Organic polymers S2218600, S2429901 and S2219200 (referred to as Polymer 1, Polymer 2 and Polymer 3, respectively) of varying toxic potential, designed for use in cosmetic aerosols, were used as model substances to predict inflammatory potential. In vivo inflammogenic potential was evaluated by assessment of inflammatory cell profile (alveolar macrophage (AM), polymorphonuclear neutrophil (PMN)) of broncho-alveolar lavage fluid (BAL) 24hrs after a single instillation of either 0.5 mg or 2 mg polymer in Sprague Dawley rats. Pro-inflammatory Minusil particles and non-inflammatory titanium dioxide (TiO2) particles were used as controls. For comparison, cultured rat NR8383 AM-like cells, human THP-1 monocyte cells or human monocyte derived macrophages were treated with polymer for 24 h and supernatants analysed for indicators of cytotoxicity and inflammatory mediator release. In addition, after 6 h treatment, gene changes in the rat lung tissue and also in the rat NR8383 alveolar macrophage cell line were assessed using microarray to analyse the entire rat genome. The in vivo studies showed that Polymer 1, Polymer 3 and Minusil caused significant PMN influx into BAL. Polymer 3 and Minusil caused a significant increase in AM number in BAL. Polymer 2 and TiO2 had no effect on BAL cell profile. BAL tumour necrosis factor-α (TNFα) and macrophage inflammatory protein-2 (MIP-2) levels were significantly increased following instillation of Polymer 3 and Minusil. Thus the polymers and particles were ranked for potential to cause pulmonary inflammation: Polymer 3 > Minusil > Polymer 1 > Polymer 2 > TiO2. In vitro studies using cultured rat NR8383 AM-like cells showed that the polymers and particles could be ranked similarly for cytotoxic potential and their ability to stimulate the release of both TNFα and MIP-2. Cultured human monocyte derived macrophages detected the pro-inflammatory abilities of Polymer 3, as measured by cytotoxic potential and ability to stimulate TNFα, interleukin-8 (IL-8) and macrophage inflammatory protein-1α (MIP-1α), however, did not detect the pro-inflammatory abilities of Polymer 1. Cultured human THP-1 cells predicted the pro-inflammatory effects of Polymer 3 in rat lungs using the cytotoxicity assay and by changes in IL-1β, MIP-1α and IL-10 levels. The human THP-1 cell line did not predict the pro-inflammatory effects of Polymer 1 that were observed the rat lungs. Electron spin resonance (ESR) detected free radicals produced by the pro-inflammatory polymers and particles which had the ability to break bonds in super-coiled DNA and deplete intracellular glutathione (GSH). Microarray analysis of the canonical pathways activated by the pro-inflammatory polymers, Polymer 1 and Polymer 3, showed that 3 similar pathways were significantly activated in the instilled rats and the rat NR8383 AM-like cells following treatment. ‘Xenobiotic metabolism’, ‘IL-10 signalling’ and ‘leukocyte extravasation signalling’ pathways were significantly changed by the pro-inflammatory polymers. Use of these cell model alternatives in an industrial setting will refine and reduce in vivo testing and as these models are further developed and used alongside future new alternatives they will provide a substantial contribution towards the replacement of animal testing.

Barrett's oesophagus (BO) arises from chronic gastro-oesophageal reflux disease(GORD). Patients have an increased risk of adenocarcinoma (ADC), which is the sixth most common cause of cancer mortality in the UK. All ADC develop from BO, and over the last twenty years there has been a marked increase in both conditions. The reasons for this are not known, however, as with some forms of gastric cancer, it is possible that there may be a bacterial aetiology. This study employed both culturebased and molecular techniques to characterise microbial communities colonising the distal oesophageal mucosae in individuals with GORD, BO and ADC, together with healthy controls. Furthermore, in vitro models were designed to create an oral microbiota, from which an oesophageal community could develop. Microbial analysis identified a shift in oesophageal population composition with disease progression, with an incremental increase in total eubacterial scores related to the metaplasia-dysplasia sequence. Additionally, an increased proportion of Gram negative species and potentially pathogenic organisms, such as Peptostreptococcus were identified. Campylobacter spp. were isolated from 75%, 50% and 60% of GORD, BO and ADC patients, respectively, compared with 20% of controls. Helicobacter pylori, which has been proposed to be protective in oesophageal disease, was significantly reduced in disease, especially in ADC patients. In vitro models were successful, with a simple oral microbiota leading to the development of unique, varied oesophageal populations representative of those found in vivo. Additionally, after exposure of this community to bile acid, population dynamics were altered, with an increase in Gram negative species, associated with a rise in haemolytic and mucinolytic activities. Exposure of oesophageal cell lines to these stressed biofilms resulted in increased cell death, and in some cases, amplified expression of p53 and COX-2. In conclusion, this research proved an association between bacterial composition and oesophageal disease. With progression to adenocarcinoma, the community becomes increasingly diversified and Gram negative in character, and therefore, is proposed to be more pathogenic. Further research is required to investigate causal relationships, through which mechanisms for disease initiation and/or maintenance can be understood.

