Le gène MLL (Mixed-Lineage Leukemia), un homologue du gène trithorax de la Drosophile, localisé à la bande chromosomique 11q23, est fréquemment réarrangé dans plusieurs types de leucémies, essentiellement suite à des translocations chromosomiques. Dans les différentes translocations chromosomiques, la partie N-terminale de MLL est fusionnée avec les séquences d’un gène partenaire. Malgré le grand nombre de partenaires de fusion rapportés, peu de fusions MLL ont été bien caractérisées sur le plan moléculaire. De plus, l’impact pronostique de plusieurs fusions moins fréquentes n’est pas bien établi. L’objectif de mon projet est de caractériser plusieurs translocations MLL qui ont été détectées dans 39 spécimens leucémiques collectés par la Banque de cellules leucémiques du Québec (www.bclq.gouv.qc.ca), et d’établir une corrélation entre les résultats de la cytogénétique et différents paramètres biologiques et cliniques des leucémies respectives. L’identification des gènes partenaires de fusion (GPF) dans notre série (30 échantillons étudiés), a révélé la fusion de MLL à un gène partenaire très récurrent dans 26 leucémies: MLLT3(AF9), AFF1(AF4), MLLT4(AF6), MLLT1(ENL), ELL; à un GPF modérément commun dans 1 leucémie : MLLT6(AF17); et à un partenaire rare de MLL dans 3 leucémies : GAS7 et AF15/CASC5 (2 cas). Nous avons poursuivi notre travail avec la caractérisation des points de cassure de deux fusions, soit MLL-ELL associée à un syndrome myéloprolifératif (une association rare), et MLL-GAS7 (une fusion rare de MLL), associée à une leucémie aiguë myéloïde. L’analyse des transcrits de fusion par RT-PCR et séquençage a révélé respectivement la fusion de l’exon 9 de MLL à l’exon 2 de ELL et des exons 7 ou 8 de MLL (deux transcrits) à l’exon 2 de GAS7. Ce travail permettra d’effectuer des études fonctionnelles et des projets de recherche translationnelle en utilisant ces spécimens de leucémies avec différents réarrangements de MLL, bien caractérisés sur le plan clinique et moléculaire. / The MLL (Mixed-Lineage Leukemia) gene, a human homolog of the Drosophila trithorax gene, located at chromosomal band 11q23, is frequently rearranged in several types of leukemia, mostly by chromosomal translocations. In different chromosomal translocations, the N-terminal part of MLL is fused to sequences of the partner gene. Despite the large number of fusion partners that have been reported, several gene fusions remain poorly characterized at the molecular level. Moreover, the prognostic impact of less frequent fusions is not well established. The aim of my project is to characterize different MLL fusions detected in 39 leukemic samples, collected by the Quebec Leukemia Cell Bank (www.bclq.gouv.qc.ca) and to correlate cytogenetics with the clinical and biological features of the corresponding leukemia. Identification of fusion partner genes in our series (30 samples studied), revealed fusion of MLL to one of the most frequent partners in 26 leukemias: MLLT3(AF9), AFF1(AF4), MLLT4(AF6), MLLT1(ENL), ELL; to a moderately common MLL fusion partner in 1 leukemia: MLLT6(AF17); and to a rare partner in 3 leukemias: GAS7 and AF15/CASC5 (2 cases). We have characterized the breakpoints of two fusions, MLL-ELL in a myeloproliferative syndrome (a rare association) and MLL-GAS7 (a rare MLL fusion) associated with acute myeloid leukemia. Fusion transcripts analysis by RT-PCR and sequencing revealed respectively, a fusion of MLL exon 9 to ELL exon 2 and of MLL exon 7 or exon 8 (two transcripts) to GAS7 exon 2. This study is essential to perform functional studies and translational research projects using these well characterized leukemic specimens with different MLL rearrangements.

