Melanoma is a highly aggressive tumour with a poor prognosis for patients with advanced disease because it is resistant to current therapies. Therefore, the development of novel strategies for melanoma treatment is important. The characterization of the molecular mechanisms underlying melanoma proliferation, progression, and survival could help the development of novel targeted melanoma treatments. The MAPK and PI3K pathways both play important roles in melanoma progression. In the MAPK pathway, DUSP6, which acts as a phosphatase to negatively control the activation of ERK1/2, is involved in the development of human cancers. The MAPK pathway also regulates expression of the DNA repair gene ERCC1 following EGF treatment. ERCC1 is essential for nucleotide excision repair, which is one of the major systems for removal of cisplatin induced DNA lesions. The aims of this project were: 1, to investigate the molecular changes in our immortal mouse melanocyte cell lines that were needed for them to form tumours in a xenograft model; 2, to investigate whether the MAPK pathway regulates ERCC1 following cisplatin treatment and protects melanoma cells from death. Through comparison of the RAS/RAF/MEK/ERK (MAPK) and the PI3K/AKT (AKT) signalling pathways between our immortal mouse melanocyte cell lines and their tumour derivatives in our xenograft model, we identified a molecularly distinct subtype of mouse melanoma characterized by reduced ERK and AKT activity and increased expression of DUSP6. Functional analyses employing ectopic overexpression indicated that increased expression of DUSP6 enhanced anchorage independent growth ability and invasive ability in our mouse melanocytes, suggesting that increased DUSP6 expression may contribute to melanoma formation in the xenograft assay. We also demonstrated that higher expression of p-ERK suppressed invasion, but not anchorage independent growth, in our subtype of mouse melanoma by enforced expression of constitutively active MEK1 and MEK2. In addition, the role of DUSP6 in classical human melanoma was investigated in this Genetic changes in melanoma progression study. Inhibition of anchorage independent growth and invasion were observed after exogenous expression of DUSP6 in human melanoma cells. This suggested that DUSP6 played different roles in classic human melanoma than in our distinct subtype of mouse melanoma. Our study also investigated the phosphorylation level of ERK1/2 and the mRNA and protein level of ERCC1 and its partner XPF in the human melanoma cell line following cisplatin treatment. Significant increases in expression of p-ERK, ERCC1 and XPF were found in cisplatin treated cells. Moreover, a MEK inhibitor inhibited ERCC1 induction by cisplatin, but did not significantly affect XPF induction. This suggested that the MAPK pathway was involved in regulation of ERCC1 but not XPF. Furthermore, the DUSP6 level decreased after cisplatin treatment and overexpression of DUSP6 inhibited ERCC1 and XPF induction and reduced resistance to cisplatin. DUSP6 seems to play a crucial role in resistance of melanoma to cisplatin. In addition, a novel larger ERCC1 transcript was identified in human cell lines and was found to be upregulated by cisplatin. The ratio of larger ERCC1 transcript relative to the normal ERCC1 transcript increased following cisplatin treatment. The functions of this larger ERCC1 transcript in cisplatin resistance deserve further study.

Mammalian cells can initiate intracellular signalling pathways that activate pro-survival changes to maintain their integrity following their exposure to a range of extracellular stresses. One group of changes preserves cellular integrity through the regulation of cytoskeletal organization. Despite the recognised importance of maintaining microtubule (MT) networks, the specific mechanisms regulating cytoskeleton organisation in response to stress remain relatively poorly explored. Among the numerous proteins that regulate MT organisation, stathmin (STMN) is a key MT destabilising protein that regulates MT disassembly through its ability to bind tubulin dimers. The actions of STMN can be regulated by a number of growth factor-activated and cell cycle regulatory protein kinases. In preliminary work, our studies suggest the potential regulation of STMN by c-Jun N-terminal Kinase (JNK) in cells exposed to stress. Specifically, we observed changes in STMN phosphorylation which were coordinated with JNK activation. / This project has explored the contribution of stress-activated c-Jun N-terminal Kinase (JNK) to STMN phosphorylation observed during osmotic stress. More detailed in vitro biochemical analysis has revealed that JNK directly phosphorylates STMN. In addition, we have compared STMN phosphorylation by different MAPK family member. In particular, our results illustrated that JNK predominantly phosphorylate STMN on serine residue 38 (S38) whereas ERK most likely targeted STMN S25. By examining specifically the phosphorylation of the four regulatory serine residues in vitro, we proposed a model of hierarchical phosphorylation among STMN serine residues. Specifically, our results demonstrated that phosphorylation of S38 was a pre-requisite for S25 phosphorylation by JNK in vitro. Furthermore, our results also demonstrated the impacts of JNK binding domain (JBD) and tubulin on STMN phosphorylation in vitro. Overall, this project identified STMN as a novel JNK substrate. The results have broadened our understanding on the JNK-mediated STMN phosphorylation as the first step to provide deeper insights into the different functions of JNK in the mammalian stress response.

