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1
Muszynska, Dorota. "Gene expression profiling in Keratoconus." Thesis, Queen's University Belfast, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.602693.
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Keratoconus (MIM#148300), a common bilateral, progressive corneal thinning disorder, is the leading indication for corneal transplantation in the developed world. Keratoconus usually arises in the teenage years and presents a significant health burden in work-age adults. Despite the visual and social impact of keratoconus, our lack of understanding of the molecular pathology of keratoconus is a major obstacle to the development of new therapeutic approaches. This study represents the first reported application of massively parallel sequencing of mRNA (RNA-Seq) to perform whole genome transcriptome analysis of keratoconic keratocytes. Genes-enrichment analysis identified several pathway maps that are disrupted in keratoconic keratocytes and associated with the pathogenesis of keratoconus. Microarray gene expression was used to validate differentially expressed genes identified by RNA-Seq in a global manner, whereas quantitative reverse transcriptase polymerase chain reaction was performed on selected candidate genes. Wnt signalling, TGF-beta signalling. ECM-matrix interactions, oxidative stress and inflammatory- related genes were specifically identified in keratoconic keratocytes and implicated in the pathogenesis of keratoconus. Analysis of individual target genes identified altered expression of both known and novel keratoconus-related genes, in particular, SFRP1, BMP4, CBS, POSTN, C0L11Al, COL4Al, SOD1, IL6, and SP3. Functional analyses and expression profiling of keratoconic keratocytes harbouring a novel heterozygous missense mutation (c.l920G>T; p.Gln640His) in the zinc finger E-box binding gene 1 (ZEB1) was also performed. The mutant ZEB1 protein was stable and localised to the nucleus resulting in an enhanced transcriptional repressor of known ZEB1 targets, involved in epithelialmesenchymal transition and collagen synthesis. This ZEB1 mutation results in a gain-In-function with enhanced transcriptional repression of a number of gene targets associated with keratoconus, corneal thickness and Fuchs endothelial corneal dystrophy. This study has identified a number of molecular targets for keratoconus and provides a significant insight into the gene pathways involved in keratoconus pathogenesis. Further functional studies can build on this evidence to interrogate disease pathogenesis, identify novel genes and develop molecular therapies for keratoconus.
2
Leonard, Pauline Catherine. "Gene expression profiling of osteosarcoma." Thesis, University College London (University of London), 2006. http://discovery.ucl.ac.uk/1445814/.
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Purpose: The aim of the work described in this thesis was to determine whether needle core and open biopsies from osteosarcoma (OS) provide sufficient quality of mRNA for cDNA array analyses which might then provide insights into the expression profile of OS. Experimental Design: Sixteen samples collected from OS and two established cell lines were used for array analyses. A primary cell culture was also established from one of the OS biopsies. Total RNA was extracted and probes generated for cDNA arrays. A reference probe was included for computational analyses. Results: cDNA probes were made for twenty five samples. Two of these samples were needle core bone biopsies. Twenty two cDNA probes were used for the generation of microarray data. Previous established statistical analysis confirmed the reliability of array data obtained in sixteen of the twenty two samples. Known genes involved in bone metabolism, osteoblast differentiation and cancer cell growth, were identified as up- or down-regulated in OS. Conclusions: Without amplification of RNA, OS tissue including small core bone biopsies, are amenable to cDNA array analysis. Known and novel putative markers for OS, that could have prognostic value, were identified.
3
Hägg, Sara. "Gene Expression Profiling of Human Atherosclerosis." Doctoral thesis, Linköpings universitet, Biologiska Beräkningar, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-52085.
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Atherosclerosis is a progressive inflammatory disease that causes lipid accumulation in the arterial wall, leading to the formation of plaques. The clinical manifestations of plaque rupture—stroke and myocardial infarction—are increasing worldwide and pose an enormous economic burden for society. Atherosclerosis development reflects a complex interaction between environmental exposures and genetic predisposition. To understand this complexity, we hypothesized that a top-down approach—one in which all molecular activities that drive atherosclerosis are examined simultaneously—is necessary to highlight those that are clinically relevant. To this end, we performed whole-genome expression profiling in multiple tissues isolated from patients with coronary artery disease (CAD). In the Stockholm Atherosclerosis Gene Expression (STAGE) study, biopsies of five tissues (arterial wall with and without atherosclerotic lesions, liver, skeletal muscle and visceral fat) were isolated from 124 CAD patients undergoing coronary artery bypass grafting surgery (CABG) at the Karolinska University Hospital, Solna and carotid lesions from 39 patients undergoing carotid artery surgery at Stockholm Söder Hospital. Detailed clinical characteristics of these patients were assembled together with a total of 303 global gene expression profiles obtained with the Affymetrix GeneChip platform. In paper 1, a two-way clustering analysis of the data identified 60 tissue clusters of functionally related genes. One cluster, partly present in both visceral fat and atherosclerotic lesions, related to atherosclerosis severity as judged by coronary angiograms. Many of the genes in that cluster were also present in a carotid lesion cluster relating to intima-media thickness (IMT) in the carotid patients. The union of all three clusters relating to extent of atherosclerosis—referred to as the “A-module”—was overrepresented with genes belonging to the transendothelial migration of leukocyte (TEML) pathway. The transcription co-factor, Lim domain binding 2 (LDB2), was identified as putative regulator of the A-module and TEML pathway in validation studies including Ldb2-/- mice. In paper 2, we investigated the increased incidence of postoperative complications in CABG patients with diabetes. Using the STAGE compendium, we identified an anti-inflammatory marker, dual-specificity phosphatase 1 (DUSP1), as a novel preoperative blood marker of risk for a prolonged hospital stay after CABG. In paper 3, plaque age was determined with C14-dating in the carotid patients. Interestingly, the strongest correlation with plaque age was not the age of the patients or IMT. Rather, the strongest correlations were with plasma insulin levels and inflammatory gene expression. Taken together, the findings in this thesis show that a top-down approach using multi-tissue gene expression profiling in CAD and C14-dating of plaques can contribute to a better understanding of the molecular processes underlying atherosclerosis development and to the identification of clinically useful biomarkers.
4
Bain, Peter A., and n/a. "Gene Expression Profiling of Cylindrospermopsin Toxicity." Griffith University. School of Biomolecular and Physical Sciences, 2007. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20080404.145834.
