Dynamic portfolio rebalancing with lag-optimised trading indicators using SeroFAM and genetic algorithms

Some common technical indicators, such as moving average convergence divergence (MACD), relative strength index (RSI), and MACD histogram (MACDH) are used in technical analyses and stock trading. However, some of them are lagging indicators, affecting the effectiveness in the stock trading and portfolio management. A forecasted MACDH (fMACDH) indicator for predicting next day price by a neuro-fuzzy network, Self-reorganizing Fuzzy Associative Machine (SeroFAM) which has been reported in the prior research work. In order to further reduce the lagging effect, two trading indicators are proposed in this paper: the optimised fMACDH indicator and the fMACDH-fRSI indicator. The optimised fMACDH indicator is derived to extend price forecasting to 1-5 days ahead as the prediction depth, using 1-5 days of historical price data as the input depth. The fMACDH-fRSI indicator is derived by combining the optimized fMACDH indicator and the forecasted RSI (fRSI) indicator. A genetic algorithm (GA) and the fitness functions are designed with the SeroFAM in this paper, which are utilised for optimising parameters of these two proposed indicators. Experiments have been conducted to evaluate and benchmark of the proposed trading indicators optimised by the GA. Two rule-based portfolio rebalancing algorithms are then proposed using the optimised fMACDH trading indicator tuned by the GA: the Tactical Buy and Hold (TBH) and the Rule-Based Business Cycle (RBBC) portfolio rebalancing algorithms. The TBH algorithm takes advantage of relative differences in risk levels to perform rebalancing during trend reversals. The RBBC portfolio rebalancing algorithm takes advantage of the offsets between the business cycles of different market sectors. Experiments have been conducted to evaluate the performance of both algorithms using two sets of portfolios consisting of different assets. The TBH portfolio rebalancing algorithm outperforms the equally weighted portfolio strategy by about 26% - 27%; as well outperforms the Buy and Hold strategy by 5% - 40%. The RBBC portfolio rebalancing algorithm outperforms the equally weighted portfolio strategy by 54% - 55%; it also outperforms 12 out of the 13 assets with the Buy and Hold strategy, by an average performance of about 166%. The results are highly encouraging with consistent performances achieved in dynamic portfolio rebalancing

Gene Expression and Phenotypic Traits

Gene expression is the most fundamental level at which genotype gives rise to phenotype, which is an obvious, observable, and measurable trait. Phenotype is dependent on genetic makeup of the organism and influenced by environmental conditions. This book explores the significance, mechanism, function, characteristic, determination, and application of gene expression and phenotypic traits

Investigating New Drug Options for Temozolomide Resistant IDH1 Mutant Glioma

Gliomas, a prevalent form of malignant brain tumors in adults, often exhibit mutations in the isocitrate dehydrogenase 1 (IDH1) gene. Temozolomide (TMZ) is a commonly used chemotherapy drug for treating gliomas; however, the development of drug resistance poses a significant challenge to its effectiveness. My study aimed to investigate new drug options for IDH1 mutant gliomas and was divided into two main parts. The first part focused on reversing TMZ resistance and identifying synergistic drugs, while the second part sought alternative treatments for IDH1 mutant TMZ-resistant gliomas. To achieve the objectives of the first part, patient-derived glioma tumorspheres (PDTs) harboring IDH1 mutations were utilized. Vehicle and TMZ treated tumor models were subjected to transcriptional, metabolic, and epigenetic analyses. Transcriptome analysis revealed the upregulation of the p53 signaling pathway and its associated transcription factor, TP53. Notably, combining the p53 activator RITA with TMZ demonstrated strong synergy in certain PDTs. Metabolome analysis uncovered that glycolytic inhibition with the glucose analog 2-DG (2-Deoxy-D-glucose) or combining Mildronate, L-carnitine biosynthesis inhibitor, with TMZ treatment showed efficacy in specific PDTs. Additionally, employing epigenetic approaches using decitabine (DAC) in combination with TMZ revealed robust synergistic effects in select PDTs. These findings underscore the significance of genetic and metabolic heterogeneity among cells in gliomas. In the pursuit of alternative drugs, a high-throughput miniaturized screening identified more than 20 potential candidate drugs, among which the YAP inhibitor Verteporfin (VP) emerged as a promising option. VP exhibited anti-tumor activity in IDH1 mutant PDTs independent of the YAP1 protein. It downregulated the nucleocytoplasmic transport pathway, with NUP107 identified as an upstream regulator associated with VP response. In conclusion, this study elucidated the intricate interplay of signaling pathways and their impact on drug sensitivity in diverse glioma cell populations. It emphasized the need to consider the complexities inherent to gliomas when devising effective therapeutic strategies. The findings provide valuable insights into the development of alternative treatments and strategies to overcome TMZ resistance in IDH1 mutant gliomas

The determination of petroleum reservoir fluid properties : application of robust modeling approaches.

