The transmission of sex pheromone-mediated signals is essential for goldfish reproduction. However, the neural pathways underlying this reproductive signalling pathway in the goldfish brain is not well described. Lesioning experiments have shown previously that two brain areas, the preoptic area (POA) and the ventral telencephali pars ventralis (Vv) in particular, are important for reproduction. We used patch clamp electrophysiology to study the electrical activities of POA and Vv neurons. Based on the intrinsic properties of these neurons, we suggest there are five different functional classes of POA neurons and a single class of Vv neurons. In addition, by electrically stimulating the olfactory bulb (OB), we were able to show that this primary sensory structure makes monosynaptic glutamatergic connections with both POA and Vv neurons. While electrophysiology measures signalling events occurring at short time scales on the order of milliseconds to minutes, we were also interested in studying sex pheromone signalling in the goldfish brain over a long time scale. Thus, we describe changes in gene expression in male goldfish exposed to waterborne sex pheromones (17alpha,20beta dihydroxy-4-pregene-3-one and Prostaglandin-F2alpha) over 6 hours. We perform cDNA microarrays on Prostaglandin-F2alpha-treated fish to study the rapid modulation of transcription and define the signalling pathways affected. Our microarrays showed that 71 genes were differentially regulated (67 up and 4 down). Through gene ontology enrichment analysis, we found that these genes were involved in various biological processes such as RNA processing, neurotransmission, neuronal development, apoptosis, cellular metabolism and sexual reproduction. RT-PCRs were performed to validate our microarrays and to facilitate direct comparisons of the effects of the two sex pheromones, 17alpha,20beta dihydroxy-4-pregene-3-one and Prostaglandin-F2alpha. By combining electrophysiology and gene expression analyses, we were able to study sex-pheromone signalling on two different time scales. One short, occurring on the order of milliseconds to minutes, that involves electrical activities in the brain through the glutamatergic amino-3-hydroxy-5-methylisoxazole-4-propionate and N-methyl-D-aspartate receptors; and the other long occurring several hours later that involves changes in the gene expression levels of calmodulin and ependymin among other genes underlying neuroplasticity. Reproductive neuroplasticity in the goldfish may therefore require the activation of glutamatergic receptors which then activate downstream signals like calmodulin and ependymin to transform the sex pheromones-mediate signal into gene expression.

Metástases em ovário geralmente se apresentam como o primeiro sinal de doença, com o tumor primário não sendo imediatamente reconhecido. A diferenciação mucinosa é o fenótipo mais comum entre essas metástases. Em algumas situações, quando essa apresentação está associada a carcinomas metastáticos capazes de simular tumores ovarianos primários, essa configuração pode levar até mesmo patologistas experientes a diagnosticar incorretamente um depósito secundário como uma neoplasia primária. A maioria dos casos problemáticos pode ser resolvida correlacionando-se os dados clínicos, as características macroscópicas, os critérios de histologia e o perfil imuno-histoquímico, mas sempre haverá alguns casos com características sobrepostas. Levando-se em conta que a invasão linfovascular conspícua é uma das características que favorecem metástase, nós hipotetizamos que diferentes padrões de microdensidade vascular intratumoral poderiam nos ajudar na definição da origem primária ou secundária do tumor. Um total de 124 casos de tumores mucinosos de ovário foram selecionados, apresentando histologia \"borderline\" e maligna. Eles foram separados em dois grupos (primários ou metastáticos), classificados de acordo com as informações clínicas disponíveis, características macroscópicas e microscópicas, e perfil imuno-histoquímico realizado em amostras de tumores em microarranjo de tecido (TMA). A densidade vascular linfática (DVL) foi analisada quantificando-se espaços vasculares intratumorais identificados pela podoplanina, um marcador endotelial linfático. De acordo com os nossos resultados a DVL foi maior nas neoplasias primárias do que nas secundárias, mas, após análise multivariada, os melhores preditores de um tumor ser secundário foram tamanho de 10,0 cm ou menos (OR 9,4; IC 95% 1,2-69,2), bilateralidade (OR 51,5; IC 95% 7,1-370,2) e negatividade para CK7 (OR 64,8; IC 95% 9,4- 447). De acordo com o conhecimento atual, a disseminação metastática não é um evento aleatório, mas um processo de várias etapas complexas e sequenciais, altamente organizado e tecido específico. É importante aprofundar a relação entre as células tumorais e seu microambiente porque as características moleculares envolvidas podem ser uma possível fonte de novos marcadores que podem permitir uma categorização mais precisa dos tumores mucinosos nos ovários / Ovarian metastases commonly present as the first sign of the disease, with the primary tumor not being immediately recognized. Mucinous differentiation is the most common phenotype among those metastases. In particular situations, when compounded by the known metastatic carcinomas capable of simulate primary tumors, this setting can lead even experienced pathologists to diagnose incorrectly a secondary deposit as a primary neoplasm. Correlating clinical data, macroscopic features, histology