We first studied factors associated with the rate of colonoscopy by primary care physicians (PCPs) in Ontario between the years 1996 and 2005. Next, we conducted an Instrumental Variable Analysis (IVA) to estimate the effect of colonoscopy on colorectal cancer (CRC) incidence and mortality on average-risk subjects aged 50-74 years. Finally, we explored two study cohorts, one by including subjects who had the outcomes during the exposure period (unselected cohort) and the other cohort by excluding those subjects (restricted cohort). We estimated the absolute risk reduction associated with colonoscopy in preventing CRC incidence and mortality using traditional regression analysis, propensity score analysis and IVA. PCPs who were Canadian medical graduates and with more years of experience were more likely to use colonoscopy. PCPs were more likely to use colonoscopy if their patient populations were predominantly women, older, had more illnesses, and if their patients resided in less marginalized neighborhoods (lower unemployment, fewer immigrants, higher income, higher education, and higher English/French fluency). Using PCP rate of discretionary colonoscopy as an instrumental variable, receipt of colonoscopy was associated with a 0.60% absolute reduction in 7-year CRC incidence and a 0.17% absolute reduction in 5-year risk of death due to CRC. The unselected cohort showed an increase in CRC incidence and mortality associated with colonoscopy, whereas the restricted cohort showed a reduction in CRC incidence and mortality associated with colonoscopy. In the restricted cohort, using different statistical models, the absolute risk reduction varied from 0.52-0.60% for CRC incidence and 0.08-0.17% for CRC mortality. There were social disparities in the use of colonoscopy by PCPs and this disparity increased as the overall use of colonoscopy increased over time. Colonoscopy is effective in reducing incidence and mortality due to CRC. Different methods of subject selection and statistical analysis provided different estimates of colonoscopy effectiveness.

We first studied factors associated with the rate of colonoscopy by primary care physicians (PCPs) in Ontario between the years 1996 and 2005. Next, we conducted an Instrumental Variable Analysis (IVA) to estimate the effect of colonoscopy on colorectal cancer (CRC) incidence and mortality on average-risk subjects aged 50-74 years. Finally, we explored two study cohorts, one by including subjects who had the outcomes during the exposure period (unselected cohort) and the other cohort by excluding those subjects (restricted cohort). We estimated the absolute risk reduction associated with colonoscopy in preventing CRC incidence and mortality using traditional regression analysis, propensity score analysis and IVA. PCPs who were Canadian medical graduates and with more years of experience were more likely to use colonoscopy. PCPs were more likely to use colonoscopy if their patient populations were predominantly women, older, had more illnesses, and if their patients resided in less marginalized neighborhoods (lower unemployment, fewer immigrants, higher income, higher education, and higher English/French fluency). Using PCP rate of discretionary colonoscopy as an instrumental variable, receipt of colonoscopy was associated with a 0.60% absolute reduction in 7-year CRC incidence and a 0.17% absolute reduction in 5-year risk of death due to CRC. The unselected cohort showed an increase in CRC incidence and mortality associated with colonoscopy, whereas the restricted cohort showed a reduction in CRC incidence and mortality associated with colonoscopy. In the restricted cohort, using different statistical models, the absolute risk reduction varied from 0.52-0.60% for CRC incidence and 0.08-0.17% for CRC mortality. There were social disparities in the use of colonoscopy by PCPs and this disparity increased as the overall use of colonoscopy increased over time. Colonoscopy is effective in reducing incidence and mortality due to CRC. Different methods of subject selection and statistical analysis provided different estimates of colonoscopy effectiveness.

