Tissue microarrays (TMAs) are a high-throughput technique that facilitates the survey of very large numbers of tumours, important both in clinical and research applications. However, the assessment of stained TMA sections is laborious and still needs to be carried manually, constituting a bottleneck in the pathologist?s work-flow. This process is also prone to perceptual errors and observer variability.Thus, there is strong motivation for the development of automated quantitative analysis of TMA image data. The analysis of breast TMA sections subjected to nuclear immunostaining begins with the classification of each spot as to the maintype of tissue that it contains, namely tumour, normal, stroma, or fat. Tumour and normal spots are then assigned a so-called quickscore composed of a pair or integer values, the first reflecting the proportion of epithelial nuclei that are stained, and the second reflecting the strength of staining of those nuclei. In this work, an approach was developed to analyse breast TMA spots subjectedto progesterone receptor immunohistochemistry. Spots were classified into their four main types through a method that combined a bag of features approachand classifiers based on either multi-layer perceptrons or latent Dirichlet allocation models. A classification accuracy of 74.6 % was achieved. Tumour and normal spots were scored via an approach that involved the computation of global features formalising the quickscore values used by pathologists, and the use of Gaussian processes for ordinal regression to predict actual quickscores based on global features. Mean absolute errors of 0.888 and 0.779 were achieved in the prediction of the first and second quickscore values, respectively. By setting thresholds on prediction confidence, it was possible to classify and score fractions of spots with substantially higher accuracies and lower mean absolute errors. Amethod for the segmentation of TMA spots into regions of different types was also investigated, to explore the generative nature of latent Dirichlet allocation models.

O carcinoma de células renais (CCR) é o tumor mais agressivo que afeta o rim de pessoas adultas. O CCR é uma doença heterogênea, com diferentes alterações moleculares e variados patrões histológicos e clínicos que apresentam evolução diferente. Atualmente apenas variáveis anatomopatológicas clássicas são utilizadas para determinar o prognóstico dos pacientes. Utilizando uma plataforma de microarranjos de DNA, nosso grupo identificou em um trabalho anterior um conjunto de genes que se encontram diferencialmente expressos em tumores de rim. Neste estudo, nove candidatos foram selecionados para avaliação como marcadores de prognóstico no CCR. Foi confirmada a alteração na expressão dos genes ARNTL, ACTN4 e EPAS1 (p < 0,05) em amostras tumorais de CCR através de PCR em tempo real. Adicionalmente, foi observada a alteração da expressão dos genes ARNTL, EPAS1 e CASP7 em linhagens celulares imortalizadas derivadas de tumores renais, recapitulando por tanto, as alterações observadas nos tumores obtidos de pacientes. Posteriormente investigamos o padrão de expressão proteica destes candidatos por imunohistoquímica utilizando microarranjos de tecidos. Foi detectada a diminuição significativa (p < 0,05) da expressão das proteínas ACTN4, ARNTL, CASP7 e EPAS1 em tumores de pacientes com CCR relativamente ao tecido renal não tumoral. Além disso, foi possível determinar valores de imunomarcação capazes de estratificar pacientes com CCR em diferentes grupos de risco quanto à sobrevida câncer-específica, que adicionalmente apresentaram associação significativa com parâmetros anatomopatológicos utilizados na clínica. As imunomarcações de ACTN4, ARNTL, e EPAS1 se mostraram parâmetros independentes de prognóstico de sobrevida dos pacientes. A imunomarcação de CASP7 foi capaz de identificar subgrupos de pacientes com pior prognóstico dentro de um conjunto de pacientes de baixo risco em função do estadio clinico, além de identificar pacientes com menor risco de morte pelo câncer entre aqueles apresentaram recorrência em até 5 após a cirurgia. O conjunto de resultados obtidos aponta para um novo conjunto de biomarcadores moleculares com potencial relevância para auxiliar no prognóstico de pacientes com carcinoma de células renais. / The renal cell carcinoma (RCC) is the most aggressive tumor that affects the kidney in adult people. The RCC is a heterogeneous disease, with many different molecular alterations and varied histological and clinical patterns with different outcome. Currently, only classic anatomopathological variables are used to determine patients\' prognosis. Using a DNA microarray platform, our group identified in a previous work a set of genes differentially expressed in renal tumors. In this study, nine candidates were selected for evaluation as prognostic biomarkers in RCC. Alteration of the gene expression in RCC tumor samples was confirmed for ARNTL, ACTN4 and EPAS1 (p < 0.05) by real time PCR. Additionally, gene