criteria and immunohistochemistry profile, can solve the majority of those problematic cases, but there will always be some cases in a gray zone with superimposed characteristics. Since conspicuous lymphovascular invasion is one of the characteristics favoring metastases, we hypothesized if different patterns of intratumoral vascular microdensity can help us in defining the tumor origin. A total of 124 cases of mucinous tumors in ovary were selected, presenting borderline and malignant histology. They were separated in two groups (primary and metastatic) classified according to the available clinical data, gross and microscopic features, and immunohistochemistry profile performed in tumor samples in tissue microarrays (TMA). The lymphatic vascular density (LVD) was analyzed using podoplanin, a lymphatic endothelial marker. According to our results LVD was greater in primary than in secondary neoplasms, but after multivariate analysis, the best predictors of a secondary deposit tumor were size 10,0 cm or less (OR 9.4; CI 95% 1.2- 69.2), bilaterality (OR 51.5; CI 95% 7.1-370.2) and CK7 negativity (OR 64.8; CI 95% 9.4-447). According to actual knowledge metastatic dissemination is not a random event, but a complex and sequential multistep process, highly organized and tissue-specific. It is important to go deeper into the relation between tumor cells and their microenvironment because its molecular features may be a possible source of new markers that could allow a more precise categorization of mucinous tumors in the ovaries

Die Etablierung von Hochdurchsatz-Technologien zur Durchführung von Genexpressionsmessungen führte in den letzten 20 Jahren zu einer stetig wachsende Menge an verfügbaren Daten. Sie ermöglichen durch Kombination einzelner Experimente neue Vergleichsstudien zu kombinieren oder Experimente aus verschiedenen Studien zu großen Datensätzen zu vereinen. Dieses Vorgehen wird als Meta-Analyse bezeichnet und in dieser Arbeit verwendet, um einen großen Genexpressionsdatensatz aus öffentlich zugänglichen T-Zell Experimenten zu erstellen. T-Zellen sind Immunzellen, die eine Vielzahl von unterschiedlichen Funktionen des Immunsystems inititiieren und steuern. Sie können in verschiedene Subtypen mit unterschiedlichen Funktionen differenzieren. Der mittels Meta-Analyse erstellte Datensatz beinhaltet nur Experimente zu einem T-Zell-Subtyp, den regulatorischen T-Zellen (Treg) bzw. der beiden Untergruppen, natürliche Treg (nTreg) und induzierte Treg (iTreg) Zellen. Eine bisher unbeantwortete Frage lautet, welche subtyp-spezifischen gen-regulatorische Mechanismen die T-Zell Differenzierung steuern. Dazu werden in dieser Arbeit zwei spezifische Herausforderungen der Treg Forschung behandelt: (i) die Identifikation von Zelloberflächenmarkern zur Unterscheidung und Charakterisierung der Subtypen, sowie (ii) die Rekonstruktion von Treg-Zell-spezifischen gen-regulatorischen Netzwerken (GRN), die die Differenzierungsmechanismen beschreiben. Die implementierte Meta-Analyse kombiniert mehr als 150 Microarray-Experimente aus über 30 Studien in einem Datensatz. Dieser wird benutzt, um mittels Machine Learning Zell-spezifische Oberflächenmarker an Hand ihres Expressionsprofils zu identifizieren. Mit der in dieser Arbeit entwickelten Methode wurden 41 Genen extrahiert, von denen sechs Oberflächenmarker sind. Zusätzliche Validierungsexperimente zeigten, dass diese sechs Gene die Experimenten beider T-Zell Subtypen sicher unterscheiden können. Zur Rekonstruktion von GRNs vergleichen wir unter Verwendung des erstellten Datensatzes 11 verschiedene Algorithmen und evaluieren die Ergebnisse mit Informationen aus Interaktionsdatenbanken. Die Evaluierung zeigt, dass die derzeit verfügbaren Methoden nicht in der Lage sind den Wissensstand Treg-spezifischer, regulatorsicher Mechanismen zu erweitern. Abschließend präsentieren wir eine Datenintegrationstrategie zur Rekonstruktion von GRN am Beispiel von Th2 Zellen. Aus Hochdurchsatzexperimenten wird ein Th2-spezifisches GRN bestehend aus 100 Genen rekonstruiert. Während 89 dieser Gene im Kontext der Th2-Zelldifferenzierung bekannt sind, wurden 11 neue Kandidatengene ohne bisherige Assoziation zur Th2-Differenzierung ermittelt. Die Ergebnisse zeigen, dass Datenintegration prinzipiell die GRN Rekonstruktion ermöglicht. Mit der Verfügbarkeit von mehr Daten mit besserer Qualität ist zu erwarten, dass Methoden zur Rekonstruktion maßgeblich zum besseren Verstehen der zellulären Differenzierung im Immunsystem und darüber hinaus beitragen können und so letztlich die Ursachenforschung von Dysfunktionen und Krankheiten des Immunsystems ermöglichen werden. / Within the last two decades high-throughput gene expression screening technologies have led to a rapid accumulation of experimental data. The amounts of information available have enabled researchers to contrast and combine multiple experiments by synthesis, one of such approaches is called meta-analysis. In this thesis, we build a large gene expression data set based on publicly available studies for further research on T cell subtype discrimination and the reconstruction of T cell specific gene regulatory events. T cells are immune cells which have the ability to differentiate into subtypes with distinct functions, initiating and contributing to a variety of immune processes. To date, an unsolved problem in understanding the immune system is how T cells obtain a specific subtype differentiation program, which relates to subtype-specific gene regulatory mechanisms. We present an assembled