Class I phosphoinositide 3-kinases (PI3K) and mammalian target of rapamycin complexes 1/2 (mTORC1/2) are enzymes that play important roles in elementary biology and disease. As a consequence, numerous small-molecule inhibitors of their catalytic activity have been developed and these have shown clinical utility in certain cancers. Unfortunately, acquired resistance to these therapies is a common phenomenon and often occurs relatively quickly following treatment. Our understanding of how resistance develops is hampered by the difficulty of measuring the circuitry and plasticity of the signalling networks that these and other kinases signal within. Advances in mass spectrometric technologies have rendered the routine quantitative interrogation of the phosphoproteome (the set of phosphorylated proteins expressed in a particular biological system at a specific time) more tractable than ever before. The aim of this project therefore, was to improve upon existing mass spectrometry (MS)-based phosphoproteomics methods, and to utilise these to contribute to our understanding of kinase signalling networks and examine their plasticity in models of acquired resistance to PI3K and mTORC1/2-targeted therapies. Novel approaches for the enrichment of phosphopeptides from complex biological matrices (and their analysis by MS) were designed, tested and optimised. These methods were then used to systematically characterise a kinase signalling network comprising the Akt/PI3K/mTOR and MEK/ERK signalling axes in MCF7 breast cancer cells. The biological relevance of this network was confirmed through the assessment of its dynamics upon EGF and IGF-1 stimulation. Finally, the plasticity of this network following chronic treatment with targeted PI3K and mTORC1/2 inhibitors (GDC-0941 and KU-0063794) was examined in cell-line models of acquired resistance to these two compounds. This revealed that these cells each remodelled this network in a different manner, thus indicating that the initial conditions of the system were not the sole determinant of how resistance was acquired.

Diss. (sammanfattning) Uppsala : Univ., 2002. / Härtill 3 uppsatser.

Background: The biological mechanisms underlying early-and advanced-stage epithelial ovarian cancers (EOCs) are still poorly understood. This study explored kinase-driven metabolic signalling in early and advanced EOCs, and its role in tumour progression and response to carboplatin-paclitaxel treatment. Methods: Tumour epithelia were isolated from two independent sets of primary EOC (n-72 and 30 for the discovery and the validation sets, respectively) via laser capture microdissection. Reverse phase protein microarrays were used to broadly profile the kinase-driven metabolic signalling of EOC with particular emphasis on the LBK1-AMPK and AKT-mTOR axes. Signalling activation was compared between early and advanced lesions, and carboplatin-paclitaxel-sensitive and -resistant tumours. Results: Advanced EOCs were characterised by a heterogeneous kinase-driven metabolic signature and decreased phosphorylation of the AMPK-AKT-mTOR axis compared to early EOC (P<0.05 for AMPK alpha T172, AMPK alpha 1 S485, AMPK beta 1 S108, AKT S473 and T308, mTOR S2448, p70S6 S371, 4EBP1 S65, GSK-3 alpha/beta S21/9, FOXO1 T24/FOXO3 T32, and FOXO1 S256). Advanced tumours with low relative activation of the metabolic signature and increased FOXO1 T24/FOXO3 T32 phosphorylation (P=0.041) were associated with carboplatin-paclitaxel resistance. Conclusions: If validated in a larger cohort of patients, the decreased AMPK-AKT-mTOR activation and phosphorylation of FOXO1 T24/FOXO3 T32 may help identify carboplatin-paclitaxel-resistant EOC patients.

