The freshwater snail Biomphalaria glabrata is an intermediate host for Schistosoma mansoni parasites, causing one of the most prevalent parasitic infections in mammals, known as schistosomiasis (Bilharzia). Due to its importance in the spread of the disease B. glabrata has been selected for whole genome sequencing and is now a molluscan model organism. In order to aid the sequencing project and to understand the structure and organisation of B. glabrata’s genome at the chromosomal level, a G-banded karyotype has been established. Unlike in any other previous reports, two heteromorphic chromosomes have been identified in the genome of B. glabrata and for the first time snail ideograms have been produced. In addition to characterising the snail chromosomes, a methodology for mapping single copy B. glabrata genes onto these chromosomes has also been established, and 4 genes have successfully been mapped using fluorescence in situ hybridisation. In the relationship between a parasite and a host organism, it is of fundamental importance to understand the basic biology and interfere with the life cycle to reveal how the parasite controls and elicits host gene expression for its own benefit. This study is also directly addressing this aspect of host – parasite interactions by investigating the effects of schistosome infection on the genome and cell nuclei of the host snail B. glabrata. Upon infection with S. mansoni miracidia, genes known to be involved in the host response to the parasite are dramatically relocated within the interphase snail nuclei. These events are in conjunction with the up-regulation of gene expression, indicating a parasite induced nuclear event. Moreover, a differential response between the schistosome-resistant and schistosome-susceptible snails is also reported. This is the first time this has been described in a host – pathogen relationship. The precise organisation of the genome is critical for its correct functioning. The genome is non-randomly organised and this level of organisation is very much influenced by the nuclear architecture. Being a molluscan model organism with the availability of a unique cell line, B. glabrata is a remarkable organism for the studies of nuclear and genome biology. For this reason, in this thesis the snail nuclear architecture was also investigated. For the first time PML bodies, transcription factories, and nuclear myosin 1 beta have been visualised in the snail nuclei. A heat shock system was also developed to study the role of these structures in the snail. Upon heat stimuli gene loci were found to reposition and co-localise with transcription factories, which was in parallel with the up-regulation of gene expression. The mechanism of this genome reorganisation was explored by investigating nuclear motor structures in the snail. By using a motor inhibitor on snail cells, gene repositioning and subsequent expression after heat shock was blocked. This is the first time this has been shown in any organism. Thus, due to the ease of use of the snails with respect to maintenance, handling, and treatments, B. glabrata is making a very useful new model organism to study spatial genomic events.

A biomarker is a measurable biological characteristic that can be evaluated as an indicator of normal (physiological) or abnormal (pathogenic) processes. In cancer research, there remains a need for the identification of new biomarkers that can be used to close the gaps in the current understanding of cancer development, progression and treatment. HLXB9 is a homeobox gene located at 7q36. It encodes a transcription factor important in embryonic development. Its accurate regulation is significant in the organogenesis of the endodermal germ layer particularly in the development of the pancreas. After development, its expression is downregulated in the majority of adult tissues. Recently, aberrant expression of HLXB9 has been found in certain cancers such as hepatocellular carcinoma, testicular cancer, pancreatic cancer and leukaemia. The location of genes and chromosomes in the nuclei of healthy human cells has been shown to be non-random, therefore understanding the mechanisms that regulate nuclear genome organisation is important in understanding of cancer biology in cases where genes are relocated. The nuclear localisation of genes as a biomarker of tumour development in cancer is a relatively new but promising field in cancer research. Previous research by our group found overexpression of HLXB9 corresponded to an altered positioning of this gene in the nucleus of paediatric leukaemia patients harbouring the translocation t(7;12)(q36;p13). In this project, HLXB9 was evaluated as a biomarker in cancer development. In the first study, a new dual colour probe for the detection of the t(7;12)(q36; p13) was validated by fluorescence in situ hybridisation (FISH) in leukaemia patient samples previously described as harbouring the translocation. The expression of HLXB9 was then analysed by RT-PCR in 48 patients diagnosed with various haematological disorders. 