Our objective was to know how the hepatic transcriptome expression of growing beef (Angus-cross) heifers (0.5 kg gain/day) was affected by the feeding of different sources of dietary (3 mg/day) Se supplements: inorganic Se (ISe, sodium selenite), organic (OSe, Sel-Plex®), or a blend (1.5 mg:1.5 mg) of ISe:OSe (Mix), compared to the adequate but non-Se supplemented “Control”. The biopsied hepatic tissues of these four groups heifers collected at day 168 (when liver Se assimilation had stabilized) after supplements of Se, was subjected to the microarray analysis to assess Se treatment effects. The results suggest that there were clear differences in the hepatic gene expression profile of the four Se treatment groups. 139 significantly treatment-induced differentially expressed transcripts were selected. Among them: 1) the gene expression profiles of Control and OSe appeared to be more similar than Control and ISe, 2) eight distinct gene expression patterns among treatments were identified and each of them indicates affected biofunctions and networks, 3) they were grouped as the expression profile relative to Control, there were solely and commonly affected transcripts for four Se treatments and they indicated different biofunctions, 4) of them, three microRNAs were identified and their predicated mRNA targets showed different biofunctions.

Diffuse large B-cell lymphoma (DLBCL), which is the most common type of lymphoma, is characterised by its aggressiveness and poor outcome without adequate treatment and also for its biological and clinical heterogeneity. It is therefore highly desirable to gain a more profound understanding of the underlying biology of the disease, as well as predictive factors for the guidance of treatment. The studies presented here attempt to gain an overall grasp on DLBCL, from the epidemiological level down to the genomic level. The tumour microenvironment consists of both tumour cells and normal infiltrating cells in a delicate interplay. By assessing the number of infiltrating mast cells (MCs) in the microenvironment, a correlation between low numbers of MCs and poorer prognosis of DLBCL was found. However, malignant cells are not only affected by environmental conditions but also by intrinsic factors, such as small non-coding microRNAs. A low expression level of microRNA-129 was found to correlate with poor survival of DLBCL and the finding remained significant even for rituximab-treated patients. An even smaller intracellular genomic unit is one single nucleotide. The single nucleotide polymorphism 309 (SNP309) is a T to G change in the promotor region of MDM2, a regulatory protein in the p53 pathway, which results in increased transcription of MDM2 and thus decreased levels of p53. It was found that homozygous T allele patients had longer overall survival, as well as disease-specific survival and disease-free survival. However, treatment with rituximab eliminated the predictive value of the SNP309 polymorphism. In the last project presented in this thesis we used epidemiological methods to analyse all DLBCL cases diagnosed 2000-2013 in Sweden. Here it was possible to categorically show that higher age is an adverse prognostic factor, and most importantly, this starts from a young age. In conclusion, within this thesis I have applied different laboratory and analysis techniques to examine DLBCL biology in relation to the clinic. I have identified potential new prognostic markers, contributed to an enhanced understanding of DLBCL biology and described epidemiological data from one of the largest DLBCL cohorts ever presented. All of these aspects provide important information for a deeper understanding of the disease DLBCL.

The first aim of this thesis is to examine relationships between microRNAs targeting gene networks, combining knowledge from microRNA prediction databases into our microRNA Data Integration Portal (mirDIP). Modeling the microRNA:transcript interactome – referred to as the micronome – to build microRNA interaction networks of signalling pathways, we find genes within signalling pathways to be co-targeted by common microRNAs suggesting an unexpected level of transcriptional control. We identify two distinct classes of microRNAs; universe microRNAs, which are involved in many signalling pathways; and intra-pathway microRNAs, which target multiple genes within one signalling pathway. We find universe microRNAs to have more targets, to be more studied and more involved in cancer signalling than their intrapathway counterparts. The second aim was to undertake a more focused view, analyzing the characteristics of microRNAs within the micronome itself beginning with a focus on the under-examined microRNA terminal loop across the micronome to determine if this region of the microRNA structure might contribute to microRNA functioning. We have identified 2 main classes of microRNAs based on loop structure – perfect and occluded, which show biological relevance. We found regulatory motifs within microRNA terminal loops and found a large number of Frequently Occurring Words (FOWs) significantly overrepresented across the micronome. Set analysis of in vitro secreted microRNAs, microRNA expression across a panel of normal tissues, and microRNAs shown to be secreted in lung cancer shows that specific microRNA loop motifs within these groups are significantly overreperesented – suggesting that microRNA terminal loops harbour sequences bearing microRNA processing and localization signals.

