Mutations in the gene encoding the bone morphogenetic protein type 2 receptor (BMPR2) are the most common genetic cause of heritable pulmonary arterial hypertension (PAH). However, given the reduced penetrance of BMPR2 mutations in affected families, a major outstanding question is the identity of additional factors or pathways that are responsible for the manifestation of clinical disease. Furthermore, limited human tissue is available for study and usually only from patients with end-stage disease, making it difficult to understand how PAH is established and progresses. Alternative human models of PAH are therefore required. This thesis describes the characterisation of the first human iPSC-derived smooth muscle cell (iPSC-SMC) model of PAH and elucidates the role of BMPR2 deficiency in establishing PAH-associated phenotypes in iPSC-derived SMCs. To achieve this, I used CRISPR-Cas9 gene editing to generate wild-type and BMPR2+/- iPSC lines with isogenic backgrounds which were subsequently differentiated into lineage-specific iPSC-SMCs that displayed a gene expression profile and responses to BMP signalling akin to those present in distal pulmonary artery smooth muscle cells (PASMCs). Using these cells, I found that the introduction of a single BMPR2 mutation in iPSC-SMCs was sufficient to recapitulate the pro-proliferative and anti-apoptotic phenotype of patient-derived BMPR2+/- PASMCs. However, acquisition of the mitochondrial hyperpolarisation phenotype was enhanced by inflammatory signalling and required an interaction between BMPR2 mutations and environmental stimuli provided by exposure to serum over time. Furthermore, I showed that BMPR2+/- iPSC-SMCs had an altered differentiation state and were less contractile compared to wild-type iPSC-SMCs, phenotypes which have not been observed previously in PAH-derived PASMCs. Finally, RNA sequencing analysis identified genes that were differentially expressed between wild-type and BMPR2+/- iPSC-SMCs and may hence provide further insights into PAH pathobiology. The iPSC-SMC model described in this study will be useful for identifying additional factors involved in disease penetrance and for validating therapeutic approaches that target BMPR2.

LKB1 is the second most commonly altered tumour suppressor gene in lung adenocarcinoma, the most prevalent form of lung cancer. LKB1 is a "master kinase" that has been shown to phosphorylate up to 13 downstream targets. We hypothesised that LKB1 loss is associated with an increased dependency on alternative, targetable pathways. The overall aims of this project were to better understand the role of LKB1 loss in lung cancer and to identify novel approaches to selectively target LKB1 mutated cells. We generated isogenic cells with or without LKB1 and used these to study the effect of LKB1 on cell proliferation. Importantly, we used a range of models including 2D culture, 3D spheroids and, sub-cutaneous and orthotopic xenograft models. To understand the role of LKB1 loss in lung cancer, the effect of LKB1 on mRNA expression was analysed using whole genome RNA Sequencing. To identify novel approaches to selectively target LKB1 mutated cells, we used biological screening methods and also investigated the effect of several metabolic inhibitors. We found that loss of LKB1 expression had no effect on cell proliferation in 2D culture, but was associated with increased growth in 3D spheroids, sub-cutaneous and orthotopic xenografts, as well as greater metastasis in a lung orthotopic model. Gene ontology analysis of the transcriptome identified that genes associated with cAMP signalling and cytoskeletal organisation were differentially expressed between LKB1 deficient and proficient cells. We confirmed that cAMP signalling was increased in LKB1 deficient cells, though there was no difference in sensitivity between LKB1 deficient and proficient cells to cAMP signalling modulators. The bioactive small molecule screen showed that LKB1 deficient cells underwent apoptosis more slowly and therefore, were less sensitive to many compounds, compared with LKB1 proficient cells. Screening in 3D spheroids was a novel approach that we used to identify microtubule inhibitors as potentially selective compounds acting in LKB1 deficient cells. Our RNASeq data suggests that there was a metabolic shift from oxidative phosphorylation to aerobic glycolysis in LKB1 deficient cells, although this did not affect sensitivity to complex I inhibitors. Importantly, LKB1 deficient cells were more sensitive to glucose and glutamine deprivation which suggests that targeting these metabolic pathways may hold the greatest promise to selectively inhibit proliferation in LKB1 mutated cells.

