Errors in DNA replication can cause chromosome instability and gross chromosomal rearrangements (GCRs). For my thesis work I investigate how chromosome instability can originate in the telomere. Here I report how defects in Cdc13, a telomere specific protein, lead to chromosome instability and GCRs in Saccharomyces cerevisiae. Using a temperature sensitive mutant of Cdc13, I find that cdc13-induced instability can be induced in a single cell cycle and synergizes with replication stress (dNTP depletion via hydroxyurea). Additionally, I find that Cdc13 has to be functional during the cell’s S phase to suppress chromosome instability. Further genetic analysis suggests that that cdc13-induced chromosome instability depends on the generation of single stranded (ss)DNA, but not on the activity of canonical double strand break (DSB) repair pathways such as homologous recombination or non-homologous end joining. Finally, I demonstrate that telomeric unstable chromosomes can later progress and trigger rearrangements at centromeric loci. This system, using the conditional nature of the cdc13 mutation, promises a more complex analysis of the ontogeny of chromosome instability: in this case from errors semi-conservative DNA replication through the telomere to the formation and resolution of unstable chromosomes.

The gain or loss of whole chromosomes, known as aneuploidy, is a distinguishing feature of cancer cells. The rapid gain or loss of hundreds of genes dramatically alters a cell's genomic landscape and is typically detrimental to cell survival under normal conditions. However, cancer cells display enhanced proliferation and overcome multiple conditions of stress, suggesting aneuploidy may increase cellular fitness. Furthermore, distinct patterns of aneuploidy are found in cancers from different anatomical sites. Despite these observations, scant research has sought to examine the role of aneuploidy in cancer, or determine whether aneuploidy is a driver or passenger mutation, or why certain aneuploidies appear to be selected for and others against. To investigate the role of aneuploidy in cancer cell fitness, we utilized the diploid colorectal cancer (CRC) cell line DLD1 and two trisomic variants carrying an extra copy of either chromosome 7 or chromosome 13, two trisomies frequently seen in colorectal cancer. To assess fitness, we compared proliferation, anchorage-independence, and invasiveness in aneuploid CRC cells versus their diploid counterpart when grown under various culture conditions, including regular media, serum-free media, cytotoxic drug-containing media, and hypoxia. We found that aneuploid cells proliferated better than diploid cells under all but standard culture conditions. Moreover, regardless of growth condition, we found that aneuploid CRC cells formed larger and more numerous colonies in soft agar (anchorage-independent growth), and displayed greater invasiveness (assessed by matrigel invasion assay). Taken together, these results indicate that aneuploidy enhances the fitness of CRC cells under stressful conditions that are likely to occur in the tumor microenvironment. / Master of Science

Chromosome Instability (CIN) is defined as an increase in the rate at which whole chromosomes or large parts are gained or lost. CIN is not only associated with virtually all tumor types, but it is associated with aggressive tumors, tumor recurrence, acquisition of multidrug resistance and poor patient prognosis. However, the genes and molecular defects that contribute to CIN are poorly understood. I hypothesize that KIF11 is an essential gene for chromosomes integrity during mitosis and therefore any defect in KIF11 expression or function will induce CIN and contribute to tumorigenesis. Accordingly, KIF11 was either silenced using siRNA or inhibited using monastrol within two distinct human cell lines and was investigated for CIN associated phenotypes. Here, I have identified and validated KIF11 as a novel CIN gene. This study represents the first steps necessary to identify and develop novel treatments design to target origins of CIN in CIN associated cancers. / February 2017

Chromosomal fragile sites are specific loci associated with a high frequency of breakage and recombination. A cell's ability to repair and/or replicate through a lesion is prerequisite to the maintenance of genomic stability. An improved understanding of fragile site biology and its contribution to replication defects and genomic instability is critical for prevention, intervention, and diagnosis of genetic diseases such as cancer. This work seeks to identify and characterize both trans and cis fragile sites associated elements involved in instability onset and progression. An array of Saccharomyces cerevisiae isogenic DNA repair deficient mutants were utilized to identify genes contributing to the stability or instability of a natural fragile site ~ 403 kb from the left telomere on chromosome VII. Findings suggest that the RAD52 epistasis group, the MRX complex, non-homologous end-joining (NHEJ) pathways, MUS81 and SGS1 helicases, translesion polymerases, and a majority of the post replication repair (PRR) proteins are all required for faithful replication of the 403 fragile site and likely other fragile sites as well. In contrast I found that MMS2, previously thought to be specific to the PRR pathway, is required to prevent the fusion of repetitive elements within the 403 site. mgs1 (homolog of the human Werner helicase interacting protein, WHIP) and pol3-13 (a subunit of the DNA polymerase delta) mutants also exhibited reduced instability in checkpoint deficient cells. These findings suggest previously uncharacterized function of Mgs1, Pol3 and Mms2 in regulation of genome regions at risk of replication damage. We further find the presence of inverted repeats (IR) are sufficient to induce instability. Two IR's proximal to the 403 site consistently fuse to generate acentric and dicentric chromosomes involving the 403 fragile site and a newly identified site on chromosome VII as well. The frequency of fusion events is aggravated by chromatin traffic stressors such as tRNA transcription induced fork stalling and replisome termination regions.

