Low-grade diffuse astrocytomas have an intrinsic tendency for malignant progression but the factors determining the kinetics of this process are still poorly understood. We report here the case of a male patient who developed a fibrillary astrocytoma at the age of 33 years and who underwent six surgical interventions over a period of 17 years without radiotherapy or chemotherapy. The first three biopsies spanned a period of 11 years and led to the diagnosis of low-grade, diffuse astrocytoma (WHO grade II), with a growth fraction (MIB-1 labeling index) of 2.3-3.7%. The fourth to sixth biopsies showed histological features of anaplastic astrocytoma (WHO grade III), with growth fractions between 5.0 and 10.5%. The fraction of gemistocytic neoplastic astrocytes also increased, from 0.3% in the first biopsy to 17.5% in the last biopsy and preceded the increase in proliferative activity and transition to anaplastic astrocytoma. The fraction of tumor cells immunoreactive to BCL-2 increased from 0.3% to 8.2%. A p53 mutation in codon 273 (CGT→TGT, Arg→Cys) was identified in the first biopsy and persisted throughout the course of the disease. However, the fraction of cells with p53 protein accumulation increased significantly during progression, from 3.2% in the first biopsy to 13.7% in the last. The absence of additional genetic alterations (PTEN mutations, loss of chromosome 10 and 19q) may be responsible for the slow progression and lack of glioblastoma features even after a 17-year disease duration.

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Ewens sampling formula is the sampling distribution for a population assumed to follow a one parameter Poisson-Dirichlet distribution, where the parameter is fixed. In this project this assumption will be loosened and we will look at the parameter as a function of the sample size. This will result in sampling from a family of Poisson-Dirichlet distributions. Estimators for this new construction will be tested using two different simulation methods. / Thesis / Master of Science (MSc)

La dégradation des protéines, appelée protéolyse, est un mécanisme essentiel pour le fonctionnement et la survie cellulaire. Elle se fait en grande partie grâce à l’ubiquitination des protéines qui permet au protéasome de les reconnaître et de les cliver. Dans le cadre de ce projet, et ce, à partir de deux cas cliniques, j’ai étudié le rôle la protéine F-box/WD repeat-containing protein 4 (FBXW4) dans ce processus de dégradation. Les patients étaient tous deux atteints d’un syndrome polymalformatif caractérisé par une ectrodactylie appelé split hand/split foot malformation de type 3 (SHFM3) et par une insuffisance rénale chronique. Ils étaient aussi tous deux porteurs d’une mutation P376Q dans FBXW4. Comme on suspectait déjà que FBXW4 appartienne à un complexe d’ubiquitination, nous avons émis l’hypothèse que la mutation affectait l’assemblage de ce complexe et causait ainsi les désordres cliniques identifiés. J’ai donc reproduit cette mutation in vitro ainsi que d’autres à cette position pour en étudier les effets dans le système d’expression des ovocytes de Xenopus laevis. J’ai constaté que FBXW4 était organisé en homomères et que la nature du résidu 376 jouait un rôle dans cet assemblage. J’ai aussi observé que la nature du résidu 376 affectait aussi la liaison de FBXW4 avec Skp1, une autre protéine qui se retrouve dans le complexe. Ces travaux ont ainsi permis d’en arriver aux conclusions suivantes : 1) la mutation des patients affecte l’assemblage oligomérique de FBXW4, 2) elle est donc fort possiblement causale, et 3) elle entraînerait la maladie dû à un désordre de l’ubiquitination de certaines protéines durant le développement. / Protein degradation, also known as proteolysis, is essential for cell function and survival. It is most often achieved through the ubiquitination of proteins, a process that allows the proteasome to recognize and cleave such proteins. In this project, I studied two clinical cases in which the protein F-box/WD repeat-containing protein 4 (FBXW4) was believed to play a role. Both patients suffered from a polymalformative syndrome characterized by an ectrodactyly called type 3 split hand/split foot malformation (SHFM3) and chronic renal failure. Both patients also bore a P376Q mutation in FBXW4. As previous studies was consistent with the possibility that FBXW4 was part of an ubiquitination complex, we hypothesized that the mutation affected the assembly of this complex and resulted in the observed clinical disorders. I therefore reproduced the mutation in vitro among others at this location and characterized the effects of such mutations in Xenopus laevis oocyte expression system. I found that FBXW4 was organized in homooligomers and that the nature of the residue of position 376 played a role in assembly of the FBXW4 containing complex. I also found that the nature of residue 376 affected the binding of FBXW4 to another protein in the complex, that is, to Skp1. These results allow us to draw the following conclusions: 1) the mutation identified affects the oligomeric assembly of FBXW4, 2) it is thus very likely to be causative, and 3) it could cause an ubiquitination disorder in which certain proteins are not properly degraded during development