Doctor of Philosophy in Chemical Engineering. University of KwaZulu-Natal, Durban 2016.Abstract available in PDF file

Molecular and functional characterization of microRNA-137 in oligodendroglial tumors.

Yang, Ling.Thesis (M.Phil.)--Chinese University of Hong Kong, 2011.Includes bibliographical references (leaves 222-244).Abstracts in English and Chinese.Acknowledgements --- p.iAwards and Presentations --- p.iiAbstract in English --- p.iiiAbstract in Chinese --- p.viiTable of Contents --- p.xList of Tables --- p.xvList of Figures --- p.xviiList of Abbreviations --- p.xxChapter CHAPTER 1 --- INTRODUCTION --- p.1Chapter 1.1 --- Gliomas --- p.1Chapter 1.1.1 --- Oligodendroglial tumors (OTs) --- p.3Chapter 1.1.2 --- Glioblastoma multiforme (GBM) --- p.3Chapter 1.1.3 --- Molecular pathology of gliomas --- p.4Chapter 1.1.3.1 --- Genetic alterations in OTs --- p.4Chapter 1.1.3.2 --- Prognostic and predictive factors in OTs --- p.7Chapter 1.1.3.3 --- Genetic alterations in GBM --- p.8Chapter 1.1.3.4 --- Prognostic and predictive factors in GBM --- p.10Chapter 1.2 --- microRNA(miRNA) --- p.13Chapter 1.2.1 --- miRNA biogenesis and function --- p.13Chapter 1.2.2 --- miRNA involvement in cancer --- p.17Chapter 1.2.2.1 --- Dysregulation of miRNAs in human malignancies --- p.17Chapter 1.2.2.2 --- Function and potential application of miRNAs --- p.17Chapter 1.2.3 --- Role of miRNAs in glioma --- p.19Chapter 1.2.3.1 --- miRNAs in OTs --- p.19Chapter 1.2.3.2 --- miRNAs in GBM --- p.20Chapter 1.3 --- miR-137 --- p.30Chapter 1.3.1 --- Biology of miR-137 --- p.30Chapter 1.3.2 --- Role of miR-137 in carcinogenesis --- p.33Chapter 1.3.2.1 --- Deregulation of miR-137 in cancer --- p.33Chapter 1.3.2.2 --- Regulation of miR-137 expression in cancer --- p.33Chapter 1.3.2.3 --- Biological functions of miR-137 in cancer --- p.37Chapter 1.3.3 --- Role of miR-137 in differentiation and neurogenesis --- p.39Chapter CHAPTER 2 --- AIMS OF STUDY --- p.43Chapter CHARPTER 3 --- MATERIALS AND METHODS --- p.45Chapter 3.1 --- Tumor samples --- p.45Chapter 3.2 --- Cell lines and culture conditions --- p.48Chapter 3.3 --- Fluorescence in situ hybridization (FISH) --- p.49Chapter 3.4 --- Cell transfection --- p.52Chapter 3.4.1 --- Transfection of oligonucleotides --- p.52Chapter 3.4.1.1 --- Oligonucleotide preparation --- p.52Chapter 3.4.1.2 --- Optimization of transfection condition --- p.52Chapter 3.4.2 --- Cotransfection of plasmids and miRNA mimic --- p.53Chapter 3.4.2.1 --- Optimization of transfection condition --- p.53Chapter 3.4.2.2 --- Procedure of transfection --- p.54Chapter 3.5 --- Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) --- p.55Chapter 3.5.1 --- RNA extraction from frozen tissues and cell lines --- p.55Chapter 3.5.2 --- qRT-PCR for miR-137 --- p.56Chapter 3.5.3 --- qRT-PCR for CSE1L and ERBB4 transcripts --- p.57Chapter 3.6 --- 5-aza-2'-deoxycytidine (5-aza-dC) and Trichostatin A (TSA) treatment --- p.61Chapter 3.7 --- Western blotting --- p.62Chapter 3.7.1 --- Preparation of cell lysate --- p.62Chapter 3.7.2 --- Measurement of protein concentration --- p.62Chapter 3.7.3 --- Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) --- p.63Chapter 3.7.4 --- Electroblotting of proteins --- p.67Chapter 3.7.5 --- Immunoblotting --- p.67Chapter 3.8 --- Dual-luciferase reporter assay --- p.70Chapter 3.8.1 --- Construction of reporter plasmids --- p.70Chapter 3.8.1.1 --- Experimental outline --- p.70Chapter 3.8.1.2 --- PCR Amplification of MREs --- p.70Chapter 3.8.1.3 --- TA cloning --- p.71Chapter 3.8.1.4 --- Transformation --- p.72Chapter 3.8.1.5 --- Blue/white screening and validation of recombinants --- p.72Chapter 3.8.1.6 --- Subcloning of 3'UTR fragments into pMIR-reproter vector --- p.73Chapter 3.8.2 --- Site-directed mutagenesis --- p.74Chapter 3.8.3 --- Plasmid and miRNA mimic cotransfection --- p.76Chapter 3.8.4 --- Determination of luciferase activity --- p.76Chapter 3.9 --- Functional assays : --- p.79Chapter 3.9.1 --- Cell growth and proliferation assay --- p.79Chapter 3.9.1.1 --- "3-(4，5-Dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay" --- p.79Chapter 3.9.1.2 --- Cell counting --- p.80Chapter 3.9.1.3 --- 5-Bromo-2'-deoxyuridine (BrdU) incorporation assay --- p.80Chapter 