Dissertations / Theses on the topic 'PTC mutation'

The peroxisome is a subcellular organelle that carries out a diverse range of metabolic functions, including the b-oxidation of very long chain fatty acids, the breakdown of peroxide and the a-oxidation of fatty acids. Disruption of peroxisome metabolic functions leads to severe disease in humans. These diseases can be broadly grouped into two categories: those in which a single enzyme is defective, and those known as the peroxisome biogenesis disorders (PBDs), which result from a generalised failure to import peroxisomal matrix proteins (and consequently result in disruption of multiple metabolic pathways). The PBDs result from mutations in PEX genes, which encode protein products called peroxins, required for the normal biogenesis of the peroxisome. PEX1 encodes an AAA ATPase that is essential for peroxisome biogenesis, and mutations in PEX1 are the most common cause of PBDs worldwide. This study focused on the identification of mutations in PEX1 in an Australasian cohort of PBD patients, and the impact of these mutations on PEX1 function. As a result of the studies presented in this thesis, twelve mutations in PEX1 were identified in the Australasian cohort of patients. The identified mutations can be broadly grouped into three categories: missense mutations, mutations directly introducing a premature termination codon (PTC) and mutations that interrupt the reading frame of PEX1. The missense mutations that were identified were R798G, G843D, I989T and R998Q; all of these mutations affect amino acid residues located in the AAA domains of the PEX1 protein. Two mutations that directly introduce PTCs into the PEX1 transcript (R790X and R998X), and four frameshift mutations (A302fs, I370fs, I700fs and S797fs) were identified. There was also one mutation found in an intronic region (IVS22-19A>G) that is presumed to affect splicing of the PEX1 mRNA. Three of these mutations, G843D, I700fs and G973fs, were found at high frequency in this patient cohort. At the commencement of these studies, it was hypothesised that missense mutations would result in attenuation of PEX1 function, but mutations that introduced PTCs, either directly or indirectly, would have a deleterious effect on PEX1 function. Mutations introducing PTCs are thought to cause mRNA to be degraded by the nonsense-mediated decay of mRNA (NMD) pathway, and thus result in a decrease in PEX1 protein levels. The studies on the cellular impact of the identified PEX1 mutations were consistent with these hypotheses. Missense mutations were found to reduce peroxisomal protein import and PEX1 protein levels, but a residual level of function remained. PTC-generating mutations were found to have a major impact on PEX1 function, with PEX1 mRNA and protein levels being drastically reduced, and peroxisomal protein import capability abolished. Patients with two missense mutations showed the least impact on PEX1 function, patients with two PTC-generating mutations had a severe defect in PEX1 function, and patients carrying a combination of a missense mutation and a PTC-generating mutation showed levels of PEX1 function that were intermediate between these extremes. Thus, a correlation between PEX1 genotype and phenotype was defined for the Australasian cohort of patients investigated in these studies. For a number of patients, mutations in the coding sequence of one PEX1 allele could not be identified. Analysis of the 5' UTR of this gene was therefore pursued for potential novel mutations. The initial analyses demonstrated that the 5' end of PEX1 extended further than previously reported. Two co-segregating polymorphisms were also identified, termed –137 T>C and –53C>G. The -137T>C polymorphism resided in an upstream, in-frame ATG (termed ATG1), and the possibility that the additional sequence represented PEX1 coding sequence was examined. While both ATGs were found to be functional by virtue of in vitro and in vivo expression investigations, Western blot analysis of the PEX1 protein in patient and control cell extracts indicated that physiological translation of PEX1 was from the second ATG only. Using a luciferase reporter approach, the additional sequence was found to exhibit promoter activity. When examined alone the -137T>C polymorphism exerted a detrimental effect on PEX1 promoter activity, reducing activity to half that of wild-type levels, and the -53C>G polymorphism increased PEX1 promoter activity by 25%. When co-expressed (mimicking the physiological condition) these polymorphisms compensated for each other to bring PEX1 promoter activity to near wild-type levels. The PEX1 mutations identified in this study have been utilised by collaborators at the National Referral Laboratory for Lysosomal, Peroxisomal and Related Genetic Disorders (based at the Women's and Children's Hospital, Adelaide), in prenatal diagnosis of the PBDs. In addition, the identification of three common mutations in Australasian PBD patients has led to the implementation of screening for these mutations in newly referred patients, often enabling a precise diagnosis of a PBD to be made. Finally, the strong correlation between genotype and phenotype for the patient cohort investigated as part of these studies has generated a basis for the assessment of newly identified mutations in PEX1.

