This thesis establishes a connection between GOMMA and STROMA – both are tools of ontology processing. Consequently, a new workflow of denoting a set of correspondences with five semantic relation types has been implemented. Such a rich denotation is scarcely discussed within the literature. The evaluation of the denotation shows that trivial correspondences are easy to recognize (tF > 90). The challenge is the denotation of non-trivial types ( 30 < ntF < 70). A prerequisite of the implemented workflow is the extraction of semantic relations between concepts. These relations represent additional background knowledge for the enrichment tool STROMA and are integrated to the repository SemRep which is accessed by this tool. Thus, STROMA is able to calculate a semantic type more precisely. UMLS was chosen as a biomedical knowledge source because it subsumes many different ontologies of this domain and thus, it represents a rich resource. Nevertheless, only a small set of relations met the requirements which are imposed to SemRep relations. Further studies may analyze whether there is an appropriate way to integrate the missing relations as well. The connection of GOMMA with STROMA allows the semantic enrichment of a biomedical mapping. As a consequence, this thesis enlightens two subjects of research. First, STROMA had been tested with general ontologies, which models common sense knowledge. Within this thesis, STROMA was applied to domain ontologies. Studies have shown that overall, STROMA was able to treat such ontologies as well. However, some strategies for the enrichment process are based on assumption which are misleading in the biomedical domain. Consequently, further strategies are suggested in this thesis which might improve the type denotation. These strategies may lead to an optimization of STROMA for biomedical data sets. A more thorough analysis will review their scope, also beyond the biomedical domain. Second, the established connection may lead to deeper investigations about advantages of semantic enrichment in the biomedical domain as an enriched mapping is returned. Despite heterogeneity of source and target ontology, such a mapping results in an improved interoperability at a finer level of granularity. The utilization of semantically rich correspondences in the biomedical domain is a worthwhile focus for future research.

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Objetivo: Verificar resposta após debridamento epitelial de córneas humanas. Métodos: Córneas normais foram submetidas a debridamento antes da cirurgia de enucleação. Realizou-se histologia, TUNEL, Ki67, SMA e microscopia eletrônica. Resultados: Seis córneas foram debridadas e preservadas entre ½ e 65 horas, apresentando apoptose nos ceratócitos do estroma anterior. Células estromais em proliferação foram observadas apenas no tempo de 65 horas. Miofibroblastos não foram encontrados. Uma córnea serviu de controle. Conclusões: Os eventos observados em córneas humanas após debridamento epitelial, apoptose e proliferação dos ceratócitos, foram semelhantes aos descritos em animais de experimentação / Purpose: To examine the early wound healing response to epithelial scrape in human corneas. Methods: Normal corneas had epithelial scrape prior to enucleation. Histology, TUNEL assay, Ki67, SMA and transmission electron microscopy were performed. Results: Epithelial scrape was performed in six corneas from ½ to 65 hours prior to preservation. Keratocyte apoptosis was detected in the anterior stroma in all scraped corneas. Keratocyte proliferation was detected exclusively 65 hours after scrape. No myofibroblast was detected. One cornea was not scraped (control). Conclusion: Results obtained in human corneas (keratocyte apoptosis and proliferation) were similar to animal models

Objetivo: Verificar resposta após debridamento epitelial de córneas humanas. Métodos: Córneas normais foram submetidas a debridamento antes da cirurgia de enucleação. Realizou-se histologia, TUNEL, Ki67, SMA e microscopia eletrônica. Resultados: Seis córneas foram debridadas e preservadas entre ½ e 65 horas, apresentando apoptose nos ceratócitos do estroma anterior. Células estromais em proliferação foram observadas apenas no tempo de 65 horas. Miofibroblastos não foram encontrados. Uma córnea serviu de controle. Conclusões: Os eventos observados em córneas humanas após debridamento epitelial, apoptose e proliferação dos ceratócitos, foram semelhantes aos descritos em animais de experimentação / Purpose: To examine the early wound healing response to epithelial scrape in human corneas. Methods: Normal corneas had epithelial scrape prior to enucleation. Histology, TUNEL assay, Ki67, SMA and transmission electron microscopy were performed. Results: Epithelial scrape was performed in six corneas from ½ to 65 hours prior to preservation. Keratocyte apoptosis was detected in the anterior stroma in all scraped corneas. Keratocyte proliferation was detected exclusively 65 hours after scrape. No myofibroblast was detected. One cornea was not scraped (control). Conclusion: Results obtained in human corneas (keratocyte apoptosis and proliferation) were similar to animal models