expression changes of ARNTL, EPAS1 and CASP7 were also observed in immortalized cell lines derived from renal tumors, recapitulating the expression changes detected in the patients\' tumors. Next, we used tissue microarrays to investigate the protein expression of the selected candidates by immunohistochemistry. Expression of the proteins ACTN4, ARNTL, CASP7 and EPAS1 was detected as significantly downregulated (p < 0.05) in patients´ tumors relative to non-tumor renal tissue. Furthermore, immunostaining patterns of the selected candidates were able to stratify patients with RCC in different risk groups according to cancer-specific survival, which also showed significant associations with anatomopathological parameters used in the clinics. ACTN4, ARNTL and EPAS1 immunostaining resulted as independent prognostic parameters of patient survival. CASP7 immunostaining was able to identify subgroups of patients with worse prognosis in a set of low risk patients as determined by their clinical stage, and also identified patients with lower risk of death from cancer amongst patients that relapsed within 5 years after surgery. Overall, these results point to a new set of molecular biomarkers with potential relevance to help in the prognosis of patients with renal cell carcinoma.

O câncer de mama é uma doença extremamente heterogênea compreendendo diferentes subtipos moleculares que resultam em evoluções clínicas e condutas terapêuticas distintas. A maior gravidade desta patologia está associada a sua capacidade de formação de metástases Mudanças no padrão de expressão gênica têm sido associadas à manifestação do fenótipo metastático. Neste trabalho, utilizamos microarranjos de tecido (TMAs) para investigar a expressão de 8 biomarcadores candidatos (CIP4, PPIL1, ITGAV, AKAP14, MICA, FXYD1, ARPC3, ABG1) e avaliar seu potencial prognóstico em pacientes com carcinoma ductal invasivo da mama. Destes, ARPC3 PPIL1 e CIP4 mostraram associações estatisticamente significativas com a sobrevida câncer específica e/ou a probabilidade de desenvolvimento de metástases. Determinamos que a expressão aumentada de CIP4 nos tumores está associada a maior probabilidade de desenvolvimento de metástases. CIP4 é uma proteína adaptadora descrita na literatura como moduladora de migração e invasão celular e portanto selecionamos este candidato para caracterização funcional detalhada. Observamos que a expressão de CIP4 encontra-se aumentada em linhagens tumorais com características invasivas. A partir do silenciamento estável e regulado de CIP4 na linhagem metastática MDA-MB-231, determinamos que CIP4 modula positivamente a ativação de MAPK-p38 e a expressão de MMP2 , sugerindo que CIP4 participe em vias de sinalização importantes para a transição epitélio-mesenquima (EMT). O silenciamento de CIP4 resultou em uma redução de aproximadamente 50% da capacidade migratória e invasiva das células tumorais in vitro , e na diminuição da formação de metástases pulmonares in vivo. Coletivamente, nossos resultados indicam que CIP4 tem potencial como marcador de prognóstico assim como um possível alvo terapêutico no controle da disseminação de metástases nos tumores da mama. / Breast cancer is an extremely heterogeneous disease comprising different molecular subtypes that result in different clinical outcomes and therapeutic procedures. The severity of this disease is mainly associated with its ability to produce metastasis. Changes in gene expression profile have been associated with the manifestation of the metastatic phenotype. In this study, we used tissue microarrays (TMAs) to investigate the expression of 8 candidate biomarkers (CIP4, PPIL1, ITGAV, AKAP14, MICA, FXYD1, ARPC3 e ABG1) and to evaluate their prognostic potential in patients with invasive ductal breast carcinoma. Among these, ARPC3, PPIL1 and CIP4 showed statistically significant associations with cancer specific survival and/or the patient\'s probability to develop metastasis. We found that increased expression of CIP4 in tumors is associated with a higher probability of developing metastasis. CIP4 is an adaptor protein described in the literature as a modulator of cell migration and invasion and therefore we selected this candidate for detailed functional characterization. We observed that CIP4 expression is increased in tumor cell lines with invasive characteristics. Following the stable and regulated knockdown of CIP4 in the metastatic line MDA-MB-231, we determined that it modulates positively the activation of MAPK-p38 and the expression of MMP2, suggesting that CIP4 participates in important signaling pathways required for the epithelial mesenchymal transition (EMT). CIP4 silencing resulted in an approximate 50% reduction of the migratory and invasive capacity of tumor cells in vitro and decreased the generation of lung metastases in vivo. Collectively, our results indicate that CIP4 has potential as a prognostic marker as well as a potential therapeutic target to control the metastatic dissemination of breast tumors.