Tetraploid cells, which typically arise from errors in mitosis, are genomically unstable and promote tumorigenesis. Recent evidence suggests that ~40% of tumors undergo a tetraploid intermediate during their evolution, with ~20% of all solid tumors maintaining a tetraploid karyotype. Consequently, tumor suppression mechanisms have evolved to limit the proliferation of tetraploid cells. However, it remains unclear how tetraploid cells are able to overcome these tumor suppression mechanisms to initiate tumorigenesis. To address this unresolved question, we developed and validated a genome-wide screening assay to comprehensively identify miRNAs whose overexpression promotes tetraploid cell proliferation. We then profiled those miRNAs to mechanistically define how each miRNA functions to overcome tetraploid induced arrest. Our results demonstrate that miRNAs can promote proliferation via multiple mechanisms, including inhibition of the p53 tumor suppressor pathway, hyperactivation of growth factor signaling, and inactivation of the Hippo tumor suppressor pathway. Additionally, we investigated mechanisms that facilitate tumorigenesis from proliferating tetraploid cells. It is well established that tetraploid cell proliferation promotes both numerical and structural chromosome abnormalities, although the precise mechanisms underlying these phenomena remain incompletely understood. Chromosome missegregation can lead to the formation of micronuclei separate from the primary nucleus, a result of either lagging or polar chromosomes. Micronuclei have been shown to rupture during interphase, leading to massive amounts of DNA damage and chromothripsis, resulting in extensive DNA breaks and rearrangements. We followed micronuclei formed from both lagging and polar chromosomes to determine whether all micronuclei are equally prone to nuclear envelope rupture. Our results show that polar micronuclei have nuclear envelopes that are significantly more stable than the nuclear envelopes of micronuclei formed from lagging chromosomes. Furthermore, micronuclei have been shown to be deficient at nuclear import of proteins. Kinetochore assembly, vital for proper chromosome segregation, is dependent upon the nuclear import of many proteins. We sought to establish whether micronuclei have defects in kinetochore assembly since without functional kinetochores, chromosomes cannot bind to the mitotic spindle. We found that chromosomes in micronuclei fail to assemble kinetochores efficiently, and thus promote additional chromosome missegregation. Overall, this dissertation identifies multiple mechanisms that facilitate tumorigenesis from tetraploid intermediates.

We have used Chinese hamster ovary (CHO)-human hybrid cells containing chromosomes 16, 18, X, and 21 to test the ability of human kinetochores to successfully bind to spindle microtubules and to be distributed to the daughter cells. We have established the intrinsic rate of non-disjunction among these human chromosomes noted above and compared these rates with those in cells presented with mitotic challenges such as taxol, nocodazole, and mitosis with unreplicated genomes (MUG). Cells were grown on culture slides, fixed and processed for immunofluorescence and fluorescence in situ hybridization (FISH). Daughter pairs were identified by staining with anti-á-tubulin to identify midbodies. Human centromere DNA probes were used for FISH in order to test for the successful passage of human kinetochores to daughter cells during anaphase. Our data indicate that different human kinetochores vary in their ability to properly engage the spindle and to be successfully distributed. In addition, mitotic challenges have been shown to affect the rate of non-disjunction. The mechanism of this effect is not yet known.

No description available.

