La leucémie myéloïde aigüe (LMA) est la forme de leucémie la plus fréquente chez l’adulte au Canada. Bien que de nombreux réarrangements chromosomiques récurrents aient été identifiés chez les patients LMA, près de la moitié des cas présentent un caryotype normal (LMA-CN). L’étude de la LMA-CN in vitro est rendue difficile par le fait que la survie des cellules primaires de patients est défectueuse sur le long terme et que les lignées cellulaires leucémiques ont un caryotype hautement anormal. En 2009, Munker et son équipe ont établi une nouvelle lignée cellulaire, CG-SH, ayant la particularité d’avoir un caryotype normal. L’objectif principal de ce projet d’étude est de caractériser plus en détail ce nouveau modèle d’étude. Nous avons identifié l’ensemble des variants génétiques présents dans CG-SH grâce au séquençage du génome entier. Les variants susceptibles de participer à la leucémogénèse ont été isolés, tels que des insertions détectées dans EZH2 et GATA2, et de nombreux variants faux-sens détectés dans des gènes pertinents pour la LMA. Nous avons montré que les cellules CG-SH sont sensibles à l’effet prolifératif d’une combinaison de cytokines, qui agissent sur le comportement des cellules en modifiant l’expression des gènes associés à la régulation de la prolifération, de l’apoptose et de la différentiation. De plus, les cytokines diminuent le taux de nécrose des cellules en culture sur le court terme. La présente étude a permis d’approfondir notre connaissance sur les caractéristiques moléculaires de la lignée cellulaire CG-SH, un nouveau modèle d’étude in vitro de la LMA-CN. / Acute myeloid leukemia (AML) is the most frequent form of leukemia in the adult population in Canada. Although many recurrent chromosomal rearrangements have been identified in AML, almost half of all adult patients will present with a normal karyotype (NK-AML). The in vitro study of NK-AML is difficult because the long-term survival of primary patient samples is deficient and AML cell lines have a highly abnormal karyotype. In 2009, Munker and collegues established a new cell line, CG-SH, with the advantage of having a normal karyotype. The main goal of this research project is to further characterize this new model system. We identified all the genetic variants present in the CG-SH cells using whole genome sequencing. We also isolated the variants that are susceptible to participate to leukemogenesis, including the insertions detected in EZH2 and GATA2, and several missense mutations occurring in relevant genes for AML. We found that a combination of cytokines promotes the proliferation of CG-SH cells, and that cytokines act on the cells behavior through expression changes of the genes involved in the regulation of proliferation, apoptosis and differentiation. Moreover, cytokines trigger a decrease of the necrotic rate of CG-SH on the short-term. The current study allowed us to better appreciate molecular characteristics of the CG-SH cell line, a new model to study NK-AML in vitro.