Stomata are cellular valves in plants that play an essential role in the regulation of gas exchange and are distributed in the epidermis of aerial organs. In Arabidopsis thaliana, stomatal production and development are coordinated by the mitogen-activated protein kinase (MAPK) signalling pathway, which modulates a variety of other processes, including cell proliferation, regulation of cytokinesis, programed cell death, and response to abiotic and biotic stress. The environment also plays a role in stomatal development, by influencing the frequency at which stomata develop in leaves. This thesis presents an analysis of stomatal development in Arabidopsis mutants in two MAPK pathways: MEKK1-MKK1/MKK2-MPK4, and MAP3K17/18-MKK3. Obtained results demonstrate the effect of stress conditions on stomatal development and specify the involvement of analysed MAPK in stomatal patterning. First, both analysed pathways modulate stomatal patterning in Arabidopsis cotyledons. Second, plant growth-promoting bacteria tested enhance stomatal density and affect guard cell morphology. Third, the sucrose or mannitol treatment increases defects in stomatal patterning. Finally, salt stress or high temperature can suppress stomatal defects in mutants of the MEKK1-MKK1/MKK2-MPK4 pathway.

Il est fréquent d’avoir recours à la radiothérapie dans le traitement des mélanomes, en adjuvant ou en métastatique, mais les résultats cliniques sont suboptimaux, car ces tumeurs présentent souvent des mutations de RAF/RAS, activant alors la voie MAPK de façon constitutive. Nous avons donc étudier si le Trametinib, un inhibiteur allostérique puissant et sélectif de MEK1/2, est en mesure d’augmenter l’efficacité de la radiothérapie. Des tests clonogéniques ont été effectués sur des lignées de mélanomes humaines mutées pour BRAF (A375), NRAS (D04,WM1631), KRAS (WM1791c) ainsi que sur une lignée sauvage (PMWK). Les effets du Tramétinib avec ou sans irradiation (IR) sur les protéines effectrices de MEK ont été quantifiés par western-blot. Les effets de l’addition du Trametinib sur le cycle cellulaire, la réparation de l’ADN, la catastrophe mitotique et la senescence ont respectivement été analysés par cytométrie de flux, étude des foyers γH2Ax, et marquage de l’activité de la β-galactosidase. Enfin, des souris immunodéficientes xenogreffées avec des cellules D04 ont été traitées par IR fractionnée après gavage de Trametinib, et la croissance tumorale a été monitorée.Une augmentation de la cytocoxité en présence de l’ajout de Trametinib à l’ IR a été observée pour toutes les lignées, exceptée PMWK. Le taux de radiosensibilisation des cellules étaient respectivement de 1.70, 1.32, 1.22, et 1.70 pour A375, D04, WM1361 et WM1791c. Le Trametinib bloquait de façon efficace la phosphrylation de ERK à des doses de l’ordre du nanomolaire. Ceci corrélait avec un arrêt prolongé des cellules en phase G1, et une réduction de la phase S, connue pour être radiosésistante, ceci jusqu’à 48 heures après IR. Dans les groupes cellulaires prétraités par Trametinib, une population plus importante de cellules étaient positives pour la β-galactosidase, et deux médiateurs