The field of proteomics has rapidly expanded due to the completion of the human genome sequence. This thesis validates affinity-purified monospecific antibodies of polyclonal origin, for protein profiling in a broad spectrum of normal tissues and cells. Validation of antibodies is crucial for development of reliable binders for target proteins and this thesis evaluates the generation and application of large sets of msAbs in different settings. MsAbs were generated towards recombinant Protein Epitope Signature Tag (PrEST) antigens using a stringent affinity-purification strategy, presented in the first study. The specificity of msAbs was studied using reverse phase protein arrays and immunohistochemistry (IHC), and results presented over 90% success rate in the protein array analysis. In IHC, 81% of the msAbs displayed apparent specific staining in normal tissues. MsAbs were also compared with commercial analogs (cAbs) using IHC and Western blot. Results presented similar outcome between msAbs and cAbs in both applications, although interpretation suggested more extensive IHC staining patterns with msAbs than with monoclonal analogs. For antibody validation, an approach called paired antibodies was presented and involved the generation of two msAbs towards non-overlapping epitopes on the same protein. Similarities in protein detection between paired antibodies were studied using three different antibody-based methods. Similar results were observed in several applications, indicating that this strategy can be a useful tool for studying known and unknown proteins. Given the reliability of msAbs, they were also applied in a study investigating the impact of tissue fixatives on protein detection. The study showed that different fixation mechanisms appeared to affect protein recognition by indicating that aldehyde-based fixation, e.g. induced by neutral buffered formalin, was preferred for tissues used in IHC and non-aldehyde based fixation was applicable for tissues used in protein extraction analysis and Western blotting. Conclusively, validation results suggest that msAbs are reliable affinity binders that can be used as valuable tools for proteome-wide protein profiling in tissues and cells.

Proteins are essential building blocks in every living cell, and since the complete human genome was sequenced in 2004, researchers have attempted to map the human proteome, which is the functional representation of the genome. One such initiative is the Human Protein Atlas programme (HPA), which generates monospecific antibodies towards all human proteins and uses these for high-throughput tissue profiling on tissue microarrays (TMAs). The results are publically available at the website www.proteinatlas.org. In this thesis, TMAs were used for analysis of expression patterns in various research areas. Different search queries in the HPA were tested and evaluated, and a number of potential biomarkers were identified, e.g. proteins exclusively expressed in islets of Langerhans, but not in exocrine glandular cells or other abdominal organs close to pancreas. The identified candidates were further analyzed on TMAs with pancreatic tissues from normal and diabetic individuals, and colocalization studies with insulin and glucagon revealed that several of the investigated proteins (DGCR2, GBF1, GPR44 and SerpinB10) appeared to be beta cell specific. Moreover, a set of proteins differentially expressed in lung cancer stroma was further analyzed on a clinical lung cancer cohort in the TMA format, and one protein (CD99) was significantly associated with survival. In addition, TMAs with tissue samples from different species were generated, e.g. for mapping of influenza virus attachment in various human and avian tissues. The results showed that the gull influenza virus H16N3 attached to human respiratory tract and eye, suggesting possible transmission of the virus between gull and human. TMAs were also used for analysis of protein expression differences between humans and other primates, and two proteins (TCF3 and SATB2) proved to be significantly differentially expressed on the human lineage at both the protein level and the RNA level.   In conclusion, this thesis exemplifies the potential of the TMA technology, which can be used for analysis of expression patterns in a large variety of research fields, such as biomarker discovery, influenza virus research or further understanding of human evolution.