Induced pluripotent stem cells (iPSCs) can be differentiated into multiple cell types in the body while maintaining proliferative capabilities. The generation of human iPSC-derived hepatocytes (iPSC-Heps) has resulted in a new source for hepatic cells. The current available options for human hepatocytes are primary human hepatocytes (PHHs) and cell lines. PHHs isolated from healthy human donors are difficult to obtain, while cell lines exhibit reduced hepatotoxic sensitivity. iPSC-Heps are being investigated as an alternative option as they are derived from a continuous, stable source and are able to maintain their original donor genotype, which opens the door for patient-specific studies. iPSC-Heps show promise for utilization in tissue engineering, hepatotoxicity studies as well as screening for patient-specific therapeutics. Various reports have concluded that iPSC-Heps exhibit reduced hepatocyte function in comparison to PHHs. Prior reports on iPSC-Heps have focused on improving their adult phenotype functions through variations in differentiation protocols or by altering their in vitro culturing environment. This thesis focuses on incorporating hepatic non-parenchymal cells to more closely mimic the tissue and cell architecture found in the liver tissue. We designed and assembled a 3D iPSC-Hep model that integrates liver sinusoidal endothelial cells, with the goal of achieving functional maturity. Hepatotoxicants were administered to our models and various hepatic markers were measured to analyze the toxic response. This work demonstrates the need for the inclusion of hepatic non-parenchymal cells in iPSC-derived liver tissues, specifically for hepatotoxicity applications. / Master of Science / Induced pluripotent stem cells (iPSCs) can be differentiated into multiple cell types in the body while maintaining proliferative capabilities. The generation of human iPSC-derived hepatocytes (iPSC-Heps) has resulted in a new source for hepatic cells. The current available options for human hepatocytes are primary human hepatocytes (PHHs) and cell lines. PHHs originating from healthy human donors are difficult to obtain, while cell lines may exhibit reduced hepatotoxic sensitivity to chemicals. iPSC-Heps are being investigated as an alternative option since they are derived from a continuous source and are able to maintain their original donor genetic make-up, allowing for patient-specific studies. iPSC-Heps can be used in tissue engineering, hepatotoxicity studies as well as screening for patient-specific therapeutics. Various reports have concluded that iPSC-Heps exhibit reduced function in comparison to PHHs. Prior reports on iPSC-Heps have focused on improving their function through variations in differentiation procedures or by changing their culture environment. This thesis focuses on incorporating other hepatic cells to more closely mimic the tissue and cell architecture found in the liver tissue. We designed and assembled a 3D iPSC-Hep model that integrates liver sinusoidal endothelial cells, with the goal of improving hepatocyte function. Chemicals were administered to our models and various hepatic markers were measured to analyze the toxic response. This work demonstrates the need for the inclusion of additional hepatic cell types in iPSC-derived liver tissues, specifically for hepatotoxicity applications.

A exposição excessiva à radiação Ultravioleta (UV) resulta em manifestações clínicas à pele humana como queimaduras, fotoenvelhecimento e câncer. A radiação UVA, preferencialmente, induz à formação de espécies reativas de oxigênio, enquanto que a radiação UVB é absorvida diretamente pelo DNA. Apesar de mecanismos endógenos auxiliarem na prevenção/reparação dos danos causados pela radiação UV, quando o dano excede a capacidade de reparação celular, diversos efeitos lesivos ocorrem na pele como alterações da matriz dérmica, resposta inflamatória e desidratação do estrato córneo. O uso de compostos fenólicos com atividade antioxidante pode auxiliar na prevenção das consequências patológicas da exposição à radiação UV. O presente trabalho teve como objetivo estudar em cultura de células da pele (HaCaT -queratinócito humano imortalizado e FHPD - fibroblasto humano primário dermal) exposta às radiações UVA e UVB a atividade fotoprotetora de 3 compostos fenólicos, ácido cafeico (AC), clorogênico (ACG) e rosmarínico (AR). Inicialmente, células HaCaT e FHPD cultivadas em monocamada foram expostas às doses crescentes de radiação UVA ou UVB e, após 24 horas, foram