Yes / The ability to either erase or update the memories of a previously learned spatial task is an essential process that is required to modify behaviour in a changing environment. Current evidence suggests that the neural representation of such cognitive flexibility involves the balancing of synaptic potentiation (acquisition of memories) with synaptic depression (modulation and updating previously acquired memories). Here we demonstrate that the p38 MAPK/MAPK-activated protein kinase 2 (MK2) cascade is required to maintain the precise tuning of long-term potentiation and long-term depression at CA1 synapses of the hippocampus which is correlated with efficient reversal learning. Using the MK2 knockout (KO) mouse, we show that mGluR-LTD, but not NMDAR-LTD, is markedly impaired in mice aged between 4 and 5 weeks (juvenile) to 7 months (mature adult). Although the amplitude of LTP was the same as in wildtype mice, priming of LTP by the activation of group I metabotropic receptors was impaired in MK2 KO mice. Consistent with unaltered LTP amplitude and compromised mGluR-LTD, MK2 KO mice had intact spatial learning when performing the Barnes maze task, but showed specific deficits in selecting the most efficient combination of search strategies to perform the task reversal. Findings from this study suggest that the mGluR-p38-MK2 cascade is important for cognitive flexibility by regulating LTD amplitude and the priming of LTP. / Professor Richard Greene at the University of Bradford - startup fund to setup electrophysiological facility and Wellcome Trust 200646/Z/16/Z to S.A.L.C.

Fibrodysplasia ossificans progressiva (FOP) is a rare autosomal dominant disease resulting in episodic but progressive extraskeletal bone formation. FOP is caused by missense mutations in the cytoplasmic domain of the type I bone morphogenetic protein (BMP) receptor ACVR1, leading to dysregulated activation. Currently there are no available drug treatments and the structural mechanism of mutant activation is still poorly characterised. To address this, a number of BMP and TGFβ receptors, including FOP mutants of ACVR1 were cloned, expressed and purified for both structural and biophysical experiments. The arginine at the site of most recurrent FOP mutation, R206H, is common across all type I receptors except BMPR1A and BMPR1B which have a lysine at this site. The novel structure of BMPR1B differed to wild-type ACVR1 showing some of the conformational changes expected of the active conformation. However, a variety of disease related ACVR1 mutant structures, including ACVR1 R206H, revealed a surprisingly persistent inactive conformation in the kinase domain. Some conformational changes suggestive of activation were observed in the mutant Q207D affecting the ATP pocket, the β4–β5 hairpin and the activation loop. Additionally, the structure of the Q207E mutant showed a slight release of the regulatory glycine-serine rich domain from its inhibitory position. These subtle changes suggest that the mutant inactive conformation is destabilised and potentially more dynamic. In agreement, all of the ACVR1 mutants showed reduced binding to the inhibitory protein FKBP12. However, mutant phosphorylation of the substrate Smad1 was not constitutive, but dependent on the co-expression of the partner ACVR2, consistent with recent evidence from transgenic knock-out mice. A novel 2-aminopyridine inhibitor scaffold with favourable specificity for ACVR1 was identified using a fluorescence-based thermal shift assay. Further derivatives were characterised with improved potency and selectivity. The crystal structures of ACVR1 bound to these inhibitors showed exquisite shape complementarity, contributing to their favourable specificity. This work has increased the understanding of FOP-associated mutant activation and provided a novel starting scaffold for potential drug development.