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Cylindrospermopsin (CYN) is a toxic alkaloid produced by several freshwater cyanobacterial species, the most prevalent in Australian waters being Cylindrospermopsis raciborskii. The occurrence of CYN-producing cyanobacteria in drinking water sources worldwide poses a potential human health risk, with one well-documented case of human poisoning attributed to the toxin. While extensive characterisation of CYN-induced toxicity has been conducted in rodents both in vivo and in primary cell cultures, little is known about mechanisms of toxicity in human cell types. This thesis describes studies undertaken to further define the molecular mechanisms of CYN toxicity in human cells. Concentration-response relationships were determined in various cultured human cell types using standard toxicity assays. As expected, CYN caused dose-dependent decreases in the growth of three cell lines, HepG2, Caco-2 and HeLa, and one primary cell type, human dermal fibroblasts, according to tetrazolium reduction assays. CYN treatment did not disrupt cellular membranes according to the lactate dehydrogenase release assay in HepG2 or Caco-2 cells after 24, 48 or 72 h exposure, but did cause membrane disruption in fibroblasts after 72 h exposure to relatively high concentrations of the toxin. Apoptosis occurred more readily in HeLa cells than HepG2 cells or fibroblasts, with 72 h exposure to 1 &mug/mL required before statistically significant rates of apoptosis occurred in the latter cell types. CYN did not appear to directly affect the structure of actin filaments or microtubules under the conditions used in the present study. The major portion of the work presented in this thesis comprises a large-scale interrogation of changes in gene expression induced by the toxin in cultured cells. To assess the effects of CYN on global gene expression, relative messenger RNA (mRNA) levels in human dermal fibroblasts and HepG2 cells after 6 h and 24 h exposure to 1 &mug/mL CYN were determined using oligonucleotide microarrays representing approximately 19 000 genes. Overall, the number of transcripts significantly altered in abundance was greater in fibroblasts than in HepG2 cells. In both cell types, mRNA levels for genes related to amino acid biosynthesis, carbohydrate metabolism, and protein folding and transport were reduced after CYN treatment, while transcripts representing genes for apoptosis, RNA biosynthesis and RNA processing increased in abundance. More detailed data analyses revealed the modulation of a number of stress response pathways—genes regulated by NF-&kappaB were induced, DNA damage response pathways were up-regulated, and a large number of genes involved in endoplasmic reticulum stress were strongly down-regulated. Genes for the synthesis and processing of mRNA, tRNA and rRNA were strongly up-regulated, indicating that CYN treatment may increase the turnover of all forms of cellular RNA. A small group of genes were differentially expressed in HepG2 cells and fibroblasts, revealing cell-specific responses to the toxin. Selected changes in transcript level were validated using real-time quantitative reverse transcriptase PCR (qRT-PCR). The modulation of stress response pathways by CYN, indicated by microarray analysis, was further investigated using other methods. The role of tumour suppressor protein p53 in CYN-mediated gene expression was confirmed by measuring the expression of known p53-regulated genes following CYN treatment of HepG2 cells and human dermal fibroblasts using qRT-PCR. Western blotting of protein extracts from CYNtreated cells showed that p53 protein accumulation occurred in HepG2 cells, providing additional evidence of the activation of the p53 pathway by CYN in this cell line. The immediate-early genes JUN and FOS were found to be induced by CYN in a concentration-dependent manner, and MYC was induced to a lesser extent. The mitogen-activated protein kinase c-Jun NH2-terminal kinase, implicated in the ribotoxic stress response initiated by damage to ribosomal RNA, appeared to become phosphorylated in HeLa cells after CYN exposure, suggesting that ribotoxic stress may occur in response to CYN in at least some cell types. The expression of a reporter gene under the control of a response element specific for NF-&kappaB was induced at the mRNA level but inhibited at the protein level. This shows that while transcription factors such as p53 and NF-&kappaB are apparently activated in response to the toxin, transactivation of target genes may not necessarily manifest a corresponding increase at the protein level. The current work contributes significantly to the current understanding of cylindrospermopsin toxicity in human-derived cell types, and provides further insight into putative modes of action.
5
Beijnum, Judith Rosina van. "Gene expression profiling of tumor angiogenesis." Maastricht : Maastricht : Universiteit Maastricht ; University Library, Maastricht University [Host], 2006. http://arno.unimaas.nl/show.cgi?fid=7710.
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Al-Halabi, Hani. "Gene expression profiling in adult Medulloblastoma." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=107616.
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Medulloblastoma (MB) represents approximately 1% of adult brain tumours, and as such is a poorly studied disease. It exhibits different clinical manifestations and outcome in adults, yet it is still treated as per pediatric protocols. Recently, gene expression profiling studies suggested the existence of at least 4 molecular subtypes in pediatric MB, characterized by distinct genetic profiles, activation of oncogenic pathways and varied clinical outcomes. This has refined our ability to classify MB, select tumors for targeted therapy and is leading the way to individualized medicine. It is unknown whether adult MB has its unique molecular signature and whether biologic differences underlie the clinical discrepancies observed in the adult population. We hypothesized that MB displays age-related biological differences and to further characterize these differences; we studied the gene expression profiles of a cohort of adult MB and compared them to a pediatric MB dataset. We found a preponderance of SHH pathway activation amongst adult MB tumours (26/31, 84%). This is in support with evolving data that have identified SHH signature in 75% of adult MB. In view of reports on the good clinical response observed with the use of selective SHH inhibitors in SHH driven MB, our results suggest that the adjuvant use of these agents may improve outcomes in adult MB and should be investigated within a prospective trial. Sonic hedgehog active adult MB represent a homogenous tumor population, which exhibits differences in molecular profiles compared to pediatric SHH driven MB. The later potentially explains the variable outcome between adults and infants with SHH MB, and outlines potential targets of MB tumorigenesis in adults. This thesis offers new insights into age based molecular differences in MB and highlights adult patients as potential targets for selective therapy targeting the SHH pathway.<br>Le médulloblastome (MB) représente environ 1% des tumeurs du cerveau adulte, et en tant que telle est une maladie peu étudiée. Il présente différentes manifestations cliniques et differents résultats chez les adultes, mais il est encore traité selon les protocoles pédiatriques. Récemment, des études d'expression de profil génétique suggére l'existence d'au moins 4 sous-types moléculaires pour le MB pédiatriques, caractérisées par des profils génétiques distincts, par l'activation des voies de signallisation oncogéniques et par des résultats cliniques variées. Cela a amélioré notre capacité de classifier le MB, a mieux sélectionné les tumeurs pour le traitement ciblé et ouvre la voie à une médecine individualisée. On ignore si le MB adulte possede une signature moléculaire unique et si ce sont des différences biologiques qui expliquent les différences cliniques observées dans la population adulte. Nous proposons que le MB possede des différences biologiques qui varie en fonction de l'âge et afin de mieux caractériser ces différences, nous avons étudié les profils d'expression génetique d'une cohorte de MB adultes et les ont comparés à une base de données de MB pédiatrique. Nous avons trouvé une prépondérance d'activation de la voie SHH parmi les tumeurs de MB adulte (26/31, 84%). Ceci supporte les données qui ont identifié la signature SHH dans 75% des MB adultes. Compte tenu des rapports sur la bonne réponse clinique observée avec l'utilisation d'inhibiteurs sélectifs de Shh dans le MB à SHH, nos résultats suggèrent que l'utilisation adjuvante de ces agents peut améliorer les résultats pour le MB adulte et devrait être étudiée dans une étude prospective. Le MB adulte avec Sonic hedgehog actif représente une population homogène de tumeur, et présente des différences dans les profils moléculaires par rapport au MB pédiatriques à SHH. Cela pourrait expliquer les résultat variable entre adultes et enfants avec le MB à SHH, et décrit des cibles potentielles de la tumorogenèse du MB chez les adultes. Cette thèse propose de nouveaux aperçus sur l'effet de l'âge sur les différences moléculaires pour le MB et met en évidence que les patients adultes representent des cibles potentielles pour la thérapie de ciblage sélectif de la voie SHH.