analisadas quanto a viabilidade, marcadores de morte celular, mediadores inflamatórios, presença de aquaporina e lesões de DNA. HaCaT quando exposta às radiações UVA e UVB são conduzidas à morte por apoptose, com aumento de Caspases 3 e 9, p53 e redução de PARP. Após a exposição à radiação UVA, HaCaT responde com aumento na liberação de IL-6, TNF-α e COX-2, internalização/redução de AQP3 da membrana, redução na liberação de MMP-2 e 9, aumento na liberação de MMP-1 e na produção de ERO. Quando expostos à radiação UVB, HaCaT aumenta a liberação de IL-6 e COX-2, promove internalização/redução de AQP3 na membrana e redução na liberação de MMP-2 e 9. FHPD são menos sensíveis à exposição a ambas as radiações, mostrando redução de viabilidade com parada de ciclo apenas frente à radiação UVA. Além disto, FHPD exposto a radiação UVA responde com aumento na liberação de IL-6 e danos no DNA do tipo 8-oxo-dG. Dentre os compostos, o ACG apresentou melhor atividade fotoquimioprotetora perante ambas as radiações UVA e UVB, pois foi capaz de reverter em HaCaT a morte celular induzida por ambas as radiações e de reverter a parada de ciclo em FHPD expostos à radiação UVA. HaCaT tratado com ACG e exposto à radiação UVA responde com aumento na expressão de AQP3 e PARP, aumento na expressão gênica de AQP3, redução na expressão gênica de CDKN1A e na liberação de MMP-1, 2 e 9. Após a radiação UVB, o tratamento com ACG aumenta a expressão gênica de AQP3, reduz a expressão gênica de CDKN1A, reduz a produção de COX-2 e aumenta a liberação de MMP-2 e 9. O tratamento com o AR apresentou atividade fotoquimioprotetora frente à radiação UVA, com HaCaT respondendo a radiação com aumento na população de células viáveis, aumento na expressão de AQP3 e PARP e na expressão gênica de AQP3, redução na liberação de MMP-1 e 9 e redução na produção de COX-2. FHPD tratados com AR apresentaram aumento na população em fase G1, na expressão de p21, e redução de danos de DNA tipo 8-oxo-dG. O tratamento de HaCaT com AC foi capaz de reverter a morte celular, aumentar a expressão de p53 e aumentar a liberação de MMP-2 e 9 frente à radiação UVB e de reduzir a produção de ERO, a expressão de p21 e a liberação de MMP-1, 2 e 9 frente à radiação UVA. Para FHPD, o tratamento com AC foi capaz apenas de reduzir a formação de danos de DNA tipo 8-oxo-dG. Os resultados indicam que o modelo proposto foi capaz de discriminar a atividade fotoprotetora dos compostos frente à radiação UVA e UVB. Além disto, foi possível demonstrar que os compostos antioxidantes se comportam de maneira distinta enquanto fotoprotetores no modelo empregado. / Excessive exposure to Ultraviolet radiation (UV) results in clinical manifestations in human skin such as burns, photo-aging and cancer. UVA radiation preferentially induces formation of reactive oxygen species, while UVB radiation is absorbed directly by the DNA. Although endogenous mechanisms are able to prevent/repair cellular damages caused by UV radiation, excess cellular damage retains cells repair capacity and also results on diverse harmful effects on skin, such as, changes in the dermal matrix, inflammatory response and dehydration of the stratum corneum. The use of phenolic compounds with antioxidant activity may help preventing pathological conditions caused by UV radiation. This work aimed to study the photoprotective activity of three phenolic compounds, caffeic (CA), chlorogenic (CGA) and rosmarinic acid (RA) in human skin cells (HaCaT - immortalized human keratinocytes and HDSF - human dermal skin fibroblast) exposed to UVA and UVB radiation. Initially, HDSF and HaCaT cells were exposed to increasing doses of UVA and UVB radiation. After 24 hours of exposure, we evaluated cell viability, cell death, inflammatory mediators, aquaporin and DNA damage. Exposure to UVA and UVB radiation in HaCaT cells results on apoptotic cell death, with an increase of caspases 3 and 9, p53 and reduction of PARP. HaCaT cells when exposed to UVA radiation resulted on increased levels of IL-6, TNF-α and COX-2, internalization of the membrane AQP3, reduction of MMP-2 and MMP-9 release, increase of MMP-1 and ROS production. After UVB radiation, HaCaT cells resulted on an increase of IL-6 and COX-2 production, it also promoted internalization of membrane AQP3 and reduced release of MMP-2 and 9. HDSF were less sensitive to both radiations. Moreover, HDSF resulted in cell viability decrease and cell cycle arrest only after UVA radiation. Furthermore, HDSF when exposed to UVA radiation resulted on an increase of