The peroxisome is a subcellular organelle that carries out a diverse range of metabolic functions, including the b-oxidation of very long chain fatty acids, the breakdown of peroxide and the a-oxidation of fatty acids. Disruption of peroxisome metabolic functions leads to severe disease in humans. These diseases can be broadly grouped into two categories: those in which a single enzyme is defective, and those known as the peroxisome biogenesis disorders (PBDs), which result from a generalised failure to import peroxisomal matrix proteins (and consequently result in disruption of multiple metabolic pathways). The PBDs result from mutations in PEX genes, which encode protein products called peroxins, required for the normal biogenesis of the peroxisome. PEX1 encodes an AAA ATPase that is essential for peroxisome biogenesis, and mutations in PEX1 are the most common cause of PBDs worldwide. This study focused on the identification of mutations in PEX1 in an Australasian cohort of PBD patients, and the impact of these mutations on PEX1 function. As a result of the studies presented in this thesis, twelve mutations in PEX1 were identified in the Australasian cohort of patients. The identified mutations can be broadly grouped into three categories: missense mutations, mutations directly introducing a premature termination codon (PTC) and mutations that interrupt the reading frame of PEX1. The missense mutations that were identified were R798G, G843D, I989T and R998Q; all of these mutations affect amino acid residues located in the AAA domains of the PEX1 protein. Two mutations that directly introduce PTCs into the PEX1 transcript (R790X and R998X), and four frameshift mutations (A302fs, I370fs, I700fs and S797fs) were identified. There was also one mutation found in an intronic region (IVS22-19A>G) that is presumed to affect splicing of the PEX1 mRNA. Three of these mutations, G843D, I700fs and G973fs, were found at high frequency in this patient cohort. At the commencement of these studies, it was hypothesised that missense mutations would result in attenuation of PEX1 function, but mutations that introduced PTCs, either directly or indirectly, would have a deleterious effect on PEX1 function. Mutations introducing PTCs are thought to cause mRNA to be degraded by the nonsense-mediated decay of mRNA (NMD) pathway, and thus result in a decrease in PEX1 protein levels. The studies on the cellular impact of the identified PEX1 mutations were consistent with these hypotheses. Missense mutations were found to reduce peroxisomal protein import and PEX1 protein levels, but a residual level of function remained. PTC-generating mutations were found to have a major impact on PEX1 function, with PEX1 mRNA and protein levels being drastically reduced, and peroxisomal protein import capability abolished. Patients with two missense mutations showed the least impact on PEX1 function, patients with two PTC-generating mutations had a severe defect in PEX1 function, and patients carrying a combination of a missense mutation and a PTC-generating mutation showed levels of PEX1 function that were intermediate between these extremes. Thus, a correlation between PEX1 genotype and phenotype was defined for the Australasian cohort of patients investigated in these studies. For a number of patients, mutations in the coding sequence of one PEX1 allele could not be identified. Analysis of the 5' UTR of this gene was therefore pursued for potential novel mutations. The initial analyses demonstrated that the 5' end of PEX1 extended further than previously reported. Two co-segregating polymorphisms were also identified, termed –137 T>C and –53C>G. The -137T>C polymorphism resided in an upstream, in-frame ATG (termed ATG1), and the possibility that the additional sequence represented PEX1 coding sequence was examined. While both ATGs were found to be functional by virtue of in vitro and in vivo expression investigations, Western blot analysis of the PEX1 protein in patient and control cell extracts indicated that physiological translation of PEX1 was from the second ATG only. Using a luciferase reporter approach, the additional sequence was found to exhibit promoter activity. When examined alone the -137T>C polymorphism exerted a detrimental effect on PEX1 promoter activity, reducing activity to half that of wild-type levels, and the -53C>G polymorphism increased PEX1 promoter activity by 25%. When co-expressed (mimicking the physiological condition) these polymorphisms compensated for each other to bring PEX1 promoter activity to near wild-type levels. The PEX1 mutations identified in this study have been utilised by collaborators at the National Referral Laboratory for Lysosomal, Peroxisomal and Related Genetic Disorders (based at the Women's and Children's Hospital, Adelaide), in prenatal diagnosis of the PBDs. In addition, the identification of three common mutations in Australasian PBD patients has led to the implementation of screening for these mutations in newly referred patients, often enabling a precise diagnosis of a PBD to be made. Finally, the strong correlation between genotype and phenotype for the patient cohort investigated as part of these studies has generated a basis for the assessment of newly identified mutations in PEX1.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
Full Text