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Die Analyse von NGS Daten ist ein zentraler Aspekt der modernen genomischen Forschung. Bei der Extraktion von Daten aus den beiden am häufigsten verwendeten Quellorganismen bestehen jedoch vielfältige Problemstellungen. Im ersten Kapitel wird ein neuartiger Ansatz vorgestellt welcher einen Abstand zwischen Krebszellinienkulturen auf Grundlage ihrer kleinen genomischen Varianten bestimmt um die Kulturen zu identifizieren. Eine Voll-Exom sequenzierte Kultur wird durch paarweise Vergleiche zu Referenzdatensätzen identifiziert so ein gemessener Abstand geringer ist als dies bei nicht verwandten Kulturen zu erwarten wäre. Die Wirksamkeit der Methode wurde verifiziert, jedoch verbleiben Einschränkung da nur das Sequenzierformat des Voll-Exoms unterstützt wird. Daher wird im zweiten Kapitel eine publizierte Modifikation des Ansatzes vorgestellt welcher die Unterstützung der weitläufig genutzten Bulk RNA sowie der Panel-Sequenzierung ermöglicht. Die Ausweitung der Technologiebasis führt jedoch zu einer Verstärkung von Störeffekten welche zu Verletzungen der mathematischen Konditionen einer Abstandsmetrik führen. Daher werden die entstandenen Verletzungen durch statistische Verfahren zuerst quantifiziert und danach durch dynamische Schwellwertanpassungen erfolgreich kompensiert. Das dritte Kapitel stellt eine neuartige Daten-Aufwertungsmethode (Data-Augmentation) vor welche das Trainieren von maschinellen Lernmodellen in Abwesenheit von neoplastischen Trainingsdaten ermöglicht. Ein abstraktes Abstandsmaß wird zwischen neoplastischen Entitäten sowie Entitäten gesundem Ursprungs mittels einer transkriptomischen Dekonvolution hergestellt. Die Ausgabe der Dekonvolution erlaubt dann das effektive Vorhersagen von klinischen Eigenschaften von seltenen jedoch biologisch vielfältigen Krebsarten wobei die prädiktive Kraft des Verfahrens der des etablierten Goldstandard ebenbürtig ist. / The analysis of NGS data is a central aspect of modern Molecular Genetics and Oncology. The first scientific contribution is the development of a method which identifies Whole-exome-sequenced CCL via the quantification of a distance between their sets of small genomic variants. A distinguishing aspect of the method is that it was designed for the computer-based identification of NGS-sequenced CCL. An identification of an unknown CCL occurs when its abstract distance to a known CCL is smaller than is expected due to chance. The method performed favorably during benchmarks but only supported the Whole-exome-sequencing technology. The second contribution therefore extended the identification method by additionally supporting the Bulk mRNA-sequencing technology and Panel-sequencing format. However, the technological extension incurred predictive biases which detrimentally affected the quantification of abstract distances. Hence, statistical methods were introduced to quantify and compensate for confounding factors. The method revealed a heterogeneity-robust benchmark performance at the trade-off of a slightly reduced sensitivity compared to the Whole-exome-sequencing method. The third contribution is a method which trains Machine-Learning models for rare and diverse cancer types. Machine-Learning models are subsequently trained on these distances to predict clinically relevant characteristics. The performance of such-trained models was comparable to that of models trained on both the substituted neoplastic data and the gold-standard biomarker Ki-67. No proliferation rate-indicative features were utilized to predict clinical characteristics which is why the method can complement the proliferation rate-oriented pathological assessment of biopsies. The thesis revealed that the quantification of an abstract distance can address sources of erroneous NGS data analysis.

Upon encounter of an antigen, epidermis-resident Langerhans cells (LCs) become activated and present the processed antigen to T cells of the draining lymph nodes, resulting in tolerogenic or inflammatory responses. In psoriasis plaques, skin homeostasis is disrupted and replaced by an inflammatory dermatitis. Topical application of the anti-viral compound, imiquimod, induces a psoriasiform inflammatory condition, partly driven by LC production of pro-inflammatory cytokines. Differentiation of the myeloid progenitor cell line, MUTZ-3, produces MUTZ-3 derived Langerhans cells (MUTZ-LCs) which can be used as an in vitro model of LCs. This project aimed to investigate the phenotype and function of imiquimod-treated MUTZ-LCs in monolayer cultures, co-culture with T cells and inserted into a 3D skin model. LC-related surface markers (HLA-DR, CD1a, CD207, CCR7) were upregulated in MUTZ-LCs after 7 days of differentiation with 40 ng/ml GM-CSF, 10 ng/ml TGF-β and 2.5 ng/ml TNF-α. Supernatants of imiquimod-treated monolayer cultures of MUTZ-LCs showed subtle concentrations of IL-6 and TNF-α, but not IL-23. mRNA expression showed no significant upregulation of IL-6, IL-23 or TNF-α after 24 h treatment with imiquimod. The presence of MUTZ-LCs in T cell co-cultures greatly increased the production of IL-2, but did not affect expression of CD25. After 16 h exposure to imiquimod, IL-6, IL-23 and TNF-α could not be detected in culture supernatants of a 3D model consisting of fibroblasts, keratinocytes and MUTZ-LCs. The model was devoid of fibroblasts after 19 days of culture, most likely compromising the immunocompetence, as LC migration in response to activation could not be detected. Further studies could refine and optimize the imiquimod-3D skin model, which has potential as a possible substitute for animal models in psoriasis research.