IL-6 production and in DNA damage (8-oxo-dG). Among the studied compounds, CGA presented better photochemiprotective activity towards UVA and UVB radiation. Also, this compound was able to reverse cell death in HaCaT after exposure to both radiations and inhibited cell cycle arrest in HDSF after UVA radiation exposure. HaCaT cells treated with CGA and exposed to UVA radiation resulted on an increase in AQP3 and PARP expression, increased in AQP3 gene expression, reduction in CDKN1A gene expression and reduction in MMP-1, 2 and 9 release. After UVB radiation, GCA treatment increases AQP3 gene expression, reduces CDKN1A gene expression, reduces COX-2 production and increase MMP-2 and 9 releases. The AR treatment showed photochemiprotective activity towards the effects of UVA radiation, with HaCaT responding with an increase on cells viability, increased in PARP and AQP3 expression and in AQP3 gene expression, decreased MMP-1 and 9 releases and reduced COX-2c production. HDSF when treated with AR showed an increase in G1 phase population, in p21 expression and reduced DNA damage-type 8-oxo-dG. HaCaT cells treated with AC reversed cell death, increased p53 expression and increased MMP-2 and 9 releases after UVB radiation and reduced ROS production, p21 expression and MMP -1, 2, 9 release after UVA radiation. HDSF treated with AC was only able to reduce the formation of 8-oxodG DNA damage. These results indicated that the proposed model was able to discriminate the photochemiprotective activity of the studied compounds against the UVA and UVB radiation. In addition, it was demonstrated that the each studied antioxidant have different photoprotective mode of action.

A exposição excessiva à radiação Ultravioleta (UV) resulta em manifestações clínicas à pele humana como queimaduras, fotoenvelhecimento e câncer. A radiação UVA, preferencialmente, induz à formação de espécies reativas de oxigênio, enquanto que a radiação UVB é absorvida diretamente pelo DNA. Apesar de mecanismos endógenos auxiliarem na prevenção/reparação dos danos causados pela radiação UV, quando o dano excede a capacidade de reparação celular, diversos efeitos lesivos ocorrem na pele como alterações da matriz dérmica, resposta inflamatória e desidratação do estrato córneo. O uso de compostos fenólicos com atividade antioxidante pode auxiliar na prevenção das consequências patológicas da exposição à radiação UV. O presente trabalho teve como objetivo estudar em cultura de células da pele (HaCaT -queratinócito humano imortalizado e FHPD - fibroblasto humano primário dermal) exposta às radiações UVA e UVB a atividade fotoprotetora de 3 compostos fenólicos, ácido cafeico (AC), clorogênico (ACG) e rosmarínico (AR). Inicialmente, células HaCaT e FHPD cultivadas em monocamada foram expostas às doses crescentes de radiação UVA ou UVB e, após 24 horas, foram analisadas quanto a viabilidade, marcadores de morte celular, mediadores inflamatórios, presença de aquaporina e lesões de DNA. HaCaT quando exposta às radiações UVA e UVB são conduzidas à morte por apoptose, com aumento de Caspases 3 e 9, p53 e redução de PARP. Após a exposição à radiação UVA, HaCaT responde com aumento na liberação de IL-6, TNF-α e COX-2, internalização/redução de AQP3 da membrana, redução na liberação de MMP-2 e 9, aumento na liberação de MMP-1 e na produção de ERO. Quando expostos à radiação UVB, HaCaT aumenta a liberação de IL-6 e COX-2, promove internalização/redução de AQP3 na membrana e redução na liberação de MMP-2 e 9. FHPD são menos sensíveis à exposição a ambas as radiações, mostrando redução de viabilidade com parada de ciclo apenas frente à radiação UVA. Além disto, FHPD exposto a radiação UVA responde com aumento na liberação de IL-6 e danos no DNA do tipo 8-oxo-dG. Dentre os compostos, o ACG apresentou melhor atividade fotoquimioprotetora perante ambas as radiações UVA e UVB, pois foi capaz de reverter em HaCaT a morte celular induzida por ambas as radiações e de reverter a parada de ciclo em FHPD expostos à radiação UVA. HaCaT tratado com ACG e exposto à radiação UVA responde com aumento na expressão de AQP3 e PARP, aumento na expressão gênica de AQP3, redução na expressão gênica de CDKN1A e na liberação de MMP-1, 2 e 9. Após a radiação UVB, o tratamento com ACG aumenta a expressão gênica de AQP3, reduz a expressão gênica de CDKN1A, reduz a produção de COX-2 e aumenta a liberação de MMP-2 e 9. O tratamento com o AR apresentou atividade fotoquimioprotetora frente à radiação UVA, com HaCaT respondendo a radiação com aumento na