Dilated Cardiomyopathy (DCM) with conduction disease and Atrial Fibrillation (AF) are the two cardiac-specific diseases associated with lamin A/C gene (LMNA) mutations. Protein Kinase C Alpha, (PKCα) functions as a nodal integrator of cardiac contractility by “sensing” intracellular calcium and signal transduction. PKCα has been implicated in heart failure and cardiac hypertrophy. Moreover, abnormal PKCα function results in irregular atrial potassium channel activity associated with chronic AF PKCα is a lamin A/C binding partner. Thus, the deregulation of PKCα signaling can contribute to the development of DCM and AF. Our hypothesis is that the AF (Thr528Met), DCM-associated (Arg541Cys) and (Arg541Gly) and DCM/AF-associated (Tyr481Stop) LMNA variants will disrupt the cellular distribution of PKCα therefore resulting in impaired PKCα function. The first objective was to phenotypically characterise Arg541Cys LMNA variant in murine skeletal myoblasts cell line (C2C12) in comparison to cellular phenotypes induced by LMNA variants associated with AF, DCM and DCM with AF. Arg541Cys lamin A and C variants formed circular and sickle-shaped lamin A/C in the nucleus of C2C12 cells. The second objective was to determine the effect of these lamin variants on cellular distribution of PKCα in C2C12 cells. PKCα mislocalized into the nucleus of C2C12 cells transfected with AF and DCM-associated variants (Thr528Met and Arg541Cys). Colocalization analysis showed significant increase in PKCα in the nucleus of AF (Thr528Met) and DCM (Arg541Cys) variants when lamin A and C, were co-transfected compared to wild-type, DCM (Arg541Gly) and DCM/AF (Tyr481Stop) variants. Densitometry analysis showed statistically significant increase in phosphorylated PKCα, the active form of PKCα, in nuclear and cytoplasmic extracts of C2C12 cells expressing Arg541Cys variant. Densitometry analysis also showed statistically significant increase in non-phosphorylated PKCα in the nuclear extract of Thr528Met variant expressing cells. The third objective was to determine the effect of AF and DCM-associated variants on the activity of PKCα. PKCα activity is quantified by measuring the phosphorylation of a known phosphorylated PKCα substrate. Alpha-6-tubulin phospho (Ser165) is phosphorylated by PKCα. Hence, this was used to quantify PKCα activity. No statistical significance was observed in the level of phosphorylated alpha-6-tubulin at (Ser165) in the C2C12 cells that were transfected with lamin A and C variants compared to wild type. Furthermore, PKCα phosphorylation state is cyclic in nature and this could have had an impact on the phosphorylation state of the chosen substrate in this study. The functional consequence of nuclear translocation of PKCα with respect to laminopathies is unknown. Abnormal activation of the Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK1/2) which are branches of the mitogen-activated protein kinase (MAPK) signalling cascade in hearts of mice, and humans prior to the onset of cardiomyopathy. These findings have been associated to cardiac disease-causing lamin A/C alteration to signal transduction pathways implicated in heart function and cardiomyopathy. Human LMNA cardiomyopathy, could lead to abnormal activation of MAPK signalling pathways via abnormal PKCα activation in cardiomyocytes.

Les mutations de TET2, IDH2 et DNMT3A, 3 gènes impliqués dans la régulation de la méthylation de l'ADN, sont fréquentes dans les lymphomes T périphériques (PTCL), mais leurs conséquences sont mal connues. Nous avons montré que les mutations d'IDH2 dans les lymphomes angioimmunoblastiques (AITL) sont restreintes aux cellules T tumorales et que l'enzyme mutée, exprimée dans des lymphocytes T, produit bien l'oncometabolite D-2 hydroxyglutarate (D-2HG). Utilisant des modèles de souris transgéniques, nous avons montré que, dans un lymphocyte T, seule la mutation IDH2R172K produit suffisamment de D-2HG pour inhiber les protéines TET et altérer la différentiation lymphoïde. Ceci peut expliquer qu'IDH2R172 soit la seule mutation d'IDH retrouvée dans les AITL. Les mutations d'IDH2 inhibant les protéines TET, ce qui conduit à une baisse de la 5 hydroxyméthylcytosine (5hmC), nous avons évalué le niveau de 5hmC dans des PTCL mutés ou non pour TET2, IDH2 et/ou DNMT3A. Par rapport aux lymphocytes T normaux, nous avons vu une perte de 5hmC dans les cellules tumorales des PTCL, qui de façon intéressante était présente dans toutes les entités étudiées, quel que soit le statut mutationnel, à l'exception des lymphomes T hépatospléniques. Dans une démarche plus transversale, nous avons montré que la fréquence élevée de mutations de TET2, IDH2 et DNMT3A dans des PTCL présentant des caractéristiques TFH permet d'apporter un argument moléculaire, qui s'ajoute aux similitudes histologiques et phénotypiques pour regrouper ces lymphomes avec les AITL. Enfin, la description de l'efficacité d'un traitement par 5 azacytidine chez une patiente atteinte de AITL mutée pour TET2, suggère que les traitements ciblant l'épigénétique pourraient être efficaces dans ces maladies