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The role of highly conserved amino acids within the carboxy-terminal hydrophobic domain of herpes simplex virus I (HSV-I) glycoprotein gB was studied by introducing point mutations using the method of site directed mutagenesis. A segment of this hydrophobic domain of glycoprotein gB contains a nuclear envelope (NE) targeting signal and the effect of these point mutations on targeting to the nuclear envelope was determined. A complementation assay was employed to determine the effect these mutations have on HSV-I infectivity .The point mutations created within the transmembrane domain of glycoprotein gB had no effect on nuclear envelope targeting and localization. However, single point mutations introduced into the first and second hydrophobic domains of glycoprotein gB, G₇₄₃R and F₇₇₀S, affected the targeting and localization of full-length glycoprotein gB at the nuclear envelope. When the transmembrane domain ofHSV-I glycoprotein gB containing the following point mutations A₇₉₀Q, A₇₉₁S, A₇₈₆S, A₇₈₆Y and A₇₉₀S, was introduced into a chimeric protein consisting of the cytoplasmic domain and ectodomain of a plasma membrane protein, vesicular stomatitis virus glycoprotein G, NE targeting and localization were affected. These point mutations may affect the targeting of glycoprotein gB by altering the structure of the targeting signal within the protein. It can be hypothesized that the presence of the cytoplasmic domain. ectodomain domain, and the first and second transmembrane domains within full-length glycoprotein gB can compensate for the effect these point mutations have on nuclear envelope targeting. since the same point mutations had no effect on the targeting · and localization of full-length glycoprotein gB. Complementation assays showed that the glycoprotein gB mutants, A₇₈₆S, A₇₈₆Y, A₇₈₆N, A₇₉₀Q, A₇₉₁S, F₇₇₀S, or G₇₄₃R, were unable to complement a gB-null virus even though these mutant proteins are localized at the nuclear envelope. These proteins may not have been incorporated into the viral capsid due to misfolding or due to the fact that sequences required for interaction with other viral proteins were lost. Another possibility is that the mutant proteins were incorporated into the HSV virion but were not biologically active. / Thesis / Master of Science (MS)

Avec les constantes avancées du séquençage de nouvelle génération (NGS), la quantité de données disponibles devient massive. En parallèle, les méthodes de détection au cancer demeurent très spécifiques et peu efficaces. De plus, le taux de survie des patients est directement relié à la progression tumorale et par conséquent, aux méthodes de détection. Malgré des avancées technologiques très importantes dans les dernières années, le taux de mortalité du cancer ne cesse d’augmenter. L’importance de développer des nouvelles méthodes de détection applicables à tous les types de cancer devient une nécessité. Jusqu’à présent, il n’existe aucun modèle permettant d’utiliser le séquençage de nouvelle génération qui permet la prédiction de caractéristiques cancéreuse (ex : récurrence, résistance, etc.). Les sections suivantes démontrent la création d’un modèle utilisant des mutations somatiques et germinales pour prédire la récurrence et son applicabilité au travers de tous les types de cancers (et même différentes maladies). En utilisant des signatures géniques (combinaisons de gènes) spécifiques à chaque cancer, nous avons été en mesure d’obtenir une précision de 90% (et plus) pour le groupe où le cancer est récurrent. De nos connaissances, ceci est la première tentative de développement de modèle permettant de prédire le pronostic du patient en utilisant le NGS. Ceci amène un nouvel aspect pour la médecine personnalisée et spécialement pour le dépistage du cancer. / With the constant progress in neext generation sequencing, the quantity of data available for investigation becomes massive. In parallel, cancer detection methods and treatments remain very specific and barely accurate. Moreover, the patients survival rate are directly linked with tumoral progression and therefore, to cancer detection methods. Despite continual technological advances in recent years, the global cancer mortality rate keeps rising. The creation of new detection methods accessible to all cancer types becomes a necessity. As of now, there is no model available that using sequencing data to predict cancer traits (ex: recurrence, resistance, etc.). The following sections demonstrate the creation of such model using somatic and germline mutations to predict recurrence and its applicability across all cancer types (and even across different diseases). By using gene signatures specific to each cancer types, we were able to obtain an accuracy of 90% (and more) for the cohort where the cancer was recurrent. To our knowledge, this is the first attempt to develop a model that can predict the patient’s prognosis using genome sequencing data. This will affect future studies and improve personalized medicine as well as cancer detection methods.