O câncer de mama é uma doença extremamente heterogênea compreendendo diferentes subtipos moleculares que resultam em evoluções clínicas e condutas terapêuticas distintas. A maior gravidade desta patologia está associada a sua capacidade de formação de metástases Mudanças no padrão de expressão gênica têm sido associadas à manifestação do fenótipo metastático. Neste trabalho, utilizamos microarranjos de tecido (TMAs) para investigar a expressão de 8 biomarcadores candidatos (CIP4, PPIL1, ITGAV, AKAP14, MICA, FXYD1, ARPC3, ABG1) e avaliar seu potencial prognóstico em pacientes com carcinoma ductal invasivo da mama. Destes, ARPC3 PPIL1 e CIP4 mostraram associações estatisticamente significativas com a sobrevida câncer específica e/ou a probabilidade de desenvolvimento de metástases. Determinamos que a expressão aumentada de CIP4 nos tumores está associada a maior probabilidade de desenvolvimento de metástases. CIP4 é uma proteína adaptadora descrita na literatura como moduladora de migração e invasão celular e portanto selecionamos este candidato para caracterização funcional detalhada. Observamos que a expressão de CIP4 encontra-se aumentada em linhagens tumorais com características invasivas. A partir do silenciamento estável e regulado de CIP4 na linhagem metastática MDA-MB-231, determinamos que CIP4 modula positivamente a ativação de MAPK-p38 e a expressão de MMP2 , sugerindo que CIP4 participe em vias de sinalização importantes para a transição epitélio-mesenquima (EMT). O silenciamento de CIP4 resultou em uma redução de aproximadamente 50% da capacidade migratória e invasiva das células tumorais in vitro , e na diminuição da formação de metástases pulmonares in vivo. Coletivamente, nossos resultados indicam que CIP4 tem potencial como marcador de prognóstico assim como um possível alvo terapêutico no controle da disseminação de metástases nos tumores da mama. / Breast cancer is an extremely heterogeneous disease comprising different molecular subtypes that result in different clinical outcomes and therapeutic procedures. The severity of this disease is mainly associated with its ability to produce metastasis. Changes in gene expression profile have been associated with the manifestation of the metastatic phenotype. In this study, we used tissue microarrays (TMAs) to investigate the expression of 8 candidate biomarkers (CIP4, PPIL1, ITGAV, AKAP14, MICA, FXYD1, ARPC3 e ABG1) and to evaluate their prognostic potential in patients with invasive ductal breast carcinoma. Among these, ARPC3, PPIL1 and CIP4 showed statistically significant associations with cancer specific survival and/or the patient\'s probability to develop metastasis. We found that increased expression of CIP4 in tumors is associated with a higher probability of developing metastasis. CIP4 is an adaptor protein described in the literature as a modulator of cell migration and invasion and therefore we selected this candidate for detailed functional characterization. We observed that CIP4 expression is increased in tumor cell lines with invasive characteristics. Following the stable and regulated knockdown of CIP4 in the metastatic line MDA-MB-231, we determined that it modulates positively the activation of MAPK-p38 and the expression of MMP2, suggesting that CIP4 participates in important signaling pathways required for the epithelial mesenchymal transition (EMT). CIP4 silencing resulted in an approximate 50% reduction of the migratory and invasive capacity of tumor cells in vitro and decreased the generation of lung metastases in vivo. Collectively, our results indicate that CIP4 has potential as a prognostic marker as well as a potential therapeutic target to control the metastatic dissemination of breast tumors.