La spleen tyrosine kinase (Syk) est une protéine kinase cytoplasmique qui intervient dans la signalisation immunitaire. Notre équipe a montré pour la première fois que Syk est exprimée aussi dans les cellules épithéliales mammaires et que son expression est perdue au cours de l’acquisition d’un phénotype invasif/métastatique. Syk agit comme un suppresseur de tumeurs et de métastases dans des modèles de xénogreffes de cancer du sein. Ces observations ont été étayées par des études cliniques qui montrent que la perte d’expression de Syk correspond à un risque accru de développement de métastases (facteur de mauvais pronostic) dans le cancer du sein et d’autres carcinomes. Par une approche de phospho-protéomique quantitative (SILAC), nous avons pu identifier de nouveaux substrats potentiels de Syk dans les cellules de cancer du sein. De façon intéressante, ressortent de nombreuses protéines impliquées dans l'adhésion intercellulaire (E-cadhérine/caténines) et la polarisation épithéliale (eg ZO3, occludine, claudine-3). Ces protéines, qui se localisent aux jonctions d'adhésion et d'occlusion, sont connues comme composants plate-formes de signalisation et exercent souvent une fonction de suppresseur de tumeur.Dans ce travail de thèse je me suis focalisé principalement sur :(i) le rôle de l’activité kinase de Syk dans la régulation du complexe E-cadhérine/caténines et(ii) les conséquences de l’invalidation conditionnelle de Syk dans la glande mammaire murine (développement mammaire et tumorigenèse).Par une approche de phosphorylation in vitro, nous avons montré que la E-cadhérine et différentes caténines sont des substrats directs de Syk. Les résidus tyrosines phosphorylés dans ces protéines ont été identifiés par spectrométrie de masse et les anticorps phospho-spécifiques correspondants ont été générés. En immunofluorescence, Syk endogène colocalise avec la E-Cadhérine au niveau des jonctions adhérentes et la surexpression de Syk stimule la phosphorylation de la E cadhérine et différentes caténines au niveau des jonctions intercellulaires. Des expériences d’immunoprécipitation montrent que les protéines E-cadhérine et caténines phosphorylées restent associées dans un complexe au niveau des jonctions adhérentes. L’extinction de Syk par shRNA dans une lignée de cancer de sein inhibe partiellement la ré-agrégation intercellulaire (2D/3D) et augmente l’invasion et la migration cellulaires et la croissance en 3D dans le Matrigel. Inversement, la surexpression de Syk inhibe la migration et l’invasion et favorise l'adhérence intercellulaire. Syk semble par la phosphorylation du complexe E-cadhérine/caténines consolider leurs interactions renforçant ainsi les jonctions intercellulaires et l’intégrité de l’épithélium, ce qui pourrait révéler un mécanisme majeur responsable de son activité anti-invasive. Leurs mécanismes moléculaires ont été explorés.Ces modèles cellulaires in vitro ont ensuite été étendus vers un modèle intégré murin. L'invalidation homozygote du gène SYK étant létale, nous avons développé un modèle d’invalidation conditionnelle de Syk dans la glande mammaire (Syk-flox:WAP-Cre). Ce modèle nous a permis tout d’abord d’étudier le rôle de Syk dans le développement et la physiologie de la glande mammaire au cours de la lactation et de l’involution, les glandes Syk-négatives montrant des défauts de développement. Il permet à plus long terme également d’évaluer l'implication de Syk dans la formation et la progression du cancer du sein chez des souris cKO Syk, après croisement ou non avec des souris transgéniques exprimant l’oncogène MMTV-Neu/Her2.Déterminer si Syk est un bona fide suppresseur de tumeurs est crucial car un inhibiteur de Syk est en cours d’étude clinique pour le traitement de l’arthrite rhumatoïde. L’identification des voies de signalisation gouvernées par Syk pourrait ultérieurement déboucher sur le développement de nouvelles thérapies ciblant ces protéines et bloquant l'évolution cancéreuse. / The spleen tyrosine kinase (Syk) is a cytoplasmic protein kinase involved in immune-response signaling. Our team showed for the first time that Syk is also expressed in mammary epithelial cells and that its expression is lost during acquisition of an invasive/metastatic phenotype. Syk acts as a tumor and metastasis suppressor in breast cancer xenograft models. Clinical studies corroborated that loss of Syk expression is correlated with a decreased survival and an increased risk of metastasis development (poor prognosis) in breast cancer and other carcinomas. Using a quantitative phospho-proteomic SILAC approach in breast cancer cells, our group identified new potential Syk substrates. Interestingly, many proteins are involved in intercellular adhesion (E-cadherin/catenin) and epithelial polarization (eg ZO3, occludin, claudin-3). These proteins are localized at the adherens and tight junctions