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Goh, Huey Tse. "Profiling cardiac gene expression during endotoxaemia." Thesis, University of Nottingham, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.523087.
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Brooks, W. M. "Profiling gene expression in Alzheimer's disease." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596943.
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Alzheimer’s disease is a debilitating neurodegenerative disease expected to increase in prevalence during the next few decades. Familial Alzheimer’s disease cases have revealed some molecules that appear to be involved in the disease pathogenesis. However, factors fully explaining the vast majority of case of Alzheimer’s disease which are sporadic, wait to be determined. The present study conducted a broad survey of gene expression in Alzheimer’s disease post mortem tissue with the aim of identifying gene expression products involved in this disease. Initially, a study was carried out to determine the effects of post mortem interval on gene expression assessment by cDNA array hybridisation. This study used mouse tissue in which the post mortem delay prior to freezing could be controlled. Observations from this study led to the conclusion that it is acceptable to assess gene expression in samples with varying PMIs. Samples derived from Alzheimer diseased and control human post mortem tissues were then compared to reveal differences in gene expression at the RNA level. The brain area under investigation was the hippocampus which is important for memory and is known to be affected in Alzheimer’s disease. Initially, five samples (2 Alzheimer’s disease, 3 controls) were screened against Affymetrix GeneChip HG-U133A arrays . The findings from this study were used, along with findings reported by other researchers, to identify candidates whose expression appeared to be altered in Alzheimer’s disease. Semi-quantitative Real-Time PCR was used to verify differential expression of the genes of interest in a greater number of samples (6 Alzheimer’s disease, 5 controls). This resulted in the identification of 13 statistically significant differentially expressed genes in Alzheimer’s disease from the 67 investigated. These included transcripts involved in ubiquitination, neurotransmission and energy metabolism amongst others. The biological significance of these findings is discussed.
9
Cleator, Susan Jane. "Gene expression profiling of breast cancers." Thesis, Institute of Cancer Research (University Of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.423120.
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10
Bain, Peter A. "Gene Expression Profiling of Cylindrospermopsin Toxicity." Thesis, Griffith University, 2007. http://hdl.handle.net/10072/367068.
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Cylindrospermopsin (CYN) is a toxic alkaloid produced by several freshwater cyanobacterial species, the most prevalent in Australian waters being Cylindrospermopsis raciborskii. The occurrence of CYN-producing cyanobacteria in drinking water sources worldwide poses a potential human health risk, with one well-documented case of human poisoning attributed to the toxin. While extensive characterisation of CYN-induced toxicity has been conducted in rodents both in vivo and in primary cell cultures, little is known about mechanisms of toxicity in human cell types. This thesis describes studies undertaken to further define the molecular mechanisms of CYN toxicity in human cells. Concentration-response relationships were determined in various cultured human cell types using standard toxicity assays. As expected, CYN caused dose-dependent decreases in the growth of three cell lines, HepG2, Caco-2 and HeLa, and one primary cell type, human dermal fibroblasts, according to tetrazolium reduction assays. CYN treatment did not disrupt cellular membranes according to the lactate dehydrogenase release assay in HepG2 or Caco-2 cells after 24, 48 or 72 h exposure, but did cause membrane disruption in fibroblasts after 72 h exposure to relatively high concentrations of the toxin. Apoptosis occurred more readily in HeLa cells than HepG2 cells or fibroblasts, with 72 h exposure to 1 µg/mL required before statistically significant rates of apoptosis occurred in the latter cell types. CYN did not appear to directly affect the structure of actin filaments or microtubules under the conditions used in the present study. The major portion of the work presented in this thesis comprises a large-scale interrogation of changes in gene expression induced by the toxin in cultured cells. To assess the effects of CYN on global gene expression, relative messenger RNA (mRNA) levels in human dermal fibroblasts and HepG2 cells after 6 h and 24 h exposure to 1 µg/mL CYN were determined using oligonucleotide microarrays representing approximately 19 000 genes. Overall, the number of transcripts significantly altered in abundance was greater in fibroblasts than in HepG2 cells. In both cell types, mRNA levels for genes related to amino acid biosynthesis, carbohydrate metabolism, and protein folding and transport were reduced after CYN treatment, while transcripts representing genes for apoptosis, RNA biosynthesis and RNA processing increased in abundance. More detailed data analyses revealed the modulation of a number of stress response pathways—genes regulated by NF-?B were induced, DNA damage response pathways were up-regulated, and a large number of genes involved in endoplasmic reticulum stress were strongly down-regulated. Genes for the synthesis and processing of mRNA, tRNA and rRNA were strongly up-regulated, indicating that CYN treatment may increase the turnover of all forms of cellular RNA. A small group of genes were differentially expressed in HepG2 cells and fibroblasts, revealing cell-specific responses to the toxin. Selected changes in transcript level were validated using real-time quantitative reverse transcriptase PCR (qRT-PCR). The modulation of stress response pathways by CYN, indicated by microarray analysis, was further investigated using other methods. The role of tumour suppressor protein p53 in CYN-mediated gene expression was confirmed by measuring the expression of known p53-regulated genes following CYN treatment of HepG2 cells and human dermal fibroblasts using qRT-PCR. Western blotting of protein extracts from CYNtreated cells showed that p53 protein accumulation occurred in HepG2 cells, providing additional evidence of the activation of the p53 pathway by CYN in this cell line. The immediate-early genes JUN and FOS were found to be induced by CYN in a concentration-dependent manner, and MYC was induced to a lesser extent. The mitogen-activated protein kinase c-Jun NH2-terminal kinase, implicated in the ribotoxic stress response initiated by damage to ribosomal RNA, appeared to become phosphorylated in HeLa cells after CYN exposure, suggesting that ribotoxic stress may occur in response to CYN in at least some cell types. The expression of a reporter gene under the control of a response element specific for NF-?B was induced at the mRNA level but inhibited at the protein level. This shows that while transcription factors such as p53 and NF-?B are apparently activated in response to the toxin, transactivation of target genes may not necessarily manifest a corresponding increase at the protein level. The current work contributes significantly to the current understanding of cylindrospermopsin toxicity in human-derived cell types, and provides further insight into putative modes of action.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>School of Biomolecular and Physical Sciences<br>Faculty of Science, Environment, Engineering and Technology<br>Full Text
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Paon, Lenaic Marie Pierre. "Gene expression profiling of metastatic gastric cancer." Thesis, University of Liverpool, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490659.