expression data set which describes a specific T cell subset, regulatory T (Treg) cells, which can be further categorized into natural Treg (nTreg) and induced Treg (iTreg) cells. In our analysis we have addressed specific challenges in regulatory T cell research: (i) discriminating between different Treg cell subtypes for characterization and functional analysis, and (ii) reconstructing T cell subtype specific gene regulatory mechanisms which determine the differences in subtype-specific roles for the immune system. Our meta-analysis strategy combines more than one hundred microarray experiments. This data set is applied to a machine learning based strategy of extracting surface protein markers to enable Treg cell subtype discrimination. We identified a set of 41 genes which distinguish between nTregs and iTregs based on gene expression profile only. Evaluation of six of these genes confirmed their discriminative power which indicates that our approach is suitable to extract candidates for robust discrimination between experiment classes. Next, we identify gene regulatory interactions using existing reconstruction algorithms aiming to extend the number of known gene-gene interactions for Treg cells. We applied eleven GRN reconstruction tools based on expression data only and compared their performance. Taken together, our results suggest that the available methods are not yet sufficient to extend the current knowledge by inferring so far unreported Treg specific interactions. Finally, we present an approach of integrating multiple data sets based on different high-throughput technologies to reconstruct a subtype-specific GRN. We constructed a Th2 cell specific gene regulatory network of 100 genes. While 89 of these are known to be related to Th2 cell differentiation, we were able to attribute 11 new candidate genes with a function in Th2 cell differentiation. We show that our approach to data integration does, in principle, allow for the reconstruction of a complex network. Future availability of more and more consistent data may enable the use of the concept of GRN reconstruction to improve understanding causes and mechanisms of cellular differentiation in the immune system and beyond and, ultimately, their dysfunctions and diseases.

INTRODUÇÃO: A deleção do cromossomo 9p tem sido encontrada em 14 a 36% dos pacientes com carcinoma renal tipo células claras (CRCC) e está associado a tumores de alto grau, estágio avançado, presença de metástases linfonodais e sistêmicas. OBJETIVOS: Avaliar se a deleção do cromossomo 9p é fator preditor independente de pior sobrevida livre de recorrência e câncer-específica em pacientes com CRCC localizado. MÉTODOS: Neste estudo de coorte retrospectivo, amostras tumorais de 94 pacientes com CRCC NX-0 M0, submetidos à nefrectomia radical ou cirurgia renal conservadora, foram analisadas através das técnicas de microarranjo tecidual e hibridização in situ com fluorescência. RESULTADOS: O tempo de seguimento médio foi de 11,6 anos e a deleção do 9p foi encontrada em cerca de 15% dos casos. A sobrevida câncer específica estimada em 5 e 10 anos foi respectivamente de 99% e 96% nos pacientes sem a referida perda cromossômica e de 71% e 57% naqueles com perda do 9p (p < 0,001). A deleção do cromossomo 9p foi fator prognóstico independente na análise multivariada, aumentando o risco de morte pela doença em 28x (IC 95% 5-155, p < 0,001). Tal deleção foi o preditor mais importante de mortalidade câncer específica, superior a qualquer fator patológico analisado, inclusive ao tamanho tumoral. Em pacientes com baixo risco de progressão, isto é, baixo escore SSIGN (0-2), baixo risco segundo a UISS e baixo risco segundo a Tríade Patológica da USP, tumores deletados do 9p estão significativamente associados com pior sobrevida câncer-específica em 10 anos: respectivamente 70%, 67% e 67% versus 98%, 97% e 98% naqueles sem a perda do 9p. CONCLUSÃO: A deleção do cromossomo 9p estabelece independentemente um pior prognóstico para pacientes com CRCC localizado, fornece informação clínica relevante adicional e pode aperfeiçoar a habilidade preditora dos principais sistemas prognósticos atuais / INTRODUCTION: Deletion of chromosome 9p has been found in 14-36% of patients with clear cell renal cell carcinoma (ccRCC) and is associated with high grade tumors, advanced tumor stage, presence of lymph node involvement and metastases. OBJECTIVES: To assess whether deletion of chromosome 9p is an independent predictor of worse recurrence-free and cancer-specific survival in patients with localized ccRCC. METHODS: In this retrospective cohort study, tumor samples of 94 patients with NX-0 M0 ccRCC undergoing radical nephrectomy or renal conservative surgery, were analyzed using tissue microarray and fluorescence in situ hybridization. RESULTS: Mean follow-up was 11.6 years and 9p deletion was found in near 15% of cases. Estimated cancer-specific survival at 5 and 10 years was, respectively, 99% and 96% in patients without such chromosomal loss and 71% and 57% in those with 9p loss (p < 0.001). Deletion of chromosome 9p is an independent prognostic factor in multivariate analysis, increasing the risk of disease-specific death in 28x (95% CI 5-155, p < 0.001). This deletion was the strongest predictor of cancer-specific mortality, superior to any analysed pathological factor, including tumor size. In patients at low risk of progression, namely low score (0-2) SSIGN, low risk UISS and low risk USP Pathological Triad, 9p-deleted tumors were associated with worse 10 years cancer-specific survival: respectively 70%, 67% and 67% versus 98%, 97% and 98% in those with no 9p loss. CONCLUSIONS: Deletion of chromosome 9p independently establishes a worse prognosis for patients with localized ccRCC, provides relevant additional clinical information and can improve the predictive ability of the main current prognostic models