Il est reconnu, depuis une centaine d’années, que des désordres de la coagulation, regroupés sous le terme de coagulopathies, sont souvent associés au développement néoplasique. Pendant de nombreuses années, ces coagulopathies furent souvent reconnues comme une simple conséquence du développement du cancer. D’ailleurs, pour les cliniciens, l’apparition de ces anomalies sanguines constitue souvent le premier signe clinique d’un cancer occulte. Toutefois, l’étude approfondie du lien existant entre le système hémostatique et le cancer indique que différents facteurs hémostatiques vont interagir avec soit l’environnement tumoral ou soit la tumeur elle-même et influencer le développement du cancer. Au cours de nos travaux, nous avons porté une attention particulière à deux protéines jouant un rôle primordial dans l’hémostase. Le facteur tissulaire (TF) et l’inhibiteur du facteur tissulaire (TFPI) peuvent jouer des rôles pro- ou anti-néoplasique, et ce indépendamment de leurs fonctions hémostatiques normales. Dans le premier volet de cette thèse, nous avons étudié les propriétés antiangiogéniques de TFPI. L’angiogenèse, soit la formation de nouveaux vaisseaux sanguins à partir du réseau pré-existant, est reconnue comme étant une étape clée du développement tumoral. D’après nos travaux, le TFPI peut inhiber la formation de structures de type capillaire des cellules endothéliales (CEs) de la veine ombilicale humaine (HUVEC), et ce à une IC 50 de 5 nM, soit la concentration physiologique de l’inhibiteur. De plus, le TFPI bloque la migration des cellules endothéliales lorsque ces dernières sont stimulées par la sphingosine-1-phosphate (S1P), une molécule relâchée lors de l’activation des plaquettes sanguines. Cette inhibition de la migration cellulaire s’explique par l’effet du TFPI sur l’adhésion des CEs. En effet, TFPI inhibe la phosphorylation de deux protéines clées participant à la formation des complexes d’adhésion focales soit FAK (focal adhesion kinase) et PAX (paxilin). L’inhibition de ces deux protéines suggère qu’il y ait une réorganisation des complexes focaux, pouvant expliquer la perte d’adhérence. Finalement, des études de microscopie confocale démontrent que les cellules traitées au TFPI changent de morphologie au niveau du cytosquelette d’actine provoquant une désorganisation des structures migratoires (pseudopodes). Les effets du TFPI au niveau de la migration, de l’adhésion et de la morphologie cellulaire sont strictement spécifiques aux cellules endothéliales humaines, puisque aucun n’effet n’est observé en traitant des cellules cancéreuses de glioblastomes (GB) humains, qui sont normalement des tumeurs hautement vascularisées. En résumé, cette première étude démontre que le TFPI est un inhibiteur de l’angiogenèse. Dans le second volet de cette thèse, nous nous sommes intéressés aux différents rôles de TF, le principal activateur de la coagulation. Cette protéine est également impliquée dans le développement néoplasique et notamment celui des médulloblastomes (MB) chez l’enfant via des fonctions hémostatiques et non-hémostatiques. Nos travaux démontrent que l’expression de TF est induite par la voie de signalisation de HGF (hepatocyte growth factor) et de son récepteur Met. Cet effet de HGF/Met semble spécifique aux MB puisque HGF ne peut stimuler l’expression de TF au niveau des cellules cancéreuses de glioblastomes. TF, exprimé à la surface des cellules médulloblastiques (DAOY), est responsable de l’activité pro-thrombogénique de ces cellules, ainsi qu’un acteur important de la migration de ces cellules en réponse au facteur VIIa (FVIIa). De plus, en étudiant 18 spécimens cliniques de MB, nous avons établi un lien entre l’intensité d’expression de TF et de Met. L’importance de cette corrélation est également suggérée par l’observation que les cellules exprimant les plus forts taux de TF et de Met sont également les plus agressives en termes d’index de prolifération et de dissémination métastatiques. En résumé, ces travaux représentent le point de départ pour la mise au point de TF comme un marqueur diagnostique clinique dans les cas de tumeurs du cerveau pédiatriques. De plus, l’élucidation de la voie de signalisation moléculaire responsable de l’expression de TF permet de mieux comprendre la biologie et le fonctionnement de ces tumeurs et de relier le profil d’expression de TF aux phénotypes agressifs de la maladie. Il est reconnu que HGF peut également jouer un rôle protecteur contre l’apoptose. Dans le troisième volet de cette thèse, nous avons remarqué que cette protection est corrélée à l’expression de TF. En réduisant à néant l’expression de TF à l’aide de la technologie des ARN silencieux (siRNA), nous démontrons que HGF ne protège plus les cellules contre l’apoptose. Donc, TF médie l’activité anti-apoptotique de HGF. TF assume cette protection en inactivant la phosphorylation de p53 sur la sérine 15, empêchant ainsi la translocation de p53 au noyau. Finalement, l’expression de TF et son interaction avec le FVIIa, au niveau des cellules médulloblastiques favorise la survie de ces dernières et ce même si elles sont soumises à de fortes concentrations de médicaments couramment utilisées en cliniques. Ce troisième et dernier volet démontre l’implication de TF en tant que facteur impliqué dans la survie des cellules cancéreuses, favorisant ainsi le développement de la tumeur. Dans son ensemble, cette thèse vise à démontrer que les facteurs impliqués normalement dans des