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Gastric cancer is one of the main cancers in the world, and is responsible for a large number of deaths each year. In Europe, the main issue is that it is only detected at latter stages, when metastases have developed. Although metastasis is the main cause of death from such tumours, the process is a very complex one and still not fully understood. In order to unravel this mechanism, microarrays have been used to study the expression pattern of a large number of genes in primary tumours and metastatic samples. These studies aim at indentifying genes that may playa role in metastasis. A number of microarray studies have already been carried out on gastric cancer to pursue knowledge. However, they have been mainly carried out in Asian populations, which are thought to present different gastric tumours than Europeans, possibly due to genetic and environmental parameters. The present thesis therefore aimed to carry out the first microarray study on gastric tumours from a European population, to identify genes that might playa role in gastric cancer metastasis, and assess whether there were any differences between Asian and European samples. In order to achieve this aim, the printing of in-house microarrays and methods to amplify and hybridise the samples first needed to be developed. This included the development of a new amplification method, the SMARTff7 protocol. Results showed that this method allowed more genes to be amplified than with an .established protocol. In addition, a microarray study published in 2003 identified a metastasis specific gene expression signature that could differentiate between metastatic and nonmetastatic primary tumours from different sites. However, this study did not include samples from gastric cancer. It was thus decided to test whether this signature could be applied to primary gastric tumours, using the new MetriGenix® platform. Although the analysis seemed to indicate that the signature did not apply to gastric tumours, technical issues meant that the results were inconclusive. On the other hand, a larger microarray analysis using the techniques developed during this project allowed the indentification of a number of genes of interest which may playa role in the metastatic spread of gastric cancer.
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Quinn, Michael Corwin James, and n/a. "Gene expression profiling of human granulosa cells." University of Otago. Department of Anatomy & Structural Biology, 2005. http://adt.otago.ac.nz./public/adt-NZDU20070501.144002.
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Human granulosa cells play an important role in the follicle, providing the oocyte with nutrients and growth factors to ensure successful ovulation. Normal granulosa cell functioning is thus crucial to human fertility. By studying their transcriptome, the mechanisms underpinning follicle development and infertility will be better understood.
In this study, granulosa cells were retrieved at the time of oocyte removal for in vitro fertilization (IVF). Cells were purified through a combination of a Percoll gradient to remove red blood cells and positive selection of granulosa cell aggregations. On average, contamination by white blood cells was 2% as measured by FACS analysis using specific white blood cell markers. Histological and electron microscopy of granulosa cell aggregations did not detect evidence of resident ovarian white blood cells. This technique provided a good source of pure, healthy granulosa cells for RNA extraction and subsequent gene expression studies.
The construction of a human granulosa cell SAGE library derived 1689 SAGEtags and 1289 discrete mRNA transcripts. SAGEtags for a number of well recognized granulosa cell genes (FSH receptor, follistatin, connexin 43) were found in addition to hormone receptors, multiple kinases, structural genes, apoptosis related genes and secreted proteins. A variety of other SAGE libraries were downloaded from SAGEmap (two ovary epithelium, ovary, white blood cell, brain, cerebellum, heart, liver, lung, kidney, pancreas and universal human reference) and compared to the human granulosa cell library. This was based on two measures: a gene specificity score (GSS) and a tissue specificity score (TSS). Three SAGEtags were identified with high levels of expression in granulosa cells, but no or low expression in the other libraries. These were retinol binding protein 1 (RBP 1), scavenger receptor class B member 1 (SCARB 1) and hydroxysteroid (11-beta) dehydrogenase 1 (11-β-HSD). Library comparisons were validated by real time RT-PCR. The TSS score revealed granulosa cells were most similar to the universal reference library and least similar to liver.
Granulosa cell samples were collected from woman undergoing IVF for a range of infertility disorders. These included polycystic ovary syndrome (PCOS), tubal disease, endometriosis and idiopathic (unknown). Gene expression was compared between these groups using real time RT-PCR. Candidate genes included RBP 1, 11-β-HSD, SCARB 1, FSH receptor, follistatin, decidual protein induced by progesterone, and progesterone membrane receptor component 1 and 2. Granulosa cell gene expression was significantly different (p<0.05) from human white blood cells. No differences were found in gene expression levels between the infertility disorders. Analysis of each patient, however, revealed individuals with marked over-expression of selected genes.
The technique of Generation of Longer cDNA fragments for Gene Identification (GLGI) was used to investigate seven SAGEtags that did match known genes or ESTs. Although no novel genes were characterized, a further 14 granulosa cell transcripts were identified by this technique.
This thesis used an integrated approach to the study of human granulosa cell gene expression. This has involved development of a purification method, the use of a high-throughput technique (SAGE), bioinformatics tools to identify candidates genes, real time RT-PCR to investigate gene expression of particular genes in infertility disorders and finally a technique with the potential to characterize unknown SAGEtags (GLGI). This systematic approach has advanced the understanding of gene expression in human granulosa cells and identified avenues for future research into folliculogenesis and human infertility.
13
Geatrell, Jenny. "Apoptosis gene expression profiling in lens development." Thesis, Cardiff University, 2007. http://orca.cf.ac.uk/54644/.
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During lens development, epithelial cells located at the equatorial region of the lens undergo terminal differentiation to form fibre cells resulting in cell elongation and degradation of all intracellular organelles. Failure to complete this process successfully can result in cataract. This process is thought to be an attenuated form of classical apoptosis. This study was completed to give a comprehensive analysis of apoptosis genes in the developing mouse lens. Macroarrays containing 243 immobilised cDNAs with a known role in apoptosis were utilised to examine the gene expression at different developmental stages. The stages examined were postnatal day 7 and postnatal day 14. Over 100 apoptosis genes were shown to be expressed above background with 20 genes demonstrating significantly differential expression (2-fold or greater change in expression, p-value < 0.05), with highest expression at PI4. PCR confirmed expression of all the genes identified from the array results, and differential expression was confirmed for 52% of the genes. Protein expression of two selected genes, axl and mcl-1, was demonstrated using western blotting. Lens morphology was examined in transgenic mice generated to contain an extended CAG repeat in the huntingtin gene (one of the genes identified from the arrays). Morphology was compared between homozygote, heterozygote and wild-type mice. The presence of the mutated gene did not affect denucleation during lens differentiation and no statistically significant difference was seen in the dimensions of the organelle free zone (OFZ) of the wild-type and homozygote mice. A cross-species comparison was completed. Gene expression of the genes shown to be highly expressed and differentially expressed from the array results was examined in embryonic chick lenses. From the results of this part of the study expression was seen for 83% of genes. These results add to the argument that the process of differentiation is similar in both mouse and chick lenses.
