This dissertation mainly focuses on interdisciplinary approaches for biomedical knowledge discovery. This required special efforts in developing systematic strategies to integrate various data... Show moreThis dissertation mainly focuses on interdisciplinary approaches for biomedical knowledge discovery. This required special efforts in developing systematic strategies to integrate various data sources and techniques, leading to improved discovery of mechanistic insights on human diseases. Chapter one looks at the possibility in which combining various bioinformatics-based strategies can significantly improve the characterization of the OPMD mouse model. We discuss that this approach in knowledge discovery, on the basis of our extensive analysis, helped us to shed some light on how this model system relates to OPMD pathophysiology in human. In Chapter two, we expand on this combinatory approach by conducting a cross-species data analysis. In this study, we have looked for common patterns that emerge by assessing the transcriptome data from three OPMD model systems and patients. This strategy led to unravelling the most prominent molecular pathway involved in OPMD pathology. The third chapter achieves a similar goal to identify similar molecular and pathophysiological features between OPMD and the common process of skeletal muscle ageing. Engaging in a study in which the focus was made on the universality of biological processes, in the light of evolutionary mechanisms and common functional features, led to novel discoveries. This work helped us uncover remarkable insights on molecular mechanisms of ageing muscles and protein aggregation. Chapters four and five take a different route by tackling the field of computational biology. These chapters aim to extend network inference by providing novel strategies for the exploitation and integration of multiple data sources. We show that these developments allow us to infer more robust regulatory mechanisms to be identified while translations and predictions are made across very different datasets, platforms, and organisms. Finally, the dissertation is concluded by providing an outlook on ways the field of systems biology can evolve in order to offer enhanced, diversified and robust strategies for knowledge discovery. Show less
Rationale Psychosis susceptibility is mediated in part by the dopaminergic neurotransmitter system. In humans, individual differences in vulnerability for psychosis are reflected in differential... Show moreRationale Psychosis susceptibility is mediated in part by the dopaminergic neurotransmitter system. In humans, individual differences in vulnerability for psychosis are reflected in differential sensitivity for psychostimulants such as amphetamine. We hypothesize that the same genes and pathways underlying behavioral sensitization in mice are also involved in the vulnerability to psychosis.Objectives The aim of the current study was to investigate which genes and pathways may contribute to behavioral sensitization in different dopaminergic output areas in the mouse brain.Methods We took advantage of the naturally occurring difference in psychostimulant sensitivity in DBA/2 mice and selected animals displaying extremes in behavioral sensitization to amphetamine. Subsequently, the dopamine output areas, prefrontal cortex, nucleus accumbens, and cornu ammonis 1 (CA1) area of the hippocampus, were isolated by laser microdissection and subjected to DNA microarray analysis 1 h after a challenge dose of amphetamine. Results A large number of genes with differential expression between high and low responders were identified, with no overlap between brain regions. Validation of these gene expression changes with real-time quantitative polymerase chain reaction demonstrated that the most robust and reproducible effects on gene expression were in the CA1 region of the hippocampus. Interestingly, many of the validated genes in CA1 are members of the cAMP response element (CRE) family and targets of the glucocorticoid receptor (GR) and myocyte enhancer factor 2 (Mef2) transcription factors.Conclusion We hypothesize that CRE, Mef2, and GR signaling form a transcription regulating network, which underlies differential amphetamine sensitivity, and therefore, may play an important role in susceptibility to psychosis. Show less
The results obtained in this thesis suggest that the most explicit differences between normal and atypical melanocytes are subtle changes in pigment biosynthesis and the functioning of the... Show moreThe results obtained in this thesis suggest that the most explicit differences between normal and atypical melanocytes are subtle changes in pigment biosynthesis and the functioning of the antioxidant system. Impairment of the antioxidant system and increased levels of pheomelanin result in increased levels of oxidative stress. It is anticipated that these increased levels of oxidative stress contribute to early melanoma development by inducing DNA mutations, but additional studies are required to prove this hypothesis. Show less
Kearns-Jonker, M.; Dai, W.D.; Gunthart, M.; Girish, N.; Pera, M.; Mummery, C.; Kloner, R.A. 2010
