mobility and expand upon why it needs to be studied further. In Chapter 2, I present in detail our method for measuring the pairing of DNA loci during HR at a site-specific DSB in Saccharomyces cerevisiae. This method utilizes live cell imaging and a chromosome tagging system in diploid yeast to visualize homologous chromosomes during HR-mediated repair. Using this method, we demonstrate that in wild type (WT) cells, homologous chromosomes come together, repair and then move apart after repair is complete. Importantly, the kinetics we observe in the pairing of homologous chromosomes match the kinetics of site-specific DSB formation and the subsequent gene conversion of that site. In Chapter 3, I describe our study that elucidates the relationship between ICM and multiple HR steps. We find a tight temporal correlation between the recruitment of the recombination proteins, ICM, the physical pairing of homologous loci, and gene conversion. Importantly, we can shift the timing of ICM by altering the initiation of DNA end resection - an early step in the HR process. Our data highlight the importance of DNA end resection as a vital precursor to ICM and demonstrate a strong temporal linkage between ICM and HR. Taken together our data support the claim that ICM is essential to HR and mechanistically involved in the process of DNA repair. In Chapter 4, we explore chromosome mobility in response to different forms of DNA damage such as spontaneous DSBs, collapsed replication forks, and ionizing radiation (IR). We find that spontaneous DSBs and collapsed replication forks do not induce a change in chromosome mobility. However, exposure to ionizing radiation results in a robust increase in global chromosome mobility that is dependent on activation of the DNA damage checkpoint. Overall, these findings demonstrate how ICM is tightly regulated and highly dependent on the circumstances surrounding the formation of the DSB. Lastly, in Chapter 5, I summarize all of my findings and discuss how they relate to one another with respect to the linkage between ICM and HR. I also provide a perspective on future experiments needed to advance the field.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder that is caused by a point mutation in the LMNA gene, resulting in production of a truncated farnesylated-prelamin A protein (progerin).We previously reported that XPAmislocalized to the progerin-inducedDNAdouble-strand break (DSB) sites, blocking DSB repair, which led to DSB accumulation,DNA damage responses, and early replication arrest inHGPS. In this study, the XPA mislocalization to DSBs occurred at stalled or collapsed replication forks, concurrent with a significant loss of PCNA at the forks, whereas PCNA efficiently bound to progerin. This PCNA sequestration likely exposed ds-ssDNA junctions at replication forks for XPA binding. Depletion of XPA or progerin each significantly restored PCNAat replication forks.Our results suggest that although PCNAismuchmore competitive than XPAin binding replication forks, PCNA sequestration by progerin may shift the equilibrium to favor XPA binding. Furthermore, we demonstrated that progerin-induced apoptosis could be rescued by XPA, suggesting that XPAreplication fork binding may prevent apoptosis in HGPS cells. Our results propose a mechanism for progerininduced genome instability and accelerated replicative senescence in HGPS. - Hilton, B. A., Liu, J., Cartwright, B.M.,Liu,Y.,Breitman,M.,Wang,Y., Jones,R.,Tang, H.,Rusinol,A.,Musich,P.R.,Zou,Y.Progerin sequestrationof PCNApromotes replication fork collapse andmislocalization ofXPAin laminopathy-related progeroid syndromes.

The exposure to high doses of ionizing radiation (>5Gy) is unequivocally associated with increased cancer risk. However, there is substantial experimental evidence showing that in response to low doses of ionizing radiation (LDR: <100mGy), cells and organisms are benefitted with delayed ageing, improved immunity and reduced cancer growth. These intriguing findings have proposed the “Radiation Hormesis” hypothesis. Herein, I studied the senescence effects of LDR exposure to normal human HFL1 cells and examined transcriptional changes. I found that HFL1 cells exposed to 10 mGy of gamma radiation had delayed senescence measured at 12 weeks post-irradiation compared to unirradiated cells. Through qPCR array analysis, I found that genes involved in human cellular senescence functions are differentially regulated in 10 mGy exposed cells at 12 weeks compared to 1-week post-exposure. A nucleolar protein, SIRT7, that belongs to the family of proteins called Sirtuins with known roles in aging, was found to be upregulated transcriptionally in LDR-exposed HFL1 cells. Knocking out SIRT7 protein significantly accelerated senescence in HFL1 cells suggesting a direct role of SIRT7 in the deceleration of senescence and potentially in mediating radiation hormesis. Furthermore, overexpression of the HRAS oncogene strongly accelerated senescence in HFL1 cells through gene expression of cell cycle regulators and checkpoint proteins. Together, my studies revealed that LDR induces unique transcriptional changes resulting in a potentially radio adaptive protective cellular response. I also discuss the HRAS overexpression system as a time-efficient cellular model that could be used to more rapidly study the effect of LDR on senescence using primary cultures.