and are known as signaling platforms and components often presenting a tumor suppressor function.In this thesis I mainly focused on:(i) the role of the Syk kinase activity in the regulation of the E-cadherin/catenin complex and(ii) the consequences of the conditional Syk knockout in the mouse mammary gland on breast development and tumorigenesis.Using in vitro kinase assays, we demonstrated that E-cadherin (E-Cdh) and different catenins are direct Syk substrates. The phosphorylated tyrosine residues were identified by mass spectrometry and corresponding phospho-specific antibodies were generated. By immunofluorescence, we observed that endogenous Syk and E-Cdh colocalize at adherens junctions (AJ) and that Syk overexpression stimulates Syk-dependent phosphorylation of E-cadherin and different catenins at AJ. Immunoprecipitation experiments indicate phosphorylated E-cadherin and catenin proteins are associated in a complex. Using functional tests, Syk knockdown by shRNA in breast cancer cells partially inhibited intercellular re-aggregation (2D/3D) and increased cell invasion, migration and 3D-growth in Matrigel. Conversely, Syk overexpression inhibited migration and invasion and promoted intercellular adhesion. Thus, Syk seems to strengthen the intercellular junctions and the integrity of the epithelium via the phosphorylation of the E-cadherin/catenin complex of which its molecular mechanisms were explored. This could be a major mechanism responsible for its anti-invasive activity.These in vitro observations were subsequently extended to an integrated mouse model. As the homozygous SYK gene knockout is lethal; we developed a conditional Syk deletion model in the murine mammary gland (Syk-flox:WAP-Cre).This model allowed us to study the role of Syk in the development and physiology of the mammary gland during lactation and involution, the Syk-negative glands showing developmental defects. On a long-term basis, it also allows to assess the involvement of Syk in the formation and progression of breast cancer in aging cKO Syk mice, bred or not with transgenic mice expressing the MMTV-Neu / Her2 oncogene.Whether Syk is a bona fide tumor suppressor is a crucial issue as Syk inhibitors are being evaluated in clinical studies for the treatment of rheumatoid arthritis. Identification of the signaling pathways governed by Syk could lead to the development of new therapies targeting these proteins and blocking tumor development and progression.

Partículas da exaustão de motores a diesel (DEP) têm propriedades toxicológicas, devido às características físico-químicas. O DEP é capaz de ativar as vias de sinalização intracelular e induzir alterações metabólicas em células e tecidos do sistema respiratório. O objetivo desta tese foi: 1) avaliar o perfil das mucinas e alterações epiteliais em explantes de traqueia de camundongo BALB/c expostos ao DEP e DEP tratado com ácido nítrico e solventes orgânicos; e 2) em cultura de células de epitélio brônquico humano (BEAS-2B) expostas ao DEP e DEP tratado com hexano (DEP/HEX) para avaliar ativação de MAPK (ERK e JNK), citotoxidade, integridade de citoesqueleto, viscoelasticidade celular e expressão gênica de enzimas envolvidas no estresse oxidativo e apoptose. Os resultados mostraram que, em explantes de traqueia, o DEP causa aumento significativo em relação ao grupo controle na quantidade de muco ácido (p= 0,001), diminuição no muco neutro (p=0,001), diminuição de muco misto (p= 0,001), aumento de vacuolização (p= 0,001), aumento de apoptose (p=0,001), ora com aumento de pERK e diminuição de pJNK, e vice-versa. Os explantes submetidos à exposição ao DEP e DEP/MET aumentaram significativamente o muco ácido (p=0,01) e DEP/HEX provocou aumento da extrusão do muco (p=0,007), provavelmente devido à ação do enriquecimento inorgânico. Para as células BEAS-2B, nos resultados obtidos com células epiteliais expostas ao DEP e DEP/HEX, foram observadas alterações na membrana citoplasmática, mitocôndrias e citoesqueleto. As células expostas apenas ao DEP em baixas concentrações (15ug/mL) apresentaram alterações na expressão de genes envolvidos no apoptose (BCL-2 e Caspase-3 (p=0,05 e p=0,01) e estresse oxidativo [(SOD1 e SOD2 e GPx. p=0,01 )], e CYP1A1 ((p=0,01) / Diesel exhaust particles (DEPs) from diesel engines have toxic properties that result from their physical and chemical characteristics. DEPs