fonctions hémostatiques (TFPI et TF) peuvent contribuer à réguler le développement tumoral. Tout système physiologique et pathologique est dépendant d’un équilibre entre activateur et inhibiteur et la participation de TF et de TFPI à la régulation du développement néoplasique illustre bien cette balance délicate. Par sa contribution anti- ou pro-néoplasique le système hémostatique constitue beaucoup plus qu’une simple conséquence du cancer; il fait partie par l’action de TF des stratégies élaborées par les cellules cancéreuses pour assurer leur croissance, leur déplacement et leur survie, alors que TFPI tente de limiter la croissance tumorale en diminuant la vascularisation. / For more then a century now, haemostatic disorders, also refered as coagulopathies, are recognized to be associated to neoplasia development. At first, these coagulopathies were often seen as the first clinical symptom of an occult malignancy and as such they were foreseen as merely consequence of cancer. However recent studies allowed to determine that a molecular link between haemostasis and cancer exists. Haemostatic protein were found to interact with the tumor environment or the tumor itself. In this thesis, we look at two important haemostatic proteins involved in anti- or pro-tumoral activities. These proteins we looked at were, tissue factor (TF), which as been identified as the main trigger of blood coagulation an its natural inhibitor which is named tissue factor pathway inhibitor (TFPI). In our investigations we focus on the non-haemostatic function of these proteins. First of all, we studied the effect of TFPI on angiogenesis. Angiogenesis, the formation of new blood vessels from pre-existing ones, is a critical component of cancer. In this first paper we demonstrate that, in addition to its anticoagulant properties, emerging data show that TFPI may also regulate endothelial cell functions via a non-haemostatic pathway. At physiological concentration, TFPI inhibits both endothelial cell migration and their differentiation into capillary-like structures in vitro. These effects were specific to endothelial cells since no inhibitory effect was observed on the migration of tumor (glioblastoma) cells. Inhibition of endothelial cell migration was correlated with a concomitant loss in cell adhesion, suggesting an alteration of focal adhesion complex integrity. Accordingly, we observed that TFPI inhibited the phosphorylation of focal adhesion kinase and paxillin, two key proteins involved in the scaffolding of these complexes and that this effect was specific to endothelial cells. These results suggest that TFPI influences the angiogenic process via a non-haemostatic pathway, by downregulating the migratory mechanisms of endothelial cells. Met, the only known receptor for hepatocyte growth factor (HGF) is a member of the receptor tyrosine kinases (RTKs) family and recently this RTK emerged as one important contributor to human neoplasia. In physiologic and pathologic conditions, Met trigger various cellular functions related to cell proliferation and migration, inhibition of apoptosis and also regulate a genetic program leading to coagulation. Since medulloblastoma (MB) express high level of tissue factor (TF), the main initiator of blood coagulation, we therefore wanted to know if there was a link between Met and TF expression in these pediatric tumors. In this work we demonstrate that stimulation of MB cells in vitro with HGF lead to overt expression of TF. These data correlate with analysis of clinical MB tumors specimens, were tumors expressing high level of Met also express high level of TF. This HGF/Met/TF pathway seems specific to MB only since no effect was observed on glioblastoma cells. TF expression in MB leads to a pro-coagulation state which could initiate thrombosis and the formation of a provisional fibrin matrix. Furthermore, TF can also mediate non-haemostatic function such as cell migration, thus helping cancer cells to form distant metastasis. Taken together these results suggest that HGF/Met pathway is responsible for TF expression in MB and explained how TF participate to tumor aggressiveness. In the third part of this thesis we look at the effect of TF on cell survival as a huge body of evidence suggest a role for TF and its natural ligand FVIIa on cells death (apoptosis) protection. In this study, we show that HGF-induce anti-apoptotic effect on DAOY MB cells is correlated to TF expression. Using TF siRNA we completely reversed this anti-apoptosis activity. TF is responsible of p53 inactivation, thus allowing DAOY to resist to very high concentrations of the chemotherapeutic drug Etoposide. These finding highlights the importance of understanding the molecular biology of MB, to achieve a better clinical management and also find new therapeutic targets. Overall, this thesis demonstrates that normal haemostatic protein such as TF and TFPI are also involved in tumor development. The different activities of TF and TFPI on cancer reflected the fact that every physiological or pathological system is dependent of a balance between activator and inhibitor. Furthermore the molecular link described in this thesis between haemostasis and cancer constitutes an argument against the fact that the haemostatic system is simply a consequence of cancer. Instead we show that TF is part of a strategy designed to improve tumor expansion while TFPI try to restrain the tumor growth by limiting tumor angiogenesis.