Human pluripotent stem cells are increasingly used for cell-based regenerative therapies worldwide, with the use of embryonic and induced pluripotent stem cells as potential treatments for a range of debilitating and chronic conditions. However, with the level of chromosomal aneuploidies the cells may generate in culture, their safety for therapeutic use could be in question. This study aimed to develop sensitive and high-throughput assays for the detection and quantification of human pluripotent stem cell aneuploidies, to assess any changes in their positioning in nuclei, as well as investigate the possible roles of lamins in the accumulation of aneuploidies. Using Droplet Digital PCR™, we optimised the detection of aneuploid cells in a predominantly diploid background. An assay was established for the sensitive detection of up to 1% of mosaicism and was used for the monitoring of low-level chromosome copy number changes across different cell lines, conditions and passages in the human pluripotent stem cells. In addition, fluorescence in-situ hybridisation was used to map genes ALB and AMELX on chromosomes 4 and X, respectively, in karyotype-stable chromosome X aneuploid lymphoblastoid cell lines. Our results demonstrated significant alternations in the gene loci positioning in the chromosome X aneuploid cell lines. Using the same established method, the positioning of ALB and AMELX was monitored, alongside the genomic instability with ddPCR™, in the different human pluripotent stem cell lines, conditions and passage. We demonstrated a highly plastic nuclear organisation in the pluripotent stem cells with many changes occurring within a single passage. Furthermore, these results were not exclusive to a single cell line or condition, regardless of the presence or absence of feeder cells and of passage number, and the flexibility of the chromatin organisation remained throughout the duration of the study. We demonstrated high levels of genomic instability with recurrent gains and losses in the AMELX copy number in the human embryonic stem cells during the course of our study, however no significant changes in their gene loci positioning from these abnormalities were observed. xvi | P a g e Additionally, we observed reduced levels of lamin B2 in the aneuploid lymphoblastoid cell lines and complete loss in some hPSC samples. Our results support recent findings that suggest a link between lamin B2 loss and the formation of chromosome aneuploidies in cell culture. In conclusion, our data demonstrates several key novel findings. Firstly, we have established a sensitive technique for the detection of up to 1% mosaicism, which to our knowledge is the most sensitive assay currently available. Secondly, we showed significant changes in the gene loci positioning between aneuploid and diploid cell lines. Thirdly, utilising our novel ddPCR™ assay, we demonstrated the karyotypical instability of hPCSs with consistent gains and/or loses of gene copy numbers in a short period of time in culture. When studying the effects of different growth conditions, we showed that the karyotypical instability was not exclusive to a single condition or a combination of conditions, and what is more, the karyotypical abnormalities detected were not observed to change the gene positioning of hPSCs significantly, with the genome organisation remaining plastic. Finally, our results support a potential association of lamin B2 loss and karyotypical instability. We conclude that more sensitive and robust techniques need to be readily used by clinicians for the screening of potential therapeutic hPSCs.

Les hélicases sont des enzymes ubiquitaires catalysant la séparation de l’ADN double-brin et impliquées dans la réplication, la réparation de l’ADN et dans le maintien des télomères. Chez l’Homme, 3 hélicases présentent des mutations responsables de syndromes cliniques : WRN pour le syndrome de Werner, BLM pour le syndrome de Bloom et RECQL4 pour le syndrome de Rothmund-Thomson. Tous ces syndromes associent un vieillissement pathologique accéléré à un risque accru de développement de cancer notamment par une augmentation de l’instabilité génomique. Les connaissances sur les mécanismes moléculaires et cellulaires impliqués dans ces maladies du vieillissement sont encore très partielles, notamment en ce qui concerne le lien entre l’instabilité génomique et le vieillissement. Au cours de ce projet, l'utilisation de prélèvements sanguins et cutanés de patients atteints de ces pathologies rares a permis de générer des modèles de cellules souches pluripotentes induites (iPS). Ces cellules présentent l’avantage de s’auto-renouveler et de pouvoir théoriquement se différencier dans tous les types cellulaires d’un organisme. Parallèlement, un témoin de sénescence a été généré de la même manière avec des cellules d’un patient souffrant du syndrome de la progéria de Hutchinson-Gilford. Après caractérisation de ces cellules, nous avons identifié des ensembles de phénotypes cellulaires et moléculaires dans le but de récapituler in vitro les pathologies. Nous avons également engagé les cellules iPS dans des voies de différenciation proches des tissus atteints dans les pathologies in vivo. Enfin, nous avons étudié la stabilité génomique de ces lignées dans les différents types cellulaires cultivés. Ainsi nous avons observé que la lignée Bloom est le siège de recombinaisons particulièrement fréquentes et est caractérisée par une instabilité du génome dans tous les types cellulaires étudiés. Egalement, la lignée Werner semblerait se distinguer par une instabilité de ses télomères. Enfin, l’ensemble des lignées des pathologies du vieillissement prématuré présenterait un défaut mitochondrial. / Helicases process the double-stranded DNA dissociation. They are involved in replication, DNA repair and maintenance of telomeres. In human, 3 helicases display mutations responsible for clinical syndromes: WRN for the Werner syndrome, BLM for the Bloom syndrome and RECQL4 for the Rothmund-Thomson syndrome. All these diseases cause premature ageing and high risk of cancer. Molecular and cellular mechanisms involved in these diseases are not well defined. Particularly, little is known concerning the link between genomic instability and ageing. During this project, we used blood samples and skin biopsies of affected patients to generate models by reprogramming cells to induced pluripotent stem cells (iPSCs). These cells have the advantage of self-renewing and theoretically could be differentiated in all cell types. At the same time, an iPSC senescence control was performed from cells of a Hutchinson-Gilford Progeria syndrome patient. iPSCs were characterized for pluripotency. In the aim of recapitulate these pathologies in vitro, we identified sets of cellular and molecular phenotypes. We also engaged differentiation of iPSCs in cell pathways closed to the affected tissues in vivo. Finally, we studied the genomic stability of iPSCs and derived cells. We observed that Bloom cells are susceptible to frequent recombinations and are characterized by a genome instability through all studied cell types. Werner cells showed an instability of telomeres length. Finally, all premature ageing diseases displayed mitochondrial defects.