In recent times, endocrine disrupting chemicals (EDCs) have been associated with the rise in neurodevelopmental disorders such as autism, attention deficit hyperactivity disorder (ADHD) and decreased intelligence quotient (IQ) in children. This effect is suspected to be induced at pre-/peri-natal development, via an alteration in hormonal signaling, thus interfering with neuronal differentiation, with subsequent effect on normal brain development and function in exposed children. This issue increases the need for chemical screening for potential developmental neurotoxicity (DNT) effect. The current available EDC induced DNT test guideline is based on in-vivo testing that requires animal use. Here, a multipotent neural progenitor cell line, the C17.2 cell-line, generated from neural stem cells of the external germinal layer of mouse cerebellum, with potential to differentiate to neurons or astrocytes, is introduced for in-vitro EDC induced DNT testing. This project focused on optimizing the C17.2 cell-line for the detection of EDC-induced DNT with emphasis on the disruption of the oestrogen, androgen, and thyroid hormone systems. It aimed at validating the involvement of oestrogen, androgen, and thyroid hormone on molecular and cellular endpoints relevant for the differentiation of the C17.2 cells.  Herein, the cells were exposed to the hormonal agonist and antagonist at a range of concentrations for a 10-day differentiation period. After exposure, LDH, viability assay and morphological changes (percentage of neurons in culture and neurite outgrowth) were evaluated. The results showed no morphological changes induced by androgen receptor (AR) agonist/antagonist at relevant physiological concentrations. The thyroid receptor (TR) agonist and antagonist on the other hand showed a response in the form of increased neurite outgrowth in relation to the negative control at a concentration range of 40-200 nM and 40 nM respectively. The oestrogen receptor (ER) antagonist at 100 nM also increased percentage neuron in culture. Additionally, in-silico analysis of microarray and RNA sequencing data were used to map out target genes regulated by ER, AR and TR and involved in neurodevelopment. With this approach, 29 marker genes were identified. Validation of the marker genes by means of gene expression (qPCR) was carried out, ER and TR agonist/antagonist were observed to modulate the expression of examined genes. In summary, the model could not be established for detecting EDC induced DNT via androgenic and oestrogenic pathway, while it is a promising model for identifying DNT induced by thyroid hormone signalling disruption.

