O câncer colorretal é uma das malignidades com maior incidência no Brasil e, na maioria dos casos, tem poucos sintomas visíveis até a doença estar em um estágio avançado. Pensando em simplificar o procedimento do exame e fazer um diagnóstico mais rápido para pacientes com câncer colorretal, este estudo teve como objetivo desenvolver um processo de diagnóstico simplificado baseado na caracterização de um biossensor eletroquímico em que fitas simples de miRNAs de interesse foram imobilizadas na superfície de eletrodos de ouro com objetivo de fazer a detecção de sua fita complementar utilizando-se dos métodos de espectroscopia de impedância eletroquímica e microbalança de cristal de quartzo. A sequência que foi imobilizada foi uma sequência de DNA que corresponde ao miRNA-224, cuja elevada expressão foi recentemente correlacionada com a agressividade e a incidência de metástase em pacientes com câncer colorretal. Os dados obtidos através da técnica de EIS foram comparados a dois modelos físicos de circuito equivalente, o circuito Randles clássico e um circuito Randles modificado, onde o capacitor foi substituído por um elemento de fase constante, tentando modelar de maneira mais eficiente a dupla camada que se forma na região de contado do eletrodo com a solução eletrolítica. O modelo modificado apresentou uma janela de funcionamento de 40,11% enquanto o circuito original apresentou uma janela de funcionamento de 23,98%; o que juntamente com o embasamento teórico do modelo de dupla camada fez com que o circuito modificado tenha sido escolhido para modelar os dados dos experimentos feitos na sequência. Tendo em vista que a imobilização das fitas simples de DNA na superfície do eletrodo de ouro é o passo chave para a obtenção de uma resposta satisfatória no biossensor, foram feitos testes alterando a proporção de DNA e espaçadores na fase de funcionalização a fim de determinar qual a proporção que otimiza a resposta do sensor. Comparando os resultados obtidos para as proporções de ssDNA:tiol total na etapa de funcionalização do eletrodo de 1:3, 1:4 e 1:5, a proporção 1:4 que corresponde a 20% de amostra no buffer de imobilização foi a que levou a uma maior variação percentual dos valores de Rct devido às hibridizações. Considerando esses como sendo os parâmetros otimizados para o sistema, foi construída então uma curva de caracterização do sensor, e o limite de detecção encontrado foi de 10pM; um valor considerado alto comparado com outros experimentos semelhantes, entretanto deve-se lembrar que o sistema aqui estudado não fez o uso de elementos amplificadores, como nanopartículas ou intercaladores de DNA. Para fins de comparação entre técnicas, foi conduzida uma análise semelhante utilizando uma microbalança de cristal de quartzo. Inicialmente foram utilizados os parâmetros encontrados como otimizados para a EIS, e posteriormente foram usados parâmetros mais próximos aos otimizados para essa técnica encontrados na literatura. Em ambos os casos foi possível observar variações referentes à hibridização das fitas complementares, entretanto como esperado, a resposta se mostrou mais expressiva para o segundo caso. Essas diferenças de resposta puderam ser relacionadas aos diferentes princípios de funcionamento dos sensores nas duas técnicas, mostrando que para a QCM o fator que influencia na resposta está relacionado à quantidade total de amostra imobilizada na superfície do eletrodo, enquanto que para a técnica de EIS o mais relevante é o quão compacta a camada se mostra. / Colorectal cancer is one of the most prevalent malignancies in Brazil and, in most cases, has few visible symptoms until the disease is at an advanced stage. In order to simplify the examination procedure and to make a faster diagnosis for patients with colorectal cancer, this study aimed to develop a simplified diagnostic process based on the characterization of an electrochemical biosensor in which single strands of miRNAs of interest were immobilized on the surface of gold electrodes with the objective of detecting their complementary strand using the methods of electrochemical impedance spectroscopy and quartz crystal microbalance. The sequence that was immobilized was a DNA sequence corresponding to miRNA-224, whose high expression was recently correlated with the aggressiveness and incidence of metastasis in patients with colorectal cancer. The data obtained through the EIS technique were compared to