TET2, IDH2 and DNMT3A, 3 genes involved in the regulation of DNA methylation, are frequently mutated in Peripheral T Cell Lymphomas (PTCL). However, the consequences of these mutations are poorly understood. Focusing on IDH2 mutation, we demonstrated that this mutation is restricted to tumor T cells within angioimmunoblastic lymphoma (AITL) tumor tissue. We also demonstrated that, in AITL, IDH2 mutated T cells had the ability to produce D-2 hydroxyglutarate (D-2HG), a metabolite that has oncogenic effect. Using transgenic mouse models, we showed that IDH2R172K was the only IDH mutation that, when expressed in T cells, produced enough D-2HG to inhibit TET proteins and impairing lymphoid differentiation. This likely explains why IDH2R172 is the only IDH mutation found in AITL. As IDH2 mutation results in TET2 inhibition, which impairs 5hmC formation, we assessed the level of 5hmC in AITL, and described 5hmC loss, compared to normal TFH, in all AITL, regardless of the TET2, IDH2 and DNMT3A mutational status. We extended these finding to main nodal and extranodal PTCL entities, showing that 5hmC loss was a general mechanism present in all PTCL, with the exception of hepatosplenic T cell lymphoma. In a translational approach, we saw that the high frequency of TET2, DNMT3A and RHOA mutations in TFH like PTCL suggest a common molecular basis shared with AITL that could argue, in addition to phenotypic and histological similarities, to group these 2 entities into a single category. Finally, we described the first complete remission of a patient with a TET2 mutated AITL with 5 azacytidine, suggesting that hypomethylating agents could be active in PTCL

Le droit de la responsabilité a évolué selon deux grandes orientations : le développement des responsabilités sans faute - l'objectivation - et la dilution de la charge des dommages reportée sur une collectivité, par le biais de la technique de l'assurance - la collectivisation -. Cette dynamique incessante entre l'assurance et la responsabilité constitue actuellement le point central du débat engage par les assureurs, selon lesquels l'extension ininterrompue du champ de la responsabilité civile grâce à l'assurance mettrait en péril conjointement ces deux institutions. Ils préconisent des lors de dissocier la responsabilité et l'indemnisation en vue d'indemniser les victimes sans étendre le domaine de la responsabilité. Concrètement, il s'agirait d'abandonner le recours à l'assurance de responsabilité pour lui substituer l'assurance directe des victimes potentielles. Or, cette technique mise à l'épreuve de l'expérience acquise en assurance construction - ou elle a été consacrée par le législateur - ainsi qu'en assurance automobile - ou elle a été spontanément imposée par le réseau conventionnel des assureurs -, laisse présager un certain nombre de bouleversements, particulièrement à propos du droit des victimes à être indemnisées et plus généralement à propos du droit de la responsabilité et de l'évolution que l'on peut craindre. Cette étude se divise en deux étapes. Dans un premier temps, l'évolution de l'assurance de responsabilité - de sa consécration a son rejet actuel - sera retracée afin de préciser les raisons structurelles (liées à la technique de l'assurance) et conjoncturelles (liées à la "crise" de la responsabilité) qui entretiennent ce débat. Cette recherche accomplie, le fonctionnement de l'assurance directe sera analysé, notamment à partir des expériences déjà acquises. Les fruits de cette analyse imposeront inévitablement une approche critique de l'assurance directe, confortée par notre réflexion sur la recherche de sa légitimité, ainsi que par nos interrogations sur l'avenir de la responsabilité dans l'hypothèse de la généralisation d'un tel système.

La NADPH oxydase du phagocyte est une enzyme impliquée dans la défense immunitaire contre les pathogènes. Après activation du phagocyte, cette enzyme produit des ions superoxyde par réduction du dioxygène par le NADPH. Elle est constituée de quatre sous- unités cytosolubles (p47phox ; p67phox ; p40phox et Rac), et deux membranaires (gp91 ; p22phox). Son activation fait intervenir un processus complexe qui met en jeu des changements d’interaction entre les protéines la constituant et qui permet l’assemblage des six sous- unités. Afin d’obtenir des informations sur les processus d’assemblage et d’activation, j’ai reconstitué le complexe dans un système cell free à l’aide de protéines recombinantes pour pouvoir contrôler tous les paramètres. Dans ce travail nous avons comparé les modes d’activation de p47phox par phosphorylation, par mutation substitutionelle sérine - aspartate en position S303,S304 et S328 pour mimer la phosphorylation et enfin par addition d’acide arachidonique (AA) activateur connu de l’enzyme in vitro mais aussi in vivo. Bien qu’il ai été montré que ces trois méthodes ouvrent la protéine vers une conformation ayant des propriétés similaires, nous avons trouvé que les effets de ces méthodes d’activation sont significativement différents. Ainsi, les changement de conformation observés par dichroisme circulaire, sont dissemblables. Pour p47phox, l’addition de AA déstructure la protéine. La phosphorylation induit un déplacement bathochrome des bandes de CD qualitativement similaire, alors que les mutations S-D de p47phox provoquent un déplacement opposé. Pour le complexe p47phox-p67phox l’addition d’AA destructure le mélange tandis que la mutation induit relativement peu de changement. Nous avons mesuré les constantes de dissociation Kd du complexe p47phox-p67phox. Alors que pour les protéines « sauvages », le Kd est faible (4±2 nM), les mutations de p47phox ainsi que l’addition d’AA augmentent cette valeur jusqu’à environ 50 nM, montrant une diminution de l’affinité entre p47phox-p67phox. De même, sur le complexe entier, l’effet de la phosphorylation de p47phox est différent de la mutation. Nous