Radiation therapy is administered to more than 50% of patients diagnosed with cancer. Mechanisms of interaction between radiation and tumour cells are relatively well understood on a molecular level, but much remains uncertain regarding how radiation interacts with the tumour as a whole. Recent studies have suggested that tumour response to radiation may in fact be regulated by endothelial cell response, consequently stressing the role of tumour blood vessels in radiation treatment response. As a result, various treatment regimens have been proposed to strategically combine radiation with vascular targeting agents. A great deal of effort has been aimed towards developing efficient vascular targeting agents. Nonetheless, no optimal method has yet been devised to strategically deliver such agents. Recent evidence suggesting that these drugs may “normalize” tumour blood vessels and enhance radiosensitivity, is supporting experiments where anti-angiogenic drugs are combined with cytotoxic therapies such as radiotherapy. In contrast, ultrasound-stimulated microbubbles have recently been demonstrated to enhance radiation therapy by biophysically interacting with endothelial cells. When combined with single radiation doses, these microbubbles are believed to cause localized vascular destruction followed by tumour cell death. Finally, a new form of ‘pro-angiogenics’ has also been demonstrated to induce a therapeutic tumour response. The overall aim of this thesis is to study the role of tumour blood vessels in treatment responses to single-dose radiation therapy and to investigate radiation-based vascular targeting strategies. Using pharmacological and biophysical agents, blood vessels were altered to determine how they influence tumour cell death, clonogenicity, and tumour growth, and to study how these may be optimally combined with radiation. Three-dimensional high-frequency power Doppler ultrasound was used throughout these studies to investigate vascular response to therapy.

Tyrosyl phosphorylation plays an important role in many fundamental cellular processes, including cell growth, differentiation and proliferation. The levels of phosphotyrosine (pY) are regulated by the opposing actions of protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs). A limitation to understanding the roles of PTPs in physiological and pathological cell signaling has been the absence of global proteomic approaches that enable the systematic and comprehensive analysis of PTP expression, regulation and function. This dissertation describes the development and application of novel proteomic methodologies that permit the global analysis of PTP expression (qPTPome), regulation (by oxidation and nitrosylation; q-oxPTPome) and substrates/binding proteins. These methods provide a workflow to begin assessing PTP function at a systems level, rather than its current targeted format. Application of these techniques will provide invaluable information to begin bridging the gap in our understanding of PTP and PTK function in normal and malignant cell signaling.

The diagnosis and monitoring of AML relies predominantly on the identification of blast cells in the bone marrow and peripheral blood. While at the time of diagnosis the identification of leukemic cells is relatively easy, during remission the identification of small numbers of blasts is problematic. This is most evident by the fact that patients who achieve complete remission frequently relapse, despite pathologic examination indicating a marked reduction in leukemic cell burden. In this thesis I have explored the potential of using serum proteins secreted by leukemic cells as a means of monitoring disease in patients. To identify proteins that might be useful for monitoring, I took advantage of published gene expression arrays and looked into online bioinformatics databases. Using specific characteristics, I was able to identify approximately 107 candidate proteins secreted by AML cells. RT-PCR analysis and ELISA assays were performed to evaluate the variability of expressions and serum level differences of twelve different proteins in the list.