A desnutrição proteica continua sendo um dos principais problemas nutricionais do mundo. Trabalhos de nosso laboratório e de outros autores evidenciam que entre as alterações presentes na desnutrição proteica, está a alteração do tecido hemopoético, com modificações em componentes da matriz extracelular, alterações no ciclo celular da célula tronco/progenitora hemopoética, redução da produção de precursores hemopoéticos, tanto na série eritrocitária como na série leucocitária, levando a anemia e leucopenia. Os mecanismos de participação do Ca2+ nas células da medula óssea são pouco conhecidos, porém, sabe-se que ele atua no processo de hemopoese. Têm sido descrito que elevações da concentração de Ca2+ citoplasmático induzem a proliferação e diferenciação de células mielóides. A ação dessa via em indivíduos desnutridos também é pouco conhecida. Este estudo tem como objetivo avaliar o estabelecimento da celularidade medular in vitro, bem como investigar mecanismos moleculares envolvidos na proliferação e diferenciação dessa celularidade, além de avaliar a ação do cálcio na presença da interleucina-3 em células-tronco hemopoéticas murinas e sua modulação para avaliar alterações na via das MAPKs. Camundongos C57BL/6, machos e adultos foram submetidos à desnutrição proteica e, após a perda de aproximadamente 20% de seu peso corporal, as células da medula óssea foram colhidas. Essas células foram imunofenotipadas, além de reagirem com anticorpos específicos para caracterização da célula-tronco hemopoética e proteínas da via de sinalização de cálcio intracelular. Observamos que a celularidade do estroma medular em cultura de longa duração de animais desnutridos é alterada, principalmente em células de origem mesenquimal, que aparecem em maior número em desnutridos ao longo dos dias de cultura. Além disso, as ondas de cálcio intracelular estavam diminuídas em animais desnutridos, bem como as proteínas p-PKC, p-PLCy, CAMKII, p-AKT e p-STAT5 não respondem ao estímulo de IL-3, levando a uma deficiência da expressão das MAPK: ERK 1/2, JNK e p38. A desnutrição proteica pode causar alterações na celularidade estromal da medula óssea e na diferenciação das células tronco hemopoéticas pela via das MAPKs estimulada por IL-3. / Protein malnutrition remains one of the world\'s major nutritional problems. Studies from our laboratory and others shown that alterations in protein malnutrition include hemopoietic tissue alterations, changes in extracellular matrix components, changes in the hemopoietic stem/progenitor cell tissue, reduction in the production of hemopoietic precursors, in the erythroid series as in the mieloyd series, leading to anemia and leukopenia. Mechanisms of Ca2+ participation in bone marrow cells are poorly understood, but no hemopoiesis has been developed. Elevations of cytoplasmic Ca2+ concentration in proliferation and differentiation of myeloid cells were included. Such an action through malnourished animals is also a little known. This study aims to evaluate the establishment of cellularity in vitro as well as investigate the molecular involvement in cell proliferation and differentiation, as well as to evaluate the action of calcium in the presence of IL-3 in hemopoietic stem cells and its modulation by analytical evaluations in the MAPKs pathway. C57BL/6, male adult mices were subjected to protein restriction and, after loss of approximately 20% of their body weight, bone marrow cells were harvested. These were immunophenotyped in addition to specific activation terms for the hemopoietic stem cell and intracellular signaling pathway proteins. We observed that the bone marrow cells in long-term culture of malnourished animals is altered, mainly in cells of mesenchymal origin, which appears in greater numbers in undernourished throughout the days of culture. In addition, as intracellular calcium waves decreased in malnourished animals, as well as the p-PKC, p-PLC, CAMKII, p-AKT and p-STAT5 proteins did not respond to IL-3, sugesting expression of the expression of MAPK: ERK 1/2, JNK and p38. Protein malnutrition may have changes in bone marrow capacity and differentiation of hemopoietic stem cells through IL-3-stimulated MAPKs.