Gene expression is a complicated process with multiple types of regulation, including binding of proteins termed transcription factors. This thesis looks at transcription factors and transcription... Show moreGene expression is a complicated process with multiple types of regulation, including binding of proteins termed transcription factors. This thesis looks at transcription factors and transcription factor binding site discovery through computational predictions and wet lab work to better elucidate their role in transcriptional regulation. This includes bioinformatics tools to extrapolate transcription factors common to a set of co-regulated sequences, such as genes differentially expressed in a microarray or next-generation sequencing experiment. It also includes a working pipeline to analyze next-generation sequencing data, used in the following projects: Next-generation sequencing of chromatin-immunoprecipitated CBP and p300 (two highly homologous transcription factors) bound DNA was performed to analyze their (different) roles in cell cycle regulation. Next-generation sequencing of RNA from differentiating muscle cells was also done to identify differential gene expression during myogenesis, as well as identify novel promoter regions (a common target of transcription factors). Taken together, computational and wet lab tools can enhance our knowledge of transcriptional regulation, as described by several applications to enhance our knowledge of myogenic and cell-cycle regulation in this thesis. Show less
Jong, M.C. de; Pramana, J.; Knegjens, J.L.; Balm, A.J.M.; Brekel, M.W.M. van den; Hauptmann, M.; ... ; Rasch, C.R.N. 2010
Purpose: The purpose of this study was to combine gene expression profiles and clinical factors to provide a better prediction model of local control after chemoradiotherapy for advanced head and... Show morePurpose: The purpose of this study was to combine gene expression profiles and clinical factors to provide a better prediction model of local control after chemoradiotherapy for advanced head and neck cancer.Material and methods: Gene expression data were available for a series of 92 advanced stage head and neck cancer patients treated with primary chemoradiotherapy. The effect of the Chung high-risk and Slebos HPV expression profiles on local control was analyzed in a model with age at diagnosis, gender, tumor site, tumor volume, T-stage and N-stage and HPV profile status.Results: Among 75 patients included in the study, the only factors significantly predicting local control were tumor site (oral cavity vs. Pharynx, hazard ratio 4.2 [95% CI 1.4-12.5]), Chung gene expression status (high vs. Low risk profile, hazard ratio 4.4 [95% CI 1.5-13.3]) and HPV profile (negative vs. Positive profile, hazard ratio 6.2 [95% CI 1.7-22.5]).Conclusions: Chung high-risk expression profile and a negative HPV expression profile were significantly associated with increased risk of local recurrence after chemoradiotherapy in advanced pharynx and oral cavity tumors, independent of clinical factors. (C) 2010 Elsevier Ireland Ltd. All rights reserved. Radiotherapy and Oncology 95 (2010) 365-370 Show less
Bio-informatica kan omschreven worden als het toepassen van algoritmen om meerwaarde te verkrijgen uit data afkomstig van biomedisch en/of biologisch onderzoek. In bio-informatica wordt onderzoek... Show moreBio-informatica kan omschreven worden als het toepassen van algoritmen om meerwaarde te verkrijgen uit data afkomstig van biomedisch en/of biologisch onderzoek. In bio-informatica wordt onderzoek gedaan met grote gegevens verzamelingen die afkomstig zijn uit biomedisch en/of biologisch experimenten. Het doel van dit onderzoek is komen tot nieuwe inzichten vanuit de gegevens verzameling. Deze inzichten komen tot stand door de goede organisatie van de data, het linken naar en integreren met complementaire gegevens verzamelingen en ontwikkelen en toepassen van analytische methodieken. Als bio-informatica groep onderzoeken wij het inrichten en ontwikkelen van een 3D spatio-temporele data omgeving voor ontwikkelingsstudies van het zebravis model organisme. De expressie van genen in spatio-temporale patronen vormt de basis van het ontwikkelingsproces. Voor onderzoekers is een begrip van deze patronen in sam enhang met de anatomische ontwikkeling belangrijk; hoe vormen de patronen de basis voor vorm verandering en welke genen kunnen bij dergelijke veranderende patronen betrokken zijn. In deze context hebben wij een omgeving ontwikkeld voor spatio-temporele gegevens uit embryonische studies van het zebravis modelsysteem. Show less