Metástases em ovário geralmente se apresentam como o primeiro sinal de doença, com o tumor primário não sendo imediatamente reconhecido. A diferenciação mucinosa é o fenótipo mais comum entre essas metástases. Em algumas situações, quando essa apresentação está associada a carcinomas metastáticos capazes de simular tumores ovarianos primários, essa configuração pode levar até mesmo patologistas experientes a diagnosticar incorretamente um depósito secundário como uma neoplasia primária. A maioria dos casos problemáticos pode ser resolvida correlacionando-se os dados clínicos, as características macroscópicas, os critérios de histologia e o perfil imuno-histoquímico, mas sempre haverá alguns casos com características sobrepostas. Levando-se em conta que a invasão linfovascular conspícua é uma das características que favorecem metástase, nós hipotetizamos que diferentes padrões de microdensidade vascular intratumoral poderiam nos ajudar na definição da origem primária ou secundária do tumor. Um total de 124 casos de tumores mucinosos de ovário foram selecionados, apresentando histologia \"borderline\" e maligna. Eles foram separados em dois grupos (primários ou metastáticos), classificados de acordo com as informações clínicas disponíveis, características macroscópicas e microscópicas, e perfil imuno-histoquímico realizado em amostras de tumores em microarranjo de tecido (TMA). A densidade vascular linfática (DVL) foi analisada quantificando-se espaços vasculares intratumorais identificados pela podoplanina, um marcador endotelial linfático. De acordo com os nossos resultados a DVL foi maior nas neoplasias primárias do que nas secundárias, mas, após análise multivariada, os melhores preditores de um tumor ser secundário foram tamanho de 10,0 cm ou menos (OR 9,4; IC 95% 1,2-69,2), bilateralidade (OR 51,5; IC 95% 7,1-370,2) e negatividade para CK7 (OR 64,8; IC 95% 9,4- 447). De acordo com o conhecimento atual, a disseminação metastática não é um evento aleatório, mas um processo de várias etapas complexas e sequenciais, altamente organizado e tecido específico. É importante aprofundar a relação entre as células tumorais e seu microambiente porque as características moleculares envolvidas podem ser uma possível fonte de novos marcadores que podem permitir uma categorização mais precisa dos tumores mucinosos nos ovários / Ovarian metastases commonly present as the first sign of the disease, with the primary tumor not being immediately recognized. Mucinous differentiation is the most common phenotype among those metastases. In particular situations, when compounded by the known metastatic carcinomas capable of simulate primary tumors, this setting can lead even experienced pathologists to diagnose incorrectly a secondary deposit as a primary neoplasm. Correlating clinical data, macroscopic features, histology criteria and immunohistochemistry profile, can solve the majority of those problematic cases, but there will always be some cases in a gray zone with superimposed characteristics. Since conspicuous lymphovascular invasion is one of the characteristics favoring metastases, we hypothesized if different patterns of intratumoral vascular microdensity can help us in defining the tumor origin. A total of 124 cases of mucinous tumors in ovary were selected, presenting borderline and malignant histology. They were separated in two groups (primary and metastatic) classified according to the available clinical data, gross and microscopic features, and immunohistochemistry profile performed in tumor samples in tissue microarrays (TMA). The lymphatic vascular density (LVD) was analyzed using podoplanin, a lymphatic endothelial marker. According to our results LVD was greater in primary than in secondary neoplasms, but after multivariate analysis, the best predictors of a secondary deposit tumor were size 10,0 cm or less (OR 9.4; CI 95% 1.2- 69.2), bilaterality (OR 51.5; CI 95% 7.1-370.2) and CK7 negativity (OR 64.8; CI 95% 9.4-447). According to actual knowledge metastatic dissemination is not a random event, but a complex and sequential multistep process, highly organized and tissue-specific. It is important to go deeper into the relation between tumor cells and their microenvironment because its molecular features may be a possible source of new markers that could allow a more precise categorization of mucinous tumors in the ovaries