avons mesuré les valeurs de EC50 relatives à p67phox pour les différentes formes de p47phox. L’activation de p47phox par phosphorylation diminue l’EC₅₀, alors que les doubles ou triple mutations augmentent sa valeur. Nous avons confirmé que la phosphorylation et la mutation sont insuffisantes pour activer l’enzyme. La présence de AA est indispensable pour le fonctionnement du complexe. L’ordre de fixation des sous unités cytosoliques semble indifférent mais il faut que tous les composants soient présents lors de l’ajout de AA. Enfin, la délétion de p47phox dans la partie C-terminale (aa 343 à 390, domaine d’interaction avec p67phox) il n’y a plus de formation du dimère mais l’enzyme fonctionne normalement. Ces résultats apportent des éléments nouveaux sur le rôle de la dimérisation p47 phox-p67 phox, non indispensable à l’activité du système et sur le rôle mineur de la phosphorylation dans l’activation de la NADPH oxydase in vitro
The NADPH oxidase of phagocytes is an enzyme involved in the innate defense of organisms against pathogens. After phagocyte activation, this enzyme produces superoxide ions by reduction of dioxygen by NADPH. It is constituted of four cytosolic sub-units (p47phox ; p67phox ; p40phox et Rac) and two membrane proteins (gp91 ; p22phox). Its activation takes place through a complex process that involves protein-protein interaction changes leading to assembly and functionning of the catalytic core. In order to obtain information on this process, I have reconstituted the enzyme in a cell free systeme using recombinant proteins, to be able to fully control all the measurement conditions. In this work, we have compared different activation modes of p47phox i) phosphorylation; ii) substitution serine - aspartate by mutations at positions S303, S304 and S328 to mimic phosphorylation; iii) addition of arachidonic acid (AA), a well known activator molecule in vitro. It has been shown that these three activating methods transform p47phox to an open configuration with similar characteristics. However, we have found that the effects of these methods are significantly different. Indeed, the conformational changes observed by circular dichroism are different. For p47phox, the addition of AA destructures the protein. Its phosphorylation induces a bathochromic displacement of the bands, whereas the mutations S-D lead to an opposite displacement. For the dimer p47phox-p67phox , the addition of AA destructures the proteins while mutations induce hardly no changes. We have measured the dissociation constant Kd of the complex p47phox-p67phox. For wild type proteins, Kd value is low (4±2 nM), while mutations of p47phox as well as addition of AA increase its value up to 50 nM, showing a decrease of affinity between p47phox and p67phox. Moreover, on the whole complex, the effect of phosphorylation of p47phox is different from mutations. We have shown that the EC50 values relative to p67phox are sensitive to the various modifications of p47phox. Phosphorylation of p47phox decreases EC₅₀, while double or triple mutations increase its value. We have confirmed that phosphorylation and mutation are not sufficient to activate the enzyme. The presence of AA is a prerequisite for the functionning of the complex, i.e. production of superoxide. The binding order of the cytosolic proteins seems random but it is necessary that all the components be present during the activation by AA. Finally, deletion of the C terminal part of p47phox (aa 343 to 390, interaction domain with p67phox) leads to the absence of dimer formation but does not affect the enzyme activity. These results bring new information on the role of dimerisation of p47-p67 and on that of phosphorylation in the activation of NADPH oxidase in vitro

Endometrial cancer (EC) is the fourth most common cancer in women in developed countries, such as North America, Europe and Australia. Patients with low-grade, early-stage disease usually have a favourable survival rate. However, patients that present at an advanced stage of disease have an average survival of only 12 months. Current treatments for these patients are radiation and chemotherapy, which offer limited clinical benefit. There is no efficient treatment for advanced EC. Improved therapeutic approaches are needed for the treatment of recurrent and metastatic endometrial cancer. Recent advances in cancer biology have resulted in the development of molecular targeted therapies. The Fibroblast Growth Factors Receptor (FGFR) family and their ligands (fibroblast growth factors, FGFs) regulate a broad spectrum of physiological processes as well as tissue patterning and organogenesis during embryogenesis. Abnormally activated FGFRs have been identified in various cancers and are emerging as potential therapeutic targets. The Pollock laboratory and other groups have demonstrated that 10-20% of endometrioid ECs carry FGFR2 mutations that may be a novel therapeutic target in endometrial carcinoma. Preclinical studies show that inhibition of FGFR can inhibit EC cell growth in vitro. However, FGFR inhibitors are not as efficient at inhibiting tumour growth in vivo. We aim to find a way to improve the efficacy of FGFR inhibition in cancer treatment. About 90% of EC patients harbour genetic aberrations in the components of the PI3K/AKT pathway which indicates this signalling pathway plays an important role in the development of EC. Work from our lab demonstrates that