two equivalent circuit models, the classic Randles circuit and a modified Randles circuit, where the capacitor was replaced by a constant phase element, trying to more efficiently model the double layer that is formed in the interface between the electrode and the electrolytic solution. The modified model presented an operating range of 40.11% while the original circuit presented an operating range of 23.98%; which along with the theoretical understanding of the double-layer model made the modified circuit to be chosen as the model to fit the data of the experiments realized in the sequence. Considering that the immobilization of the simple DNA strands on the surface of the gold electrode is the key step to obtain a satisfactory response in the biosensor, tests were performed by altering the ratio of DNA and spacers in the functionalization phase in order to determine which the ratio that optimizes the sensor response. Comparing the results obtained for the proportions of ssDNA:total thiol in the functionalization stage of the electrode of 1:3, 1:4 and 1:5, the ratio 1:4 corresponding to 20% of sample in the immobilization buffer was the one that led to a greater percentage variation of Rct values due to hybridizations. Considering these as the optimized parameters for the system, a sensor characterization curve was built, and the limit of detection found was 10pM; a value considered high compared to other similar experiments, however it must be remembered that the system studied here did not make use of amplifying elements, such as nanoparticles or DNA intercalators. For purposes of comparing techniques, a similar analysis was conducted using a quartz crystal microbalance. Initially, the parameters found as optimized for the SIS were used, and later parameters that were closer to those optimized for this technique found in the literature were. In both cases it was possible to observe variations related to the hybridization of the complementary tapes, however, as expected, the response was more expressive for the second case. These differences in optimization parameters for the two techniques could be related to the different principles of sensor operation, showing that for the QCM the factor that influences the response is related to the total amount of sample immobilized on the surface of the electrode, while for the EIS technique the most relevant parameter is how compact the layer is.

Aniridia is a rare genetic disorder that affects the development of the eye and is caused in most cases by mutations in the PAX6 gene. Patients with a heterozygous mutation in their PAX6 gene are born without irises. Aniridia patients are also prone to other eye diseases over their lifetimes such as cataracts and glaucoma. Aniridia’s progressive nature suggests that therapeutic intervention aimed at restoring PAX6 expression may be effective at ameliorating the progression of this disease. PAX6 is necessary for the development and maintenance not only of the eye, but also the pancreas. Patients with aniridia have an increased likelihood of developing glucose intolerance and diabetes. Indeed, genetic studies in rodents have confirmed that haploinsufficient animals for Pax6 develop glucose intolerance due to an ongoing requirement for Pax6 expression in the pancreas and gut. This thesis is a proof-of-concept study designed to determine the effects of repressing miRNA regulation of murine Pax6. Pax6 is regulated by miRNA-7 and miRNA-375. I hypothesized that repression of miRNA-7 and miRNA-375 would restore Pax6 expression and that this strategy might be useful in treating some of the progressive symptoms that emerge in aniridia patients in adulthood. As a first step towards evaluating miRNA inhibition as a therapeutic strategy for the treatment of aniridia, my first objective was to confirm whether miRNA-7 and miRNA-375 regulate Pax6 expression in pancreatic cells and tissue. My second objective was to determine whether these miRNAs could be efficiently inhibited. My third objective was to determine whether repression of miRNA-7 or miRNA-375 alters endogenous PAX6 protein levels in pancreatic cell lines. My final objective was to determine whether target protectors, delivered to explants of pancreatic islets through an adeno-associated virus (AAV) vector, could be used to restore Pax6 expression in murine haploinsufficient islets. From this study, I have confirmed that miRNA-7 and miRNA-375 regulate Pax6 in pancreatic cells that these miRNAs can be specifically inhibited, and that inhibition leads to an increase in Pax6 on both the reporter and protein levels. I have shown that target protectors against the miRNA-7 and miRNA-375 binding sites within the Pax6 3’UTR are effective at increasing the levels of PAX6 protein in pancreatic cell lines. Finally, I have also shown that a target protector against the miRNA-7 binding site can increase PAX6 protein levels in islets from murine haploinsufficient islets to near wild-type levels. My thesis lays the groundwork for the development of anti-miRNA-based therapies aimed at restoring PAX6 expression in the eye and pancreas. / Graduate

Ovine herpesvirus 2 (OvHV-2) is a gammaherpesvirus of domestic sheep and causes the lymphoproliferative disease malignant catarrhal fever (MCF) in susceptible ruminants, including cattle. Sheep are latently infected but do not develop disease. MCF is characterised by proliferation of non-antigen specific cytotoxic large granular lymphocytes which leads to necrosis of infiltrated tissues and death. The molecular basis underlying MCF pathogenesis is poorly understood and it is unknown what controls the differences in the clinical outcome of infection between sheep and cattle, two closely related species. microRNAs (miRNAs) are short noncoding RNAs that post-transcriptionally regulate gene expression through targeting of mRNA. A number of herpesviruses have been shown to encode miRNAs that are capable of regulating of both viral and cellular gene expression which can often have an effect on the pathogenesis of the virus. Following RNA seq analysis of an OvHV-2-infected bovine T-cell line (BJ1035) forty-five miRNAs were predicted to be encoded. Eight miRNAs were previously validated by northern blotting, and a further twenty-seven were confirmed using two PCR methods described in this project. It was hypothesised that these virus-encoded miRNAs may differentially target cellular genes in sheep and MCF-susceptible species. Previous work using the technique CLASH (Crosslinking Ligation and Sequencing of Hybrids) identified Delta-like 1 (DLL1), a ligand for Notch signalling, as a potential target of ovhv2-miR-17-2. Initially, differential targeting of DLL1 between sheep and cattle was hypothesised due to differences in the sequence and number of binding sites for ovhv2-miR-17-2. The sheep DLL1 mRNA was shown to be targeted however, due to incorrect annotation of the sheep genome, targeting of DLL1 is likely in both sheep and cattle. One OvHV-2-encoded miRNA, ovhv2-miR-73-1, has partial homology to a mammalian miRNA, miR-216a. Based on this homology it was predicted that ovhv2-miR-73-1 may target Phosphatase and Tensin Homolog (PTEN) and Y Box Binding Protein 1 (YB-1), as they are known targets of miR-216a. A GFP-reporter system was used to demonstrate that despite having similar seed sequences, ovhv2-miR-73-1 does not target PTEN or YB-1. Bioinformatic prediction was used to identify MHC class II genes as potential targets of OvHV-2-encoded miRNAs. Two miRNAs, ovhv2-miR-17-25 and ovhv2-miR-17-9 were shown to target sheep MHC class II genes (DRA and DQB respectively) using a luciferase reporter system. These miRNAs were not predicted to target the equivalent genes in cattle indicating that these genes may be differentially regulated between sheep and cattle. It was also shown that two OvHV-2-encoded miRNAs, ovhv2-miR-17-10 and ovhv2-miR-61-1, target the viral protein Ov2. Ov2 is predicted to contain a basic leucine zipper (bZIP) domain and is therefore likely to be a transcription factor. Other closely related gammaherpesviruses encode proteins that contain bZIP domains and these play major roles in the reactivation of the virus from latency. Immunofluorescence and confocal microscopy was performed to confirm the nuclear localisation of Ov2. RT-qPCRs were performed to investigate whether Ov2 could regulate the expression of any cellular genes. Of the two genes investigated, one of these, Jagged (JAG1), was downregulated in the presence of an Ov2-EGFPN1 construct compared to a control plasmid. JAG1 is another ligand for Notch signalling indicating that the virus may manipulate Notch signalling using multiple methods. Immunoprecipitation and mass spectrometry analysis of an Ov2HA-pcDNA3.1+ construct was performed and a number of potential interacting partners of Ov2 were identified.

Low fertility is a major cause of lost productivity in the cattle industry. In addition, cattle provide a convenient model to study ovarian physiology in monovular species including humans. Our previous microarray studies in the bovine ovary showed the upregulation of two clusters, miR-212-132 and miR-183-96-182, in luteal relative to follicular tissues. The studies in this thesis were aimed at establishing the functional involvement of these miRNAs during the follicle-luteal transition using a bovine model as well as human tissues. The aim of the first study was to characterise the expression of miR-132 and miR-96 within luteal tissue using ISH and FACS. The expression of miR-132 was detected in most luteal compartments while miR-96 was not detectable using ISH. Further examination using FACS showed that miR-212-132 expression remained unchanged in sorted endothelia (CD144+) and steroidogenic (CD144-Nile Red (NR) +) cell fractions. In contrast, expression of miR-183 and miR-96 was significantly increased in CD144+ compared to CD144-NR+ fractions. To elucidate potential roles of these miRNAs in the CL, I used existing online databases to identify putative miRNA targets. I identified 3042 predicted bovine gene targets of these miRNAs as well as 174 miRNA targets that had been experimentally validated in human, mouse and/or rat. I also identified putatively targeted signalling pathways primarily involved in cell survival, proliferation and differentiation. For further investigation, I narrowed my list of targets to FOXO1 and ADCY6, the expression of which was naturally down- regulated during luteinisation. The second study used an in vitro model of bovine granulosa cell luteinisation. Levels of miR-183-96-182 and miR-212-132 increased significantly (P < 0.05) during the first 4 days of luteinisation in vitro. The function of miR-132 and miR-96 during luteinisation in vitro was studied. Transfection of bovine granulosa cells with specific miRNA inhibitors or mimics of miR-132 and miR-96 led, respectively, to abolished expression and a significant increase in the levels of these miRNAs (P < 0.01) within 4 days. These changes in miRNA levels did not have any effect on transcript levels of the predicted mRNA targets, FOXO1 and ADCY6, during luteinisation. However, progesterone production by luteinising granulosa cells decreased (P < 0.05) on day 2 after transfection with miR-132 inhibitor. The results demonstrated that putative miRNA target genes remained unchanged during in vitro luteinisation which was not consistent with in vivo results. The third study aimed to elucidate the effect of miRNA inhibition in bovine luteal cells in culture. The loss of miR-132 led to an increase (P < 0.05) in FOXO1 transcript but not protein levels. In contrast, inhibition of miR-96 increased protein but not transcript levels of FOXO1. Moreover, miR-96 inhibition induced an increase in the caspase 3/7 response of luteal cells to serum deprivation indicating an anti-apoptotic effect of this miRNA on these cells. In the fourth study, I investigated the role of miR-132 and miR-96 in human luteinised granulosa cells obtained from IVF patients. The levels of FOXO1 protein were significantly increased following depletion of miR-132 and miR-96, whereas caspase3/7 increased in response to miR-96 inhibition, regardless of whether cells had been serum deprived or not. Similarly, using Annexin V and Trypan blue staining an increase in numbers of apoptotic cells was observed in response to miR- 96 inhibition. In addition, reduction of FOXO1 with the siRNA inhibited the apoptotic effect of miR-96 inhibition. Interestingly, inhibition of pooled miR-132 and miR-96 reduced progesterone secretion. However, this effect was prevented by transfecting cells with FOXO1 siRNA. These results suggest that the effects of these miRNAs on cell survival and progesterone production are mediated through targeting FOXO1. In summary, my results identify miR-96 and miR-132 as potentially critical factors in ensuring luteal cell survival and steroidogenesis in both cattle and human.

Regulation of gene expression is a complex process in mammalian cells with many levels of control. In recent years non-coding RNAs in the form of microRNAs (miRNA) have surfaced as important regulators of protein coding genes, with biologically important roles in development, differentiation and cell growth. In this dissertation the complex interactions between miRNAs and mRNAs in ovarian cancer are investigated using a combination of computational and experimental techniques. In vitro studies and current models predict that increases in levels of miRNA should result in corresponding decreases in the levels of targeted mRNAs due to miRNA induced degradation. Profiling the global miRNA and mRNA expression patterns in epithelial ovarian cancer cells from patients and surface epithelial cells from normal ovaries reveal only ~11% of predicted targets of miRNAs are inversely correlated in vivo. In an effort to dissect the mechanisms behind these unexpected observations single miRNA transfection experiments are carried out followed by gene expression profiling. Analysis of genes altered following these transfections reveal majority of the altered genes are not direct targets of the miRNAs. Network analysis however suggests that miRNAs may target "hub genes" to cause altered expression in downstream transcripts. Pathway enrichment analysis of altered genes demonstrates miRNAs may regulate specific pathways rather than causing random off-target effects. Finally investigation of miRNA regulation reveals miRNAs may also affect the levels of other miRNAs, which may indirectly affect more genes downstream. Together these results provide a detailed view of the mechanisms employed by miRNAs to regulate the expression of hundreds of genes in ovarian cancer cells.

miRNAs are important regulators of gene expression. These small RNAs function throughout development and regulate translation of a number mRNAs. miRNAs exert their affect on translation as part of the RNP complex RISC. RISC can affect translation of transcripts at both the level of translation initiation, and post-initiation. Although mechanisms of repression mediated by miRNAs have been intensively studied, repression is not well characterized. In order to understand how miRNAs regulate translation in Drosophila, we first characterized miRNA-mediated repression in the ovary. We developed an ovarian assay sensitive to regulation by miRNAs and found that regulated transcripts localize to cytoplasmic puncta distinct from sponge bodies, cytoplasmic RNP structures consisting of proteins implicated in miRNA-mediated regulation. In addition, we devised a genetic screen to identify genes involved in miRNA-mediated regulation. Seven mutants were isolated from the screen, and two mutants were subsequently mapped to separate 1Mb genomic regions. Both these regions are devoid of genes implicated in miRNA-mediated regulation, suggesting our mutants identify novel components involved in repression. The oskar mRNA encodes for the Oskar protein, which is vital in establishing the posterior axis of the Drosophila embryo. In addition to its protein coding function, the osk mRNA has another essential role: it is required for egg chamber progression through oogenesis. This role of oskar is mediated by its 3ʼ UTR, but how it functions in this role is unknown. Here, we investigate the function of the 3ʼ UTR and discover that the well-defined BRE sequences are required for egg chamber progression through oogenesis. The BREs mediate translational repression of the highly regulated oskar mRNA and were previously defined by their ability to bind Bruno, which represses translation of the oskar mRNA. We also provide evidence that the osk BREs sequester Bruno, potentially inhibiting Bruno from binding and misregulating other mRNAs. Our results suggest a novel regulatory loop, where oskar sequesters and inhibits Bruno from misregulating mRNAs, and Bruno, in turn, regulates translation of the oskar mRNA. / text

Cell proliferation is a fundamental biological process, and the ability of human cells to transition from a quiescent to proliferative state is essential for tissue homeostasis. Most cells in eukaryotic organisms are in a quiescent state, but on appropriate physiological or pathological stimuli, many types of somatic cells may exit quiescence, re-enter the cell cycle and begin to proliferate. The ability of cells to remain viable while quiescent, exit quiescence and re-enter into the cell cycle is the basis for varied physiological processes such as wound healing, lymphocyte activation and hepatocyte regeneration, but is also a hallmark of cancer. The transition of mammalian cells from quiescence to proliferation is accompanied by the differential expression of several microRNAs (miRNAs) and transcription factors. Our understanding of miRNA biology has significantly improved, but the miRNA regulatory networks that govern cell proliferation are still largely unknown. We characterized a miR-22 Myc network that mediates proliferation through regulation of the interferon response and multiple cell cycle arrest genes. We identified several cell cycle arrest genes that regulate the effects of the tumor suppressor p53 as direct targets of miR-22, and discovered that miR-22 suppresses interferon gene expression. We go on to show that miR-22 is activated by the transcription factor Myc as quiescent cells enter proliferation, and that miR-22 represses the Myc transcriptional repressor MXD4, mediating a feed forward loop to elevate Myc expression levels. To more effectively determine miRNA targets, we utilized a combination of RNA-induced silencing complex immunoprecipitations and gene expression profiling. Using this approach for miR-191, we constructed an extensive transcriptome wide miR-191 target set. We show that miR-191 regulates proliferation, and targets multiple proto-oncogenes, including CDK9, NOTCH2, and RPS6KA3. Recent advances in determining miRNA targetomes have revealed widespread non-canonical miRNA-target pairing. We experimentally identified the transcriptome wide targets of miR-503, miR-103, and miR-494, and observed evidence of non-canonical target pairing for these miRNAs. We went on to confirm that miR-503 requires pairing outside of the canonical 5' seed region to directly target the oncogene DDHD2. Further bioinformatics analysis implicated miR-503 and DDHD2 in breast cancer tumorigenesis. / text