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Dennis, Jayne L. "Gene expression profiling and classification of adenocarcinoma." Thesis, University of Glasgow, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.411836.
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Sharp, Margaret. "Global gene expression profiling of canine lymphoma." Thesis, Sharp, Margaret (2017) Global gene expression profiling of canine lymphoma. PhD thesis, Murdoch University, 2017. https://researchrepository.murdoch.edu.au/id/eprint/38017/.
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Lymphoma, a cancer of lymphoid tissue, is a relatively common form of canine malignancy, typically affecting middle-aged to older dogs, with a higher prevalance among certain breeds. Treatment choices and more precise diagnosis and classification for this disease are currently limited by deficiencies in our understanding of the underlying pathogenic mechanisms and by a lack of useful biomarkers. As with other forms of cancer, canine lymphoma is likely to be a molecular disease resulting from the abnormal expression of genes involved in fundamental cell processes such as cell differentiation, proliferation and apoptosis. Thus, molecular tools such as gene expression microarrays, which permit the analysis of thousands of genes in parallel, have the potential to greatly enhance our understanding of lymphoma pathogenesis in the dog, as previously achieved for human lymphoma.
In this study, gene expression profiling (GEP) of 45 canine lymphomas (36 B cell and 9 T cell) and 10 clinically normal canine lymph nodes was carried out using the Affymetrix Canine Genome 2.0 GeneChip microarray system. This showed that canine B cell lymphoma and T cell lymphoma could easily be distinguished from each other, as well as from non-diseased lymph node tissue. Within the B lymphoma specimens, which were dominated by DLBCL cases, there was a close molecular similarity and B lymphoma samples with a histological diagnosis of Burkitt-like (BL) were generally indiscernible as a subgroup. Significantly, however, gene expression profiling could subdivide the B cell lymphomas overall into two closely related molecular subgroups (designated B1 and B2). Direct comparison of this data with previously published canine lymphoma microarray data (the Frantz cohort), upheld these B lymphoma subgroups and confirmed the existence of two previously identified T lymphoma subgroups (high grade T-LBL and low grade TZL), in which all 9 T lymphoma specimens in this study corresponded to the high grade T-LBL subgroup.
Comparison of gene expression patterns of both the B cell and T cell lymphomas with non-diseased lymph nodes, revealed a preponderance of cell cycle genes and genes encoding components of various lymphocyte signalling pathways. A similar result was seen within the T lymphomas when the high-grade (T-LBL) subgroup was compared with the low grade (TZL) specimens. This was strongly indicative of tumour cells with drastically altered proliferative and survival capabilities. The B lymphomas also showed a marked decrease in gene transcripts associated with cell adhesion. An attempt to identify a gene signature common to both B cell and T cell lymphomas identified relatively few genes. However, among these were several coding for haemoglobin molecules, suggesting that an ability to scavenge oxygen in a hypoxic tumour environment might be an important feature of lymphomas in general. The discovery of highly related, yet discernible, canine B lymphoma (mainly DLBCL) subgroups prompted additional assessment of whether the B lymphomas would segregate according to two key molecular signatures defined for human DLBCL, namely stromal-1 (mesenchymal-like with strong extracellular matrix representation) and stromal-2 (angiogenic with increased blood vessel density). While a direct correspondence between human and canine was not readily apparent, a canine B lymphoma subgroup, largely congruent with identified subgroup B2 and referred to as the stromal subgroup, was revealed which appeared somewhat analogous to human stromal-1 signature with very high expression of genes associated with the extracellular matrix together with diffuse collagen staining histologically. This signature, which included the key regulator CTGF (connective tissue growth factor) as well as genes involved in cell adhesion, may underlie those canine tumours exhibiting a fibrotic reaction.
Using a set of 25 genes (16 on the full cohort of specimens and 9 on subsets of the cohort), the microarray data were validated by use of the independent technique of quantitative reverse transcription PCR (qRT-PCR) analysis. To further extend the study, the possibility of using routine archival formalin-fixed paraffin-embedded (FFPE) lymphoma specimens for qRT-PCR was explored. Using modified techniques for extraction of suitable RNA from FFPE tissue, highly valid results were obtained, although a lower signal-to-noise ratio compared to using unfixed tissue necessitated the use of higher cDNA template concentrations and effectively precluded the analysis of genes that exhibited only a low fold-change in mRNA expression. The ability to use archival FFPE tissues for measurement of gene expression has great potential for large-scale retrospective studies to aid the discovery of disease classifiers and therapeutic targets in canine lymphoma.
In summary, this study has shown at a molecular level that canine lymphoma has some degree of similarity with its human counterpart and that it can be stratified into distinct molecular subgroups on the basis of gene expression profiling. A better understanding of the pathogenesis of this tumour type will facilitate efforts to improve classification, discover diagnostic and prognostic biomarkers, and guide treatment decision-making, with the overall aim of improving lymphoma management and clinical outcomes.
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Gould, Barbara. "The genomics of labour : global gene expression profiling and oxytocin receptor gene expression." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84251.