Abstract Pancreatic cancer remains one of the deadliest malignancies, with dismal prognosis. Pancreatic cancer arises from precursor lesions called pancreatic intraepithelial neoplasia. Toll-like receptors (TLR) are receptors of the innate immunity responsible for initiating immune responses against invading pathogens. Their involvement in cancer progression is becoming evident. Hypoxia is a typical characteristic of pancreatic cancer and linked to poor prognosis. Typically, pancreatic cancer has an abundant desmoplastic stroma that contributes to the hypoxia and poor delivery of anti-tumor drugs to the cancer cells. Tenascin-C and fibronectin are proteins of the extracellular matrix. They are involved in normal organ development, but in recent years, their involvement in various cancers has become evident. This thesis examined the involvement of Toll-like receptors, hypoxia markers HIF-1alpha and Carbonic anhydrase 9 (CAIX) as well as stromal markers tenascin-C and fibronectin in pancreatic cancer. Furthermore, the prognostic effect of each protein was evaluated. The material consisted of whole section tissue samples of surgically treated patients with pancreatic ductal adenocarcinoma. The expression of the proteins was evaluated using immunohistochemical stainings. TLR, HIF-1alpha, CAIX, tenascin-C and fibronectin were all abundantly expressed in pancreatic cancer. High TLR9 associated with improved prognosis while weak HIF-1alpha indicated poor prognosis. In a subgroup analysis consisting of only T1 and T2 tumors, high tenascin-C associated with poor prognosis. There was no significant correlation between TLR and hypoxia marker expression. Based on these results, TLR2, TLR4 and TLR9 are expressed in pancreatic cancer, and high TLR9 associates with improved survival of the patients. Weak HIF-1alpha associated with poor prognosis, suggesting that other factors than hypoxia might be involved in the regulation of HIF-1alpha expression. Tenascin-C and fibronectin are not associated with patient prognosis in pancreatic cancer. / Tiivistelmä Haimasyövällä on kaikista syövistä yksi huonoimmista ennusteista. Haimasyöpä kehittyy tiehyidensisäisistä muutoksista, joita kutsutaan englanninkielisellä nimellä pancreatic intraepithelial neoplasia (PanIN). Tollin kaltaiset reseptorit (TLR) ovat luontaisen immuniteetin reseptoreja, ja niiden tehtävä on aloittaa elimistön puolustusvaste tunkeutuvia taudinaiheuttajia vastaan. Tollin kaltaisten reseptorien osuus on osoitettu eri syövissä. Hypoksia on tyypillistä haimasyövälle, ja se on yleensä yhteydessä huonontuneeseen ennusteen. Tyypillisesti haimasyövällä on voimakas sidekudosreaktio, joka osaltaan lisää kasvaimen hapenpuutetta ja vaikeuttaa sytostaattien kulkeutumista syöpäsoluihin. Tenaskiini ja fibronektiini ovat solunulkoisen tilan proteiineja, jotka osallistuvat normaaliin elimistön kehitykseen. Viime aikoina niillä on huomattu olevan osuutta myös erilaisten syöpien kehittymiseen. Tässä väitöskirjassa on tutkittu Tollin kaltaisten reseptorien, hypoksiamerkkiaineiden HIF-1alpha ja hiilihappoanhydraasi 9 (CAIX) sekä sidekudosmerkkiaineiden tenaskiini ja fibronektiini ilmentymistä haimasyövässä. Lisäksi tutkimuksessa selvitettiin näiden proteiinien osuutta haimasyövän ennusteeseen. Tutkimuksen materiaali koostuu haimasyöpäpotilaiden syöpäkudosnäytteistä. Näytteinä käytettiin kokoleikenäytteitä. Näytteille tehtiin immunohistokemialliset värjäykset, joista eri proteiinien ilmentymistä arvioitiin. Tollin kaltaiset reseptorit, HIF-1alpha, CAIX, tenaskiini ja fibronektiini ilmenivät kaikki haimasyövässä. Korkea TLR9 oli yhteydessä parantuneeseen ennusteeseen, kun taas heikko HIF-1alpha oli yhteydessä huonontuneeseen ennusteeseen. Huomioitaessa vain T1- ja T2-kasvaimet korkea tenaskiini oli yhteydessä huonontuneeseen ennusteeseen. Tollin kaltaisten reseptorien ja hypoksiamerkkiaineiden välillä ei ollut merkittävää yhteyttä. Tulosten perusteella haimasyövässä on runsaasti Tollin kaltaisia reseptoreita, ja korkea TLR9 on yhteydessä parantuneeseen ennusteeseen. Matala HIF-1alpha on yhteydessä huonoon ennusteeseen. Tenaskiinilla ja fibronektiinilla ei ole vaikutusta potilaiden ennusteeseen.