3.9.2 --- Apoptosis assay --- p.82Chapter 3.9.3 --- Anchorage-independent growth assay --- p.82Chapter 3.9.4 --- Wound healing assay --- p.83Chapter 3.9.5 --- Matrigel invasion assay --- p.84Chapter 3.9.6 --- Cell differentiation assay --- p.85Chapter 3.10 --- Immunohistochemical analysis --- p.86Chapter 3.10.1 --- H&E staining --- p.86Chapter 3.10.2 --- Detection of Ki-67 expression --- p.87Chapter 3.10.3 --- Detection of CSE1L expression --- p.87Chapter 3.10.4 --- Scoring methods --- p.88Chapter 3.11 --- Bioinformatic analysis --- p.90Chapter 3.12 --- Statistical analysis --- p.92Chapter CHAPTER 4 --- RESULTS --- p.93Chapter 4.1 --- Expression of miR-137 in glioma cells and clinical significance --- p.93Chapter 4.1.1 --- Description of 36 OT samples --- p.93Chapter 4.1.2 --- miR-137 level in oligodendroglial tumors and glioma cells --- p.102Chapter 4.1.3 --- "Association of miR-137 expression with clinicopathological features, lp/19q status and Ki-67 expression" --- p.104Chapter 4.2 --- miR-137 levels in glioma cells after demethylation treatment --- p.113Chapter 4.3 --- Biological effects of miR-137 overexpression in glioma cells --- p.118Chapter 4.3.1 --- Cell growth --- p.118Chapter 4.3.1.1 --- Cell viability --- p.118Chapter 4.3.1.2 --- Cell number --- p.123Chapter 4.3.1.3 --- Cell cycle analysis : --- p.127Chapter 4.3.2 --- Anchorage-independent cell growth --- p.130Chapter 4.3.3 --- Cell apoptosis --- p.134Chapter 4.3.4 --- Cell motility --- p.136Chapter 4.3.5 --- Cell differentiation : --- p.142Chapter 4.4 --- Identification of miR-137 targets --- p.144Chapter 4.4.1 --- In silico prediction of potential miR-137 targets --- p.144Chapter 4.4.2 --- Experimental validation of miR-137 targets by dual-luciferase reporter assay --- p.147Chapter 4.4.3 --- "Expression of miR-137 candidate targets, CSE1L and ERBB4 in glioma cells" --- p.152Chapter 4.4.4 --- Effects of miR-137 on CSE1L transcript and protein levels --- p.154Chapter 4.5 --- Expression of CSE1L in OTs --- p.156Chapter 4.5.1 --- CSE1L expression in OTs by qRT-PCR and IHC --- p.156Chapter 4.5.2 --- Correlation of CSE1L expression with clinicopathological features --- p.165Chapter 4.6 --- Effects of CSE1L knockdown in glioma cells --- p.168Chapter 4.6.1 --- Cell growth --- p.170Chapter 4.6.1.1 --- Cell viability --- p.170Chapter 4.6.1.2 --- Cell number --- p.173Chapter 4.6.1.3 --- Cell cycle analysis --- p.176Chapter 4.6.2 --- Anchorage-independent cell growth --- p.179Chapter 4.6.3 --- Cell apoptosis --- p.182Chapter 4.6.4 --- Cell motility --- p.184Chapter CHAPTER 5 --- DISCUSSION --- p.190Chapter 5.1 --- Expression of miR-137 transcript level in OTs and glioma cell lines --- p.190Chapter 5.2 --- Association of miR-137 expression with OT clinical and molecular parameters --- p.192Chapter 5.3 --- Prognostic significance of clinical features and miR-137 expression in OTs --- p.194Chapter 5.4 --- Inactivation mechanisms of miR-137 in glioma --- p.196Chapter 5.5 --- Biological effects of miR-137 overexpression in glioma cells --- p.198Chapter 5.6 --- CSE1L is a novel miR-137 target in glioma --- p.200Chapter 5.7 --- Expression of CSE1L in glioma --- p.203Chapter 5.8 --- Intracellular distribution of CSElL in OTs --- p.206Chapter 5.9 --- Correlation of CSE1L expression with clinicopathological and molecular features in OTs --- p.208Chapter 5.10 --- CSE1L mediates effects of miR-137 in glioma cells --- p.210Chapter 5.11 --- Biological roles of CSE1L in glioma cells 226}0Ø. --- p.212Chapter 5.11.1 --- CSE1L in glioma cell proliferation --- p.212Chapter 5.11.2 --- CSE1L in glioma cell apoptosis --- p.213Chapter 5.11.3 --- CSE1L in glioma cell invasion --- p.215Chapter CHAPTER 6 --- CONCLUSIONS --- p.216Chapter CHAPTER 7 --- FUTURE STUDIES --- p.219Chapter 7.1 --- Expression Molecular mechanisms for miR-137 inactivation in glioma --- p.219Chapter 7.2 --- Identification of more miR-137 targets in glioma --- p.219Chapter 7.3 --- Role of miR-137 and CSE1L in drug-induced apoptosis in glioma --- p.220Chapter 7.4 --- Deciphering dysregulated and clinical relevant miRNAs in glioma --- p.220Chapter 7.5 --- Effects of miR-137 in vivo and the therapeutic potential in glioma treatment --- p.221REFERENCES --- p.22