Avec la chimiothérapie et la chirurgie, la radiothérapie fait partie intégrante de l'arsenal thérapeutique pour lutter contre le cancer. Afin de potentialiser l’efficacité des rayonnements ionisants, la radiochimiothérapie s’est développée mais en raison des résultats insuffisants de cette stratégie, de nouvelles voies permettant une modulation de la radiosensibilité tumorale sont évaluées. C’est dans ce contexte d’amélioration de l’efficacité de la radiothérapie que s’inscrit ce travail de thèse. Nous avons évalué l’intérêt thérapeutique de l’association d’inhibiteurs de la réparation de l’ADN à la radiothérapie sur un modèle orthotopique de cancer bronchique et sur un modèle orthotopique de cancer de la tête et du cou. En raison de son rôle prépondérant dans la réparation des cassures simple brin, PARP1 a été ciblé dans un premier temps pour éprouver cette stratégie, à l’aide d’un inhibiteur chimique l’Olaparib. Le rationnel consistait à inhiber la réparation de dommages induits par l’irradiation, pouvant ainsi conduire à la mort des cellules tumorales. Les résultats obtenus in vitro ont montré que l’inhibition de PARP1 permettait en effet de potentialiser les effets de la radiothérapie. Cette association thérapeutique a, par la suite, été évaluée in vivo et a montré une très faible radiosensibilisation, limitée par une toxicité induite par cette association. Afin d’augmenter l’efficacité de cette stratégie thérapeutique, un inhibiteur d’ATR (AZD6738), une des protéines majeures de la réponse aux dommages de l’ADN et au stress réplicatif, a été ajouté à la combinaison initiale. Il a en effet été montré que Chk1, la cible principale d’ATR, était activée dans les cellules traitées avec l’Olaparib et/ou irradiées. Nous avons démontré in vitro et in vivo, que l’AZD6738 améliorait l’efficacité de la combinaison irradiation et Olaparib dans nos deux modèles tumoraux, suggérant le potentiel de cette triple combinaison en clinique. Enfin, en raison du rôle de l’irradiation et de PARP1 dans différents processus immunitaires, nous avons étudié de façon préliminaire l’influence de nos différentes combinaisons thérapeutiques sur l’infiltrat immunitaire tumoral. Sachant que l’efficacité de l’association Olaparib/irradiation avait été démontrée dans des modèles tumoraux implantés en sous-cutané, ce travail de thèse montre l’importance et la pertinence de modèles précliniques plus proches de la pathologie humaine, comme les modèles orthotopiques. En effet, il est très probable que les toxicités observées au cours de ce travail soit la conséquence d’une détérioration avancée des muqueuses présentes dans le champ d’irradiation et que celles-ci ne puissent être observées lors d’irradiation localisée de tumeurs implantées en sous-cutané. / With chemotherapy and surgery, radiotherapy is part of anti cancer therapeutic strategy. To increase ionizing radiations effects, radiochemotherapy has emerged, but because of inefficient results, new pharmacological strategies for modulation of radiosensitization has been assessed. My thesis project is part of this context of improvement of radiotherapy efficiency. We have evaluated therapeutic interest of association of DNA repair inhibitors and radiotherapy on lung cancer model and head and neck cancer model. Because of its implication in single strand break repair, PARP1 has been first, targeted to assess this strategy, with the chemical inhibitor Olaparib. The rational was to inhibit radio-induced damages, leading to cellular death. In vitro, we have demonstrated that Olaparib was promising for enhancing radiation efficacy, but has an in vivo limited radiosensitization, plus we observed with this association a toxicity. Non toxic association has been found by decreasing Olaparib dose, but association efficiency has been limited, meaning that Olaparib, in our model, has a restrained therapeutic index.To increase the efficiency of this combination, we have added an ATR inhibitor (AZD6738), one of the key proteins implicated in response to DNA damages and replicative stress. In fact it has been demonstrated, that ATR main target, Chk1, was activated in Olaparib-treated and/or irradiated cells. We have demonstrated in vitro and in vivo, that AZD6738 improved efficiency of Olaparib and radiotherapy combination in both models, suggesting the potential of this triple combination in clinic.Finally, because of effects of PARP1 and radiation on different immune processes, we have preliminary studied, the influence of this different combinations on immune infiltrate.Knowing that efficiency of the association Olaparib and radiotherapy has already been demonstrated in subcutaneous models, this work has shown the importance and relevance of preclinical models, closer to human pathologies, as orthotopic models. In fact, it is likely that toxicities observed during this work, are the consequence of mucous membrane damaging in the field of irradiation, which cannot be observed with localized irradiation of subcutaneous tumors.

Following low levels of UV exposure, Escherichia coli cells deficient in nucleotide excision repair recover and synthesize DNA at near wild type levels, an observation that formed the basis of the post replication recombination repair model. In this study, we characterized the DNA synthesis that occurs following UV-irradiation in the absence of nucleotide excision repair and show that although this synthesis resumes at near wild type levels, it is coincident with a high degree of cell death. We confirm that the replication occurring under these conditions involves extensive levels of strand exchange. However, cells undergoing this form of replication accumulate strand exchange intermediates that fail to resolve into discrete molecules, resulting in grossly filamentous, multinucleate cells. Taken together the results demonstrate that the DNA synthesis that occurs in UV-irradiated nucleotide excision repair mutants is aberrant and suggests that post replication repair is not an efficient mechanism to promote survival in the absence of nucleotide excision repair. The role that nucleotide excision repair plays in the recovery of replication following UV-induced DNA damage was further characterized by examining the specific role of UvrD in processing and restoring UV-arrested replication forks. UvrD is a helicase with functions associated with nucleotide excision repair and replication. UvrD catalyzes the removal of the damaged region by nucleotide excision repair proteins and removes the stretch of DNA incised during methyl-directed mismatch repair during replication. Recent biochemical studies have led to the proposal that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forks in vivo has not been directly examined. In this study, we show that UvrD is required for DNA synthesis to recover. However, in the absence of UvrD, the displacement and partial degradation of the nascent DNA at the arrested fork occurs normally. In addition, damage-induced replication intermediates persist and accumulate in uvrD mutants in a manner that is similar to that observed in other nucleotide excision repair mutants. These data indicate that following arrest by DNA damage, UvrD is not required to catalyze fork regression in vivo and suggest that the failure of uvrD mutants to restore DNA synthesis following UV-induced arrest relates to its role in nucleotide excision repair.

DNA end-resection and nuclear actin-based movements orchestrate clustering of double-strandbreaks (DSBs) into homology-directed repair (HDR) domains. Using genomic approaches, we analyze how actin nucleation by ARP2/3 affects damage-dependent and -independent 3D genome reorganization and facilitates pathologic repair. Chromosome conformation capture techniques (Hi-C) reveal multi-scale alterations in genome organization following damage, including changes in chromatin insulation and compartmentalization. Nuclear actin polymerization promotes interactions between DSBs, which in turn facilitates aberrant intra- and inter-chromosomal rearrangements as visualized by high-throughput translocation assays (HTGTS). Notably, BRCA1 deficiency, which decreases end-resection, DSB mobility, and subsequent HDR, nearly abrogates recurrent translocations between AsiSI DSBs. In contrast, loss of functional BRCA1 yields unique translocations genome-wide, reflecting a critical role in preventing spontaneous genome instability and subsequent rearrangements. Our work establishes that the assembly of DSB repair domains is coordinated with multiscale alterations in genome architecture that enable HDR despite increased risk of translocations with pathologic potential.

Indiana University-Purdue University Indianapolis (IUPUI) / The overexpression of the multi-domain enzyme fatty acid synthase (FASN) has long been associated with poor clinical prognosis and treatment outcome in various cancers. Previous research in the Zhang lab has determined a role for FASN in mediating increases in non-homologous end-joining (NHEJ) DNA double-strand break repair activity allowing for increased cancer cell survival, and this mechanism was found to involve inhibition of NF-kB/p65. The mechanism responsible for the regulation of NF-kB/p65 by FASN in cancer cells, however, remains unknown. To this end, I was able to determine that FASN negatively regulates both the expression and activity of NF-kB/p65 in breast cancer cells, and that this effect was likely mediated by the 16-carbon saturated fatty acid palmitate, the end product of FASN catalytic activity. Specifically, FASN was found to negatively regulate p65 expression by disrupting its protein stability as a result of an increase in poly-ubiquitination of p65 protein and subsequent proteasomal degradation. Further, I found that the phosphorylation site Thr254 of p65 is involved in the regulation of p65 protein stability by FASN, in that mutation of this residue resulted in a disruption in p65 stability. Finally, I was able to determine that FASN likely inhibits the ability of the peptidyl-prolyl cis/trans isomerase Pin1 to assist in maintaining p65 stability, in that both siRNA knockdown and pharmacological inhibition of Pin1 resulted in a reduction of p65 expression in FASN shRNA knockdown cells. The determination of this signaling mechanism serves to expand our understanding of the role of FASN in breast cancer cells and has the potential to assist in uncovering more effective ways to target the oncogenic FASN pathway to kill breast tumor cells and to overcome resistance to drug treatment.