INTRODUÇÃO: Deve-se considerar que cerca de 70 a 80% dos pacientes portadores de carcinoma colorretal estádio II podem ser curados apenas com cirurgia. Por outro lado, a despeito do tratamento empregado e dos benefícios alcançados com a evolução dos tratamentos adjuvantes, cerca de 20 a 35% dos pacientes tratados com doença em estádio III vêm a falecer por recidiva tumoral. É provável que existam características biomoleculares intrínsecas que possam conferir maior agressividade e resistência ao tratamento adjuvante. A família de proteínas ErbB formam um grupo de receptores de membrana, cuja função é ativar a via de sinalização intracelular em resposta ao sinal extracelular e é formada por quatro receptores: EGFR/ErbB1, ErbB2/HER2, ErbB3/HER3 e ErbB4/HER4. O complexo de receptores ErbB é uma das vias de transmissão de sinal celular mais amplamente estudada, porém poucos estudos interessados em avaliar a expressão dos quatro receptores da família ErbB e sua correlação prognóstica no câncer de cólon e reto foram realizados até o momento. Nosso objetivo foi avaliar a expressão imunoistoquímica de EGFR, ErbB2, ErbB3 e ErbB4 e seu papel como fator prognóstico para sobrevida livre de doença e sobrevida global em carcinoma de cólon e reto estádio II de alto risco e estádio III submetidos a tratamento cirúrgico radical. CASUÍSTICA E MÉTODOS: vi Trata-se de um estudo retrospectivo que avaliou uma série de 118 indivíduos portadores de adenocarcinoma de colón e reto alto estádio II com fatores de alto risco ou estádio III. Foram analisadas variáveis clínicopatológicas e as expressões de EGFR, ErbB2, ErbB3 e ErbB4 foram determinadas através de imunoistoquímica pelo dispositivo técnico Tissue Microarray (TMA). RESULTADOS: O tempo de seguimento mediano foi de 58,8 meses. A sobrevida global da amostra foi de 71,2% em 5 anos. A sobrevida livre de doença foi de 67,8% em 5 anos. As expressões imunoistoquímicas positivas de EGFR, ErbB2, ErbB3, em membrana de ErbB4 e em citoplasma de ErbB4 foram encontradas em respectivamente 59,3%, 7,6%, 71,2%, 10,2% e 20,3% dos casos. Houve diferença significativa na expressão de EGFR em relação à localização da neoplasia, onde 75% dos pacientes com tumor em reto apresentaram expressão positiva, contra 52,4% entre os tumores de cólon (p=0,02). Em relação à expressão ErbB2, houve diferença significativa no que refere ao estadiamento, onde 1,8% dos pacientes com estádio II apresentavam expressão positiva, contra 12,7% entre os pacientes com estádio III (p=0,03). A expressão de ErbB3 teve diferença significativa em relação à presença de embolização linfática, com expressão positiva em 79,5% dos pacientes com ausência de embolização linfática frente a 46,7% dos com presença de embolização linfática (p=0,001). Em relação à expressão de ErbB4, não houve diferença significativa entre todas as variáveis estudadas, tanto para expressão em membrana quanto em citoplasma. Observamos que presença de embolização vascular linfática, presença de invasão perineural, expressão imunoistoquímica negativa de ErbB3 e positiva de ErbB4 em membrana influenciaram negativamente a sobrevida livre de doença em cinco anos na análise univariada. No modelo multivariado, a expressão negativa de ErbB3 (RR: vii 2,43; IC 95%: 1,26 4,66) e a expressão positiva de ErbB4 em membrana (RR: 3,03; IC 95%: 1,31 6,98) mantiveram-se como fator independente para risco de recaída. Observamos ainda que idade igual ou maior que 65 anos, presença de embolização linfática e expressão negativa de ErbB3 influenciaram negativamente a sobrevida global em 5 anos na análise univariada. No modelo multivariado, a idade igual ou maior que 65 anos (RR 2,83; IC 95%: 1,36 5,90) e a expressão negativa de ErbB3 (RR: 2,52; IC 95%: 1,28 4,97) mantiveram-se como fator independente para risco de óbito. CONCLUSÕES: A expressão positiva de ErbB4 em membrana foi variável de risco independente para recidiva e a expressão negativa de ErbB3 foi variável de risco independente para recidiva e óbito. As expressões imunoistoquímicas de ErbB3 e de ErbB4 em membrana podem selecionar pacientes portadores de câncer colorretal estádios II e III submetidos a tratamento cirúrgico radical que tenham maior risco de recidiva e óbito / INTRODUCTION: In spite of multidisciplinary treatment, survival after 5 years in these subgroups is under 60 and 70%. Probably, some patients have recurrence due to microscopic residual disease resistant to the adjuvant treatment received. However, other patients do not have recurrent disease even without adjuvant treatment as they have already been cured by surgery alone. Thus, there is a need to identify biological tumoral characteristics that may predict poor outcome and guide the development of new adjuvant treatments. The epidermal growth factor receptor (EGFR/ErbB1), ErbB2/HER2, ErbB3/HER3 and ErbB4/HER4 are a group of subtype I tyrosine-kinases sharing structural homologies, especially at the intracellular domain. Protein kinases are enzymes that play a key regulation role in nearly every aspect of cell biology. There have been only a few studies that explored the expression of ErbB family in colorectal cancers. The present study was designed to investigate the expression of ErbB family in high risk colorectal cancer (high risk stage II and stage III) submitted to radical surgery and their role as a prognostic factor to recurrence and survival. MATERIALS AND METHODS: We studied 118 individuals with high risk stage II and stage III colorectal cancer submitted to radical surgery. Clinico-pathological data were reviewed. ErbB family protein expression in ix tumor tissue was assessed by immunohistochemistry using Tissue Microarray technique. RESULTS: The median follow-up time was 58,8 months. The five-year overall survival was 71,2% and five-year disease free survival was 67,8%. The immunohistochemical expression was considered positive for EGFR, ErbB2, ErbB3, ErbB4 membrane and ErbB4 cytoplasmic in respectively 59,3%, 7,6%, 71,2%, 10,2% and 20,3% of the patients. EGFR expression was associated with tumor localization, ErbB2 expression with stage III and ErbB3 negative expression with lymphovascular invasion. Membranous positive ErbB4 expression was an independent prognostic factor only for recurrence. ErbB3 negative expression was an independent prognostic factor for recurrence and survival in the multivariate analysis. EGFR, ErbB2 and cytoplasmic ErbB4 expression was not associated with prognosis. CONCLUSIONS: Membranous positive ErbB4 expression was an independent prognostic factor for recurrence and ErbB3 negative expression was an independent prognostic factor for recurrence and survival. The immunohistochemical expression of ErbB3 and ErbB4 may be used to identify a subgroup of patients with stage II and III colorectal tumors at higher risk of recurrence and death