THE GENETICS OF ADAPTATION IN DROSOPHILA SECHELLIA

Drosophila sechellia, an ecological specialist on the ripe fruit of Morinda citrifolia (Morinda), displays a suite of adaptations which allow it to both prefer and tolerate Morinda and its toxic compounds. Other Drosophilids, like D. melanogaster, find Morinda repellent and toxic. Despite years of effort to dissect the genetic basis of this behavioral and physiological divergence, we still do not understand what genes allow D. sechellia to prefer and tolerate Morinda and what genes drive aversion in other species. In this dissertation I dissect the genetic basis of preference and tolerance using both traditional genetic and molecular tools along with new whole genome sequencing methods. I find that preference is genetically complex (Chapter Two), requiring up to 27 different genetic loci (Chapter Three). At the same time, however, a gene expressed in the fly's peripheral nervous system, gustatory receptor 22c, Gr22c, is responsible for nearly 50% of the transition between aversion and preference (Chapter Four). Surprisingly, extant D. sechellia Gr22c is likely a pseudogene, suggesting that preference evolution proceeded in two steps: loss of aversion then gain of preference. Finally, I, along with collaborators, introgress D. sechellia Morinda tolerance factors into a D. simulans genome and identify 17 candidate genes, among then three Odorant binding proteins (Chapter Five). We find that tolerance alone is not enough to confer altered behavior, conflicting with evolutionary models that predict preference and tolerance loci would evolve to be genetically linked. In sum, this dissertation shows that the genetic basis of D. sechellia specialism on Morinda is complex and suggests that the evolution of preference and tolerance occurred in multiple steps: loss of aversion, gain of tolerance, and finally gain of preference.Doctor of Philosoph