população de células viáveis, aumento na expressão de AQP3 e PARP e na expressão gênica de AQP3, redução na liberação de MMP-1 e 9 e redução na produção de COX-2. FHPD tratados com AR apresentaram aumento na população em fase G1, na expressão de p21, e redução de danos de DNA tipo 8-oxo-dG. O tratamento de HaCaT com AC foi capaz de reverter a morte celular, aumentar a expressão de p53 e aumentar a liberação de MMP-2 e 9 frente à radiação UVB e de reduzir a produção de ERO, a expressão de p21 e a liberação de MMP-1, 2 e 9 frente à radiação UVA. Para FHPD, o tratamento com AC foi capaz apenas de reduzir a formação de danos de DNA tipo 8-oxo-dG. Os resultados indicam que o modelo proposto foi capaz de discriminar a atividade fotoprotetora dos compostos frente à radiação UVA e UVB. Além disto, foi possível demonstrar que os compostos antioxidantes se comportam de maneira distinta enquanto fotoprotetores no modelo empregado. / Excessive exposure to Ultraviolet radiation (UV) results in clinical manifestations in human skin such as burns, photo-aging and cancer. UVA radiation preferentially induces formation of reactive oxygen species, while UVB radiation is absorbed directly by the DNA. Although endogenous mechanisms are able to prevent/repair cellular damages caused by UV radiation, excess cellular damage retains cells repair capacity and also results on diverse harmful effects on skin, such as, changes in the dermal matrix, inflammatory response and dehydration of the stratum corneum. The use of phenolic compounds with antioxidant activity may help preventing pathological conditions caused by UV radiation. This work aimed to study the photoprotective activity of three phenolic compounds, caffeic (CA), chlorogenic (CGA) and rosmarinic acid (RA) in human skin cells (HaCaT - immortalized human keratinocytes and HDSF - human dermal skin fibroblast) exposed to UVA and UVB radiation. Initially, HDSF and HaCaT cells were exposed to increasing doses of UVA and UVB radiation. After 24 hours of exposure, we evaluated cell viability, cell death, inflammatory mediators, aquaporin and DNA damage. Exposure to UVA and UVB radiation in HaCaT cells results on apoptotic cell death, with an increase of caspases 3 and 9, p53 and reduction of PARP. HaCaT cells when exposed to UVA radiation resulted on increased levels of IL-6, TNF-α and COX-2, internalization of the membrane AQP3, reduction of MMP-2 and MMP-9 release, increase of MMP-1 and ROS production. After UVB radiation, HaCaT cells resulted on an increase of IL-6 and COX-2 production, it also promoted internalization of membrane AQP3 and reduced release of MMP-2 and 9. HDSF were less sensitive to both radiations. Moreover, HDSF resulted in cell viability decrease and cell cycle arrest only after UVA radiation. Furthermore, HDSF when exposed to UVA radiation resulted on an increase of IL-6 production and in DNA damage (8-oxo-dG). Among the studied compounds, CGA presented better photochemiprotective activity towards UVA and UVB radiation. Also, this compound was able to reverse cell death in HaCaT after exposure to both radiations and inhibited cell cycle arrest in HDSF after UVA radiation exposure. HaCaT cells treated with CGA and exposed to UVA radiation resulted on an increase in AQP3 and PARP expression, increased in AQP3 gene expression, reduction in CDKN1A gene expression and reduction in MMP-1, 2 and 9 release. After UVB radiation, GCA treatment increases AQP3 gene expression, reduces CDKN1A gene expression, reduces COX-2 production and increase MMP-2 and 9 releases. The AR treatment showed photochemiprotective activity towards the effects of UVA radiation, with HaCaT responding with an increase on cells viability, increased in PARP and AQP3 expression and in AQP3 gene expression, decreased MMP-1 and 9 releases and reduced COX-2c production. HDSF when treated with AR showed an increase in G1 phase population, in p21 expression and reduced DNA damage-type 8-oxo-dG. HaCaT cells treated with AC reversed cell death, increased p53 expression and increased MMP-2 and 9 releases after UVB radiation and reduced ROS production, p21 expression and MMP -1, 2, 9 release after UVA radiation. HDSF treated with AC was only able to reduce the formation of 8-oxodG DNA damage. These results indicated that the proposed model was able to discriminate the photochemiprotective activity of the studied compounds against the UVA and UVB radiation. In addition, it was demonstrated that the each studied antioxidant have different photoprotective mode of action.