majeurs de la sénescence, p53 et pRb se trouvaient être activés. Les souris recevant le traitement combiné (Trametinib 1mg/kg et IR sur 3 jours) avaient un volume tumoral réduit en comparaison du groupe recevant du Trametinib seul (p=0.016), ou une IR seule (p=0.047). Il n’y avait pas de toxicité notable dans le groupe recevant le traitement combiné.Le Trametinib radiosensibilise les lignées cellulaires de mélanomes mutées pour RAF/RAS en induisant un arrêt prolongé en phase G1 du cycle cellulaire, provoquant ainsi une sénescence prématurée. Associer Trametinib et IR semble être parfaitement toléré, mais ne ralentit la croissance tumorale que modestement in vivo. / Radiotherapy is used frequently in patients with melanoma, but results are suboptimal as these tumours frequently exhibit constitutive activation of the MAPK pathway through mutations involving RAS/RAF. Thus, we studied whether Trametinib, a potent and selective allosteric inhibitor of the MEK1/2 enzymes could improve efficacy of radiotherapy.Clonogenic survival assays were carried out in human BRAF (A375), NRAS (D04,WM1631), KRAS (WM1791c) mutant and wild type (PMWK) melanoma. The effects of Trametinib with and without irradiation (IR) on protein levels of MEK effectors were quantitated by immunoblot analyses. Cell cycle effects, DNA damage repair, mitotic catastrophe and senescence were measured using flow cytometry, γH2Ax, nuclear fragmentation and β-galactosidase staining, respectively. Additionally, nude mice with D04 flank tumours were treated with fractionated RT after gavage with Trametinib and monitored for tumours’ growth. All cell lines but PMWK exhibited enhanced cytotoxicity with IR and Trametinib compared to either agent alone. The sensitizer enhancement ratios were 1.70, 1.32, 1.22, and 1.70 for A375, D04, WM1361 and WM1791c, respectively. Trametinib efficiently blocked IR-induced phosphorylation of ERK at doses in the nanomolar range. This increased susceptibility correlated with a prolonged G1 arrest and reduction in the radioresistant S phase up to 48 hours following IR. A larger population of senescence activated β-galactosidase-positive cells was seen in the Trametinib pretreated group, and this correlated with an activation of two of the major mediator of induced senescence, p53 and pRb. Mice receiving the combination treatment (Trametinib 1mg/kg and IR ober 3 days) showed a reduced mean tumour volume compared with mice receiving Trametinib alone (p=0.016), or IR alone (p=0.047). No overt signs of drug toxicity were observed.Trametinib radiosensitized RAF/RAS mutated melanoma cells to radiation by inducing a prolonged G1 arrest and premature senescence. Combining Trametinib and IR is well tolerated but only moderately induces tumour growth inhibition in vivo.

BACKGROUND:General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.RESULTS:For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value<0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value<0.001) including, 9nucleotide binding / ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.CONCLUSIONS:The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.