Blood-flow-induced shear stress plays an important role in cardiovascular development and disease. How endothelial cells sense shear stress remains to be elucidated. We postulated that the primary... Show moreBlood-flow-induced shear stress plays an important role in cardiovascular development and disease. How endothelial cells sense shear stress remains to be elucidated. We postulated that the primary cilium is a component of the endothelial shear sensor. This luminal cell protrusion contains microtubules and is connected to the microtubular cytoskeleton. We identified cilia on endothelial cells of the embryonic heart in areas of low or oscillatory shear stress. This shear-related distribution is reminiscent of the distribution of atherosclerotic lesions in the adult arterial system, as lesions develop at sites of low or oscillating shear (athero-prone flow). Ciliated endothelial cells are exclusively present at these atherosclerotic predilection sites in adult mice. Athero-prone (oscillatory) but not athero-protective (steady or pulsatile) flow induces ciliation of cultured endothelial cells. Moreover, the endothelial shear response is dependent on the microtubular cytoskeleton and primary cilia sensitise the endothelium for shear. Taken together, these data demonstrate that primary cilia are induced by athero-prone flow and that ciliated cells are more sensitive to shear stress. We conclude that the endothelial biosensor for shear stress is the microtubular cytoskeleton and that the attached primary cilium functions as a signal amplifier in areas subjected to athero-prone flow. Show less
Total mesorectal excision (TME) is the standard treatment for rectal cancer, while transanal endoscopic microsurgery (TEM) is a recently introduced surgical approach for the treatment of rectal... Show moreTotal mesorectal excision (TME) is the standard treatment for rectal cancer, while transanal endoscopic microsurgery (TEM) is a recently introduced surgical approach for the treatment of rectal adenomas. Incorrect preoperative staging before TEM is a problem. Therefore the aim of this thesis was to identify molecular differences between rectal tumors of different stages, using gene expression profiling and genomic analysis. First protocols and data analysis algorithms for a new type of SNP array were developed. These studies showed that reliable LOH and copy number changes could be obtained from both frozen and paraffin embedded material. Consequently SNP arrays were used to type groups of TEM and TME treated samples. Five genomic events were found which could make a clear discrimination between adenomas and carcinomas. Early carcinomas treated by TEM, which were not recognized preoperatively as carcinomas, showed already carcinoma-associated aberrations. Analysis of tree core biopsies per patient showed a large degree of intra- tumor heterogeneity; although a good correlation was obtained between the biopsy with the largest number of aberrations and its corresponding tumor fraction. Gene expression array analysis was performed on the same samples as the SNP array series. A high concordance between chromosomal aberrations and changes in gene expression was observed. Finally a clinical application of these data is discussed in the preoperative staging of rectal tumours. Show less
Using newly developed single cell A3243G mutation load assays a novel mechanism of mtDNA segregation was identified in which the multi-copy mtDNA nucleoid takes a central position. Furthermore,... Show moreUsing newly developed single cell A3243G mutation load assays a novel mechanism of mtDNA segregation was identified in which the multi-copy mtDNA nucleoid takes a central position. Furthermore, likely due to low level changes in gene expression, no genes or gene sets could be identified with gene wide expression analysis that would hint to the molecular pathways that are altered upon loss of mitochondrial ATP production as a consequence of A3243G mtDNA mutation. Extensive post-transcriptional adaptation in the form of global translation repression, was however apparent. A comparison between two mtDNA haplotypes indicated, that these presumably neutral sequence variants can affect the nuclear expression program, which tentatively indicates that mtDNA haplotype can affect phenotype. Show less
Arsenic (As) is a notoriously poisonous metalloid with known hazardous effects to human health. The project described in this thesis was aimed at elucidating the probable mechanism of As-induced... Show moreArsenic (As) is a notoriously poisonous metalloid with known hazardous effects to human health. The project described in this thesis was aimed at elucidating the probable mechanism of As-induced neurotoxicity in vivo and in vitro. The animal studies in this thesis were designed to answer questions about the effect of As on the peripheral nervous system after sub-acute and chronic intoxication of laboratory rats. Protein composition analysis showed compositional changes in sciatic nerves proteins. Protein expression of neurofilament heavy (NF-H) and neurofilament medium (NF-M) remained unchanged. Neurofilament protein light (NF-L) expression was reduced, while _- and m-calpain protein expression was increased, both in a dose/time pattern. Furthermore, NF-H protein was hypophosphorylated; while NF-L and microtubule-associated protein tau (MAP-tau) proteins were phosphorylated. In the in vitro studies, effects of As species were tested in various cell culture models and the manner of their hyperphosphorylation was further studied for a better understanding of the disruption of neuroskeletal integrity by As. In vitro studies showed that the compositional changes were not caused by the changes on RNA expression levels, rather a post-translational activity. Cells treated with arsenite showed cleavage of p35 to p25 by calpain, which is mediated by an increase of Ca2+ in the cells. Over expression of calpain results in hyperphosphorylation of NF-L and activated calpain is also responsible for NF-L degradation. Show less