New technologies to probe the global output of the normal and cancer genomes have recently reached widespread use. The resulting genomewide gene expression profiles, e.g, a gene expression measurement per gene and per tissue sample, remain challenging to analyze and interpret, but have already provided new insights into the pathophysiology of cancer and towards personalized care. In vitro cell culture-based experimental models are used to elucidate cancer onset and progression because experimentation in humans is difficult practically and ethically unacceptable, and because they provide simplified, reproducible and controlled systems to test hypotheses. The thyroid tumors and their in vitro experimental models are particularly suited to compare the molecular phenotypes of experimental models and tumors. From one type of cell, the thyrocyte, at least five distinct benign and malignant tumors can arise. In addition, many immortalized tumor-derived cell lines and primary cultures models of these cells exist. This thesis has focused on the bioinformatic comparison of these in vitro models to the in vivo tumors, from the point of view of their gene expression profiles, to gain insight into the pathogenesis of thyroid tumors, and of tumors in general. In a first study, we showed that primary cultures of freshly isolated normal thyroid cells where proliferation and differentiation through the TSHR/cAMP pathway was chronically activated experimentally resemble specifically the autonomous thyroid adenomas, a type of benign thyroid tumor, and provide insight into a general mechanism of tumor progression: the suppression of negative feedbacks that normally restrain excessive cell division. Subsequently, we found that immortalized thyroid tumor-derived cell lines have converged to a common phenotype regardless of their tumor subtype of origin. A TSHR/cAMP thyroid cell differentiation signature, derived from data obtained for the first study, was used to show that the cell lines were dedifferentiated. Accordingly, we showed that the cell lines resemble most the phenotype of the more dedifferentiated, clinically aggressive anaplastic thyroid cancers. Finally, using large databases of gene expression profiles publicly available, we extended the comparison of cell lines and tumors to cancers of five other organs: breast, colon, kidney, ovary and lung. We discuss the correct use of these models and advance an hypothesis regarding the nature of the state to which these cells have converged: they could represent a surviving subpopulation of tumors cells, cancer stem cells, capable of initiating and maintaining tumor growth. As other technologies designed to perturb the genome in experimental models are emerging, careful characterization and validation of the experimental models are needed to extrapolate the results in vivo. Although many differences exist between the experimental models and their in vivo disease counterparts, focusing on the similarities could provide a path to design successful therapeutic interventions more systematically.

New technologies to probe the global output of the normal and cancer genomes have recently reached widespread use. The resulting genomewide gene expression profiles, e.g, a gene expression measurement per gene and per tissue sample, remain challenging to analyze and interpret, but have already provided new insights into the pathophysiology of cancer and towards personalized care. In vitro cell culture-based experimental models are used to elucidate cancer onset and progression because experimentation in humans is difficult practically and ethically unacceptable, and because they provide simplified, reproducible and controlled systems to test hypotheses. The thyroid tumors and their in vitro experimental models are particularly suited to compare the molecular phenotypes of experimental models and tumors. From one type of cell, the thyrocyte, at least five distinct benign and malignant tumors can arise. In addition, many immortalized tumor-derived cell lines and primary cultures models of these cells exist. This thesis has focused on the bioinformatic comparison of these in vitro models to the in vivo tumors, from the point of view of their gene expression profiles, to gain insight into the pathogenesis of thyroid tumors, and of tumors in general. In a first study, we showed that primary cultures of freshly isolated normal thyroid cells where proliferation and differentiation through the TSHR/cAMP pathway was chronically activated experimentally resemble specifically the autonomous thyroid adenomas, a type of benign thyroid tumor, and provide insight into a general mechanism of tumor progression: the suppression of negative feedbacks that normally restrain excessive cell division. Subsequently, we found that immortalized thyroid tumor-derived cell lines have converged to a common phenotype regardless of their tumor subtype of origin. A TSHR/cAMP thyroid cell differentiation signature, derived from data obtained for the first study, was used to show that the cell lines were dedifferentiated. Accordingly, we showed that the cell lines resemble most the phenotype of the more dedifferentiated, clinically aggressive anaplastic thyroid cancers. Finally, using large databases of gene expression profiles publicly available, we extended the comparison of cell lines and tumors to cancers of five other organs: breast, colon, kidney, ovary and lung. We discuss the correct use of these models and advance an hypothesis regarding the nature of the state to which these cells have converged: they could represent a surviving subpopulation of tumors cells, cancer stem cells, capable of initiating and maintaining tumor growth. As other technologies designed to perturb the genome in experimental models are emerging, careful characterization and validation of the experimental models are needed to extrapolate the results in vivo.