The diagnosis and monitoring of AML relies predominantly on the identification of blast cells in the bone marrow and peripheral blood. While at the time of diagnosis the identification of leukemic cells is relatively easy, during remission the identification of small numbers of blasts is problematic. This is most evident by the fact that patients who achieve complete remission frequently relapse, despite pathologic examination indicating a marked reduction in leukemic cell burden. In this thesis I have explored the potential of using serum proteins secreted by leukemic cells as a means of monitoring disease in patients. To identify proteins that might be useful for monitoring, I took advantage of published gene expression arrays and looked into online bioinformatics databases. Using specific characteristics, I was able to identify approximately 107 candidate proteins secreted by AML cells. RT-PCR analysis and ELISA assays were performed to evaluate the variability of expressions and serum level differences of twelve different proteins in the list.

Therapeutic response assessment is a key component in adaptive image-guided radiotherapy. Conventional anatomic measures of response offer little information about the spatial distribution of tumor change. Recently developed voxel-wise response assessment methods operating on functional and biological imaging are better capable of evaluating the heterogeneity of response within the tumor, and thus may yield greater sensitivity than conventional approaches. However, voxel-wise analyses are limited by local registration uncertainties inherent to longitudinal imaging of tumors with changing morphology. A multi-resolution local histogram (LH) moment-based measure of voxel similarity was developed for the purpose of assessing the strength of correspondence between voxels of serial tumor images. This measure was first benchmarked through a series of experiments designed to establish robustness to image intensity variation and sensitivity to alterations in tissue structure through application of simulated deformations. The LH similarity method was subsequently developed as a means of mapping the spatial extent of structural change in tumors through the incorporation of an estimate of image complexity. The change maps were applied to a voxel-wise analysis of diffusion-weighted magnetic resonance imaging of patients with glioblastoma, acquired pre- and post-chemoradiotherapy. The sensitivity of the voxel-wise analysis in differentiating responding/stable patients from non-responding/progressing patients was improved by stratifying the analysis voxels according to regions of interest (ROI) based on the LH similarity-based estimate of tumor change. Meaningful correspondence relationships between evaluated voxels are essential for accurate image-based quantification of tumor structure and function with voxel-wise analysis techniques. The LH similarity methods developed here can robustly evaluate the quality of spatial and temporal voxel correspondence relationships and provide an automated tool for ROI selection and voxel change stratification. It is readily extendable to the analysis of the wide array of anatomic, functional and biological imaging currently used to characterize tumors, guide therapy and assess response.

Therapeutic response assessment is a key component in adaptive image-guided radiotherapy. Conventional anatomic measures of response offer little information about the spatial distribution of tumor change. Recently developed voxel-wise response assessment methods operating on functional and biological imaging are better capable of evaluating the heterogeneity of response within the tumor, and thus may yield greater sensitivity than conventional approaches. However, voxel-wise analyses are limited by local registration uncertainties inherent to longitudinal imaging of tumors with changing morphology. A multi-resolution local histogram (LH) moment-based measure of voxel similarity was developed for the purpose of assessing the strength of correspondence between voxels of serial tumor images. This measure was first benchmarked through a series of experiments designed to establish robustness to image intensity variation and sensitivity to alterations in tissue structure through application of simulated deformations. The LH similarity method was subsequently developed as a means of mapping the spatial extent of structural change in tumors through the incorporation of an estimate of image complexity. The change maps were applied to a voxel-wise analysis of diffusion-weighted magnetic resonance imaging of patients with glioblastoma, acquired pre- and post-chemoradiotherapy. The sensitivity of the voxel-wise analysis in differentiating responding/stable patients from non-responding/progressing patients was improved by stratifying the analysis voxels according to regions of interest (ROI) based on the LH similarity-based estimate of tumor change. Meaningful correspondence relationships between evaluated voxels are essential for accurate image-based quantification of tumor structure and function with voxel-wise analysis techniques. The LH similarity methods developed here can robustly evaluate the quality of spatial and temporal voxel correspondence relationships and provide an automated tool for ROI selection and voxel change stratification. It is readily extendable to the analysis of the wide array of anatomic, functional and biological imaging currently used to characterize tumors, guide therapy and assess response.