inhibition of FGFR results in abrogation of MAPK activation in sensitive EC cells, however, the PI3K/AKT signalling pathway remains unaffected. PI3K/AKT signalling plays a vital role in cancer cell proliferation and survival, furthermore crosstalk between the MAPK and PI3K/AKT signalling pathways is associated with resistance to targeted therapies. Thus, the first aim of this study was to examine whether combination of the FGFR inhibitor (BGJ398) with various different PI3K inhibitors was synergistic in FGFRi sensitive EC cells. We present data that the combination of the pan-FGFR inhibitor (BGJ398) with pan-PI3K inhibitors (GDC-0941, BKM120) or a p110α-selective PI3K inhibitor (BYL719) was synergistic in inhibiting cell growth. Significantly more cell death and inhibition of long-term cell survival was observed in the combination treatments compared to each of the single drug treatments. Importantly, these effects could also be observed at lower concentrations. This study is the first to indicate that partial inhibition of the PI3K signalling pathway could significantly increase cell death when combined with the FGFR inhibitor BGJ398 in FGFR2 mutant EC cells. These data provide evidence that sub-therapeutic doses of PI3K inhibitors could enhance the efficacy of anti-FGFR therapies and a combination therapy may represent a superior therapeutic treatment in FGFR2 mutant EC patients. The in vivo work (conducted by Dr Vanessa Bonazzi) shows that the combination of BGJ398 and GDC-0941 and BYL719 resulted in tumour regression, while single drug treatment only slowed tumour growth. Interestingly, BYL719 alone resulted in increased tumour growth in tumour xenografts of AN3CA but not JHUEM2. In the first results chapter we further investigated the mechanism of enhanced cell death from the combination of BGJ398 and PI3K inhibitors. The activation of ERK and AKT has been inhibited by the combination of BGJ398 and PI3K inhibitors. However, the combination of the MEK inhibitor trametinib and the PI3K inhibitors induced less cell death than inhibition of the FGFR and PI3K signalling pathways. BGJ398 but not trametinib or GDC-0941 inhibited the activity of PLCγ1. We have also found trametinib up-regulated PLCγ1 activity, which is a novel finding in the field. We next employed several pharmacological inhibitors to investigate whether PLCγ1 is involved in the cell death observed following the combination of BGJ398 and GDC-0941 treatment. As there is no PLCγ1 inhibitor available currently, we used two different pan-PLC inhibitors, manoalide and U73122. Co-inhibition of the MAPK, PI3K/AKT and PLC signalling recapitulated cell growth inhibition seen with the combination of FGFR and PI3K inhibitor in both cell lines. Cell death induced by the combination of PLC inhibitors with trametinib and GDC0941 was similar as the combination BGJ398 and GDC0941 in AN3CA, but significantly less than the combination BGJ398 and GDC0941 in JHUEM2. Unfortunately, Western blotting was unable to show inhibition of PLCγ1 bringing into question whether these PLC inhibitors inhibited PLC function sufficiently, and whether the phenotypic effects of manoalide and U73122 when added to the trametinib and GDC0941 combination are due to inhibition of PLCγ1. The second results chapter reports efforts to identify the mechanism of intrinsic resistance to FGFR inhibition in EC cell lines carrying FGFR2 activating mutations but showing intrinsic resistance to FGFR inhibition (EI, EN1078D, and MFE319) with comparisons to the two sensitive EC cell lines (JHUEM2 and AN3CA). We have observed sustained activation of ERK in the resistant cells after treatment with an FGFR inhibitor, while ERK was inhibited in the sensitive cells. Inhibition of the MAPK signalling pathway could not sensitise the resistant cells to FGFR inhibition. Although several other receptor tyrosine kinases (RTKs) were hyperactivated in these cells, pharmacological inhibition did not show they were reliant on these RTKs. Co-inhibition of these kinases did not sensitise these cells to BGJ398. Knockdown of FGFR2 by shRNA in the sensitive cells induced moderate cell death, but limited cell death in the resistant cells. Interestingly, co-inhibition of the MAPK, PI3K/AKT and PLC signalling pathways has induced markedly less cell growth inhibition in the resistant cells compared to the sensitive cells, suggesting the resistant cells are less dependent on these central signalling pathways than the sensitive cells. Western blotting results showed that FGFR2 expression was considerably lower in the resistant cells than in the sensitive cells. Based on these results we have concluded that FGFR2 mutation status is not the only factor that determines sensitivity to FGFR inhibition, high expression of mutant FGFR2 is also important. This is a novel finding in the field and one which could guide patient select criteria in future clinical trials. Lastly, we show that FGFR2 knockdown in medium containing 10% FBS has little impact on downstream ERK phosphorylation whereas pan FGFR inhibition with BGJ398 could totally abrogate ERK phosphorylation. In cells grown overnight in serum starved conditions, FGFR2 knockdown did reduce downstream ERK phosphorylation but not to the same extent as pan FGFR inhibition in full growth medium. These data suggest that inhibition of FGFR2 alone is insufficient and that inhibition of multiple FGFRs will be more effective as a cancer treatment.