are able to activate intracellular signaling pathways and induce metabolic changes to cells and tissues of the human respiratory system. This dissertation sought to evaluate: 1) the profile of mucins and the epithelial changes to the tracheal explants of BALB/c mice exposed to both DEP and DEP treated with nitric acid and organic solvents (50 and 100 ug/mL; and 2) human bronchial epithelial cells (BEAS-2B) in culture after their exposure to both DEP and DEP treated with hexane (DEP/HEX) at 100 ug/mL in order to determine MAPK (ERK/JNK) activation, cytotoxicity, cytoskeletal integrity, cell viscoelasticity and gene expression of the enzymes involved in oxidative stress and apoptosis. The results show that, in tracheal explants, DEP causes a significant increase (compared to the control) in the quantity of acidic mucus (p=0.001), a decrease in alkaline mucus (p=0.001), a decrease in mixed mucus (p=0.001), an increase in vacuolization (p=0.001), an increase in apoptosis (p=0.001), along with an increase in pERK and a decrease in pJNK, and vice versa. The explants that were exposed to DEP and DEP/MET were found to have significantly higher quantities of acidic mucus (p=0.01), and DEP/HEX caused an increase in mucus extrusion (p=0.007), which was likely due to inorganic enrichment. In the case of BEAS-2B cells, the results obtained from epithelial cells exposted to DEP and DEP/HEX revealed alterations in the cytoplasmic membrane, the mitochondria, and the cytoskeleton. The cells exposed to DEP alone at low concentrations (15 ug/mL) experienced alterations in the genes involved in apoptosis (BCL-2 and Caspase-3; p=0.05 and p=0.01, respectively), as well as oxidative stress [(SOD1, SOD2, and GPx; p=0.01 )], and changes to CYP1A1 (p=0.01)

Partículas da exaustão de motores a diesel (DEP) têm propriedades toxicológicas, devido às características físico-químicas. O DEP é capaz de ativar as vias de sinalização intracelular e induzir alterações metabólicas em células e tecidos do sistema respiratório. O objetivo desta tese foi: 1) avaliar o perfil das mucinas e alterações epiteliais em explantes de traqueia de camundongo BALB/c expostos ao DEP e DEP tratado com ácido nítrico e solventes orgânicos; e 2) em cultura de células de epitélio brônquico humano (BEAS-2B) expostas ao DEP e DEP tratado com hexano (DEP/HEX) para avaliar ativação de MAPK (ERK e JNK), citotoxidade, integridade de citoesqueleto, viscoelasticidade celular e expressão gênica de enzimas envolvidas no estresse oxidativo e apoptose. Os resultados mostraram que, em explantes de traqueia, o DEP causa aumento significativo em relação ao grupo controle na quantidade de muco ácido (p= 0,001), diminuição no muco neutro (p=0,001), diminuição de muco misto (p= 0,001), aumento de vacuolização (p= 0,001), aumento de apoptose (p=0,001), ora com aumento de pERK e diminuição de pJNK, e vice-versa. Os explantes submetidos à exposição ao DEP e DEP/MET aumentaram significativamente o muco ácido (p=0,01) e DEP/HEX provocou aumento da extrusão do muco (p=0,007), provavelmente devido à ação do enriquecimento inorgânico. Para as células BEAS-2B, nos resultados obtidos com células epiteliais expostas ao DEP e DEP/HEX, foram observadas alterações na membrana citoplasmática, mitocôndrias e citoesqueleto. As células expostas apenas ao DEP em baixas concentrações (15ug/mL) apresentaram alterações na expressão de genes envolvidos no apoptose (BCL-2 e Caspase-3 (p=0,05 e p=0,01) e estresse oxidativo [(SOD1 e SOD2 e GPx. p=0,01 )], e CYP1A1 ((p=0,01) / Diesel exhaust particles (DEPs) from diesel engines have toxic properties that result from their physical and chemical characteristics. DEPs are able to activate intracellular signaling pathways and induce metabolic changes to cells and tissues of the human respiratory system. This dissertation sought to evaluate: 1) the profile of mucins and the epithelial changes to the tracheal explants of BALB/c mice exposed to both DEP and DEP treated with nitric acid and organic solvents (50 and 100 ug/mL; and 2) human bronchial epithelial cells (BEAS-2B) in culture after their exposure to both DEP and DEP treated with hexane (DEP/HEX) at 100 ug/mL in order to determine MAPK (ERK/JNK) activation, cytotoxicity, cytoskeletal integrity, cell viscoelasticity and gene expression of the enzymes involved in oxidative stress and apoptosis. The results