O carcinoma de células renais (CCR) é o tumor mais agressivo que afeta o rim de pessoas adultas. O CCR é uma doença heterogênea, com diferentes alterações moleculares e variados patrões histológicos e clínicos que apresentam evolução diferente. Atualmente apenas variáveis anatomopatológicas clássicas são utilizadas para determinar o prognóstico dos pacientes. Utilizando uma plataforma de microarranjos de DNA, nosso grupo identificou em um trabalho anterior um conjunto de genes que se encontram diferencialmente expressos em tumores de rim. Neste estudo, nove candidatos foram selecionados para avaliação como marcadores de prognóstico no CCR. Foi confirmada a alteração na expressão dos genes ARNTL, ACTN4 e EPAS1 (p < 0,05) em amostras tumorais de CCR através de PCR em tempo real. Adicionalmente, foi observada a alteração da expressão dos genes ARNTL, EPAS1 e CASP7 em linhagens celulares imortalizadas derivadas de tumores renais, recapitulando por tanto, as alterações observadas nos tumores obtidos de pacientes. Posteriormente investigamos o padrão de expressão proteica destes candidatos por imunohistoquímica utilizando microarranjos de tecidos. Foi detectada a diminuição significativa (p < 0,05) da expressão das proteínas ACTN4, ARNTL, CASP7 e EPAS1 em tumores de pacientes com CCR relativamente ao tecido renal não tumoral. Além disso, foi possível determinar valores de imunomarcação capazes de estratificar pacientes com CCR em diferentes grupos de risco quanto à sobrevida câncer-específica, que adicionalmente apresentaram associação significativa com parâmetros anatomopatológicos utilizados na clínica. As imunomarcações de ACTN4, ARNTL, e EPAS1 se mostraram parâmetros independentes de prognóstico de sobrevida dos pacientes. A imunomarcação de CASP7 foi capaz de identificar subgrupos de pacientes com pior prognóstico dentro de um conjunto de pacientes de baixo risco em função do estadio clinico, além de identificar pacientes com menor risco de morte pelo câncer entre aqueles apresentaram recorrência em até 5 após a cirurgia. O conjunto de resultados obtidos aponta para um novo conjunto de biomarcadores moleculares com potencial relevância para auxiliar no prognóstico de pacientes com carcinoma de células renais. / The renal cell carcinoma (RCC) is the most aggressive tumor that affects the kidney in adult people. The RCC is a heterogeneous disease, with many different molecular alterations and varied histological and clinical patterns with different outcome. Currently, only classic anatomopathological variables are used to determine patients\' prognosis. Using a DNA microarray platform, our group identified in a previous work a set of genes differentially expressed in renal tumors. In this study, nine candidates were selected for evaluation as prognostic biomarkers in RCC. Alteration of the gene expression in RCC tumor samples was confirmed for ARNTL, ACTN4 and EPAS1 (p < 0.05) by real time PCR. Additionally, gene expression changes of ARNTL, EPAS1 and CASP7 were also observed in immortalized cell lines derived from renal tumors, recapitulating the expression changes detected in the patients\' tumors. Next, we used tissue microarrays to investigate the protein expression of the selected candidates by immunohistochemistry. Expression of the proteins ACTN4, ARNTL, CASP7 and EPAS1 was detected as significantly downregulated (p < 0.05) in patients´ tumors relative to non-tumor renal tissue. Furthermore, immunostaining patterns of the selected candidates were able to stratify patients with RCC in different risk groups according to cancer-specific survival, which also showed significant associations with anatomopathological parameters used in the clinics. ACTN4, ARNTL and EPAS1 immunostaining resulted as independent prognostic parameters of patient survival. CASP7 immunostaining was able to identify subgroups of patients with worse prognosis in a set of low risk patients as determined by their clinical stage, and also identified patients with lower risk of death from cancer amongst patients that relapsed within 5 years after surgery. Overall, these results point to a new set of molecular biomarkers with potential relevance to help in the prognosis of patients with renal cell carcinoma.