25% of patients analysed expressed HLXB9. Additionally, HLXB9 expression in leukaemia was found in patients with normal copies of chromosome 7 suggesting HLXB9 expression can occur independently of chromosome 7 abnormalities. An attempt was made to evaluate the link between HLXB9 expression and its nuclear localisation in these patients. Four online databases were interrogated to identify cancer types and subtypes that exhibit differential HLXB9 expression. HLXB9 expression was not altered in the majority of cancer cases investigated. However, aberrant HLXB9 expression was found in cancer types not previously reported as showing differential HLXB9 expression such as kidney cancer, lung cancer and endometrial cancer. The identification of aberrant expression of HLXB9 in these cancer types provides a new avenue for research into understanding cancer development and progression in these tumour types. Finally, the expression of HLXB9 was analysed in four breast cancer cell lines by quantitative RT-PCR and immunofluorescence. Additionally, the prognostic significance of HLXB9 expression was evaluated in publicly available breast cancer survival databases (Kaplan Meier plotter and BreastMark). Altogether, the findings emerging from this thesis work show that, although the potential for HLXB9 to be used as biomarker is appealing, further work is required to confirm the value of this biological parameter in the diagnosis, prognosis and progression of cancer.

L'ADN peut être endommagé par des facteurs environnementaux ou intrinsèques au fonctionnement des cellules. Ces facteurs induisent différents types de lésions dont les cassures double brins (CDBs). Les CDBs sont particulièrement dangereuses pour les cellules et une réparation inefficace ou non précise de ces cassures peut entraîner des mutations ou des translocations qui peuvent être à l'origine de cancer. Afin d'éviter l'instabilité génétique que peuvent induire les CDBs, les cellules ont développé deux principaux mécanismes de réparation: la ligature d'extrémités non homologues (NHEJ pour non homologous end joining) et la recombinaison homologue (HR pour homologous recombination). L’utilisation de l’un ou de l’autre de ces mécanismes est finement régulée et une dérégulation de cet équilibre induit une importante instabilité génomique.Tous ces mécanismes ont lieu dans le noyau des cellules qui, chez les mammifères est fortement hétérogène, comportant différents compartiments et des régions où la chromatine est plus ou moins compacte. Cette hétérogénéité implique que la réparation de l’ADN doit pouvoir être efficace dans différents contextes nucléaires. Au cours de ma thèse, j’ai étudié l’influence de l’architecture nucléaire sur le choix des mécanismes de réparation des CDBs. J’ai montré d’une part que la protéine appartenant au pore nucléaire Nup153 influence l’équilibre entre HR et NHEJ et d’autre part que la position d’une CDB influe sur le choix du mécanisme de réparation.Mes résultats démontrent que l’organisation des gènes dans le noyau est un nouveau paramètre à prendre en compte dans l’étude des mécanismes de réparation de l’ADN et de tumorigénèse. / DNA is constantly assaulted by various damaging agents, leading to different types of lesions including double-strand breaks (DSBs). DSBs are the most harmful lesions to the cells and their inaccurate or inefficient repair can trigger genomic instability and tumorigenesis. To cope with DSBs, cells evolved several repair pathways, including non-homologous end joining (NHEJ) and homologous recombination (HR). A fine regulation of the balance between these two pathways is necessary to avoid genomic instability.All of these mechanisms happen in the nucleus, which is highly heterogeneous in mammalian cells. Indeed, it encompasses several compartments and regions of various chromatin compaction levels. My PhD project focused on the influence of nuclear architecture on DNA repair pathway choice. I demonstrated on one hand that the nuclear pore protein Nup153 influences the balance between HR and NHEJ and on the other hand that the position of a DSB influences the choice of the repair pathway that will be used.My results demonstrate that gene positioning is a new important parameter in the study of DNA repair and tumorigenesis.