show that, in tracheal explants, DEP causes a significant increase (compared to the control) in the quantity of acidic mucus (p=0.001), a decrease in alkaline mucus (p=0.001), a decrease in mixed mucus (p=0.001), an increase in vacuolization (p=0.001), an increase in apoptosis (p=0.001), along with an increase in pERK and a decrease in pJNK, and vice versa. The explants that were exposed to DEP and DEP/MET were found to have significantly higher quantities of acidic mucus (p=0.01), and DEP/HEX caused an increase in mucus extrusion (p=0.007), which was likely due to inorganic enrichment. In the case of BEAS-2B cells, the results obtained from epithelial cells exposted to DEP and DEP/HEX revealed alterations in the cytoplasmic membrane, the mitochondria, and the cytoskeleton. The cells exposed to DEP alone at low concentrations (15 ug/mL) experienced alterations in the genes involved in apoptosis (BCL-2 and Caspase-3; p=0.05 and p=0.01, respectively), as well as oxidative stress [(SOD1, SOD2, and GPx; p=0.01 )], and changes to CYP1A1 (p=0.01)

Class I PI3Ks are a family (α, β, δ and γ) of ubiquitous lipid kinases that can be activated by cell surface receptors to 3-phosphorylate PI(4,5)P2 (phosphatidylinositol(4,5)-bisphosphate) and generate the signalling lipid PI(3,4,5)P3. The PI(3,4,5)P3 signal then activates a diverse collection of effector proteins involved in regulation of cell migration, metabolism and growth. The importance of this network is evidenced by the relatively high frequency with which cancers acquire gain-of-function mutations in this pathway and huge efforts to make PI3K inhibitors to treat cancer. The canonical model describing these events suggests class I PI3Ks are activated at the plasma membrane and generate PI(3,4,5)P3 in the inner leaflet of the plasma membrane where its effectors are activated. The PI(3,4,5)P3 signal can be terminated directly, by the tumour-suppressor and PI(3,4,5)P3-3-phosphatase PTEN, or modified to a distinct PI(3,4)P2 signal, by SHIP-family 5-phosphatases. The PI(3,4)P2 is removed by INPP4-family 4-phosphatases. Published work has shown that PI(3,4,5)P3 signalling can also occur in endosomes and nuclei, however, there is very little data defining the intracellular distribution of endogenous class I PI3Ks that supports these ideas; this is as a result of technical problems such as; their very low abundance, poor antibody-based tools and artefacts generated by overexpression of PI3Ks. Past work has indicated that, in PTEN-null mouse models of prostate tumour progression, either PI3Kβ or PI3Ks α and β, have important roles. Furthermore, the cell types and mechanism involved remained unclear. Recent published work in the host laboratory had indicated that there is an unexpectedly large accumulation of PI(3,4)P2 in PTEN-null cells that might be an important part of its status as a major tumour suppressor. The explanation and prevalence of this observation was unclear but potentially a result of PTEN also acting as a PI(3,4)P2 3-phosphatase in vivo. MEFs were derived from genetically-modified mice expressing endogenous, AviTagged class I PI3K subunits and used in experiments to define the subcellular localisation of class I PI3Ks. We found that following stimulation with PDGF, class IA PI3K subunits were unexpectedly depleted from the adherent basal membrane, in contrast, p85α and p110α, but not p85β and p110β, accumulated transiently in the nucleus. Interestingly, p110β, but none of the other subunits, was constitutively localised in the nucleus. These results support the idea that class I PI3K and PI(3,4,5)P3 signalling occurs in the nucleus. In organoids derived from WT, PI3Kγ-null or PTEN-null mouse prostate, application of PI3K-selective inhibitors revealed that PI3Kα had a dominant role in generating PI(3,4,5)P3 in prostate epithelial cells. The levels of PI(3,4)P2 were also elevated substantially in PTEN-null, compared to WT prostate organoids, use of PI3K-selective inhibitors suggested that it was also generated by PI3Kα. These data were consistent with the idea that PTEN can act as a PI(3,4)P2 3-phosphatase. Surprisingly, raising the pH of the organoids medium dramatically increased accumulation of PI(3,4,5)P3 and PI(3,4)P2, although the cause of this effect was unclear, we hypothesised the pH of the local environment may influence signalling via class I PI3Ks.