Kolorektal cancer (CRC) är en av de vanligaste cancersjukdomarna i världen med cirka 1 miljon nya detekterade fall per år. Special AT-rich sequence-binding protein1 (SATB1) är ett celltyp-specifikt kärnmatrix-associerat DNA-bindande protein, vilket utgörs av AT-rika DNA sekvenser. Det har tidigare demonstrerats att en annan medlem i SATB-familjen, SATB2, uttrycks på ett vävnadsspecifikt sätt i normal mukosa i nedre mag-tarmkanalen och i CRC. β-catenin är en intracellulär mediator i Wnt/β-catenin signaleringsvägen, som spelar en viktig roll i kolorektal carcinogenes. Uttryck av SATB1, SATB2 och β-catenin har studerats i tissue microarrays med tumörprover från 270 CRC patienter. Deras inbördes korrelation samt koppling till recidivfri överlevnad har studerats med hjälp av Spearman´s korrelationstest respektive Kaplan-Meier analys och log-rank test. Resultatet från immunhistokemiska färgningar visar att det finns en korrelation mellan de analyserade markörerna. Därutöver fann vi att SATB1 uttryck är kopplat till kortare recidivfri överlevnad i tumörer med lågt SATB2 uttryck. / Colorectal cancer (CRC) is one of the most common cancers in the world with about 1 million new cases annually. Special AT-rich sequence binding protein 1 (SATB1), is a cell type specific nuclear matrix associated DNA binding protein, which consists of AT-rich DNA sequences. It has previously been demonstrated that another member in SATB-family, SATB2, is expressed in a tissue-specific manner in normal mucosa in the lower gastrointestinal tract and in CRC. β-catenin is an intracellular mediator of the Wnt/ β-catenin signaling pathway and plays an important role in colorectal carcinogenesis. Expression of SATB1, SATB2 and β-catenin was analyzed in tissue microarrays with tumors from 270 CRC patients. Spearman´s correlation test was used to assess the correlations and the impact of SATB1 and SATB2 on recurrence free survival was assessed by Kaplan-Meier analysis and log-rank test. The result of immunohistochemical staining shows that there is a correlation between the analyzed markers and that SATB1 expression is a poor prognostic factor in tumors expressing low levels of SATB2.

Die vorliegende Arbeit beinhaltet umfangreiche histologische Untersuchungen an verschiedenen Tumoren bezüglich ihrer Infiltration durch Makrophagen-Subpopulationen, Granulozyten und Lymphozyten. Hierfür wurden 18 Gewebe-Mikroarrays mit jeweils 200 - 300 Tumorstanzen aus insgesamt 27 Organen des Gastrointestinaltraktes, des Urogenitaltraktes, des Respirationssystems und des endokrinen Systems angefertigt. Da alle Proben mit derselben Technik (Gewebe-Mikroarrays, Immunhiostochemie) ausgewertet wurden, bestand nun erstmalig die Möglichkeit eines direkten Vergleiches zwischen den verschiedenen Tumoren unterschiedlicher Organe. Für die immunhistochemischen Untersuchungen wurden fünf verschiedene Antikörper (anti-KP1, anti-PG-M1, anti-MRP8, anti-MRP14, anti-MRP8/14) eingesetzt. Die Antikörper gegen die Epitope PG-M1 und KP1 gelten als Pan-Makrophagen-Marker. Die Antikörper anti-MRP8, anti-MRP14 und anti-MRP8/14 gelten als Marker für entzündlich aktivierte Makrophagen. Diese Makrophagen wurden in einen aktiven inflammatorischen Typ (MRP14+, MRP8/14+), der proinflammatorische Zytokine wie TNF-a und Sauerstoffradikale bildet, und in einen chronisch inflammatorischen Typ (MRP8+) eingeteilt. Die Formation des MRP8/14-Heterodimers korreliert mit der zellulären Aktivierung wie z. B. mit der Aktivierung der NADPH-Oxidase. Es wurde beschrieben, dass diese Makrophagen auf Grund ihrer Eigenschaften eventuell die Tumorzellproliferation inhibieren und zytotoxische Wirkungen auf Tumorzellen ausüben können. Für die