Investigating the expression of genes and proteins in Glioblastoma during hypoxia

Glioblastoma multiforme (GBM), grade IV Astrocytoma, is the most common and deadly form of brain cancer. Despite the low incidence rate (3.2 per 100.000 people), patient’s median survival is only 14 months. Notwithstanding all new diagnostic tools, GBM remains a therapeutic challenge, being extremely difficult to prevent recurrence. Therefore, it is essential to conduct research in order to understand the molecular pathways in the core of GBM aggressiveness and swift evolution. GBM is often characterized by hypoxic regions where oxygen levels are extremely low. As a natural consequence of tumour growth and expansion, some areas of the tumour become distanced from the blood vessels and consequently, from the oxygen supply. In such a critical environment, cells activate pro-survival and malignancy mechanisms such as the metabolic switch, invasion and angiogenesis. Hence we investigated the expression of genes featuring these survival mechanisms and identified a panel of hypoxia-driven-malignancy markers. To conduct this study, two GBM patient´s biopsy-derived cell lines (UP-029 and SEBTA-023) were used and cultured under hypoxic conditions for a selected set of time-points (time-course). To characterize the hypoxic response of these cells, hypoxia profiler microarrays were ran for normoxia, 6 and 48 hours of hypoxia (1% O2). Once identified the induced and repressed genes, these were analyzed and validated through qRT-PCR assays. Finally, western-blot analysis was performed to detect target proteins and correlate with the previously obtained gene expression data. Our study validated ANGPTL4, PIGF, VEGFA, GLUT1, PFKB4, PFKB3, BNIP3, DDIT4, NDRG1 and CAIX genes as relevant in GBM’s hypoxia-mediated response. We also pointed out MXI1, HNF4A genes as likely significant factors in GBM hypoxia. Furthermore, we hypothesize PFKB3 as an adaptive resistance marker in GBM and the repression of TFRC as required mechanism for GBM progression.O Glioblastoma multiforme (GBM) é a forma mais comum e letal de cancro no sistema nervoso central. Devido às suas caraterísticas altamente invasivas e malignas, o Glioblastoma foi considerado pela World Health Organization (WHO) como um Astrocitoma grau IV. Contrariamente a outros tipos de cancro de igual grau, a capacidade de invasão do GBM é limitada ao tecido cerebral. Apesar dos avanços nas tecnologias de diagnóstico e dos constantes progressos na investigação do cancro, o tratamento do GBM é meramente paliativo. A seletividade farmacológica da barreira hemato-encefálica, a elevada heterogeneidade tumoral e influência destrutiva do tumor no tecido nervoso, refletemse na ineficiência das terapias aplicadas. Clinicamente, o GBM manifesta-se através de pressão intracranial, cefaleias e/ou défices neurológicos tais como, alterações visuais, alterações da fala, dificuldades cognitivas e até modificações na personalidade. Embora, menos frequentes, convulsões também se encontram descritas como um dos sintomas. A taxa de incidência deste tipo de carcinoma é de facto baixa, sendo que em 100000 apenas 3.2 pessoas são afetadas. Não obstante, a média de sobrevida destes pacientes é somente 14 meses. Conduzir investigações no sentido de entender os mecanismos moleculares que se encontrar subjacentes à expansão e agressividade do GBM torna-se, portanto, essencial. Uma das características mais proeminentes do GBM são as regiões hipóxicas, onde os níveis de oxigénio são extremamente baixos. Esta é uma consequência natural, derivada da expansão tumoral e do incremento da distância de difusão de oxigénio. Estabelecido um microambiente como este, crítico para a sobrevivência celular, as células tumorais ativam mecanismos de malignidade tais como “switch” metabólico, angiogénese e invasão. Desta forma as células adquirem vantagem clonal e capacidade migratória para invadirem zonas de tecido cerebral saudável. Para além do incremento da malignidade, a elevada capacidade invasiva destas células constitui um risco em termos de recorrência. De um modo geral, a hipóxia integra-se como um marcador de mau prognostico. Para este estudo, duas linhas celulares obtidas através de biópsias de pacientes com GBM (UP-029 e SEBTA-023), foram incubadas a diferentes tempos de hipóxia. Após extração de ácido ribonucleico (ARN), realizou-se um microarray de perfil de hipóxia a três amostras em diferentes condições: normóxia (controlo), 6 e 48 horas. O método do microarray baseia-se na tecnologia de reações de polimerase em cadeia e em tempo real (RT-PCR). Este, por sua vez, é um método de quantificação de expressão génica através da geração de cópias (por ciclo de PCR) a partir de um ADN molde. Isto origina uma correlação entre a quantidade inicial de cópias e a quantidade acumulada a cada ciclo. Desta maneira, foi possível quantificar a expressão génica