Two-dimensional (2D) in vitro models of tissues and organs have long been used as one of the main tools to understand human physiology and for applications such as drug discovery. But there is a huge disparity between in vivo conditions and these models which has created the need for better models. It has been shown that making three-dimensional models with dynamic environments that provide proper physical and chemical cues for cells, can bridge this gap between 2D models and in vivo conditions but the toolbox for creating such models has been imperfect and rudimentary. Introduction of tissue engineering concept and advent of biofabrication tools to meet its demands has provided new possible avenues for in vitro modeling but many of these tools are specifically designed to create tissue and organ replacements and lack features such as the ability to investigate cellular behavior with ease that are necessary for in vitro modeling purposes. The objective of this doctoral thesis was to introduce a novel toolbox of biofabrication techniques, based on bioprinting and bioassembly, that together are capable of recapitulating anatomical and physiological requirements of different tissue in in vitro setups in a more relevant way while creating the possibility of investigating cellular behavior. A bioprinting technique was developed that allowed formation of large constructs with proper mechanical stability, perfusion, and direct access to cells in different locations. The second technique was based on bioassembly of collagenous grafts in micro-molds and cells from different tissues with the ability to control cell positioning and create tissue-relevant cell densities with higher degree of similarity to human tissues compared to previous techniques. The third technique was based on bioassembled stand alone and dense cell-sheets for cells capable of fusion. These techniques were subsequently used for modeling a few chosen biological phenomenon to showcase the advantages of the techniques over previously developed ones and to further shed light on possible shortcomings of each of the techniques in their application for those specific tissues. In conclusion, our techniques may serve as valuable and easy to use tools for researchers, specifically biologists to investigate different aspects of human biology and disease mechanism in more details. / Thesis / Doctor of Philosophy (PhD) / Experimentation on humans is unethical, therefore in order to understand how human body works and test new therapeutic drugs researchers have used animals and cells isolated from animals or humans. Animals are inherently different from humans and isolated cells are culture in conditions different than human body, therefore a huge gap exists between the knowledge derived from these models and what happens in human body. Since there is no one-size-fits-all technique to model all of the human tissues, the objective of current study was set to build a toolbox of techniques that each could create better environment in the lab for cells isolated from different tissues and organs with more similarity to original tissues, to bridge the gap and eliminate the need to use animal models entirely. During the course of this PhD studies, three different techniques that can be used to make such models for different tissues and organs, as well as different diseases, were developed and characterized. These techniques were also used to shed light on some of the cellular behavior that are already observed in human body but either are not explained or aren’t re-created in the lab for mechanistic studies. Certain questions regarding selected tissues were chosen and the technique most compatible with that tissue was used for the modeling purposes. For example, one investigated niche was the origin of the bone sensory cells which could be important to heal damaged bones or prevent osteoporosis. The first technique was deemed most suitable for this question while for the next question, how the fat and muscle cells are affecting each other that can be useful to better understand conditions such as diabetes and obesity, the second technique was the best option. Overall, a variety of tools were developed that can be used by biologists to create better models of human tissues in the lab as platforms to study human physiology and as media for developing treatments for different diseases.

Le récepteur à l'IGF1 (IGF-1R) ainsi que ses voies de régulation sous-jacentes ont été largement étudié pour leur importance au cours du développement et leur rôle mitotique sur divers types cellulaires. A l'échelle de la peau, l'IGF-1R contribue à l'homéostasie épidermique et est souvent associé au compartiment basal pour son effet pro-prolifératif. Très peu d'études ont montré son implication au niveau de la différenciation épidermique et celles-ci présentent des résultats contradictoires. Au cours du vieillissement, la peau s'amincit et la barrière épidermique présente des défauts de perméabilité. Parallèlement, l'activité de l'IGF- 1R, maximale à l'adolescence, diminue avec l'âge. Cette étude a contribué à éclaircir le rôle de l'IGF-1R sur la différenciation épidermique et à montrer un lien entre vieillissement, perte en qualité de la peau et diminution d'activité de l'IGF-1R. L'élaboration de modèles 2D et 3D mimant le vieillissement par diminution d'activité de l'IGF-1R, nous a permis de confirmer le rôle mitotique de l'IGF-1R sur les kératinocytes et les progéniteurs et de démontrer son effet régulateur sur la différenciation épidermique par augmentation ou