L'auteur n'a pas fourni de résumé en français / L'auteur n'a pas fourni de résumé en anglais

La formation des souvenirs repose sur un dialogue entre l’hippocampe et le cortex préfrontal médian (CPFm) qui se met en place progressivement et durablement après l’encodage de l’information. La lésion des noyaux reuniens et rhomboïde (ReRh), relai anatomo-fonctionnel entre ces deux structures, perturbe la consolidation à long terme d’un souvenir spatial. A ce jour, les mécanismes mis en jeu ne sont, pas connus. Nous avons donc étudié les processus moléculaires impliqués dans la formation d’un souvenir spatial, au sein de l’hippocampe et du CPFm, et les conséquences induites par la lésion des noyaux ReRh. Pour cela, nous avons lésé les noyaux ReRh de rats, puis nous les testés dans une tâche de piscine de Morris pendant trois jours. Nous avons alors effectué un séquençage des ARNm des sous-régions hippocampiques CA1 dorsale et ventrale, une analyse par RT-qPCR des ARNm du CPFm, ainsi qu’une analyse de l’activation de ces structures par quantification de la protéine issue du gène immédiat c-fos. Nos résultats montrent que la lésion des noyaux ReRh modifie les processus transcriptionnels et traductionnels qui prennent place dans l’hippocampe et le CPFm, dès trois jours d’apprentissage spatial. Ces résultats pourraient expliquer la non persistance d’un souvenir spatial et les déficits comportementaux qui en résultent à la suite d’une lésion des noyaux ReRh. / Memorization relies on a dialogue between the hippocampus and the medial prefrontal cortex (mPFC). This dialog takes place progressively after the encoding of an event. Given their connectivity, the thalamic nuclei named reuniens and rhomboid (ReRh) may modulate the functional loop between these two structures. Indeed, a lesion of these nuclei impairs the persistence of a spatial memory. The mechanisms underlying this process are still unknown. Therefore, we analyzed the molecular mechanisms underlying spatial memory consolidation within the hippocampus and the mPFC, and the consequences of a lesion of the ReRh nuclei. After a stereotaxic lesion of the ReRh nuclei, rats were subjected to three days of a spatial training in the Morris water maze. We then performed a RNA sequencing of the dorsal and ventral hippocampus (CA1 regions), RT-qPCR analysis of the mPCF, and a quantification of the expression of c-fos in these two structures. Results show that ReRh nuclei lesion impairs the transcriptional and translational mechanisms within the hippocampus and the mPFC as soon as after three days of a spatial learning. These alterations could lead to the retrieval deficit observed after a long post-acquisition delay.

RNA splicing is a process where introns are removed and exons are joined together. Human adenovirus type 2 pre-mRNAs undergoes intensive alternative splicing and produce more than 40 differently spliced mRNAs.  This thesis work is focused on the identification of new splice sites in adenovirus. By virtue of Illumina mRNA sequencing technology we have identified 255 splice sites. Splice site analysis of the introns revealed the presence of three types of splice sites GT-AG (61.2%), GC-AG (25.9%) and AT-AC (12.9%). Among 255 splice sites, 224 were new. Significantly, more than 50% of the new splice sites were located in the major late transcription unit on the positive strand of adenovirus DNA. Three new splice sites; 17452-29489 (GC-AG) located on the negative strand of adenovirus DNA in the E2 region, 9668-20346 (AT-AC) and 9699-30505 (GC-AG) on the positive strand of adenovirus DNA in the major late transcription unit were further confirmed by PCR analysis. / Adenovirus replication and transcriptome

Background: Canine babesiosis is a tick-borne disease causing detrimental health effects on the domestic dogs with huge economic impact on the owners. The most complicated form of canine babesiosis is caused by a pathogenic Babesia rossi parasite. Canine babesiosis induced by B. rossi still remains the cause of mortality and morbidity in South African dogs, yet, the transcriptomic and genomic information of this parasite species is still not available. The transcriptomic and genomic information is essential in the disease development and processes for the design of effective disease control strategies. Consequently, our understanding of the mechanisms underlying the pathogenesis of the different genotypes of B. rossi remains limited. A previous study suggested a relationship between the parasite genotype and the disease phenotype. To date, thirteen B. rossi genotypes have been identified and associated with diverse clinical signs in their hosts. Hence the aim of this study was to sequence RNA from samples representing B. rossi genotypes, 19, 29 and 31, in order to have insight on the overall transcriptome of this parasite and to establish if there would be significant differences among the genotypes. Methodology: To screen for B. rossi positive samples, total DNA was extracted from 20 blood samples collected from sick domestic dogs presented at the Onderstepoort Veterinary Academic Hospital (OVAH). Babesia rossi infections were confirmed using the PCR-Reverse Line Blot (RLB) hybridization assay. Further confirmation of infection status was done by amplification of the B. rossi Erythrocyte Membrane Antigen 1 (BrEMA1) gene in all the DNA samples using qualitative PCR (qPCR), followed by sequencing of PCR products. Subsequently, total RNA was extracted from the 20 B. rossi-infected blood samples collected from the same dogs in which DNA was extracted. Three samples representing B. rossi genotypes 19, 29 and 31 were selected for transcriptome analysis. RNA sequencing was performed using the Illumina HiSeq 2000 to allow transcriptome analysis. De novo assembly was performed independently for all three transcriptomes using the Trinity software. The unigenes generated from specific transcriptome assemblies were subjected to global functional annotation using Blast2GO version 2.8.0 software, followed by KEGG database for annotation of biological pathways, and DAVID version 6.7, for COG classification to predict and classify their functions. Results: The sample representing B. rossi genotype 31 was excluded in the transcriptome analysis due to low RNA mass, which usually compromises the quality of the library used in RNA sequencing.Thus, a total of 26 747 238 and 25 709 627 paired-end reads were obtained from B. rossi genotypes 19 and 29, respectively. De novo transcriptome assembly produced a total of 3019 unigenes, with an average length of 419 bp and N50 of 362 bp in B. rossi genotype 19, and 2727 unigenes with an average length of 441 bp and N50 of 362 in B. rossi genotype 29. A total of 1193 unigenes were common between B. rossi genotype 19 and 29, while 1828 unigenes were exclusively detected in B. rossi genotype 19; and 1534 were specific to B. rossi genotype 29. Between the two B. rossi genotypes, a total of 4553 unigenes were obtained, representing the overall B. rossi transcriptome. From the overall transcriptome, 12.3% (n=558) of the unigenes could be annotated with 53 different gene ontology (GO) functional categories. About 34% (n=1550) of the unigenes represented in the overall transcriptome mapped to 237 KEGG pathways and only 2.5% (114) could be annotated in the COG database. Conclusion: Although, there were no striking differences in the transcriptomes of B. rossi genotypes 19 and 29, this study presents the first transcriptomic resource for B. rossi, which will highly contribute to our genetic understanding of B. rossi and provide a platform for future gene expression studies. Hypothetical proteins identified in this study will require further characterization as they may have a critical role in the biology and pathogenicity of B. rossi parasite. / Life and Consumer Sciences / M. Sc. (Life Sciences)

Recent advances in sequencing technology have given access to information extracted on a single cell level. Single cell RNA sequencing enables for transcriptomes to be sequenced, allowing for studies within and between cell types. A recently developed protocol, based on Smart-seq2, and the Proximity ligation essay, allows for the detection of protein data from single cells, in parallel with RNA. The combination of the transcriptomic and proteomic data will enhance researchers’ ability to explore cell states. In this study, we are comparing a new pulldown protocol with the widely-used Smart-seq2, as well as against FACS sorted cells. Our results show differences in the RNA sequenced between the two protocols, as well the prediction of cell cycle state based on their data. Using RNA extracted from the pulldown protocol in different time points, we also calculate the direction of development for the cells. We expect that the incorporation of proteomic data will shed light to relevant biological questions related to the cell function.

Vascular smooth muscle cell (VSMC) accumulation is a hallmark of atherosclerosis and vascular injury. However, fundamental aspects of proliferation and the phenotypic changes within individual VSMCs, which underlie vascular disease remain unresolved. In particular, it is not known if all VSMCs proliferate and display plasticity, or whether individual cells can switch to multiple phenotypes. To assess whether proliferation and plasticity in disease is a general characteristic of VSMCs or a feature of a subset of cells, multi-colour lineage labelling is used to demonstrate that VSMCs in injury-induced neointimal lesions and in atherosclerotic plaques are oligo-clonal, derived from few expanding cells, within mice. Lineage tracing also revealed that the progeny of individual VSMCs contribute to both alpha Smooth muscle actin (aSma)-positive fibrous cap and Mac-3-expressing macrophage-like plaque core cells. Co-staining for phenotypic markers further identified a double-positive aSma+ Mac3+ cell population, which is specific to VSMC-derived plaque cells. In contrast, VSMC-derived cells generating the neointima after vascular injury generally retained expression of VSMC markers and upregulation of Mac3 was less pronounced. Monochromatic regions in atherosclerotic plaques and injury-induced neointima did not contain VSMC-derived cells expressing a different fluorescent reporter protein, suggesting that proliferation-independent VSMC migration does not make a major contribution to VSMC accumulation in vascular disease. Similarly, VSMC proliferation was examined in an Angiotensin II perfusion model of aortic aneurysm in mice, oligo-clonal proliferation was observed in remodelling regions of the vasculature, however phenotypic changes were observed in a large proportion of VSMCs, suggesting that the majority of VSMCs have some potential to modulate their phenotype. To understand the mechanisms behind the inherent VSMC heterogeneity and observed functionality, the single cell transcriptomic techniques Smart-seq2 and the Chromium 10X system were optimized for use on VSMCs. The work within this thesis suggests that extensive proliferation of a low proportion of highly plastic VSMCs results in the observed VSMC accumulation after injury, and the atherosclerotic and aortic aneurysm models of cardiovascular disease.