The transmission of sex pheromone-mediated signals is essential for goldfish reproduction. However, the neural pathways underlying this reproductive signalling pathway in the goldfish brain is not well described. Lesioning experiments have shown previously that two brain areas, the preoptic area (POA) and the ventral telencephali pars ventralis (Vv) in particular, are important for reproduction. We used patch clamp electrophysiology to study the electrical activities of POA and Vv neurons. Based on the intrinsic properties of these neurons, we suggest there are five different functional classes of POA neurons and a single class of Vv neurons. In addition, by electrically stimulating the olfactory bulb (OB), we were able to show that this primary sensory structure makes monosynaptic glutamatergic connections with both POA and Vv neurons. While electrophysiology measures signalling events occurring at short time scales on the order of milliseconds to minutes, we were also interested in studying sex pheromone signalling in the goldfish brain over a long time scale. Thus, we describe changes in gene expression in male goldfish exposed to waterborne sex pheromones (17alpha,20beta dihydroxy-4-pregene-3-one and Prostaglandin-F2alpha) over 6 hours. We perform cDNA microarrays on Prostaglandin-F2alpha-treated fish to study the rapid modulation of transcription and define the signalling pathways affected. Our microarrays showed that 71 genes were differentially regulated (67 up and 4 down). Through gene ontology enrichment analysis, we found that these genes were involved in various biological processes such as RNA processing, neurotransmission, neuronal development, apoptosis, cellular metabolism and sexual reproduction. RT-PCRs were performed to validate our microarrays and to facilitate direct comparisons of the effects of the two sex pheromones, 17alpha,20beta dihydroxy-4-pregene-3-one and Prostaglandin-F2alpha. By combining electrophysiology and gene expression analyses, we were able to study sex-pheromone signalling on two different time scales. One short, occurring on the order of milliseconds to minutes, that involves electrical activities in the brain through the glutamatergic amino-3-hydroxy-5-methylisoxazole-4-propionate and N-methyl-D-aspartate receptors; and the other long occurring several hours later that involves changes in the gene expression levels of calmodulin and ependymin among other genes underlying neuroplasticity. Reproductive neuroplasticity in the goldfish may therefore require the activation of glutamatergic receptors which then activate downstream signals like calmodulin and ependymin to transform the sex pheromones-mediate signal into gene expression.

In the last decade, molecular biology has expanded from a reductionist view to a systems-wide view that tries to unravel the complex interactions of cellular components. Owing to the emergence of high-throughput technology it is now possible to interrogate entire genomes at an unprecedented resolution. The dimension and unstructured nature of these data made it evident that new methodologies and tools are needed to turn data into biological knowledge. To contribute to this challenge we exploited the wealth of publicly available high-throughput genomics data and developed bioinformatics methodologies focused on extracting information at the pathway rather than the single gene level. First, we developed Gene Set Variation Analysis (GSVA), a method that facilitates the organization and condensation of gene expression profiles into gene sets. GSVA enables pathway-centric downstream analyses of microarray and RNA-seq gene expression data. The method estimates sample-wise pathway variation over a population and allows for the integration of heterogeneous biological data sources with pathway-level expression measurements. To illustrate the features of GSVA, we applied it to several use-cases employing different data types and addressing biological questions. GSVA is made available as an R package within the Bioconductor project. Secondly, we developed a pathway-centric genome-based strategy to reposition drugs in type 2 diabetes (T2D). This strategy consists of two steps, first a regulatory network is constructed that is used to identify disease driving modules and then these modules are searched for compounds that might target them. Our strategy is motivated by the observation that disease genes tend to group together in the same neighborhood forming disease modules and that multiple genes might have to be targeted simultaneously to attain an effect on the pathophenotype. To find potential compounds, we used compound exposed genomics data deposited in public databases. We collected about 20,000 samples that have been exposed to about 1,800 compounds. Gene expression can be seen as an intermediate phenotype reflecting underlying dysregulatory pathways in a disease. Hence, genes contained in the disease modules that elicit similar transcriptional responses upon compound exposure are assumed to have a potential therapeutic effect. We