Myelodysplastic syndromes (MDS) are regarded as clonal disorders of haematopoietic stem cells (HSC). Recent evidence demonstrates that stromal microenvironment, in addition to HSC defects, plays a particular role via its direct contact with haematopoietic precursor cells (HPC). This thesis aims at evaluating the putative growth deficiencies of mesenchymal stromal cells (MSC) from MDS individuals compared with normal controls, exploring their adhesion profile, assessing the adhesion process-involved molecular substrates, and establishing correlations with their growth patterns and HPC dysfunctions. Functional assays revealed that MSC from MDS are intrinsically pathological, show a continuous decline of proliferation over a 14-day culture and a reduced clonogenic capacity in the absence of signals from HPC. MSC growth defects significantly correlate with decreased CD44 and CD49e expression. Moreover, stroma-dependent adhesion mechanisms control HPC clonogenic potential and CD49e might be one of the molecules involved in this process. Qualitative and quantitative abnormalities of focal adhesion (FA) proteins paxillin and pFAK [Y397] and of two regulatory proteins, HSP90αβ and p130CAS were identified via immunofluorescence analysis. Paxillin, pFAK [Y397] and HSP90αβ increased expression, besides its stronger nuclear colocalization in MSC from RAEB correlates with a consistent proliferative advantage and has a negative impact on HPC clonogenic capacity. These results open interesting opportunities, e.g. HPC-to-MSC interactions involve FA proteins signalling, and, as FAK is an HSP90αβ-client protein, it may enhance the utility of HSP90αβ inhibitors as adjuvant therapy in MDS

Dans les tumeurs, les cellules cancéreuses invasives induisent l’expression de la métalloprotéase matricielle 11 (MMP-11) dans les adipocytes adjacents (cancer-associated adipocytes) entrainant leur « dédifférenciation » en fibroblastes, la MMP-11 régulant négativement l’adipogénèse. Au cours de ma thèse, j’ai étudié la fonction de la MMP-11 sur le développement mammaire postnatal. La structure de la glande ainsi que la production de lait sont altérées dans les souris déficientes pour la MMP-11. De plus, la MMP-11 régule l’homéostase du collagène. In vivo, des transplantations montrent une fonction locale paracrine de la MMP-11 essentielle à la morphogenèse mammaire. In vitro, la MMP-11 adipocytaire favorise le branchement d’organoïdes primaires. Ainsi, la MMP-11 est un facteur paracrine majeur pour le développement de la glande mammaire. Enfin, pour poursuivre ces travaux, j’ai établi des souris transgéniques conditionnelles ciblant l’expression de la MMP-11 dans les adipocytes. / In tumors, invasive cancer cells induce matrix metalloproteinase 11 (MMP-11) expression in adjacent adipocytes (cancer-associated adipocytes), leading to their « dedifferentiation » into fibroblast-like cells. Indeed, MMP-11 is a negative regulator of adipogenesis. During my PhD, I have investigated MMP-11 function during postnatal mammary gland development. The ductal tree and alveolar structures, and milk production are reduced in MMP-11-deficient mice. Moreover, MMP-11 plays a role in collagen homeostasis. Transplantation experiments show that MMP-11 exerts an essential local paracrine function for ductal morphogenesis. Using primary mammary organoids, I show that adipocyte-related MMP-11 is a pro-branching factor in vitro. Thus, MMP-11 is a master paracrine factor during mammary gland development. Finally, to further investigate the adipocyte-related MMP-11 function, I have developed conditional transgenic mice targeting MMP-11 expression specifically into adipocytes.