Made available in DSpace on 2014-12-17T14:03:41Z (GMT). No. of bitstreams: 1 HelaineCS_DISSERT.pdf: 3181905 bytes, checksum: 5c020989070824dc8493d5f191c83a23 (MD5) Previous issue date: 2013-01-29 / Ag?ncia Brasileira da Inova??o / Sugarcane (Saccharum spp.) is a plant from Poaceae family that has an impressive ability to accumulate sucrose in the stalk, making it a significant component of the economy of many countries. About 100 countries produce sugarcane in an area of 22 million hectares worldwide. For this reason, many studies have been done using sugarcane as a plant model in order to improve production. A change in gravity may be one kind of abiotic stress, since it generates rapid responses after stimulation. In this work we decided to investigate the possible morphophysiological, biochemical and molecular changes resulting from microgravity. Here, we present the contributions of an experiment where sugarcane plants were submitted to microgravity flight using a vehicle VSB-30, a sounding rocket developed by Aeronautics and Space Institute teams, in cooperation with the German Space Agency. Sugarcane plants with 10 days older were submitted to a period of six minutes of microgravity using the VSB-30 rocket. The morphophysiological analyses of roots and leaves showed that plants submitted to the flight showed changes in the conduction tissues, irregular pattern of arrangement of vascular bundles and thickening of the cell walls, among other anatomical changes that indicate that the morphology of the plants was substantially influenced by gravitational stimulation, besides the accumulation of hydrogen peroxide, an important signaling molecule in stress conditions. We carried out RNA extraction and sequencing using Illumina platform. Plants subjected to microgravity also showed changes in enzyme activity. It was observed an increased in superoxide dismutase activity in leaves and a decreased in its activity in roots as well as for ascorbate peroxidase activity. Thus, it was concluded that the changes in gravity were perceived by plants, and that microgravity environment triggered changes associated with a reactive oxygen specie signaling process. This work has helped the understanding of how the gravity affects the structural organization of the plants, by comparing the anatomy of plants subjected to microgravity and plants grown in 1g gravity / A cana-de-a??car (Saccharum spp.) ? um planta da fam?lia Poaceae que possui uma impressionante capacidade de armazenar sacarose no colmo, o que a torna um significante componente da economia de muitos pa?ses. Aproximadamente 100 pa?ses produzem cana-de-a??car em uma ?rea de 22 milh?es de hectares no mundo. Por essas raz?es, diversos estudos sobre a resposta de culturas a estresse ambiental contemplam a cana-de-a??car. Uma mudan?a na gravidade pode ser um tipo de estresse abi?tico, uma vez que ? capaz de gerar respostas r?pidas ap?s a estimula??o gravitacional. No presente trabalho procurou-se investigar as poss?veis altera??es morfofisiol?gicas, bioqu?micas e moleculares decorrentes da microgravidade. Aqui s?o apresentadas as contribui??es do experimento de submiss?o de plantas de cana-de-a??car ? microgravidade atrav?s de voo em um ve?culo VSB-30, Plantas de cana-de-a??car cultivadas em condi??es controladas, com 10 dias de desenvolvimento, foram assim submetidas a um per?odo de seis minutos de microgravidade real. As an?lises morfofisiol?gicas de ra?zes e folhas mostraram que as plantas sofreram altera??o nos tecidos de condu??o da seiva e ?gua, padr?o de disposi??o irregular de feixes vasculares, espessamento de paredes celulares, entre outras modifica??es anat?micas que indicam que a morfologia das plantas foi substancialmente influenciada pela aus?ncia de est?mulo gravitacional, al?m do ac?mulo de per?xido de hidrog?nio, importante mol?cula de sinaliza??o em condi??es de estresse. Foi realizada a extra??o do RNA e o sequenciamento do RNA atrav?s da plataforma Illumina, e estas sequencias est?o sendo analisadas. Foram tamb?m observadas altera??es nas atividades enzim?ticas, com aumento na atividade de super?xido dismutase em folhas e redu??o da atividade de super?xido dismutase e ascorbato peroxidase em ra?zes. Assim, estes resultados permitem concluir que a altera??o da gravidade foi percebida pelas plantas de cana-de-a??car e o ambiente de microgravidade desencadeou altera??es associadas a um processo de sinaliza??o por meio de esp?cies reativas de oxig?nio em condi??es de estresse. O presente trabalho auxiliou, portanto, a compreender como a gravidade interfere na organiza??o estrutural das plantas, atrav?s da compara??o da anatomia de plantas submetidas ? microgravidade e plantas crescidas em gravidade 1g

Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also been applied to highthroughput RNA sequencing (RNA-seq) data in order to find loci associated with different levels of gene expression, called expression quantitative trait loci (eQTL). Because of the large amount of data that is required for such high-resolution eQTL studies, most of them have so far been carried out in humans, where the cost of data collection could be justified by a possible future impact in human health. However, due to the rapidly falling price of high-throughput sequencing it is now also becoming feasible to perform high-resolution eQTL studies in higher model organisms. This enables the study of gene regulation in biological contexts that have so far been beyond our reach for practical or ethical reasons, such as early embryonic development. Taking advantage of these new possibilities, we performed a high-resolution eQTL study on 80 inbred fruit fly lines from the Drosophila Genetic Reference Panel, which represent naturally occurring genetic variation in a wild population of Drosophila melanogaster. Using a 3′ Tag RNA-sequencing protocol we were able to estimate the level of expression both of genes as well as of different 3′ isoforms of the same gene. We estimated these expression levels for each line at three different stages of embryonic development, allowing us to not only improve our understanding of D. melanogaster gene regulation in general, but also investigate how gene regulation changes during development. In this thesis, I describe the processing of 3′ Tag-Seq data into both 3′ isoform expression levels and overall gene expression levels. Using these expression levels I call proximal eQTLs both common and specific to a single developmental stage with a multivariate linear mixed model approach while accounting for various confounding factors. I then investigate the properties of these eQTLs, such as their location or the gene categories enriched or depleted in eQTLs. Finally, I extend the proximal eQTL calling approach to distal variants to find gene regulatory mechanisms acting in trans. Taken together, this thesis describes the design, challenges and results of performing a multivariate eQTL study in a higher model organism and provides new insights into gene regulation in D. melanogaster during embryonic development.