Maintenance of genomic integrity is essential for the survival of an organism and its ability to pass genetic information to its progeny. However, DNA is constantly exposed to exogenous and endogenous sources of damage, which demands cells to possess DNA repair mechanisms. Of the many forms of DNA damage, double-strand breaks (DSBs) are particularly cytotoxic DNA lesions that cause genome instability and cell lethality, but also provide opportunities to manipulate the genome via repair. One of the major DSB repair pathways shared between single-celled yeast and humans is homologous recombination (HR). HR is initiated by the evolutionarily conserved Mre11-Rad50-Xrs2/Nbs1 (MRX in yeast, MRN in mammals) complex. The MRX complex has a multitude of functions such as damage sensing, adduct removal from DSB ends, and end tethering – a process to maintain the two ends of a DSB in close proximity. The role of the MRX complex has been uncovered by studying the repair of DSBs generated from meganucleases such as HO and I-SceI. However, it is unclear if this knowledge translates to the repair of DSBs from genome editing nucleases such as TALEN and CRISPR-Cas9 (Cas9), as these nucleases create DSBs with different end polarities. While the repair efficiencies and outcomes of TALEN and Cas9 are actively studied, less is known about the earlier stages of repair. The objective of this thesis is to examine the role of the MRX complex in repair processes at both ends of a DSB after cleavage with I-SceI, TALEN, and Cas9 in vivo using the model organism Saccharomyces cerevisiae. In Chapter 1, I describe the importance of DSB repair, a summary of HR and its sub-pathways, the functions of the MRX complex, and properties of I-SceI, TALEN, and Cas9. The materials and methods used in this thesis are detailed in Chapter 2. The work described in Chapter 3 focuses on end tethering and recruitment of downstream repair proteins in haploid cells. I find that DSB ends from the three nucleases all depend on the MRX complex for end tethering, and that initial end polarity does not affect tethering. DSBs created by Cas9 show greater dependence on the Mre11 nuclease of the MRX complex for Rad52 recruitment compared to DSBs from I-SceI and TALEN. Despite Mre11-dependent end processing and Rad52 recruitment at Cas9-induced DSBs, Cas9 stays bound to one DNA end after cleavage, irrespective of the MRX complex. These results suggest that Mre11 exonuclease activity required for adduct removal from DSB ends is not critical for Rad52 recruitment, and that Mre11 endonuclease activity may be driving processing of Cas9-bound DSBs. I also find that MRX tethers DSB ends even after Rad52 recruitment, and unexpectedly, untethered ends are processed asymmetrically in the absence of MRX for all three nucleases. In Chapter 4, I explore the interaction of DSB ends with their repair template, the intact homologous chromosome, in diploid cells. The primary goal is to monitor interhomolog contact in real time from homology search to completion of HR. Although technical limitations make it difficult to capture the entire HR program from DSB formation to repair, I show that untethered ends interact with the homolog separately in the absence of the MRX complex. Similar to haploids, diploid cells display defects in end tethering and end processing without the MRX complex. Repair outcomes of WT cells show an even distribution of G2 crossovers and non-crossovers, while pre-replication crossovers and break-induced replication are undetected. Overall, the results in this thesis provide insight into the functions of the MRX complex in repairing different DSB ends created by I-SceI, TALEN, and Cas9. In Chapter 5, I summarize all of these findings and discuss the motivation for future cell biology studies of HR.

Damage to DNA from a variety of sources can lead to damaged proteins, genomic instability, aneuploidy, and cancer. It is therefore essential to repair DNA damage, and to do so a variety of DNA repair mechanisms have evolved. One of the repair mechanisms, known as homologous recombination (HR) repair, uses an undamaged sister chromatid as a template to make error free repairs to double-strand (ds) DNA breaks. While many proteins are involved in HR, this work focuses on testing the interactions of a subset of these proteins known as the Rad51 paralogs. The goal of this study is to determine if the putative Rad51 paralogs in Drosophila melanogaster are sufficiently conserved as to function in the same manner as their human counterparts. This research is part of a larger project to determine if Drosophila melanogaster is a good model organism for studying HR in humans (Hs). The D. melanogaster Rad51 gene, and its four paralogs Spn D, Spn B, Rad51D, XRCC2 (the last 2 identified by sequence homology), and human hsRad51D and hsXRCC2, were cloned into Invitrogen's TOPO protein expression vector. When induced with IPTG, the resulting fusion proteins contains either aN-terminal Xpress TM epitope or a C-terminal V5 epitope. The fusion proteins were used in immunoprecipitation assays with antibodies against the epitope tags to test for proteinprotein interactions. While many of the assays were inconclusive and are still being optimized, the interaction of the C-terminally tagged dmXRCC2 with theN-terminally tagged hsRad51D gave a positive result. This single interspecies result suggests that homologous recombination is highly conserved between D. melanogaster and humans.