The overall objective of this work was to increase the knowledge regarding American hybrid grapes and wine-making techniques relevant to the State of Texas, specifically to investigate grape chemistry of hybrid grapes, to evaluate the effects of micro-oxygenation on wine chemistry, and to elucidate anti-cancer effects of wine compounds and extract in colon cancer cells in vitro. The methods used include HPLC-PDA-EIS-MSn and molecular bioassays. The American hybrid grapes, Black Spanish (Vitis aestivalis hybrid) and Blanc Du Bois (Vitis aestivalis hybrid), were compared to Cabernet Sauvignon and Merlot (Vitis vinifera) in their phytochemical composition. Total phenolics were similar in red grape varieties, but lower in white grapes. In Black Spanish grapes, anthocyanins and antioxidant capacity (ORAC) exhibited the highest values. Non-anthocyanin polyphenolics did not show qualitative differences in the four grape varieties. The presence of anthocyanins diglucosides was unique to Black Spanish grapes. The second experiment involved application of micro-oxygenation with oak inner staves to evaluate the effect of this new vinification technology on the stability of anthocyanins. Overall, anthocyanins exhibited significant decreases over time in the following order: control, wine with oak pieces, oak barrel, and micro-oxygenation. The anti-cancer effect of a combination of wine compounds, resveratrol/quercetin (RQ), and a polyphenolic extract from Black Spanish wine were investigated in colon cancer cells HT-29. RQ reduced the generation of reactive oxygen species (ROS), whereas the ORAC increased. RQ reduced cancer cell viability and proliferation, induced caspase-3-cleavage, and increased PARP-cleavage. Additionally, Sp1, Sp3, Sp4, and survivin were down-regulated at mRNA and protein levels. Furthermore, RQ decreased microRNA-27a (miR-27a) and induced ZBTB10, suggesting that RQ interactions with the miR-27a-ZBTB10-axis play a role in Sp down-regulation. Similar results were obtained for the wine extract. This work will provide valuable information regarding grape varieties, potential health benefits of wine, and wine production techniques to the wine industry in Texas and beyond.

Les cellules souches mésenchymateuses (CSM) sont des cellules stromales présentes dans différents types de tissus. En plus de leur capacité à se différencier en plusieurs lignées (chondrocytes, adipocytes et ostéoblastes), les CSM présentent également des propriétés immunosuppressives. Bien que ces mécanismes soient loin d'être entièrement compris, leur capacité immunosuppressive a récemment été démontrée comme étant modulée par des miARN. L'arthrose est la forme la plus courante de maladies articulaires sans traitement curatif et se caractérise principalement par la dégradation du cartilage articulaire, avec des altérations osseuses sous-chondrales et une inflammation synoviale. Les CSM pourraient offrir un potentiel thérapeutique intéressant pour le traitement de l'arthrose.Nos travaux ont montré qu'une injection autologue de CSM d'origine adipeuse (ASC) dans une articulation arthrosique améliore la douleur et les niveaux fonctionnels chez les patients. Nous avons souligné la tolérance immunitaire systémique induite à la suite d'injections intra-articulaires d'ASC. Enfin, nous avons étudié le profil d'expression des miARN des CSM humaines lors de leur stimulation par des cellules mononuclées du sang préalablement activés. Nous avons identifié le miR-29a et le PSAT1 comme de nouveaux candidats pour réguler l'activité immunosuppressive médiée par les CSM. / Mesenchymal Stem Cells (MSCs) are stromal cells present in a number of different tissue types. In addition to their ability to differentiate into multiple lineages (chondrocytes, adipocytes and osteoblasts), MSCs also display immunosuppressive properties. Whilst these mechanisms are far from fully understood, their immunosuppressive capacity has recently been shown to be modulated by miRNAs. OA is the most common form of joint diseases without curative treatment and mainly characterized by the degradation of articular cartilage, with subchondral bone alterations and synovial inflammation. MSC might provide therapeutic potential for treatment of OA.Here, we showed that an autologous injection of adipose-derived MSC (ASC) into an osteoarthritic joint improved pain and function levels in patients. We underscored the systemic immune tolerance induced following intra-articular injections of ASCs. Finally, we investigated the miRNA expression profile of human MSCs upon their stimulation by peripheral blood mononuclear cells. We identified miR-29a and PSAT1 as new candidates to regulate immunosuppressive activity mediated by MSCs.

