MicroRNAs (miRNAs) have now been identified in a vast array of organisms and a great deal of research has been carried out to elucidate the role they play. The dysregulation of miRNA expression has been implicated in a number of disease states and their importance has been highlighted by the beginning of their utilisation as therapeutics. The focus of this study was to identify the role played by miRNAs encoded by the Marek’s disease vaccine viruses, Marek’s disease virus serotype 2 (MDV-2) and Herpesvirus of turkeys (HVT). In order to better understand the functions of these miRNAs we wanted to identify their targets within the host cell. Using a combination of bioinformatic and biochemical approaches we were able to build up a library of potential targets. Three viral miRNA targets; AKT3, RAP1A and DEK, were further validated using dual-luciferase assays to highlight the exact site of miRNA targeting, and western blots to demonstrate an effect of miRNA targeting on protein abundance. An attempt at using label-free proteomics to observe the viral miRNA mediated changes in the host proteome is also described, however this proved to be unsuccessful. Additionally the function of one particular MDV-2 miRNA, mdv2-miR-M21, was explored in more detail, describing its role as a potential ortholog of the host miRNA; gga-miR-29b. By using the observation that the viral miRNA contained an identical 'seed' region to the host miRNA, we were able to use the data collected from existing studies on miR-29b to search for targets of mdv2-miR-M21. We demonstrated that mdv2-miR-M21 targeted DNMT3B, crucial for epigenetic modification of the genome. The final part of this study aimed to understand the wider context the viral miRNAs played in the viral biology and protective ability of the vaccine viruses. The miRNAs were deleted from the viruses, and then the miRNA-deletion viruses were used to vaccinate birds before challenge with the oncogenic Marek's disease virus serotype 1 (MDV-1), survival rates to the 'wild-type' MDV-2 and HVT vaccine viruses were then compared.

Acute myeloid leukemia (AML) is a very heterogeneous disease associated with cytogenetic aberrations and genetic mutations. Many of these changes have been revealed and their detection became usual part of the diagnostic process today. However, changes of expression profiles of small, noncoding RNAs, so called microRNAs (miRNAs), are less known and not used for diagnostics yet. These RNAs, 19-24 nucleotides long, take part in the regulation of expression of different genes through complementary base pairing to the 3'non- translated region (3'UTR) of the target messenger RNA (mRNA). They can influence key processes of the cell, like differentiation, proliferation or apoptosis. The changes in expression of different miRNAs are known from different types of cancers. In solid tumors, they are usually detected from bioptic samples; but also plasma samples are now in the center of attention as so called liquid biopsies providing the information about molecular genetic events in the organism. Many studies have revealed deregulated miRNAs in the bone marrow, full blood or isolated progenitor cells (CD34+) of AML patients, only four of them have analyzed plasma samples. We focused on the plasma samples and we targeted on such miRNAs, which levels differ at AML diagnosis and after the chemotherapy. Out of...

Acute myeloid leukemia (AML) the most common acute leukemia in adults is characterized by various cytogenetic and molecular abnormalities. However, the genetic etiology of the disease is not yet fully understood. MicroRNAs (miRNAs) are small single- stranded noncoding RNAs that are negative regulators of gene expression. miRNAs influence processes of proliferation, differentiation and apoptosis. Deregulation of miRNAs expression can contribute to human disease. Circulating miRNAs are emerging biomarkers in many diseases and cancers such as breast cancer, colorectal cancer and lung cancer. However, defining a plasma miRNA signature in AML that could serve as a biomarker for diagnosis has been conducted only once. We studied miRNA expression in plasma of 8 AML patients in first detection of the disease and repeatedly after achieving remission using TaqMan miRNA microarray for 750 human miRNA. The plasma expression level of 25 miRNA was down-regulated whilst that of 20 miRNA was up-regulated in the AML group at diagnosis when compared to healthy controls. The plasma expression level of 21 miRNA was down-regulated whilst that of 13 miRNA was up-regulated in the AML group in remission compared to healthy controls. Keywords acute myeloid leukemia (AML), biomarker, microRNA (miRNA), plasma, TaqMan Low...

Les petits ARN interférents (siRNA) sont encore rarement utilisés chez les vertébrés transgéniques pour inhiber l'expression de gènes. En effet, les vecteurs contenant un promoteur de type ARN polymérase III comme ceux des gènes U6 et H1 qui permettent une expression élevée des gènes codant pour des ARNi dans des cellules sont souvent silencieux in vivo. Dans cette thèse, divers vecteurs exprimant des petits ARN double brins (shRNA) ont été testés dans des cellules en culture et chez des souris transgéniques pour inhiber l'ARN m du gène précoce IE du virus de la pseudo rage porcine responsable de la maladie d'Aujeszky. La quantité et la séquence des si RNA produits ont été étudiées par qPCR. Dans des cellules CHO transfectées pour une expression transitoire, les vecteurs contenant les gènes U6-shRNA ont été de loin les plus efficaces pour inhiber le gène IE en raison du niveau élevé de siRNA produit. Par ailleurs, deux constructions contenant le promoteur de type ARN polymérase II, le promoteur du gène eF1-α etune séquence de shRNA bordée par 5T ou introduite dans un gène de microARN (miRNA) le miR30 ont permis d'obtenir une inhibition significative mais limitée de l'ARNm du gène IE. Ceci parait être du au niveau relativement faible de siRNA produit. Le siRNA produit par le gène du miRNA s'est avéré aussi efficace que ceux obtenus à partir des constructions U6-shRNA bien que ces derniers soient un peu plus longs. Ces diverses constructions ont été utilisées pour obtenir des souris transgéniques. Des souris contenant la séquence du shRNA n'ont pu être obtenues qu'à partir de la construction miRNA. Ceci peut être du au fait que les siRNA produits par les autres constructions ont exercé un effet inhibiteur sur des cibles aspécifiques (off-targeting) qui ne s'est pas produit avec le siRNA provenant de la construction miRNA car il contient quelques nucléotides en moins. Les souris transgéniques contenant la construction miRNA ont été soumises à une infection par le virus de la pseudo rage porcine. Bien que les souris exprimaient le gène shRNA qu'à un faible niveau. Quelques souris transgéniques ont résisté à l'infection. La seconde partie de la thèse a consisté à sélectionner d'autres séquences de shRNA capables d'inhiber l'expression du gène IE sans exercer des effets aspécifiques. Deux séquences de shRNA ont permis une telle inhibition. L'une est dirigée contre la région 5'UTR du gène IE et l'autre contre la région 3'UTR. Ces données suggèrent que (1) l'efficacité d'un shRNA n'est pas déterminée par sa séquence d'une manière totalement prévisible (2) l'efficacité d'un siRNA est d'autant plus élevé que sa séquence cible dans l'ARNm est en structure double brin (3) un effet inhibiteur intense et optimum peut être obtenu avec des concentrations faibles d'un siRNA (4) les effets secondaires et en particulier le off-targeting peuvent avoir lieu à faible concentration du siRNA mais ils ont d'autant plus de chance de se produire que la concentration du si RNA est plus élevée (5) un siRNA destiné à être utilisé chez des animaux transgéniques devrait être choisi pour sa capacité à inhiber efficacement un gène à faible concentration pour réduire ses effets secondaires.

Indiana University-Purdue University Indianapolis (IUPUI) / My thesis comprises of two individual projects which revolve around the importance of post-transcriptional regulation in liver. My first project is studying the integrated miRNA – mRNA network in NAFLD. For fulfillment of the study we conducted a genome-wide study to identify microRNAs (miRs) as well as the miR-mRNA regulatory network associated with hepatic fat and NAFLD. Hepatic fat content (HFC), miR and mRNA expression were assessed in 73 human liver samples. Liver histology of 49 samples was further characterized into normal (n=33) and NAFLD (n=16). Liver miRNome and transcriptome were significantly associated with HFC and utilized to (a) build miR-mRNA association networks in NAFLD and normal livers separately based on the potential miR-mRNA targeting and (b) conduct pathway enrichment analyses. We identified 62 miRs significantly correlated with HFC (p < 0.05 with q < 0.15), with miR-518b and miR-19b being most positively and negatively correlated with HFC, respectively (p < 0.008 for both). Integrated network analysis showed that six miRs (miRs-30b*, 612, 17*, 129-5p, 204 and 20a) controlled ~ 70% of 151 HFC-associated mRNAs (p < 0.001 with q < 0.005). Pathway analyses of these HFC-associated mRNA revealed their key effect (p<0.05) in inflammation pathways and lipid metabolism. Further, significant (p<2.47e-4, Wilcoxon test) reduction in degree of negative associations for HFC-associated miRs with HFC-associated mRNAs was observed in NAFLD as compared to normal livers, strongly suggesting highly dysfunctional miR-mRNA post-transcriptional regulatory network in NAFLD. Our study makes several novel observations which provide clues to better understand the pathogenesis and potential treatment targets of NAFLD. My second project is based on uncovering important players of post-transcriptional regulation (RBPs) and how they are associated with age and gender during healthy liver development. For this study, we performed an association analysis focusing on the expression changes of 1344 RNA Binding proteins (RBPs) as a function of age and gender in human liver. We identify 88 and 45 RBPs to be significantly associated with age and gender respectively. Experimental verification of several of the predicted associations in the mouse model confirmed our findings. Our results suggest that a small fraction of the gender-associated RBPs (~40%) are likely to be up-regulated in males. Altogether, these observations show that several of these RBPs are important developmentally conserved regulators. Further analysis of the protein interaction network of RBPs associated with age and gender based on the centrality measures like degree, betweenness and closeness revealed that several of these RBPs might be prominent players in liver development and impart gender specific alterations in gene expression via the formation of protein complexes. Indeed, both age and gender-associated RBPs in liver were found to show significantly higher clustering coefficients and network centrality measures compared to non-associated RBPs. The compendium of RBPs and this study will help us gain insight into the role of post-transcriptional regulatory molecules in aging and gender specific expression of genes.