Metastatic melanoma is an aggressive, incurable cancer with historically few therapeutic options. The discovery that 60% of melanomas harbor the oncogenic BRAF_V600E mutation, which constitutively activates the MAPK pathway, has provided a promising new therapeutic axis. Although MAPK pathway inhibitor therapy has shown striking clinical results in BRAF_V600-mutant melanoma, this approach faces three limitations. First, 10-20% of BRAF_V600-mutant melanomas never achieve meaningful response to MAPK pathway inhibitor therapy (intrinsic resistance). Second, among BRAF_V600-mutant melanomas initially responding to MAPK pathway inhibitor therapy, relapse is universal (acquired resistance). Third, approximately 40% of melanomas lack BRAF_V600 mutations and so are not currently candidates for MAPK pathway inhibitor therapy. We sought to address each of these problems: by characterizing the phenomenon of intrinsic MAPK pathway inhibitor resistance, by finding ways to perturb mechanisms of acquired MAPK pathway inhibitor resistance, and by identifying novel dependencies in melanoma outside of the MAPK pathway. Intriguingly, the NF-kappa B pathway emerged as a common theme across these investigations. In particular, we establish that MAPK pathway inhibitor sensitive and resistant melanomas display distinct transcriptional signatures. Unlike most BRAF_V600-mutant melanomas, which highly express the melanocytic lineage transcription factor MITF, MAPK pathway inhibitor resistant lines display low MITF expression but high levels of NF-kappa B signaling. These divergent transcriptional states, which arise in melanocytes from aberrant MAPK pathway activation by BRAF_V600E, remain plastic and mutually antagonistic in established melanomas. Together, these results characterize a dichotomy between MITF and NF-kappa B cellular states as a determinant of intrinsic sensitivity versus resistance to MAPK pathway inhibitors in BRAF_V600-mutant melanoma. In separate investigations, we have shown that, NFKB1 p105, a member of the NF-kappa B family, intimately regulates levels of COT, a known effector of resistance to MAPK pathway inhibitors. Moreover, we have used shRNA screening to nominate particular nodes within the NF-kappa B pathway, including MYD88 and IRF3, as candidate melanoma lineage-specific dependencies. Cumulatively, although these studies use diverse approaches to investigate the limitations of MAPK pathway inhibitor therapy in melanoma, they converge in nominating the NF-kappa B pathway as a previously underappreciated feature of melanoma biology and suggest the relevance of this pathway for future investigation.

Colorectal cancer is the second most common cause of cancer death in Western Europe and North America. Current therapies are largely ineffective and are associated with considerable morbidity. Activating mutations in KRAS and BRAF genes are frequent in colorectal cancer, especially at later stages of the disease, and result in constitutive activity of the MAPK pathway, leading to increased proliferation and tumour survival. The MEK1/2 inhibitor AZD6244, that targets the MAPK pathway downstream of these mutations, has been tested as novel therapy for colorectal cancer. However, clinical trials have been disappointing due to an apparent intrinsic and/or acquired resistance to treatment. Mechanisms underlying this resistance have been studied using cell lines and tumour xenografts. However, the relevance of these data to advanced human colorectal cancer is unclear. One of the difficulties in testing and developing novel therapies for colorectal cancer is the lack of representative models of human disease. Thus, the initial aim of my PhD was to develop a method to culture human colorectal cancers ex vivo in order to use this as a platform for investigating response to AZD6244 and other therapies. These studies indicated that regardless of growth conditions, colonic tumour explants suffered extensive apoptosis in the first 24h in culture, which limited their application in drug response assays. Therefore, as an alternative to long term culture of human colorectal explants, I tested the effects of AZD6244 using acute treatments. Twenty three fresh colonic tumours were obtained from patients and treated for 1h with AZD6244 ex vivo in dose response studies. In all samples, MEK1/2 inhibition occurred within 1h of treatment. In one group of particularly sensitive tumours, the drug also had a distinct phenotypic effect. In these tumours, I found that the agent induced a dose-dependent decrease in proliferation and increase in apoptosis within 1h of treatment. Analysis of markers for this sensitivity indicated it was not clearly dependent of the presence of KRAS or BRAF mutations, which have previously been shown to confer sensitivity. Other markers of sensitivity / resistance were also examined. In addition to studies with AZD6244 alone, I examined the combined effects of this agent and aspirin in colon cancer cells lines and in tumour explants, with promising results. Whilst the use of fresh patient tumour tissue has some technical and logistical challenges, these data suggest that such methodologies are worthy of further investigation as a means to examine determinants of sensitivity and resistance to novel therapies, or their likely activity in combination.