de 84 genes previamente descritos na literatura como relacionados na resposta hipóxica em diversos tipos de cancro. Este ensaio permitiu-nos identificar em larga escala diversos marcadores de hipóxia que foram diferencialmente expressos com significância. Do painel analisado, destacaram-se os genes ANGPTL4, NDRG1, CAIX, PFKB4 e VEGFA como relevantemente induzidos tanto nas UP-029 como nas SEBTA-023. Para além destes, os genes MXI1, HNF4A e TFRC foram estabelecidos como significativamente sub-expressos durante a hipóxia nas duas linhas celulares de GBM. Continuando com a análise, estudámos através de ensaios de RT-PCR quantitativo os vários genes distinguidos acima, tal como outros apenas diferencialmente expressos numa das linhas celulares durante a hipóxia. Cada gene foi analisado em quatro condições diferentes: normóxia, 6, 24 e 48 horas de hipóxia, em pelo menos três corridas diferentes. O método de 2-ΔΔCT foi usado para calcular o fold-change de cada gene, que nos transmite a magnitude biológica da expressão de um gene relativamente a um controlo. De modo a estudar a significância estatística dos resultados, usámos Students T-test (tipo 2, cauda 2) para calcular os P-values de cada amostra. Considerámos três níveis de significância para P-values inferiores que 0.05 (*), 0.01 (**) e 0.001 (***). Desta análise de RT-PCR quantitativo, para além dos genes previamente distinguidos, também os genes PIGF, PDK1, PFKB3, BNIP3, DDIT4 e SLC16A3 foram detetados como significativamente induzidos nas linhas celulares UP-029 e SEBTA-023. Validámos, também, o gene TFRC como significativamente subexpresso durante a hipóxia. De modo a analisar a expressão de proteínas de alguns deste fatores, realizaram-se ensaios de Western-blot. Esta é uma técnica vastamente usada em laboratório que permite a identificação de proteínas específicas de uma amostra de proteína total. Este método consiste na separação de proteínas por pesos moleculares através da aplicação de voltagem. Para tal, a amostra proteica é desnaturada através de calor e posteriormente pipetada num gel de eletroforese. As proteínas (carga negativa) migram através do gel na direção do polo positivo, assim que aplicada voltagem. Desta forma, as moléculas menores migram mais rapidamente e facilmente para a base do gel que as de maior peso molecular, que ficam mais próximas do topo. Após separação e transferência para uma membrana de nitrocelulose, é possível sinalizar estas proteínas através de complexos de anticorpos e fluoróforos. Assim, pudemos detetar a expressão proteica de alguns genes de interesse em diferentes condições: normóxia, 1, 2, 3, 6, 24 e 48 horas de hipóxia. Realizou-se uma análise de expressão proteica de HIF1a para confirmar a indução da resposta hipóxica. Uma vez que é regulado a nível da proteína, foram detetadas, de facto, bandas de HIF1a durante a hipóxia , apesar de não se observarem induções significantes da expressão génica. Como CAIX, foi significativamente expresso a nível do gene, foram também realizados blots para a proteína correspondente. A proteína CAIX foi detetável nas amostras de 6, 24 e 48 horas de hipóxia, especialmente nas células SEBTA-023. A proteína EGFR, vastamente descrita em GBM, foi também analisada. Curiosamente não foi detetável nas células UP-029, mas sim nas SEBTA-023, em todas as amostras. À semelhança de EGFR, os blots das proteínas UpaR, VEGFC e S100A10 foram também analisados. As proteínas UpaR e S100A10 foram detetadas em ambas as linhas celulares, com distinção nas amostras SEBTA-023. Nas células UP-029 a baixa deteção de proteína pode-se justificar por uma activação mais tardia da expressão de factores de invasão. Curiosamente a expressão de VEGFC, detetável em ambas as linhas, diminuí em simultaneidade com o aumento de horas de hipóxia. Em suma, o nosso estudo identificou ANGPTL4, NDRG1, CAIX, PFKB4, VEGFA, PIGF, PDK1, PFKB3, PFKB4, BNIP3, CAIX, DDIT4, NDRG1 e SLC16A3 como genes significativamente induzidos e HNF4A e TFRC como genes significativamente sub-expressos em GBM. Extrapolámos, que por vezes a indução das expressões de genes e proteínas de invasão é uma resposta tardia após um período considerado crónico de hipóxia. De futuro, deveriam ser estudados tempos de hipóxia mais prolongados, como 72 e 96 horas. Sugerimos, também, PFKB3 como um provável marcador de resistência à terapia, uma vez que já se encontra descrito noutros tumores, e neste estudo foi significativamente induzido. Conjuntamente, propõe-se o TFRC como um possível fator importante no impedimento da progressão do GBM, uma vez que foi sub-expresso nas diferentes análises. Estudos relativos a estes dois genes deverão ser conduzidos no futuro, para confirmar as hipóteses acima. Seria também relevante repetir este estudo aumentando o número de linhas celulares de modo a elevar a sensibilidade da seleção de possíveis novos marcadores de invasão em hipóxia