Tese de mestrado em Bioquímica, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2013
A Fibrose Quística (FQ) é a doença recessiva autossómica letal mais comum na população caucasiana e apresenta, na Europa, uma taxa de incidência de 1 em 3500 recém nascidos, enquanto que em Portugal, 1 em cada 6000 novos nados-vivos apresenta a doença. A doença é causada por mutações no gene CFTR (do inglês Cystic Fibrosis Transmembrane Conductance Regulator) que levam à formação de uma pro-teína (com o mesmo nome) com função anormal ou reduzida ou até à completa inibição da expressão da mesma). A CFTR exerce a sua função de canal de cloreto e de outros aniões na membrana apical de células epiteliais de vários tecidos. Do ponto de vista clínico, a FQ é caracterizada por um rápido declínio da função pulmonar devido à obstrução das vias respiratórias causada por infeções bacterianas recorrentes e persistentes. Devido ao ambiente hiper-inflamatório provocado por estas infeções, a remodelação do tecido pulmonar ocorre a um ritmo aumentado, que culmina na formação de fibrose no tecido e na consequente perda de função. Este fenótipo pulmonar é o principal responsável pela morbilidade e mortalidade dos doentes com FQ. Para além do tecido pulmonar, outros órgãos e tecidos são igualmente afetados, sendo que os pacientes apresentam frequentemente problemas digestivos graves e são geralmente inférteis (todos os homens e uma grande percentagem das mulheres). Até à data, foram identificadas mais 1900 alterações no gene CFTR sendo a maioria causadora de doença, sendo a deleção do resíduo de fenilalanina na posição 508 da cadeia peptídica a mais comum das detetadas em pacientes e portadores (~90% de todos os casos). Mutações nonsense levam, na maioria dos casos, à degradação total ou quase total dos transcritos de CFTR, ao desencadearem o mecanismo de degradação do mRNA denominado NMD (do inglês Nonsense-Mediated mRNA De-cay). Estudos recentes, realizados com gene que codifica para a β-globina, demonstraram que a presença de codões stop prematuros em proximidade com o codão de início da tradução não desencadeiam a degradação dos transcritos uma vez que não levam à ativação de NMD. No entanto persiste a dúvida se tal sucederá em genes bastante maiores como é o caso do gene CFTR. O principal objetivo deste trabalho passou, portanto, por uma maior compreensão do mecanismo de degradação NMD, no contexto de genes de grandes dimensões, usando como modelo o gene CFTR. Mais concretamente, pretendeu-se caracterizar várias mutações nonsense, previamente detetadas em doentes com FQ e/ou portadores, localizadas em proximidade com o codão AUG (Q2X, S4X e Q39X), usando minigenes de CFTR gerados através de engenharia genética, bem como validar esse modelo para o estudo de NMD, ao induzir este mesmo mecanismo com a mutação G542X, tal como haveria sido reportado em estudos prévios. Pretendeu-se ainda testar capacidade de vários fármacos em induzir o read-through das várias mutações nonsense. Foram gerados vários plasmídeos codificando minigenes de CFTR, contendo intrões normais e artificialmente construídos, com as várias mutações estudadas e em seguida estabelecido um modelo de expressão estável e isogénica desses mesmos minigenes em células HEK 293. Através de RT-PCR foi demonstrado que a presença da mutação G542X na sequência do minigene de CFTR levou à ativação de NMD e consequente degradação dos transcritos de CFTR, enquanto os transcritos dos variantes com mutações próximas do codão de iniciação não foram degradados. Foi observada, a partir da análise por imunodeteção, a ocorrência da reiniciação da tradução da CFTR nos variantes resistentes à degradação por NMD, e que proteína produzida, apesar de não possuir a região N-terminal era capaz de migrar para a membrana celular. Ensaios de efluxo de iodeto indicaram que a proteína truncada apresentava atividade reduzida e retardada. Não foram no entanto bem-sucedidas as tentativas de promover através de fármacos o read-through dos codões de stop prematuros em nenhum dos variantes.