Noonan spectrum disorders belong to the RASopathies, a group of clinically related developmental disorders caused by dysregulation of the RAS-MAPK pathway. This thesis describes genetic and clinical investigations of six families with Noonan spectrum disorders. In the first family, the index patient presented with severe Noonan syndrome (NS) and multiple café-au-lait (CAL) spots, while four additional family members displayed multiple CAL spots only. Genetic analysis of four RAS-MAPK genes revealed a de novo PTPN11 mutation and a paternally inherited NF1 mutation, which could explain the atypically severe NS, but not the CAL spots trait in the family. The co-occurrence of two mutations was also present in another patient with a severe/complex NS-like phenotype. Genetic analysis of nine RASopathy-associated genes identified a de novo SHOC2 mutation and a maternally inherited PTPN11 mutation. The latter was also identified in her brother. Both the mother and the brother displayed mild phenotypes of NS. The results from these studies suggest that an additive effect of co-occurring mutations contributes to severe/complex NS phenotypes. The inherent difficulty in diagnosing Noonan spectrum disorders is evident in families with neurofibromatosis-Noonan syndrome (NFNS). An analysis of nine RASopathy-associated genes in a five-generation family with NFNS revealed a novel NF1 mutation in all affected family members. Notably, this family was initially diagnosed with NS and CAL spots. The clinical overlap between NS and NFNS was further demonstrated in three additional NFNS families. An analysis of twelve RASopathy-associated genes revealed three different NF1 mutations, all segregating with the disorder in each family. These mutations have been reported in patients with NF1, but have, to our knowledge, not been associated with NFNS previously. Together, these findings support the notion that NFNS is a variant of NF1. Due to the clinical overlap between NS and NFNS, we propose screening for NF1 mutations in NS patients negative for mutations in NS-associated genes, preferentially when CAL spots are present. In conclusion, this thesis suggests that co-occurrence of mutations or modifying loci in the RAS-MAPK pathway contributes to the clinical variability observed within Noonan spectrum disorders and further demonstrates the importance of accurate genetic diagnosis.

abstract: In somatic cells, the mitotic spindle apparatus is centrosomal and several isoforms of Protein Kinase C (PKC) have been associated with the mitotic spindle, but their role in stabilizing the mitotic spindle is unclear. Other protein kinases such as, Glycogen Synthase Kinase 3â (GSK3â) also have been shown to be associated with the mitotic spindle. In the study in chapter 2, we show the enrichment of active (phosphorylated) PKCæ at the centrosomal region of the spindle apparatus in metaphase stage of 3T3 cells. In order to understand whether the two kinases, PKC and GSK3â are associated with the mitotic spindle, first, the co-localization and close molecular proximity of PKC isoforms with GSK3â was studied in metaphase cells. Second, the involvement of inactive GSK3â in maintaining an intact mitotic spindle was shown. Third, this study showed that addition of a phospho-PKCæ specific inhibitor to cells can disrupt the mitotic spindle microtubules. The mitotic spindle at metaphase in mouse fibroblasts appears to be maintained by PKCæ acting through GSK3â. The MAPK pathway has been implicated in various functions related to cell cycle regulation. MAPKK (MEK) is part of this pathway and the extracellular regulated kinase (ERK) is its known downstream target. GSK3â and PKCæ also have been implicated in cell cycle regulation. In the study in chapter 3, we tested the effects of inhibiting MEK on the activities of ERK, GSK3â, PKCæ, and á-tubulin. Results from this study indicate that inhibition of MEK did not inhibit GSK3â and PKCæ enrichment at the centrosomes. However, the mitotic spindle showed a reduction in the pixel intensity of microtubules and also a reduction in the number of cells in each of the M-phase stages. A peptide activation inhibitor of ERK was also used. Our results indicated a decrease in mitotic spindle microtubules and an absence of cells in most of the M-phase stages. GSK3â and PKCæ enrichment were however not inhibited at the centrosomes. Taken together, the kinases GSK3â and PKCæ may not function as a part of the MAPK pathway to regulate the mitotic spindle. / Dissertation/Thesis / Ph.D. Molecular and Cellular Biology 2012

The field of systems biology has become very popular as a means to deal with cancer as well as other complex biological issues. It enables scientists to gain an insight into difficult conditions through mathematical approaches that have been developed. Prostate cancer is the second leading cause of death among men after skin cancer and its heterogeneity makes it a complex disease. In this study we focus on three pathways known to play crucial roles in the formation of prostate cancer. By using a mathematical model that combines all of them we describe the interactions taking place during signal transduction in the prostate under normal and cancer conditions.