Placental dysfunction affects approximately 1 in 10 pregnant women in both the developed and developing worlds. Most commonly, it is manifested as preeclampsia or fetal growth restriction. Over the past two decades, an increasing body of research into the developmental biology of the placenta has been amassed, which points to defects in the differentiation of the trophoblast cell lineage as a key player in the pathophysiology of placental dysfunction. A number of clinical parameters are known to be associated with an elevated risk of placental dysfunction. These include maternal risk factors (such as chronic hypertension, renal disease, and lupus), history of placental dysfunction in a prior pregnancy, abnormalities in the levels of certain proteins in the maternal blood that are commonly used to estimate the risk of fetal genetic defects, and abnormalities in uterine artery Doppler waveforms. These current methods have significant drawbacks, including low specificity and sensitivity, high cost, lack of widespread availability, and lack of validity early in pregnancy. In order to provide a more cost-effective and reliable method to detect an elevated risk for placental dysfunction early in pregnancy, we explored the potential for extracellular RNAs (exRNA) in the maternal serum to be used as biomarkers. In our study, we used next generation sequencing technologies to compare extracellular microRNA (miRNA) levels in serum samples of pregnant women of different gestational ages, nonpregnant women, and placental tissue samples. We discovered that the large majority of microRNAs that were present at higher levels in pregnant serum samples than nonpregnant serum samples and were likely of placental origin. We also found that these pregnancy-specific miRNAs were enriched for miRNAs encoded on chromosomes (Chr) 14 and 19, with changes in the relative expression of these two groups of miRNAs throughout pregnancy. Moreover, the miRNA signatures of late gestational pregnant samples correlated more closely with placental tissue samples than those of early pregnant samples, which could be related to the increasing impact of a larger placenta on the maternal serum exRNA profile. Our results demonstrate the potential utility of next generation sequencing technologies in regards to differentiating between different conditions using clinical samples.

MicroRNAs (miRNAs) represent a major system of post-transcriptional regulation, by either preventing translational initiation or by targeting messenger RNA transcripts for storage or degradation. miRNA deregulation has been reported in neurodegenerative disorders, such as Huntington’s disease (HD) and Parkinson’s disease (PD), which may impact gene expression and modify disease progression and/or severity. To assess the relationship of miRNA levels to HD, small RNA sequence analysis was performed for 26 HD and 36 non-disease control samples derived from human prefrontal cortex. 75 miRNAs were differentially expressed in HD brain as compared to controls at genome-wide significance (FDR q<0.05). Among HD brains, nine miRNAs were significantly associated with the extent of neuropathological involvement in the striatum and three of these significantly related to a continuous measure of striatal involvement, after statistical adjustment for the contribution of HD gene length. Five miRNAs were identified as having a significant, inverse relationship to age of motor onset, in particular, miR-10b-5p, the mostly strongly over-expressed miRNA in HD cases. Although prefrontal cortex was the source of tissue profiled in these studies, the relationship of miR-10b-5p levels to striatal involvement in the disease was independent of cortical involvement. In blood plasma from 26 HD, 4 asymptomatic HD gene carriers and 8 controls, miR-10b-5p levels were significantly elevated in HD as compared to non-diseased and preclinical HD subjects, demonstrating that miRNA alterations associated with diseased brain may be detected peripherally. Using small RNA sequence analysis for 29 PD brains, 125 miRNAs were identified as differentially expressed at genome-wide significance (FDR q<0.05) in PD versus controls. A set of 29 miRNAs accurately classified PD from non-diseased brain (93.9% specificity, 96.6% sensitivity, 4.8% absolute error). In contrast to HD, among PD cases, miR-10b-5p was significantly decreased and had a significant, positive association to onset age independent of age at death. These studies provide a detailed miRNA profile for HD and PD brain, identify miRNAs associated with disease pathology and suggest miRNA changes observed in brain can be detected in blood. Together, these findings support the potential of miRNA biomarkers for the diagnosis and assessment of progression for neurodegenerative diseases.