Cystic Fibrosis is the most common lethal autosomic recessive disorder in the Caucasian population, affecting 1 in 6000 newborns in Portugal, and is caused by mutations in the CFTR gene which encodes for the CFTR protein. Since its recognition, more than 1900 CFTR mutations have been identified, being the deletion of a phenylalanine at position 508 the most prevalent of all. Most nonsense mutations lead to complete loss of protein expression due to transcript quick degradation via NMD pathway. However recent studies of the β-globin gene showed some nonsense variants with AUG-proximal PTCs are resistant to this degradation mechanism. The principle aims of this study were to generate and validate a CFTR minigene model that could be used for the study of NMD in the context of CFTR, a far larger gene than β-globin (~190kb vs ~4 kb), to characterize, using said model, naturally occurring AUG-proximal CFTR nonsense mutations, and test the efficacy several pharmacological read-through promoting agents. CFTR plasmid minigenes containing normal and artificially constructed introns as well as several naturally occurring nonsense mutations (Q2X, S4X, Q39X and G542X) were generated and a model for stable and isogenic expression of these minigenes in HEK 293 cells established. By RT-PCR analysis we showed that the presence of the mutation G542X, was at the minigene sequence was able to activate NMD, while CFTR transcripts with AUG-proximal nonsense mutations were not degraded. It was shown by western blot essays that AUG-proximal nonsense variants expressed a truncated form of CFTR lacking the N-terminus region which probably resulted from the occurrence of translation re-initiation. Residual levels of this truncated form of CFTR were also detected at the cytoplasmic membrane and iodide efflux essays indicated that it possessed reduced and delayed channel function. However, attempts of pharmacologically promote PTC read-through in any nonsense variant were deemed unsuccessful.

This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.

These technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.

No
The surface expression and regulated endocytosis of kainate (KA) receptors (KARs) plays a critical role in neuronal function. PKC can modulate KAR trafficking, but the sites of action and molecular consequences have not been fully characterized. Small ubiquitin-like modifier (SUMO) modification of the KAR subunit GluK2 mediates agonist-evoked internalization, but how KAR activation leads to GluK2 SUMOylation is unclear. Here we show that KA stimulation causes rapid phosphorylation of GluK2 by PKC, and that PKC activation increases GluK2 SUMOylation both in vitro and in neurons. The intracellular C-terminal domain of GluK2 contains two predicted PKC phosphorylation sites, S846 and S868, both of which are phosphorylated in response to KA. Phosphomimetic mutagenesis of S868 increased GluK2 SUMOylation, and mutation of S868 to a nonphosphorylatable alanine prevented KA-induced SUMOylation and endocytosis in neurons. Infusion of SUMO-1 dramatically reduced KAR-mediated currents in HEK293 cells expressing WT GluK2 or nonphosphorylatable S846A mutant, but had no effect on currents mediated by the S868A mutant. These data demonstrate that agonist activation of GluK2 promotes PKC-dependent phosphorylation of S846 and S868, but that only S868 phosphorylation is required to enhance GluK2 SUMOylation and promote endocytosis. Thus, direct phosphorylation by PKC and GluK2 SUMOylation are intimately linked in regulating the surface expression and function of GluK2-containing KARs.

DNA methylation is an epigenetic modification that is nearly ubiquitous. Eukaryotic DNA methylation contributes to the regulation of gene expression and maintaining genome integrity. In mammals, DNA methylation occurs primarily on the C5 carbon of cytosine in a CpG dinucleotide context and is catalyzed by the DNA methyltransferases, DNMT1, DNMT3A and DNMT3B. While dnmt3a and dnmt3b genes are highly homologous, the enzymes have distinct functions. Some previous reports suggested differences in the enzymatic behavior of DNMT3A and 3B, which could affect their biological roles. The goal of my thesis work was to characterize kinetics mechanisms of DNMT3A and 3B, and to identify the similarities and differences in their catalytic properties that contribute to their distinct biological functions. Given the sequence similarity between the enzymes, we asked whether DNMT3B was kinetically similar to DNMT3A. In a series of experiments designed to distinguish between various kinetics mechanisms, we reported that unlike DNMT3A, DNMT3B methylated tandem CpG on DNA in a processive manner. We also reported that the disruption of the R-D interface, critical for the cooperativity of DNMT3A, had no effect on DNMT3B activity, supporting the non-cooperative mechanism of this enzyme.

DNMT3A is frequently mutated in numerous cancers. Acute Myeloid Leukemia (AML) is a malignancy of hematopoietic stem cells in which numerous patients exhibit a high frequency of the heterozygous somatic mutation Arg882His in DNMT3A. Through thorough consensus motif building, we discovered a strong similarity in CpG flanking sequence preference between DNMT3A Arg882His variant and DNMT3B enzyme. Moreover, we found that the variant enzyme has the same kinetics mechanism as DNMT3B, indicating a gain-of-function effect caused by the mutation. This change is significant because the variant enzyme can aberrantly methylate DNMT3B targets in AML cells and effect global gene expression. In particular, given that DNMT3B has been shown to have oncogenic properties, this suggests that the Arg882His variant can acquire similar oncogenic properties and drive AML development.

Taken together, my thesis work provides novel insights into the relationship between the biochemical properties and the biological functions of DNMT3A and 3B.