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Premature labour and subsequent premature birth is a leading cause of neonatal morbidity and mortality. We studied marine labour at term and preterm with models of intrauterine infection and ovariectomy using Affymetrix microarray U74Av2 (containing 12,488 probe sets) and real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) to identify novel candidate genes involved in normal and preterm labour. Strict statistical analysis revealed 320, 188, and 74 genes to be significantly induced or suppressed during normal, infection-induced, and ovariectomy-induced labour, respectively. Novel genes identified include: associated with normal labour: alpha fetoprotein, apolipoprotein A1, fibrinogen polypeptides, cytochrome P45011a, Purkinje cell protein 4 (PCP4), and chloride channel calcium activated 3; associated with infection: numerous inflammatory mediators, alpha fetoprotein, apolipoprotein Al, and fibrinogen polypeptides. Small proline-rich protein 2 family genes were induced by ovariectomy and infection. PCP4 gene was induced after ovariectomy, but suppressed at normal labour. Only seven genes were significantly regulated (each induced) at labour in all models implying that unique gene networks are involved in normal and preterm labour induced by various stimuli. These included genes for plasminogen activator inhibitor 1 and for contraction associated proteins (CAPS) required for uterine activation and uterotonin stimulation of contractions.<br>The oxytocin receptor (OTR) gene encodes one such CAP. Northern blot and real-time RT-PCR demonstrated its up-regulation prior to labour in each model, preferentially in normal labour. Uterine contraction promotes increased central and peripheral oxytocin release and synaptic plasticity. To further examine the role of the OTR, we developed an OTR-lacZ reporter mouse. We mapped, by X-gal histochemistry, the distribution of OTR gene expression in the early postparturient mouse brain and identified novel regions of expression. These included the piriform cortex, entorhinal cortices, and parasubiculum, which support memory function. Dorsal tegmental, vestibular, and lateral reticular nuclei expression suggests the transmission of locomotor inputs. Hypoglossal, facial, and spinal trigeminal nuclei support maternal behaviours. We also more accurately demarcated OTR gene expression in the solitary tract nucleus responsible for relaying contraction stimulation of oxytocin release.<br>These studies provide a more accurate knowledge base for the development of successful therapies to decrease the incidence of premature labour.
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Liu, Zhilin. "Gene expression profiling of bovine ovarian follicular selection." Diss., Columbia, Mo. : University of Missouri-Columbia, 2006. http://hdl.handle.net/10355/4490.
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Thesis (Ph.D.)--University of Missouri-Columbia, 2006.<br>The entire dissertation/thesis text is included in the research.pf file; the official abstract appears in the short.pf file (which also appears in the research.pf); a non-technical general description, or public abstract, appears in the public.pf file. Title from title screen of research.pf file (viewed on May 6, 2009) Vita. Includes bibliographical references.
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Smith, Nolan R. "Gene Expression Profiling in Heat Stressed Scaphirhynchus Sturgeon." OpenSIUC, 2020. https://opensiuc.lib.siu.edu/theses/2759.
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The pallid sturgeon (Scaphirhynchus albus) is a federally endangered species, endemic to the Mississippi River drainage, stretching from the upper Missouri River in Montana to the Mississippi River, and continuing to the Gulf of Mexico. They are largely sympatric throughout this range with a close congener, the shovelnose sturgeon (S. platorhynchus), although speciation may have occurred when they were isolated in different refugia. In this study, we examined gene expression differences among pallid and shovelnose sturgeon families in response to heat stress. Gene expression can be considered a phenotype, and therefore, variability in expression can have an adaptive role in species. Additionally, we compared our results to a previous expression study that utilized RNA-Seq. We developed viable primer pairs for five genes in order to conduct RT-qPCR assays. There were significant differences in heat stress response between pallid and shovelnose sturgeon, potentially indicative of different evolved stress response pathways. Our species results contrasted with results from the previous study, indicating that further research is needed to improve the robustness of the results. Additionally, we found that offspring of hatchery and wild pallid sturgeon demonstrate different responses to heat stress, and potentially general stress that can occur in a hatchery environment. Overall, this study lays the groundwork for future research that can incorporate a larger suite of families to improve the robustness necessary to make actionable management recommendations.
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Arlinde, Christina. "Gene expression profiling in animal models of alcoholism /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-133-4/.
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Dhoogra, Minishca. "Gene expression profiling of polyamine-depleted Plasmodium falciparum." Diss., Pretoria : [s.n.], 2007. http://upetd.up.ac.za/thesis/available/etd-12132007-103643/.
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Hughes, B. "Gene expression profiling of quiescent peripheral T lymphocytes." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604742.
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The <i>lymphopenia </i>mutation, a key factor in the development of autoimmune diabetes mellitus in the BB rat, reduces the <i>in vitro </i>life-span of TCR<sup>hi </sup>single-positive thymocytes and peripheral T cells due to an increased rate of apoptosis. It was proposed that the <i>lymphopenia </i>mutation prevents the accumulation of a normal T cell pool, including regulatory subsets, without preventing the activation and proliferation of reactive T cells, thereby creating conditions appropriate for the development of uncontrolled autoimmune disease. To understand the processes affecting the loss of quiescent peripheral T cells in the lymphopenic rat we must first understand the maintenance and survival of peripheral T cells isolated from ‘normal’ rats. This has broader implications for understanding the genetic maintenance of a healthy peripheral T cell population and avoidance of disease phenotypes (autoimmune and infectious) throughout life. Resting and activated peripheral T cells, isolated from the lymph nodes of the PVG-<i>RT1<sup>u</sup>, </i>RT7<sup>b</sup> rat, were separated by FACSDiVa cell sorting. Total RNA isolated from these cell populations was used in subsequent gene expression profiling experiments with the aim to identify genes involved in the maintenance of T cell quiescence. This thesis describes the process of obtaining highly pure populations of resting and activated T cells for gene expression profiling, using high-density macroarrays. The processes of experimental design, sample preparation, hybridisation, image acquisition, normalisation and data analysis are explained. Profiling results were verified using SYBR Green Real Time PCR.
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Warner, Giles C. "Gene expression profiling of head and neck cancer." Thesis, Queen Mary, University of London, 2004. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1857.
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The purpose of this study was to classify oral squamous cell carcinomas (OSCCs) based on their gene expression profiles, to identify differentially expressed genes in these cancers, and to correlate genetic deregulation with clinical-histopathological data and patient outcome. After conducting proof of principle experiments utilizing six head and neck squamous cell carcinomas (HNSCCs) cell lines, the gene expression profiles of 20 OSCCs and subsequently an additional 8 OSCCs were determined using cDNA microarrays containing 19,200 sequences and the Binary Tree-Structured Vector Quantization (BTSVQ) method of data analysis. Two sample clusters were identified in the group of 20 tumors that correlated with T3-T4 category of disease (P=0.035) and nodal metastasis( p=0.035). Samplec lustering of 28 OSCCsa nd the 6 cell lines revealed a correlation with disease free survival. BTSVQ analysis identified a subset of 23 differentially expressed genes with the lowest quantization error scores in the cluster containing more advanceds taget umors from the 20 OSCC dataset.T he expressiono f six of these differentially expressedg enesw as validated by quantitative real-time RT-PCR. Statistical analysis of quantitative real-time RT-PCR data was performed and, after Bonferroni correction, CLDNI (p = 0.007) over-expressionw as significantly correlated with the cluster containing more advanced stage tumors. Despite the clinical heterogeneity of OSCC, molecular subtyping by cDNA microarray analysis was able to identify distinct patternso f genee xpressiona ssociatedw ith relevant clinical parameters. The application of this methodology represents an advance in the classification of oral cavity tumors, and may ultimately aid in the development of more tailored therapies for oral carcinoma.