Drosophila lethal giant larvae (lgl) encodes a conserved tumor suppressor with established roles in cell polarity, asymmetric division, and proliferation control. Lgl's human orthologs, HUGL1 and HUGL2, are altered in human cancers, however, its mechanistic role as a tumor suppressor remains poorly understood. Based on a previously established connection between Lgl and Fragile X protein (FMRP), a miRNA-associated translational regulator, we hypothesized that Lgl may exert its role as a tumor suppressor by interacting with the miRNA pathway. Consistent with this model, we found that lgl is a dominant modifier of Argonaute1 overexpression in the eye neuroepithelium. Using microarray profiling we identified a core set of ten miRNAs that are altered throughout tumorigenesis in Drosophila lgl mutants. Among these are several miRNAs previously linked to human cancers including miR-9a, which we found to be downregulated in lgl neuroepithelial tissues. To determine whether miR-9a can act as an effector of Lgl in vivo, we overexpressed it in the context of lgl knock-down by RNAi and found it able to reduce the overgrowth phenotype caused by Lgl loss in epithelia. Furthermore, cross-comparisons between miRNA and mRNA profiling in lgl mutant tissues and human breast cancer cells identified thrombospondin (tsp) as a common factor altered in both fly and human breast cancer tumorigenesis models. Our work provides the first evidence of a functional connection between Lgl and the miRNA pathway, demonstrates that miR-9a mediates Lgl's role in restricting epithelial proliferation, and provides novel insights into pathways controlled by Lgl during tumor progression.

(English) Oocyte-to-embryo transition (OET) is one of the most complex developmental events where a differentiated oocyte gives rise to a totipotent zygote. During the growth phase an oocyte prepares for fertilization and progression to zygotic genome activation. It does so by transcribing and storing the necessary mRNAs till a fully-grown oocyte attains transcriptional quiescence. Therefore, transcriptome regulation in a fully-grown oocyte is of utmost importance. Study of post-transcriptional regulatory pathways revealed that the small-RNA mediated regulatory pathways exist in a unique conformation in mouse oocytes. Endogenous RNAi pathway is essential for mouse female germline while miRNA pathway which is ubiquitously present in most cell types is dispensable for oocyte maturation and fertilization. My PhD project was aimed at understanding the constraints of the miRNA pathway in the oocyte which makes it non-functional. As a fully-grown oocyte is a huge cell with a proportionally large maternal transcriptome we analysed the miRNA: mRNA stoichiometry changes that occur from growing to the fully-grown mouse oocyte. Inability of miRNAs to accumulate during oocyte growth phase leads to their dilution in fully-grown oocyte rendering them inactive. Low miRNA concentrations were also observed in rat,...

Head and neck cancers represent a group of tumors with two different etiologies. The first type is associated with the viral HPV infection, the second one is virus-independent and it is associated with smoking and alcohol consumption as two main risk factors. Numerous studies show that HPV-positive tumors are more frequent in younger patients, as well as that the prognosis and overall survival of these patients is remarkably better. Therefore, the modification of the treatment is considered. For this, however, specific, sensitive and clinically relevant biomarkers for accurate identification of tumor etiology is needed. Suitable candidates for such biomarkers are miRNAs, small non-coding regulatory molecules stable in archived samples, that have been shown as differentially expressed in human cancers and the expression pattern seems specific for tumors of different origin. The submitted thesis focuses on miRNA profiling in HPV-positive and HPV-negative tonsillar tumors and cervical carcinomas with the aim to find out the differences between regulation of important carcinogenetic pathways of tumors of viral and non-viral etiology. Our data have shown very large heterogeneity of the miRNA expression profiles of these tumors. Despite the well characterized and uniform samples collection, we have found...