applied the strategy to gene expression data of human islets from diabetic and healthy individuals and identified four potential compounds, methimazole, pantoprazole, bitter orange extract and torcetrapib that might have a positive effect on insulin secretion. This is the first time a regulatory network of human islets has been used to reposition compounds for T2D. In conclusion, this thesis contributes with two pathway-centric approaches to important bioinformatic problems, such as the assessment of biological function and in silico drug repositioning. These contributions demonstrate the central role of pathway-based analyses in interpreting high-throughput genomics data. / En l'última dècada, la biologia molecular ha evolucionat des d'una perspectiva reduccionista cap a una perspectiva a nivell de sistemes que intenta desxifrar les complexes interaccions entre els components cel•lulars. Amb l'aparició de les tecnologies d'alt rendiment actualment és possible interrogar genomes sencers amb una resolució sense precedents. La dimensió i la naturalesa desestructurada d'aquestes dades ha posat de manifest la necessitat de desenvolupar noves eines i metodologies per a convertir aquestes dades en coneixement biològic. Per contribuir a aquest repte hem explotat l'abundància de dades genòmiques procedents d'instruments d'alt rendiment i disponibles públicament, i hem desenvolupat mètodes bioinformàtics focalitzats en l'extracció d'informació a nivell de via molecular en comptes de fer-ho al nivell individual de cada gen. En primer lloc, hem desenvolupat GSVA (Gene Set Variation Analysis), un mètode que facilita l'organització i la condensació de perfils d'expressió dels gens en conjunts. GSVA possibilita anàlisis posteriors en termes de vies moleculars amb dades d'expressió gènica provinents de microarrays i RNA-seq. Aquest mètode estima la variació de les vies moleculars a través d'una població de mostres i permet la integració de fonts heterogènies de dades biològiques amb mesures d'expressió a nivell de via molecular. Per il•lustrar les característiques de GSVA, l'hem aplicat a diversos casos usant diferents tipus de dades i adreçant qüestions biològiques. GSVA està disponible com a paquet de programari lliure per R dins el projecte Bioconductor. En segon lloc, hem desenvolupat una estratègia centrada en vies moleculars basada en el genoma per reposicionar fàrmacs per la diabetis tipus 2 (T2D). Aquesta estratègia consisteix en dues fases: primer es construeix una xarxa reguladora que s'utilitza per identificar mòduls de regulació gènica que condueixen a la malaltia; després, a partir d'aquests mòduls es busquen compostos que els podrien afectar. La nostra estratègia ve motivada per l'observació que els gens que provoquen una malaltia tendeixen a agrupar-se, formant mòduls patogènics, i pel fet que podria caldre una actuació simultània sobre múltiples gens per assolir un efecte en el fenotipus de la malaltia. Per trobar compostos potencials, hem usat dades genòmiques exposades a compostos dipositades en bases de dades públiques. Hem recollit unes 20.000 mostres que han estat exposades a uns 1.800 compostos. L'expressió gènica es pot interpretar com un fenotip intermedi que reflecteix les vies moleculars desregulades subjacents a una malaltia. Per tant, considerem que els gens d'un mòdul patològic que responen, a nivell transcripcional, d'una manera similar a l'exposició del medicament tenen potencialment un efecte terapèutic. Hem aplicat aquesta estratègia a dades d'expressió gènica en illots pancreàtics humans corresponents a individus sans i diabètics, i hem identificat quatre compostos potencials (methimazole, pantoprazole, extracte de taronja amarga i torcetrapib) que podrien tenir un efecte positiu sobre la secreció de la insulina. Aquest és el primer cop que una xarxa reguladora d'illots pancreàtics humans s'ha utilitzat per reposicionar compostos per a T2D. En conclusió, aquesta tesi aporta dos enfocaments diferents en termes de vies moleculars a problemes bioinformàtics importants, com ho son el contrast de la funció biològica i el reposicionament de fàrmacs "in silico". Aquestes contribucions demostren el paper central de les anàlisis basades en vies moleculars a l'hora d'interpretar dades genòmiques procedents d'instruments d'alt rendiment.

Σκοπός της παρούσης διατριβής είναι να προτείνει ένα τυπικό πλαίσιο για μια μεθοδολογία ανάλυσης που να ενσωματώνει ποσοτικά, και λειτουργικά δεδομένα και στοχεύει στο σχεδιασμό πειραμάτων για την επιβέβαιωση μεταγραφικών παραγόντων που δεσμεύονται σε ένα λειτουργικά ενεργό μοτίβο στον υποκινητή γονιδίων. Το πλαίσιο αυτό που βασίζεται στη Bayesian πιθανοκρατική θεωρία όπως αυτή θεμελιώνεται στη θεωρία λήψης αποφάσεων, εφαρμόζεται σε ένα πρόβλημα από το ερευνητικό πεδίο της ανοσοβιολογίας. Συγκεκριμένα μελετούμε την ανίχνευση μεταγραφικών παραγόντων που ενέχονται στην αρνητική ρύθμιση της γονιδιακής έκφρασης κατά τη διαδικασία ενεργοποίσης των Τ λεμφοκυττάτων. Η υιοθέτηση του προτεινούμενου πλαισίου σμιλεύει μαι αυστηρή διαδοχή διεξαγωγής in vitro και in silico πειραμάτων που ξεκινά από τεχνικές μαζικής ανάλυσης γονιδιακής έκφρασης, περνά μέσα από βάσεις δεδομένων μεταγραφικών παραγόντων και μέσω πειραμάτων ηλεκτροφορητικής κινητικότητας (Electromobility Shift Assays) στοχεύεται στην επιβεβαίωση που προσφέρουν τα πειράματα διαμόλυνσης (transfection and reporter assays). Κατά την τυποποίηση της λογικοφανούς αυτής προσέγγισης ανακύπτει ένα από τα γνωστότερα προβλήματα της εφαρμοσμένης στατιστικής, το πρόβλημα των "δύο μέσων