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Hime, Audrey Elise. "Gene expression-based profiling for studying dystonia pathogenisis." Thesis, Boston University, 2012. https://hdl.handle.net/2144/12421.
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Thesis (M.A.)--Boston University
PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>This project mainly focuses on DYT6 dystonia and its causative gene: THAP1, which encodes a proposed transcription factor, THAP1, which exhibits sequencespecific and zinc-dependent DNA-binding activity. Over 50 pathogenic mutations have been identified in THAP1, and various clinical manifestations of DYT6 have been reported. The target genes of THAP1 are not fully understood, although some genes involved in cell cycle regulation have been shown to respond transcriptionally to changes in THAP1 levels. While a connection between THAP1 and cellular proliferation has been suggested, the exact relationship is still unclear, and there is an on-going interest in finding out more about the normal function(s) of THAP1 and how these functions are affected by DYT6 mutations. It can be difficult to interpret results from gene expression profiling to further understand a protein's biochemical activities and its basis for pathogenesis. Therefore this project uniquely inputs DYT6 gene expressionbased profiling data into the Connectivity Map, a signature profile reference database and software matching system, to identify known compounds that predict similar and opposite biological signatures as patients with DYT6. The results of this CMAP query show that compounds with strong positive scores, including HDAC inhibitors, HSP90 inhibitors, and phenothiazines, all are associated in the literature with antiproliferative effects. Compounds with strong negative scores show evidence of promoting cell cycle re-entry as well as neurogenesis, which may be considered to be part of a reverse signature of decreased proliferation. Hence bioinformatics analysis may provide clues to THAP1 and its biochemical mechanism of action, specifically in relation to proliferation and the cell cycle.
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Nathanson, Jason Lawrence. "Cell type specific gene expression profiling and targeting /." Diss., View abstract only; access to full text of dissertation for UC campuses will be available after September 1, 2010, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3320635.
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Thesis (Ph. D.)--University of California, San Diego, 2008.<br>Title from first page of PDF file (viewed September 24, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 135-150).
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Ståhlberg, Nina. "Gene expression profiling in molecular studies of hormone actions /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-706-1/.
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Lam, Chi-leung David. "Gene expression profiling in non-small cell lung cancer." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/hkuto/record/B38585777.
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Tan, Wei Min. "Single cell gene expression profiling of human epidermal keratinocytes." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609685.
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Mulaw, Medhanie Assmelash. "Early target genes of CALM/AF10 as revealed by gene expression profiling." Diss., kostenfrei, 2009. http://edoc.ub.uni-muenchen.de/10480/.
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Forsman, M. (Minna). "Histological characteristics and gene expression profiling of Dupuytren’s disease." Doctoral thesis, Oulun yliopisto, 2016. http://urn.fi/urn:isbn:9789526211671.
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Abstract Dupuytren’s disease is a Caucasian male-dominant disease that affects the palmar fascia. Incidence grows with age, but persons with strong diathesis seem to develop the disease at an earlier age than the majority of the diseased. Myofibroblasts are histopathologically the main cell type in DD tissue. Despite scientific research, the aetiology of the disease is still unrevealed. Only genetic susceptibility is generally accepted as predisposing to DD. Available treatment has thus far been unsatisfactory, because only symptoms can be cured to date.The disease recurs. With genetic susceptibility the recurrence rates are high (even up to 70%) and the time to recurrence is inevitably shorter. This behaviour is considered the aggressive type of DD. To be able to predict the behaviour of DD, whether it is an aggressive or conventional type, twenty-one Dupuytren samples were gathered and compared with five controls by means of immunohistochemical stainings. It was found that cellularity was better expresented in aggressive and recurred samples. Alfa-SMA and Ki-67 showed more activity in the aggressive tissue type of DD. Tenascin was vaguely expressed in aggressive-type samples. To compare the gene and protein expressions and to obtain a more profound understanding of the disease, a microarray technique was used. With a microarray it is possible to compare nucleotide pair hybridisations to resolve the genome of the tissues. In this study RT-PCR was used to examine mRNA levels to determine gene expression changes. Twelve DD palmar fascia samples were compared with three healthy control samples. Both myoglobin and ROR2, which we considered as the most valuable results, were found in the DD samples. ROR2 acts as a receptor or co-receptor for the Wnt system. The Wnt signalling pathway transfers signals from outside of the cell through cell surface receptors, and plays a significant role in proliferation processes such as in fibrotic conditions. To evaluate a possible chromosomal imbalance behind the aetiology of the disease, eighteen DD palmar fascia samples were compared with two reference samples. However, we were not able to detect any chromosomal imbalance in the DD samples. The method used was Oligonucleotide aCGH Agilent’s 60-mer oligonucleotide-based microarray according to the manufacturer’s instructions, which can reveal gains and losses of approximately 35 kilobases in the whole genome. The result does not exclude copy number changes entirely; a small presence of aberrant cells will not be detected if the change is less than 50%. In conclusion, we revealed elements in DD tissue that would enable us to predict the nature of the disease; whether the disease is aggressive with a stronger tendency to recur. Histological differences could be detected, and this can be used to benefit patients. As a new element, ROR2 was discovered in DD tissue.The genome-wide analysis with the 44K oligonucleotide-based array method revealed no changes of DNA number sequences<br>Tiivistelmä Kämmenkalvon kuroumatauti eli Dupuytrenin kontraktuura on valkoihoisen miehen kämmenkalvon sairaus. Sairastumisen todennäköisyys lisääntyy ikääntymiseen liittyen, mutta vahva sukurasitus poikkeuksellisesti altistaa sairaudelle jo tavanomaista nuoremmalla iällä. Myofibroblastit ovat tärkein ja edustetuin solutyyppi Dupuytren kudoksessa. Huolimatta runsaasta tutkimustyöstä ei etiologiaa ole saatu vielä selvitettyä. Sukurasitus näyttää selkeästi altistavan taudille. Toistaiseksi kyetään hoitamaan ainoastaan sairauden aiheuttamat seuraukset, mutta ei perussyytä. Lisäksi tauti uusiutuu. Dupuytrenin sukurasitus lisää uusiutumista suurella todennäköisyydellä. Myös uusiutumisaika on tuolloin tavanomaista nopeampi, ja kyseessä katsotaan olevan ns.aggressiivisempi taudin muoto. Väitöskirjatyössäni pyrittiin löytämään mahdollisia tekijöitä, joiden perusteella voitaisiin ennustaan onko kyseessä