The molecular basis for central nervous system primitive neuroectodermal tumour development

PhD ThesisCentral nervous system primitive neuroectodermal tumours (CNS-PNETs) are highly aggressive tumours with similar histopathological features to other intracranial PNETs (medulloblastomas). These two tumours have accordingly been treated using unified approaches, but CNS-PNETs have a dismal prognosis. Few studies have investigated the genetic features of CNS-PNETs. The molecular basis of CNS-PNET was therefore investigated in a cohort containing CNS-PNETs from children (n=33) and adults (n=5), to aid improvements in disease classification and treatment. The common medulloblastoma molecular defects were investigated in CNS-PNETs, and showed RASSF1A promoter hypermethylation is a frequent event (18/22, 82%), and MYC family gene amplification occurs in a subgroup (MYCN: 3/25 (12%), MYCC: 0/25 (0%)). In contrast and in distinction to medulloblastoma, chromosome 17p loss is not a common feature (2/23, 9%), whilst p53 pathway signalling appears to play a major role (20/22, 91%), and associated with TP53 mutations (4/22, 18%). Aberrant Wnt signalling was identified in 2 cases (2/22, 9%) and coupled with CTNNB1 mutation in a single case. IDH1 mutations (2/25, 8%) however, appear to occur in adult but not childhood CNS-PNETs or medulloblastoma. Subsequent genome-wide investigations of the CNS-PNET DNA methylome aimed at a wider characterisation of the molecular features of CNS-PNETs and its relationships to other childhood tumours identified CNS-PNETs as a heterogenous disease group without defined sub-clusters, which were predominantly distinct from medulloblastomas, but exhibited overlap with high-grade gliomas. A panel of 76 tumour-specific methylation events were identified as disease markers. The combination of either RASSF1A hypermethylation or HLA-DPB1 hypomethylation discerned normal brain from CNS-PNET in 94% of cases (64/68). In addition, hypermethylation of TAL1, MAP3K1 and IGFBP1 is associated with non-infant disease. In conclusion, this study has shown CNS-PNETs are a heterogenous group of tumours that are molecularly distinct from medulloblastomas, and has implicated developmental pathways and genetic events in their tumorigenesis. The associations between molecular events identified and clinical features warrant further investigation to aid classification and treatment advancements.North of England Children’s Cancer Research Fund (NECCR), Clic Sargent and the Samantha Dickinson Brain Tumour Trust (SDBTT

Glioma

The tittle 'Glioma - Exploring Its Biology and Practical Relevance' is indicative of its content. This volume contains 21 chapters basically intended to explore glioma biology and discussing the experimental model systems for the purpose. It is hoped that the present volume will provide supportive and relevant awareness and understanding on the fundamental advances of the subject to the professionals from any sphere interested about glioma