M. Tech. (Department of Biotechnology, Faculty of Applied and Computer Sciences), Vaal University of Technology. / Obesity has steadily increased and represents a major public health problem worldwide, reducing quality of life and causing a range of health problems. Obesity has emerged as the fifth leading risk of global deaths. Annually, 2.8 million adults die as a result of being overweight or obese. The increase of obesity remains inexplicable in terms of genetic susceptibility to obesity. The genetic loci identified by genome-wide association studies (GWASs) explains about 2% of the heritability for obesity. Perhaps other factors such as epigenetics may be involved in the increase of obesity and may offer solutions for the management of obesity. Epigenetics is defined as a heritable change in gene expression without altering the genome sequences. It may help in providing a logical explanation between the genome and environment which shapes obesity risk and may help to explain the "missing heritability". Epigenetics may affect two mechanisms, namely: i) DNA methylation,and ii) histone modifications. DNA methylation might give scientists a link to the rise in obesity.The study aimed to investigate the effect of sugars used as sweeteners in sugar-sweetened beverages (SSB) on DNA methylation in a Caco-2 cell line in vitro. Four major objectives were pursued in the study which were to:(1) stimulate the Caco-2 cells with varying concentrations of sugar sweeteners and assess the morphological changes of the cells; (2) evaluate the cytotoxicity of different concentrations of the sugar sweetener on the Caco-2 cell line using the Alamar blue and LDH assay; (3) obtain genomic DNA from the treated Caco-2 cell line and perform bisulfite conversion and rest; and (4) amplify the WT1, MEG3, TNFRSF9, ATP10A, and CD44 obesity-associated genes and ascertain their degree of methylation. Caco-2 cells were stimulated with sugar sweeteners at varying concentrations (low, medium and high) for an incubation period of 62 days,and images of the cells were captured for morphological characterisation. The incubation condition entailed cells plated in a 12 or 96 well plate, incubated in a humidified 5% CO2 incubator at 37 °C and there is nutrient renewal every three days.Alamar blue, a cell proliferation colourimetric assay and lactate dehydrogenase assays (LDH), a homogenous membrane fluorimetric assay were used for the cytotoxicity studies. The results of the characterisation showed that different concentrations of sugar sweeteners affected the morphology of the cells as the incubation period progressed. The cytotoxicity results of both LDH and Alamar blue depicted low concentration of sweeteners that had low-to-moderate toxicity and the medium and high concentration of the sweeteners had a moderate to high toxicity on the Caco-2 cells. DNA from the Caco-2 cells was extracted. Techniques used to study DNA methylation such as bisulfite conversion, PCR amplification and restriction enzymes that have differential sensitivity to 5-methyl-cytosine were performed. The quality of DNA extracted was good. The bisulfite conversion was conducted andno amplification was observed, as a contingency plan Normal PCR was performed to amplify the CpG islands, and there was amplification. In conclusion, the study showed that a low concentration of a sugar sweetener (fructose: glucose) used in beverages had low toxicity to the Caco-2 cell line and prolonged exposure of the low concentration might have an adverse effect on the cells' morphology. At medium concentrations, the sugar sweetener used in beverages had medium toxicity to Caco-2 cells; prolonged exposure may lead to morphological changes. These findings indicated that control of dietary glucose intake is an important strategy in combating the development of obesity and type-2 diabetes. DNA methylation could not be established.

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No description available.

Lack of host-specific cell cultures necessitated initiation of primary cell cultures from ictalurid catfish. Cell cultures from the fin tissues of hybrid catfish ( channel catfish x blue catfish) were developed, characterized, and species of origin molecularly authenticated. Blue catfish alloherpesvirus (BCAHV) is an Ictalurid herpesvirus. When BCAHV was inoculated onto various fish cell lines from different families, the cytopathic effects were restricted to cell lines from family Ictaluridae indicating the host-specificity of virus. A virus challenge using channel, blue, and hybrid catfish indicated mortality due to BCAHV was significantly higher in blue and hybrid catfish. Crowding influenced BCAHV pathogenesis indicated by significantly higher mortality in highly stocked tanks. Host susceptibility to BCAHV differed with age. Temperature had a significant role in the activation and pathogenesis of BCAHV. The enhanced virulence of BCAHV in blue and hybrid catfish reveals its potential to be a significant pathogen in catfish culture.

A doubly resonant cavity was used to search for nonlinear radiofrequency (RF) energy conversion in a range of biological preparations, thereby testing the hypothesis that living tissue can demodulate RF carriers and generate baseband signals. The samples comprised high-density cell suspensions (human lymphocytes and mouse bone marrow cells); adherent cells (IMR-32 human neuroblastoma, G361 human melanoma, HF-19 human fibroblasts, N2a murine neuroblastoma (differentiated and non-differentiated) and Chinese hamster ovary (CHO) cells) and thin sections or slices of mouse tissues (brain, kidney, muscle, liver, spleen, testis, heart and diaphragm). Viable and non-viable (heat killed or metabolically impaired) samples were tested. Over 500 cell and tissue samples were placed within the cavity, exposed to continuous wave (CW) fields at the resonant frequency (f) of the loaded cavity (near 883 MHz) using input powers of 0.1 or 1 mW, and monitored for second harmonic generation by inspection of the output at 2f. Unwanted signals were minimised using low pass filters (</= 1 GHz) at the input to, and high pass filters (>/= 1 GHz) at the output from, the cavity. A tuned low noise amplifier allowed detection of second harmonic signals above a noise floor as low as -169 dBm. No consistent second harmonic of the incident CW signals was detected. Therefore, these results do not support the hypothesis that living cells can demodulate RF energy, since second harmonic generation is the necessary and sufficient condition for demodulation.