verschiedenen Tumorgewebe wurden höhere Makrophagendichten im Vergleich zum Normalgewebe und eine vergleichsweise geringe Dichte an MRP+ Makrophagen sowie signifikante Korrelationen zwischen den verschiedenen Makrophagen-Subpopulationen festgestellt. Die Dichte der Lymphozyten korrelierte negativ mit steigendem Tumorzellanteil und mit fortgeschrittenem Tumorstadium. Die Abnahme der Lymphozyten (Gastrointestinal- und Respirationstrakt) im Tumorgewebe im Vergleich zum tumorfreien Gewebe sowie die geringe Anzahl der potenziell tumoriziden MRP8/14+ Makrophagen lässt vermuten, dass die Immunantwort gegen den Tumor unterdrückt wird. Die positive Assoziation zwischen Makrophagen und Lymphozyten weist jedoch darauf hin, dass Makrophagen nicht am Rückgang der Lymphozyten beteiligt sind . Eine Korrelation der Makrophagen mit klinisch relevanten Parametern (pT-Stadium, UICC-Stadium, Lymphknotenmetastasen) zeigten ein voneinander abweichendes Infiltrationsmuster der CD68+ und MRP+ Makrophagen, was auf unterschiedliche Funktionen hinweist. Ferner liegen zahlreichen funktionelle Untersuchungsergebnisse anderer Arbeitsgruppen vor, welche darauf hinweisen, dass Makrophagen durch Hypoxie angezogen werden und im hypoxischen Tumorgewebe schließlich an der Neubildung von Blut- und Lymphgefäßen beteiligt sind. Um einen möglichen Zusammenhang zu zeigen, wurde mit den Antikörpern anti-CD31 und anti-CD34 die Gefäßdichte in Tumoren untersucht. Es zeigten sich zahlreiche positive Korrelationen zwischen Gefäßen und Makrophagen, jedoch konnte in den tumorfreien Geweben kein Zusammenhang zwischen beiden Größen gefunden werden. Das Vorkommen größerer Makrophagendichten in Tumoren mit wenig Nekrose als in Tumoren ohne Nekrose, die positive Korrelation zwischen der Anzahl der Gefäße und der Zahl der Makrophagen in Tumoren und die Unabhängigkeit von Makrophagen und Gefäßen im tumorfreien Gewebe legt die Vermutung nahe, dass TAM die Angiogenese begünstigen. Trotz vieler ähnlicher Charakteristika zwischen den Tumoren unterschiedlichen Ursprungsgewebes wurden auch Unterschiede festgestellt, die besonders die Anzahl der Makrophagen-Subpopulationen betreffen. Weitere Studien zur Aufklärung der Funktion unterschiedlicher Makrophagen-Subpopulationen (z. B. Immunsuppression, Neoangiogenese) sind notwendig, um deren Relevanz für das Tumorwachstum und die Tumorprogression aufzuklären.

Dans un contexte où des technologies et matériels nouveaux permettent un traitement en masse d'échantillons et où les données acquises sont de plus en plus partagées entre équipes de recherche, les scientifiques sont confrontés à un problème majeur d'exploitation de données. Plus précisément, utiliser ces données par des outils de fouille de données ou les replacer dans une démarche expérimentale classique nécessite une appréhension préalable de l'espace informationnel disponible afin de diriger le processus. Or cette appréhension de données est un problème complexe, peu supporté par les outils informatiques actuels. <br /><br />L'objectif de cette thèse est de proposer une solution à ce problème d'appréhension des données scientifiques. Illustrée dans le domaine applicatif des Tissue MicroArrays, la proposition se base sur la notion de synthèse, inspirée des paradigmes de Recherche d'Information. Le modèle de synthèse envisagé, qui donne un rôle central à l'étude que le chercheur veut mener, par la notion de tâche, permet l'opérationnalisation d'un concept de Recherche d'Information orientée tâche par un prototype. Le prototype mis en place est validé par des étude de cas et une étude utilisateurs et ouvre des perspectives intéressantes d'extension du modèle ou d'extension à d'autres domaines applicatifs.