Deciphering the functionality encoded in the genome constitutes an essential first step to understanding the context through which mutations can cause human disease. In this dissertation, I present multiple studies based on the use or development of comparative genomics techniques to elucidate function (or lack of function) from the genomes of humans and other animal species. Collectively, these studies focus on two biological entities encoded in the human genome: genes related to human disease susceptibility and those that encode microRNAs - small RNAs that have important gene-regulatory roles in normal biological function and in human disease. Extending this work, I investigated the evolution of these biological entities within animals to shed light on how their underlying functions arose and how they can be modeled in non-human species. Additionally, I present a new tool that uses large-scale clinical genomic data to identify human mutations that may affect microRNA regulatory functions, thereby providing a method by which state-of-the-art genomic technologies can be fully utilized in the search for new disease mechanisms and potential drug targets. The scientific contributions made in this dissertation utilize current data sets generated using high-throughput sequencing technologies. For example, recent whole-genome sequencing studies of the most distant animal lineages have effectively restructured the animal tree of life as we understand it. The first two chapters utilize data from this new high-confidence animal phylogeny - in addition to data generated in the course of my work - to demonstrate that (1) certain classes of human disease have uncommonly large proportions of genes that evolved with the earliest animals and/or vertebrates, and (2) that canonical microRNA functionality - absent in at least two of the early branching animal lineages - likely evolved after the first animals. In the third chapter, I expand upon recent research in predicting microRNA target sites, describing a novel tool for predicting clinically significant microRNA target site variants and demonstrating its applicability to the analysis of clinical genomic data. Thus, the studies detailed in this dissertation represent significant advances in our understanding of the functions of disease genes and microRNAs from both an evolutionary and a clinical perspective.

There has been much interest in recent years about the potential of microRNA as a new source of biomarkers for the diagnosis of disease. The delivery of new diagnostic tools based on this potential has been limited by shortcomings in current microRNA detection techniques. This thesis explores the development of a new method of microRNA detection through the incorporation of conductive particles into oligonucleotide-functionalised polymers to form oligonucleotide cross-linked polymer composites. Such composites could provide a simple, rapid, and low-cost means of microRNA detection that could be easily multiplexed, providing a valuable tool for point-of-care medical diagnostics. This work presents oligonucleotide-functionalised carbon/polyacrylamide composites which demonstrate a selective swelling response in the presence of analyte oligonucleotide sequences and for which the electrical conductivity decreases with swelling. The composites were synthesised via UV-initiated free-radical polymerisation of carbon/- monomer mixtures upon custom electrode devices, consisting of interdigitated platinum electrodes fabricated upon a silicon substrate. The optimal cross-linker density and carbon loading concentration were determined as well as the best means of dispersing the carbon particles within the polymer. Various types of carbon particles, with differing sizes and aspect ratios, were compared and their performances as conductive additives for polymer swelling transduction evaluated. The swelling behaviour of these composites was evaluated by analysing images of composite microdroplets as they swell. The electrical characteristics of the composites were determined by measuring either the two-terminal resistance or the complex impedance of composite microdroplets on the electrode devices. Alternating and direct current measurement techniques were compared to determine the best approach for the transduction of composite swelling. The volumetric and electrical responses of oligonucleotide-functionalised carbon/polyacrylamide composites were analysed in solutions of analyte oligonucleotide and non-complementary controls. It has been demonstrated that, using carbon nanopowder composites and a direct current two-terminal resistance measurement, it is possible to differentiate between analyte and control solutions to concentrations as low as 10 nM, with single-base precision, in less than three minutes. However, the inability to detect at concentrations below this value, difficulties in differentiating between different analyte concentrations and thermal instability mean that, in their current form, oligonucleotide cross-linked polymer composites are unsuitable for the detection of circulating microRNA at clinically relevant concentrations. Potential avenues of work to address these challenges are discussed. Also presented are collaborative results for oligonucleotide-responsive polymers functionalised with morpholino nucleic acid analogues, in what is believed to be the first example of such a material. These morpholino-functionalised polymers offer significant advantages, in terms of stability and sensitivity, over their nucleic acid equivalents for bio-responsive polymer applications.

MicroRNAs are small non-coding RNA molecules with length of about 22 nt. These molecules participate on regulation of gene expression at the post-transcriptional level. They represent the largest group of regulators in the cell and therefore are also involved in all key processes such as proliferation, differentiation or apoptosis. Moreover, they participate in tumor transformation. These small molecules have a great potential to be diagnostic markers or assist in the treatment and prevention of diseases. This research was focused on the development of isolation method using magnetic particles with subsequent electrochemical detection of microRNA. Optimization steps were performed and then the entire method was successfully applied to real samples of HEK293 cells expressing increased levels of miR-124. The developed method proved to be sufficiently specific and applicable to the analysis of microRNA.