In developmental biology, the expression of genes is studied to understand development, phenotypes and to construct models to understand disease. In this thesis, we explore and validate biological... Show moreIn developmental biology, the expression of genes is studied to understand development, phenotypes and to construct models to understand disease. In this thesis, we explore and validate biological as well as computerized tools, to address research questions in developmental biology. Based on these techniques, we developed a workflow to generate a large number of 3D spatio-temporal patterns of gene expression. Though several techniques for gene expression analysis are available, most spatial gene expression data are only in 2D. In order to study gene expression and differentiation of structures during development at the same time, both spatial 3D information, and temporal data are essential. These spatio-temporal patterns of gene expression have to be generated. To that end, we have developed a workflow based on fluorescent in situ hybridization (FISH) (ZebraFISH;), confocal laser scanning microscopy (CLSM) and subsequent three-dimensional modeling with, in our case, TDR-3Dbase software- resulting in a large amount of 3D spatio-temporal patterns of gene expression, obtained in a straightforward and non-destructive manner. In the work described in this thesis, we applied the workflow to 30 genes in 5 developmental processes. 3D modeling and data mining software are used to analyse gene expression patterns in zebrafish embryos and across species Show less
Through evolution the social amoebas have developed mechanisms to adapt to environmental changes and ensure survival. This thesis explores the evolutionary origins of cAMP signalling and regulation... Show moreThrough evolution the social amoebas have developed mechanisms to adapt to environmental changes and ensure survival. This thesis explores the evolutionary origins of cAMP signalling and regulation of developmental decisions in the model organism Dictyostelium discoideum. It also shows the first molecular-based phylogeny of the Dictyostelids. Development in Dictyostelium is characterized by the formation of a multicellular structure, the fruiting body, with a well-defined temporal and spatial pattern. cAMP, normally used as intracellular second messenger, in Dictyostelium is used also as an extracellular signal (chemoattractant) to mediate cell movement and cell differentiation. The study of the different components that control the formation of a multicellular fruiting body at a molecular level and from an evolutionary perspective shows that extracellular cAMP signalling was originally developed to control fruiting body morphogenesis. Furthermore it reinforces the idea that Dictyostelium is a simple but yet robust model to study the origins of multicellularity. Do to cAMP being so prevalent in Dictyostelium development I have studied the regulation of cAMP production during particular developmental stages showing in this thesis novel roles for the adenylyl cyclases that produce cAMP and their specific patters of expression during development. A thorough pharmacological analysis of these enzymes is also present in this work. Show less
Glomerulosclerosis is a general term describing the process of scarring of the glomeruli, the functional units in the kidney that filter urine from the blood. This severe, irreversible complication... Show moreGlomerulosclerosis is a general term describing the process of scarring of the glomeruli, the functional units in the kidney that filter urine from the blood. This severe, irreversible complication can occur secondary to various already established systemic or local diseases. However, not all patients with renal diseases show progression to end stage renal disease (ESRD). Thus renal patients can be subdivided into progressors and non-progressors based on clinical parameters1. Why patients with renal diseases become progressors or non-progressors is unclear, and better insight into the pathogenesis of glomerulosclerosis may improve our understanding of the process towards progression. However, the pathogenesis of glomerulosclerosis is complex and still poorly understood, although genetic factors probably play a role, given the considerable variation among individuals in both the risk of developing glomerulosclerosis and the rate of progression. Therefore, the first aim of the work described in this thesis was to identify genes involved in the progression and repair of glomerulosclerosis, using an animal model that allows a clear distinction between progression and repair after renal injury. The second aim was to gain better insight into the pathogenesis of glomerulosclerosis by investigating the expression and activity of fibrosis-related molecules in an animal model and in patients with renal diseases. Show less