Orientador: Jose Andres Yunes / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-10T05:42:02Z (GMT). No. of bitstreams: 1 Laranjeira_AngeloBrunelliAlbertoni_M.pdf: 2767287 bytes, checksum: 8b66a1e06cad088fa256103c24e955a7 (MD5) Previous issue date: 2007 / Resumo: A resistência intrínseca ou adquirida aos compostos quimioterápicos é uma das mais importantes causas dos insucessos no tratamento das LLAs pediátricas. A interação da LLA com o microambiente da medula óssea contribui para a proliferação e resistência ao regime quimioterápico das células leucêmicas através de uma grande variedade de mecanismos celulares que provavelmente incluem: aumento da expressão de transportadores celulares, aumento no processo de reparo do DNA, diminuição na regulação dos alvos das drogas, mudanças na regulação do ciclo celular e alteração nas vias apoptóticas. No presente estudo observou-se que a interação estabelecida entre células estromais e células de LLA-B, promoveu a ativação destas como avaliado pela análise das moléculas de superfície das células leucêmicas ao longo dos períodos de cultivo, além da sobrevivência e/ou proliferação em mais de 60% dos casos in vitro. A comunicação entre os dois tipos celulares também mostrou a influência do estroma na modulação da expressão transcricional de 17 genes relacionados com a resistência e sensibilidade a quimioterápicos em células de LLA-B. A modulação teve como conseqüência o aumento nos níveis de expressão da maioria dos genes de resistência e a queda de expressão da maioria dos genes de sensibilidade. Sendo assim, a LLA, pela interação com as células estromais, apresentaram uma alteração que as levou a um fenótipo característico de células resistentes. Essa alteração de expressão mediada pelo contato com o estroma foi confirmada por estudos funcionais de dois genes relacionados com a resistência. O gene KCNN4 em linhagens celulares, que quando submetidas à ação do clotrimazol apresentaram maior viabilidade na presença do que na ausência do estroma; e a adição da proteína recombinante IGFBP-7 no sistema de co-cultura promoveu a resistência e até mesmo proliferação na presença da L-asparaginase. Esta proteína também se mostrou atuante na proliferação das células estromais. Estes resultados mostram dois genes de LLA, que quando modulados pelo contato com o estroma podem contribuir com a maior resistência ao regime quimioterápico, podendo vir a ser usados como alvo para posteriores terapias / Abstract: The intrinsic or acquired chemotherapy resistance composites one of the most important causes of failures in the treatment of pediatric ALL. The ALL and bone marrow microenvironment nteraction contributes for the proliferation and resistance to the chemotherapy regimen of leukemic cells probably through a great variety of cellular mechanisms, including increase of the expression of cellular transporters, increase in the process of DNA repair, downregulation of drugs targets, changes in the regulation of cellular cycle and alteration in the apoptotic ways. In the present study it was observed that the interaction established between stromal cells and pre-B ALL, evaluated through analysis of surface molecules in leukemic cells throughout the periods of culture, were important for the survival and/or proliferation in more than 50% of the cases in vitro. This interaction also showed the influence of stroma in the transcriptional profile of 17 genes related with the resistance and sensitivity to chemotherapeutic agents in pre-B ALL cells. The modulation had as consequence the increase in the levels of expression of the majority of the resistance genes and the decrease of expression of the majority of the sensitivity genes. Being thus, these cellular types, for the interaction with the stromal cells, had presented an alteration that took them to one phenotype characteristic of resistant cells. This stroma-mediated alteration was confirmed by functional studies of two genes related with the resistance. Gene KCNN4 three leukemic cell lines, that when submitted to the action of clotrimazole they had presented greater viability in the presence than in the absence of stroma; and the addition of recombinant protein IGFBP-7 in the co-culture system promoted the resistance and proliferation of primary ALL cells in the presence of the L-asparaginase. This protein also induced proliferation of stromal cells. These results show two genes of ALL, that when modulated for the contact with stroma, can contribute with a resistance to the chemotherapic regimen, becoming possible targets for posterior therapies / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular