Aortic valve (AV) disease is a major cause of cardiovascular-linked deaths globally. In addition, AV disease is a strong risk factor for additional cardiovascular events; however, the mechanism by which it initiates and progresses is not well-understood. We hypothesize that low and oscillatory flow is present on the fibrosa side of the AV and stimulates ECs to differentially regulate microRNA (miRNA) and mRNAs and influence AV disease progression. This hypothesis was tested employing both in vitro and in vivo approaches, high throughput microarray and pathway analyses, as well as a variety of functional assays. First, we isolated and characterized side-dependent, human aortic valvular endothelial cells (HAVECs). We found that HAVECs express both endothelial cell markers (VE-Cadherin, vWF, and PECAM) as well as smooth muscle cell markers (SMA and basic calponin). Using microarray analysis on sheared, side-specific HAVECs, we identified side- and shear-induced changes in miRNA and mRNA expression profiles. More specifically, we identified over 1000 shear-responsive mRNAs which showed robust validation (93% of those tested). We then used Ingenuity Pathway Analysis to identify key miRNAs, including those with many relationships to other genes (for example, thrombospondin and I&B) and those that are members of over-represented pathways and processes (for example, sulfur metabolism). Furthermore, we validated five shear-sensitive miRNAs: miR-139-3p, miR-148a, miR-187, miR-192, and miR-486-5p and one side-dependent miRNA, miR-370. To prioritize these miRNAs, we performed in silico analysis to group these key miRNAs by cellular functions related to AV disease (including tissue remodeling, inflammation, and calcification). Next, to compare our in vitro HAVEC results in vivo, we developed a method to isolate endothelial-enriched, side-dependent total RNA and identify and validate side-dependent (fibrosa vs. ventricularis) miRNAs in porcine aortic valvular endothelium. From this analysis, we discovered and validated eight side-dependent miRNAs in porcine endothelial-enriched AV RNA, including one miRNA previously identified in vitro, miR-486-5p. Lastly, we determined the relationship between important miRNAs (specifically miR-187 and miR-486-5p) and AV disease by modulating levels of miRNAs and performing functional assays. Preliminary studies overexpressing miR-187 in HAVECs have shown a reduction in inflammatory state through monocyte adhesion (p<0.05). Further, miR-486-5p overexpression reveals an increase in migration (p<0.05) and a trend for a decrease in early apoptosis, linking miR-486-5p to tissue remodeling in the AV. Better understanding of AV biology and disease in terms of gene-regulation under different hemodynamic conditions will facilitate the design of a tissue-engineered valve and provide alternative treatment options.

microRNAs (miRNAs) are small (20-23 nt), non-coding single stranded RNA molecules that play an important role in post-transcriptional regulation of protein-coding genes. miRNAs have been found in all animal lineages, and have been implicated as critical regulators during development in multiple species. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development due to their well-characterized transcriptional gene networks, ease of working with their embryos in the laboratory and phylogenetic position as invertebrate deuterostomes. Literature on miRNAs in echinoderm embryogenesis is limited. It has been shown that RNAi genes are developmentally expressed and regulated in sea urchin embryos, but no study in the sea urchin has examined the expression of miRNAs. The goal of my work has been to study miRNA regulation in echinoderm developmental gene networks. I have identified developmentally regulated miRNAs in sea urchin and sea star embryos, using a combination of computational and wet lab experimental techniques. I developed a probabilistic model (named HHMMiR) based on hierarchical hidden Markov models (HHMMs) to classify genomic hairpins into miRNA precursors and random stem-loop structures. I then extended this model to make an efficient decoder by introduction of explicit state duration densities. We used the Illumina Genome Analyzer to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of S. purpuratus and P. miniata. We developed a computational pipeline for analysis of these miRNAseq data to reveal the miRNA populations in both species, and study their differential expression. We also used northern blots and whole mount in situ hybridization experimental techniques to study the temporal and spatial expression patterns of some of these miRNAs in sea urchin embryos. By knocking down the major components of the miRNA biogenesis pathway, we studied the global effects of miRNAs on embryo morphology and differentiation genes. The biogenesis genes selected for this purpose are the RNAse III enzyme, Dicer and Argonaute. Dicer is necessary for the processing of mature miRNAs from hairpin structures while Ago is a necessary part of the RISC (RNA interference silencing complex) assembly, which is required for the miRNA to hybridize to its target mRNA site. Knocking down these genes hinders normal development of the sea urchin embryo and leads to loss of the larval skeleton, a novel phenotype not seen in sea stars, as well as abnormal gastrulation. Comparison of differentiation gene marker expression between control and Ago knocked down sea urchin embryos shows interesting patterns of expansion and suppression of adjoining some embryonic territories, while ingression of larval skeletogenesis progenitors does not occur.

La Fibrose Pulmonaire idiopathique (FPI) est une maladie fibroproliférative pour laquelle il n’existe aucun traitement efficace. Les mécanismes à l’origine de cette pathologie sont méconnus et impliquent plusieurs types cellulaires et facteurs de croissance, comme le TGF-β responsable de la différenciation de fibroblastes en myofibroblastes. Pour mieux comprendre ces mécanismes physiopathologiques, nous nous sommes intéressés à l’implication des miARN dans ce processus. Une analyse par puces à ADN de l’ensemble des miARN modulés dans des échantillons pulmonaires de souris, résistantes ou sensibles à la fibrose pulmonaire induite par la bléomycine, nous a permis d’identifier miR-199a-5p comme le meilleur candidat associé à la fibrose pulmonaire mais aussi fibrose rénale et hépatique. J’ai ensuite démontré que l’expression de miR-199a-5p était induite par le TGF-β in vitro, et que sa surexpression ectopique induisait la différenciation des fibroblastes. Une combinaison d’approche in silico et expérimentale, m’a permis d’identifier la Cavéoline-1 (CAV-1) comme cible de ce miARN. La CAV-1 est impliquée dans la dégradation du récepteur TGF-β. Ainsi, l’inhibition de CAV-1 par miR-199a-5p constitue une boucle de rétrocontrôle positif exacerbant la voie TGF-β. De manière intéressante, l’inhibition de miR-199a-5p in vitro régule la différenciation, la prolifération et la migration des fibroblastes pulmonaires par le TGF-β. Par ailleurs, nos résultats précliniques indiquent que l’inhibition de ce miARN diminue les marqueurs de fibrose, permettant d’envisager le développement de nouvelles approches thérapeutiques dans le traitement de la FPI et d’autres maladies fibroprolifératives. / Idiopathic Pulmonary Fibrosis (IPF) is a fibroproliferative disease with poor prognosis and for which no effective treatment exists. The mechanisms of this disease remain poorly understood and involve numerous cell types and growth factors such as TGF-β, which leads to the activation of lung fibroblasts into myofibroblasts; the key cell type driving the fibrogenic process. In this context, we focused the involvement of miRNAs in fibrosis process. To identify miRNAs with potential roles in lung fibrogenesis, we performed a genome-wide assessment of miRNA expression in lungs from two different mouse strains known for their distinct susceptibility to lung fibrosis after bleomycin exposure. We identified miR- 199a-5p as the best candidate associated with lung fibrosis but also kidney and liver fibrosis. I observed that miR-199a-5p expression was induced upon TGF-β exposure, and that its ectopic expression was sufficient to promote the pathogenic activation of pulmonary fibroblasts. Using combination of targets miRNA prediction tools and a transcriptomic approach we identified the Caveolin-1 (CAV-1), a critical mediator of pulmonary fibrosis, as a specific target of miR-199a-5p. Thus, we shown that miR-199a-5p is a key effector of TGF-β signaling in lung fibroblasts by regulating CAV1. Interestingly, inhibition of miR-199a-5p in vitro prevents the differentiation, proliferation and migration of fibroblasts after TGF-β stimulation. Finally, our preclinical results indicate that inhibition of this miRNA decreases fibrosis markers. Thus, miR-199a-5p behaves as a major regulator of tissue fibrosis with therapeutic potency for the treatment of IPF and fibroproliferative diseases.

Orientador: Winston Bonetti Yoshida / Resumo: Introdução: O Angiossarcoma (AS) é um tumor vascular maligno raro. As vias moleculares associadas ao desenvolvimento e progressão do AS ainda são pouco entendidas. miRNAs são moléculas reguladoras da expressão gênica com papel importante na tumorigênese e constituem biomarcadores em potencial, podendo definir prognóstico e tratamento de pacientes com câncer. A identificação de perfis de expressão de miRNAs e das vias moleculares reguladas por miRNAs pode contribuir para a elucidação dos mecanismos de tumorigênese em AS. Objetivos: Identificação da expressão global de miRNAs e vias moleculares em AS. Identificar miRNAs alterados em AS; identificar genes-alvo regulados pelos miRNAs e mapear miRNAs e genes alvo relacionados ao desenvolvimento vascular. Material e Métodos: Realizamos uma meta-análise segundo a Declaração de Prisma e utilizando as principais bases de dados, PubMed e EMBASE. Após a aplicação de critérios de inclusão e exclusão específicos, um estudo (incluindo 5 amostras de AS) foi considerado elegível e selecionado para extração dos dados. Deste, foram identificados os miRNAs significativamente desregulados (FC>=1,5 e p<0,05). A seguir, os dados de expressão de miRNAs foram analisados utilizando as ferramentas de bioinformática miRWalk v.2.0 para predição de genes-alvo regulados pelos miRNAs e STRING e Cytoscape v.3.1.1/BINGO para identificação de redes de interação (miRNAs-mRNAs-alvo) e funções biológicas, respectivamente. Resultados: 59 miRNAs estavam com expres... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Orientador: Teresa Cristina Cardoso da Silva / Banca: Roberto Gameiro de Carvalho / Banca: Andréa Fontes Garcia / Resumo: As células mesenquimais derivadas da geleia de Wharton isoladas da matriz do cordão umbilical canino tem sido sugeridas como uma fonte promissora de MSCs para serem usadas nas aplicações clínicas em ciência veterinária, como uma ferramenta potencialmente efetiva na regeneração óssea. MicroRNA (miARN) é um regulador pós-transcricional da expressão gênica em várias condições fisiológicas, incluindo a osteogênese. Neste estudo, as MSCs caninos (cMSCs) isoladas da geléia de Wharton foram induzidos a osteogênese e a transcrição de miR-106b foi avaliada em 0, 7, 14 e 21 dias após a indução. Em outro experimento, as cMSC foram transfectadas com um imitador de miR106b e um inibidor e induzidos a osteogênese. Morfologicamente, cMSCs transfectadas com um inibidor de miR-106b produziram células semelhantes a osteócitos quando comparadas às mesmas células transfectadas com o mímico de miR-106b. cMSCs apresentaram transcrição de miR-106b após 7 dias de osteoindução em um nível baixo em comparação com o controle positivo, enquanto as células transfectadas com o mímico de miR-106b mostraram que o miR-106b deveria ser regulado positivamente. Após a inibição da expressão de miR-106b em cMSCs osteoinduzidas, a atividade da fosfatase alcalina (ALP) foi aumentada. A transcrição do mRNA de osteocalcina, osteopontina e RUNX2 foi regulada positivamente aos 21 dias após a osteoindução, após a inibição de miR106b. Esses achados, pela primeira vez, mostraram que a expressão de miR106b regula negativam... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Wharton's jelly derived-MSCs isolated from canine umbilical cord matrix have been suggested as a promising source of MSCs to be used for clinical applications in veterinary science, as a potentially effective tool in bone regeneration. MicroRNA (miRNA) is a post-transcriptional regulator of gene expression in several physiological conditions, including osteogenesis In this study, canine MSCs (cMSCs) isolated from Wharton's jelly were induced to osteogenesis and miR-106b transcription was measured at 0, 7, 14 and 21 days following induction. In another experiment, cMSCs were transfected with a miR106b mimic and an inhibitor and induced to osteogenesis. Morphologically, cMSCs transfected with an inhibitor of miR-106b appeared as osteocyte-like cells when compared to the same cells transfected with the mimic of miR-106b. cMSCs showed miR-106b transcription after 7 days of osteoinduction was at a low level compared to the positive control, whereas transfected cells with the miR-106b mimic showed miR-106b to be upregulated. After inhibition of miR-106b expression in osteoinduced cMSCs, alkaline phosphatase (ALP) activity was increased. Osteocalcin, osteopontin and RUNX2 mRNA transcription were upregulated at 21 days after osteoinduction following miR-106b inhibition. These findings have, for the first time, shown that the expression of miR-106b negatively regulates osteogenesis in canine MSCs derived from Wharton's jelly and seems to interfere with cell differentiation. / Mestre

Orientador: Ney Lemke / Resumo: MicroRNAs (miRNAs) são pequenas moléculas de RNA que regulam pós-transcricionalmente a expressão de genes, modelando o transcriptoma e a produção de proteínas. Em geral, os miRNAs são conservados no genoma de eucariotos, sendo considerados elementos vitais em diversos processos biológicos durante o desenvolvimento, tais como crescimento, diferenciação e morte celular. A grande diversidade de miRNAs identificados está restrita a poucas espécies e apenas uma parte do total de alvos de miRNAs preditos foi caracterizada funcionalmente. Nesse contexto, o uso da tecnologia de sequenciamento de alto rendimento (high throughput sequencing) atrelada à análise de nível transcricional por RT-qPCR possibilitam a identificação do microRNoma. A tilápia do Nilo, Oreochromis niloticus, é considerada um excelente modelo biológico para o estudo de miRNAs em vertebrados devido à sua importância econômica e evolutiva. O presente trabalho teve como objetivos: organizar os dados do sequenciamento dos miRNAs da tilapia do Nilo; disponibilizá-los em forma de uma base de dados para a comunidade científica; integrar as informações dos miRNAs identificados com outros bancos de dados de miRNAs; analisar os dados através de análises de bioinformática para determinação de agrupamentos definidos pelo nível de expressão de cada miRNA em seis tipos de tecido (músculo branco, músculo vermelho, testículo, ovário, fígado, olho, cérebro e coração) com distinção entre os gêneros e nas fases do desenvolvimento (2,... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

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Fundação de Apoio a Pesquisa e à Inovação Tecnológica do Estado de Sergipe - FAPITEC/SE / Diabetes mellitus type 2 (DM2) is characterized by defects in the action and secretion of insulin and in the regulation of hepatic glucose production. The physical exercise appears as one of the main ways of prevention and control of DM2. The literature suggests that circulating microRNAs (126, 146a and 155) have an inversely proportional relationship between glycemic rates and the pro-inflammatory state resulting from DM2. Thus, the aim of this study was to analyze the acute effect of two types of interventions (cardiovascular and neuromuscular) on the total concentrations of circulating of the miRs 126, 146a and 155 in elderly patients with DM2. The study included 23 individuals (68.23±5.31 years), of both genders, 13 patients with DM2 (controlled) and 10 non-diabetics, referred to, Group 1 and 2, respectively. These were subjected to two types of interventions: neuromuscular circuit and walk oriented, carried out with the intensity between 60% to 70% of heart rate reserve. The expression of miRNAs was performed using the method Real Time Quantitative PCR (qPCR) and was adopted the analysis of covariance (ANCOVA) whereas the measurements of baseline as co-variable. In all analyzes was used a significance level of 5%. While main results verify that the baseline (co-variable), is significantly related with the magnitude of the effect of miR-146a forward to intervention neuromuscular F (1, 23) = 166.31; p<0.001. There was also a significant effect on circulating levels of miR-146a in the face of the patient or may not be a diabetic with elevations substantially higher than the elevations shown by the non-diabetics, in front of the intervention 1, F (2, 23) = 54.33, p<0.001. It is concluded that neuromuscular intervention, when performed as a circuit, changes the total circulating levels of miR-146a and may reduce the inflammatory levels resulting from DM2. / O diabetes mellitus do tipo 2 (DM2) caracteriza-se por defeitos na ação e secreção da insulina e na regulação da produção hepática de glicose. O exercício físico aparece como uma das principais formas de prevenção e controle do DM2. A literatura vem sugerindo que os MicroRNAs circulantes (126, 146a e 155), apresentam uma relação inversamente proporcional entre taxas glicêmicas e o estado pró-inflamatório decorrentes do DM2. Assim, o objetivo do presente estudo foi analisar o efeito agudo de dois tipos de intervenções (cardiovascular e neuromuscular) sobre as concentrações circulantes totais dos miRs 126, 146a e 155 em idosos portadores do DM2. Participaram do estudo 23 idosos (68,23±5,31 anos), de ambos os sexos, sendo 13 portadores do DM2 (controlados) e dez não diabéticos denominados, respectivamente, Grupo 1 e 2. Estes foram submetidos a dois tipos de intervenções: circuito neuromuscular e caminhada orientada, realizadas com a intensidade entre 60% a 70% da frequência cardíaca de reserva. A expressão dos miRNAs foi realizada através do método Real Time Quantitative PCR (qPCR) e foi adotado a análise de covariância (ANCOVA) considerando os valores basais como co-variável. Em todas as análises foi utilizado nível de significância de 5%. Enquanto principais resultados verificam-se que os valores basais (co-variável), está significativamente relacionada com a magnitude do efeito do miR-146a frente a intervenção neuromuscular F (1, 23) = 166,31; p<0,001. Também houve um significativo efeito nos níveis circulantes do miR-146a em face de o paciente ser ou não diabético com elevações substancialmente maior que os incrementos exibidos pelo os não diabéticos, frente a intervenção 1, verificando-se F (2, 23) = 54,33; p<0,001. Conclui-se que a intervenção neuromuscular, quando realizada em forma de circuito, altera os níveis circulantes totais do miR-146a, podendo reduzir os níveis inflamatórios decorrentes do DM2.

Orientador: Marcelo Menossi Teixeira, Andréa Akemi Hoshino / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-18T07:51:32Z (GMT). No. of bitstreams: 1 Mattos_RaphaeldeSouza_M.pdf: 5526068 bytes, checksum: 090cb9f141a5a7dd324df049c18bf9c1 (MD5) Previous issue date: 2011 / Resumo: A cana-de-açúcar é uma das mais importantes espécies vegetais cultiváveis do mundo, sendo o Brasil o principal produtor. É uma fonte eficiente e de baixo custo para a obtenção de açúcar e etanol, que é considerado o mais promissor substituto do petróleo como fonte de energia a médio prazo, especialmente nos transportes. A seca é um dos principais estresses que reduzem a produtividade da cana e a produção de variedades tolerantes não só representa ganhos econômicos como contribui para a sustentabilidade dos canaviais. Embora a base genética da tolerância à seca ainda seja pouco conhecida, variedades desenvolvidas em programas de melhoramento tem apresentado progresso, apesar do ritmo ser mais lento que o desejado. Genômica funcional e desenvolvimento de marcadores colaboram aumentando a eficiência do melhoramento tradicional, mas ainda existem elementos do genoma que podem ser aproveitados de novas formas. Foram descobertos recentemente genes de função regulatória chamados microRNAs (miRNA) que também desempenham um papel na adaptação de plantas a diferentes estresses. Utilizando ESTs de cana-de-açúcar, sequenciamento de nova geração e microarranjos para avaliar a expressão de miRNAs sobre estresse hídrico foram descobertos novos miRNAs associados à seca e possíveis genes de miRNAs ligados à tolerância a este tipo de estresse / Abstract: Sugarcane (Saccharum spp.) is amongst the most relevant crops in the world and Brazil is the most prominent producer. It is an inexpensive and efficient source for commodities such as sugar and ethanol, the latter being increasingly considered the most promising immediate energy source substitute for oil, mainly in transportation. Apart from being very productive, it is largely affected by stress-related yield losses, notably from abiotic triggers. Drought stress is determinant for every crop field, and this is true for sugarcane as well. Although the molecular basis drought stress tolerance lacks further elucidation, newly developed cultivars have successfully reduced yield loss due to water shortage, albeit not at the desirable pace. Functional genomics and molecular markers development assist new cultivar selection programs by identifying and locating agronomically relevant alleles and QTL's, but there are other elements in the genome which can provide new ways to approach crop field improvement. The recently discovered microRNAs (miRNA) are regulatory genes found to have an important role in plants adaptation under different kinds of stresses. By using sugarcane ESTs, deep-sequencing and microarray technology to access stress induced miRNA expression, we have found novel sugarcane miRNA participating in the drought stress response and identified possible tolerance related miRNA genes / Mestrado / Genetica Vegetal e Melhoramento / Mestre em Genética e Biologia Molecular

Le virus de l’immunodéficience humaine de type 1 (VIH-1) induit une activation généralisée des réponses de l'hôte impliquant les lymphocytes T mais aussi les cellules du microenvironnement comme les cellules endothéliales. Les microvésicules (MV) sont des vésicules extracellulaires impliquées dans la communication intercellulaire décrites comme des vecteurs de microARNs (miARNs). Dans ce travail, nous avons émis l'hypothèse que l'infection par le VIH-1 induit l'expression de miARNs dans les lymphocytes T CD4 qui peuvent être vectorisés par les MV et transférés de manière paracrine aux CE. Ces MV joueraient un rôle important dans la pathogenèse de l’infection en contrôlant à distance l'homéostasie endothéliale. Nos résultats montrent que le miR-146-5p est uprégulé à la fois dans les lymphocytes T CD4 de patients infectés par le VIH-1, naïfs de traitement et dans les MV issues de ces lymphocytes. En utilisant un modèle de MV d’une lignée lymphocytaire T enrichie en miR-146-5p (miR-146b-MV), nous montrons que ces MV sont capables de : 1) de protéger leur contenu en miARNs de la dégradation par les RNases, 2) de transférer le miR-146b-5p mimic à des HUVEC et 3) réduire la réponse inflammatoire endothéliale in vitro et in vivo, dans les poumons de souris qui ont reçu une injection systémique de miR-146b-MV. Ce transfert est responsable d’une diminution de l’expression d’ICAM-1 et VCAM-1, à travers une down-régulation d’IRAK1 et de TRAF6. L’ensemble de ces résultats montre que le miR-146-5p transféré par des MV peut diminuer les réponses inflammatoires endothéliales et constituer ainsi un mécanisme de défense de l’hôte contre les altérations vasculaires induites par le VIH-1. / Human immunodeficiency virus type 1 (HIV-1) promotes a generalized activation of host responses that involves CD4 T cells, but also cells of the micro-environnement that are not directly infected such as endothelial cells. Microvesicles (MV), implicated in cell-to-cell communication, have been recently described as vectors of microRNAs (miRNAs). We hypothesized that HIV-1 infection induce cellular miRNAs expression in CD4 T cells which may be vectorized by MV and transferred in a paracrine manner to endothelial cells to regulate vascular homeostasis. Using a miRNome quantitative RT-PCR analysis, we showed that HIV-1 infection leads to a dysregulation of several miRNAs and identified miR-146b-5p as upregulated in both CD4 T cells and CD4 T cells derived-MV from antiretroviral therapy (ART)-naive HIV-1 infected patients, compared to age- and sex-matched healthy subjects. Using a CEM T cell line transfected with miR-146b-5p mimic, we demonstrated that MV from CEM overexpressing miR-146b-5p mimic (miR-146b-MV): 1/ protect their miRNA cargo from RNase degradation, 2/ transfer miR-146b-5p mimic into HUVEC, and 3/ reduce endothelial inflammatory response in vitro and in vivo, in lungs from mice injected with miR-146b-MV. This paracrine control of endothelial inflammatory response mediated by MV involved a decreased expression of NF-κB responsive molecules ICAM-1 and VCAM-1, through down-regulation of IRAK1 and TRAF6. Collectively, these findings demonstrate that miR-146b-5p transferred by MV counteract IRAK1- and TRAF6-mediated endothelial inflammatory responses in HIV-1 infection and could be considered as a host defence mechanism against HIV-1-associated vascular alterations.