όρων" ή πρόβλημα Behrens-Fisher. Για τη λύση αυτού του προβλήματος προτείνονται νέα μαθηματικά εργαλεία τα οποία αξιοποίηθηκαν για την κατασκευή αντίστοιχου λογισμικού. Με την εφαρμογή αυτών των εργαλείων στο εφαρμοσμένο ανοσοβιολογικό πρόβλημα προέκυψε μια μη αναμενόμενη σχέση μεταξύ δυο φαινομενικά μη συνδεόμενων συστημάτων¨των γονιδίων των κυτταροκινών και του ιού HIV. Μέσω της περιγραφόμενης μεθοδολογίας κατέστη εφικτή μια υποθεσο-εξαρτώμενη προσέγγιση σε ένα σημαντικό πρόβλημα το οποίο δεν ήταν δυνατό να λύθέί με κλασσικές βιοχημικές τεχνικές λόγω τεχνικών δυσκολιών / The current disertation concerns the description of a formal framework and an analytic methodology which aims to validate transcription factors controlling gene expression through functional and quantitative data. This Bayesian decision theory inspired framework is applied to a specific immunobiological problem. The problem targetted was the discovery of transcriptional repressors implicated in the negative control of T cell activation. Adopting the proposed framework leads one to a staged experimental strategy which starts from high-throughput gene expression data and transcription factor databases and through Electrophoretic Mobility Shift Assays targets the design of transfection and reporter gene assays. The formalization of the proposed approach, led to one of the famous applied statistics problems i.e. the two means or Behrens - Fisher problem. In order to deal with the computational aspects of this problem, we applied a novel integral transformations and ported them to software. The application of these tools to the immunobiological problem led to an unexpected connection between two seemingly unrelated systems: cytokine gene protomers and HIV LTR. The proposed methodology enabled a hypothesis-driven approach to an important basic immunobiological problem which could not be solved by standard biochemical techniques.

INTRODUÇÃO: A deleção do cromossomo 9p tem sido encontrada em 14 a 36% dos pacientes com carcinoma renal tipo células claras (CRCC) e está associado a tumores de alto grau, estágio avançado, presença de metástases linfonodais e sistêmicas. OBJETIVOS: Avaliar se a deleção do cromossomo 9p é fator preditor independente de pior sobrevida livre de recorrência e câncer-específica em pacientes com CRCC localizado. MÉTODOS: Neste estudo de coorte retrospectivo, amostras tumorais de 94 pacientes com CRCC NX-0 M0, submetidos à nefrectomia radical ou cirurgia renal conservadora, foram analisadas através das técnicas de microarranjo tecidual e hibridização in situ com fluorescência. RESULTADOS: O tempo de seguimento médio foi de 11,6 anos e a deleção do 9p foi encontrada em cerca de 15% dos casos. A sobrevida câncer específica estimada em 5 e 10 anos foi respectivamente de 99% e 96% nos pacientes sem a referida perda cromossômica e de 71% e 57% naqueles com perda do 9p (p < 0,001). A deleção do cromossomo 9p foi fator prognóstico independente na análise multivariada, aumentando o risco de morte pela doença em 28x (IC 95% 5-155, p < 0,001). Tal deleção foi o preditor mais importante de mortalidade câncer específica, superior a qualquer fator patológico analisado, inclusive ao tamanho tumoral. Em pacientes com baixo risco de progressão, isto é, baixo escore SSIGN (0-2), baixo risco segundo a UISS e baixo risco segundo a Tríade Patológica da USP, tumores deletados do 9p estão significativamente associados com pior sobrevida câncer-específica em 10 anos: respectivamente 70%, 67% e 67% versus 98%, 97% e 98% naqueles sem a perda do 9p. CONCLUSÃO: A deleção do cromossomo 9p estabelece independentemente um pior prognóstico para pacientes com CRCC localizado, fornece informação clínica relevante adicional e pode aperfeiçoar a habilidade preditora dos principais sistemas prognósticos atuais / INTRODUCTION: Deletion of chromosome 9p has been found in 14-36% of patients with clear cell renal cell carcinoma (ccRCC) and is associated with high grade tumors, advanced tumor stage, presence of lymph node involvement and metastases. OBJECTIVES: To assess whether deletion of chromosome 9p is an independent predictor of worse recurrence-free and cancer-specific survival in patients with localized ccRCC. METHODS: In this retrospective cohort study, tumor samples of 94 patients with NX-0 M0 ccRCC undergoing radical nephrectomy or renal conservative surgery, were analyzed using tissue microarray and fluorescence in situ hybridization. RESULTS: Mean follow-up was 11.6 years and 9p deletion was found in near 15% of cases. Estimated cancer-specific survival at 5 and 10 years was, respectively, 99% and 96% in patients without such chromosomal loss and 71% and 57% in those with 9p loss (p < 0.001). Deletion of chromosome 9p is an independent prognostic factor in multivariate analysis, increasing the risk of disease-specific death in 28x (95% CI 5-155, p < 0.001). This deletion was the strongest predictor of cancer-specific mortality, superior to any analysed pathological factor, including tumor size. In patients at low risk of progression, namely low score (0-2) SSIGN, low risk UISS and low risk USP Pathological Triad, 9p-deleted tumors were associated with worse 10 years cancer-specific survival: respectively 70%, 67% and 67% versus 98%, 97% and 98% in those with no 9p loss. CONCLUSIONS: Deletion of chromosome 9p independently establishes a worse prognosis for patients with localized ccRCC, provides relevant additional clinical information and can improve the predictive ability of the main current prognostic models