diminution de ces marqueurs. L'IGF-1R renforce l'adhésion cellulaire sur différentes matrices, impliquant de possibles interactions avec les intégrines α6 et β1. Ces résultats ont été corrélés aux observations de biopsies de peaux jeunes et âgées. Nous avons aussi montré que l'IGF-1R conférait un état sénescent aux cellules soumises à de fortes doses d'H2O2. Ces travaux montrent ainsi que l'IGF-1R est nécessaire pour le processus de différenciation épidermique et pour en assurer sa protection face au stress oxydant / Insulin-like growth factor 1 receptor (IGF-1R) and its signaling pathway have been widely studied for their growth promoting role on many cell types and their implication in development. On skin, the IGF-1R function has been associated to basal proliferation and contributes to epidermal morphogenesis, but very little is known about its involvement on keratinocytes differentiation and the few studies existing depict contradictory results. IGF-1R activity is maximal during teenage and tend to decrease during aging. Aged skin depicts major thinning and defects in permeability of skin barrier. Our work consisted in clarifying IGF-1R role on epidermal differentiation process and emphasized a correlation between aging, loss of skin quality and IGF-1R activity. By building 2D and 3D aging like models with low IGF-1R activity, we confirmed IGF-1R mitogenic role on both basal and progenitor-like keratinocytes. We demonstrated that IGF-1R activity regulated keratinocytes differentiation by either enhancing or slowing down differentiation markers deposition. More importantly, we highlighted the importance of IGF-1R activity for keratinocytes adhesion on both laminin-332 and collagen I/IV coatings, implying possible interactions with α6 and β1 integrins. This relationship was further correlated on skin biopsies of young and aged donors. In a parallel study, we showed that IGF-1R could induce cell senescence under acute H2O2 stress. Taken together, IGF-1R is necessary for the epidermal differentiation process and protects epidermis from acute oxidative stress induced damages

Na etapa inicial do desenvolvimento de novos fármacos, a avaliação do metabolismo e da toxicidade é fundamental para definir seu potencial emprego como candidato a fármaco. Nestes estudos, diversos modelos in vitro são empregados, dentre eles linhagens de hepatoma humano. Entretanto, uma grande limitação ao uso deste modelo in vitro é a baixa expressão das enzimas do sistema citocromo P450. O carotenóide bixina, componente majoritário do anato (urucum), apresentou em estudos in vivo, a capacidade de induzir algumas isoformas do sistema citocromo P450, com a vantagem de apresentar baixa toxicidade. Neste trabalho, a fração lipossolúvel do anato (bixina) e hidrossolúvel (norbixina) foram avaliadas como indutores do sistema citocromo P450 em linhagens de hepatoma humano. Ensaios de MTT, empregando as linhagens HepG2, C3A e SK-HEP-1 indicaram que bixina e norbixina em concentrações abaixo de 0,22 mM são seguras quanto à citotoxicidade. A expressão dos genes CYP 1A1, 1A2, 2C9, 2B6, 2E1 e 3A4 foi avaliada, através de ensaios de RT-PCR em tempo real, em linhagens de hepatoma humano submetidas a tratamento com os compostos bixina e norbixina. Os resultados mostraram que células HepG2 e C3A tratadas com bixina nas concentrações de 0,05 e 0,1 mM, por períodos de 24 e 48 horas, apresentaram aumento de expressão da CYP 1A1 e CYP 1A2. Porém, a exposição de células HepG2 e C3A ao composto norbixina não resultou em aumento de expressão das isoformas avaliadas neste estudo. Os resultados deste trabalho indicaram o potencial emprego de bixina como agente indutor das CYPs 1A1 e 1A2, em linhagens de hepatoma humano utilizadas como modelo in vitro, para estudo de compostos cuja metabolização envolva uma destas vias, entretanto, estudos adicionais são fundamentais, a fim de avaliar a ação deste composto sobre outras isoformas do sistema citocromo P-450, bem como outros sistemas enzimáticos. / In the early development stage of the new drugs, the pharmacological and toxicological properties are critical to define the potential use of the candidate drug. During this stage, several in vitro models systems are employed, including human hepatoma cell lines. However, the main limitation of the use of cell lines as in vitro model is the low expression level of cytochrome P450 enzymes. A carotenoid knowed as bixin, the main pigment in the annatto (urucum), it has been reported to induce some isoforms of cytochrome P450 in rats, with the advantage of its low toxicity. In this work, the oil-soluble (bixin) and aqueous soluble extracts (norbixin) were evaluated as inducers of the cytochrome P450 system in human hepatoma cell lines (HepG2, C3A, SK-HEP-1). The results of MTT assays showed that bixin concentrations below 0.22 mM were not cytotoxic in HepG2, C3A and SK-HEP-1 cell lines. Expression changes in CYP 1A1, 1A2, 2C9, 2B6, 2E1 and 3A4 were evaluated, by real time RT-PCR and the results showed that the exposition to 0,05 mM and 0,1 mM bixin, for 24 and 48 hours of treatment, lead to an increase in CYP 1A1 and CYP 1A2 expression level. By contrast, the cytochrome P450 isoforms were not affected by the exposition to norbixin. In conclusion, this work indicated the potential use of bixin induced hepatoma cell lines as in vitro model for studies of biotransformation and toxicity of drugs involving CYP 1A, however, further studies are necessary to evaluate the effect of bixin on the other cytochrome P450 isoforms as well as other enzymatic systems.