Le raccourcissement télomérique est la source majeure de l'instabilité chromosomique (CIN) au cours de la progression tumorale. Nous avons montré que les cellules humaines embryonnaires de rein (cellules HEK) ayant traversé une période de CIN subissent des vastes changements dans l'expression des microARNs, ce qui induit une transition épithélio-mésenchymateuse (TEM), un processus permettant aux cellules cancéreuses épithéliales migrer et envahir de nouveaux tissus et former des métastases. Notre travail a aussi suggéré que les cellules ayant subi une TEM étaient capables de former des tumeurs dans un microenvironnement sénescent. De surcroît, cette évolution dans la capacité tumorale était associée à une dérégulation supplémentaire des microARNs et à l'acquisition des propriétés des cellules souches. Afin d'étudier comment ce potentiel est mis en place au cours de l'instabilité chromosomique et au contact avec le microenvironnement sénescent, nous avons modulé les niveaux d'expression de miR-145 et avons démontré que la répression de miR-145 était nécessaire pour le développement des caractéristiques des cellules souches. Afin de mieux comprendre l'impact de CIN sur le programme génétique des cellules épithéliales, nous avons utilisé des approches de haut débit et avons caractérisé les changements des paysages chromatiniens et leur mise en place dans les cellules ayant traversé une période de CIN. Nos résultats révèlent pour la première fois que l'instabilité télomérique modifie profondément la distribution des marques d'histones en conduisant aux changements d'expression des gènes et au processus de transformation des cellules épithéliales pré-tumorales. / Telomere shortening is a major source of chromosome instability (CIN) at early stages during carcinogenesis. However, the mechanisms through which telomere-driven CIN (T-CIN) contributes to the acquisition of tumor phenotypes remain uncharacterized. We have shown that human epithelial kidney (HEK) cells undergo massive microRNA deregulation upon CIN, in particular a miR-200-dependent epithelial-mesenchymal transition (EMT), which is thought to enable epithelial cancer cells to migrate and invade other tissues to form metastases. Our work also indicated that CIN+ cells that underwent EMT were able to form tumors in a senescent microenvironment. Notably, this progression in tumor capacity was associated with further microRNA deregulation and the manifestation of enhanced stem-like properties. To investigate how stem-like properties are acquired in CIN+ cells in the contact with senescent microenvironment we adapted knockdown and overexpression approaches to modulate miR-145 expression, and demonstrated that enhanced stem-like properties depended on miR-145 repression. To fully apprehend the impact of CIN on the genetic program of epithelial cells, we used an unbiased approach to characterize the chromatin state of HEK CIN+ cells and uncover genome wide redistributions that were in direct correlation with gene expression changes. Our results reveal for the first time that T-CIN profoundly modifies the chromatin landscape genome-wide thereby fueling the transformation process of pre-tumor epithelial cells.