aggressiivisempi vai tavanomainen taudin muoto. Tätä varten tutkittiin kaksikymmentä yksi Dupuytren kudosnäytettä ja viisi tervettä kämmenkalvon näytettä immunohistologisilla värjäyksillä, ja voitiin todeta, että soluisuus oli selkeästi koholla aggressiivisten ja taudin uusineiden potilaiden näytteissä. Tulos oli samanlainen myös alfa-SMA ja Ki-67 suhteen. Tenaskiiniä voitiin löytää edellisiä niukemmin aggressiivisista näytteistä. Dupuytrenin taudin luonteen lisäselvittelemiseksi geeni- ja proteiinitasolla tehtiin mikroarray, jossa emäsparien pariutumisen avulla selvitetään taudin genomia ja myös sitten tästä aiheutuvien proteiinien ilmentymistä. Kahtatoista Dupuytren potilaan kämmenkalvon kudosnäyttettä verrattiin kolmeen terveeseen verrokki kudosnäytteeseen ja voitiin todeta myoglobiinin ja ROR2:n selkeät pitoisuuden muutokset terveisiin näytteisiin verrattaessa. ROR2 toimii solujen välisten viestien välityksen reseptorina, eli siirtää signaalin solun ulkopuolelta sen sisäpuolelle solun pinnalla olevan kiinnittymiskohdan avulla. Sillä on selkeä merkitys ja tehtävä proliferatiivisissä tapahtumissa, kuten sidekudoksen lisääntymisessä. Mahdollisia kromosomin määrän muutoksia Dupuytren kudoksessa selviteltiin kahdeksantoista kudosnäytteen tutkimisella ja löydösten tulosta verrattiin sitten kahteen normaaliin verrokki kudosnäytteen tulokseen. Tutkimuksessa ei saatu selville kromosomien määrän muutosta, kun muutosten kokonaismäärä on vähäinen tai ainakin alle 50 % kokonaismäärää alhaisempi. Yhteenvetona voidaan todeta, että löytyi histologisia kudoselementtejä, joiden perusteella voidaan ennustaa, onko Dupuyrenin tauti aggressiivisempi ja todennäköisemmin uusiutuva luonteeltaan. ROR2 ei ole aikaisemmin yhdistetty Dupuytrenin kontraktuuraan. Dupuytren kudoksesta ei voitu 44K oligonukleotide mikroarray tekniikalla paljastaa geenimäärien muutoksia
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Rysä, J. (Jaana). "Gene expression profiling in experimental models of cardiac load." Doctoral thesis, University of Oulu, 2008. http://urn.fi/urn:isbn:9789514287664.
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Abstract
Cardiac hypertrophy provides an adaptive mechanism to maintain cardiac output in response to increased workload, and although initially beneficial, hypertrophy eventually leads to heart failure, a major cause of morbidity and mortality in Western countries. The hypertrophic response in cardiac myocytes is accompanied by e.g. activation of signal transduction pathways, such as mitogen-activated protein kinases (MAPKs), and complex changes in gene programming. The purpose of this study was to characterize gene expression patterns in experimental models of cardiac load by using high-throughput DNA microarray technologies.
In the present study, changes in gene expression were evaluated in response to acute pressure overload and prolonged hypertension as well as during the development of left ventricular hypertrophy (LVH) and the transition to diastolic heart failure in an animal model of genetic hypertension, the spontaneously hypertensive rat (SHR). Increased expression of several immediate early genes was seen in response to acute hemodynamic overload in vivo. The transition from LVH to diastolic hypertensive heart failure was almost exclusively associated with changes in genes encoding extracellular matrix proteins and their regulatory processes showing the importance of progressive extracellular matrix remodeling.
The effect of p38 MAPK activation on gene expression patterns in vivo was elucidated. Cardiac-specific overexpression of p38 MAPK resulted in upregulation of genes controlling cell division and inflammation as well as cell signaling and adhesion. Accordingly, the functional role of p38 MAPK was related to myocardial cell proliferation, inflammation and fibrosis.
Finally, temporal analysis of mechanical stretch induced gene expression changes in neonatal rat cardiomyocyte cultures in vitro indicated that mechanical stretch induced complex gene expression profiles, demonstrating that both positive and negative regulators are involved in the hypertrophic process. Many novel stretch responsive genes were identified, and a subset of them may be putative downstream targets of p38 MAPK.
In conclusion, in the present study a number of well-established gene expression changes of cardiac hypertrophy were observed and novel modulators associated with increased cardiac load, such as thrombospondin-4, were identified. The study provides a better understanding of molecular mechanisms associated with increased cardiac load, and may indicate potential targets for novel therapeutic interventions.
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Lam, Chi-leung David, and 林志良. "Gene expression profiling in non-small cell lung cancer." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B38585777.
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Bergman, Julia. "Aspects of Gene Expression Profiling in Disease and Health." Doctoral thesis, Uppsala universitet, Molekylär och morfologisk patologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-312939.
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The aim of this thesis is to in various ways explore protein expression in human normal tissue and in cancer and to apply that knowledge in biomarker discovery. In Paper I the prognostic significance of RNA-binding motif protein 3 (RBM3) is explored in malignant melanoma. To further evaluate the prognostic significance of RBM3 expression was assessed in 226 incident cases of malignant melanoma from the prospective populationbased cohort study Malmö Diet and Cancer Study using tissue microarray technique (TMA). RBM3 was shown to be down regulated in metastatic melanoma and high nuclear expression in the primary tumor was an independent marker of prolonged over all survival. As a tool to facilitate clinical biomarker studies the Human Protein Atlas has created a tissue dictionary as an introduction to human histology and histopathology. In Paper II this work is introduced. A cancer diagnosis can be a complex process with difficulties of establishing tumor type in localized disease or organ of origin in generalized disease. Immunohistochemically assisted diagnosis of cancer is common practice among pathologists where its application combined with known protein expression profiles of different cancer types, can strengthen or help dismiss a suspected diagnosis. In Paper III the diagnostic performance of 27 commonly used antibodies are tested in a predominantly metastatic, multicancer cohort using TMA technique. Overall these 27 diagnostic markers showed a low sensitivity and specificity for its intended use, highlighting the need for novel, more specific markers. Breast, ovarian, endometrial and ovarian cancers affect predominantly women. Differential diagnostics between these cancer types can be challenging. In Paper IV an algorithm, based on six different IHC markers, to differentiate between these cancer types is presented. A new diagnostic marker for breast cancer, namely ZAG is also introduced. In Paper V the transcriptomic landscape of the adrenal gland is explored by combining a transcriptomic approach with a immunohistochemistry based proteomic approach. In the adrenal gland we were able to detect 253 genes with an elevated pattern of expression in the adrenal gland, as compared to 31 other normal human tissue types analyzed. This combination of a transcriptomic and immunohistochemical approach provides a foundation for a deeper understanding of the adrenal glands function and physiology.
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Chang, Xiaoqing. "Bayesian Mixtures and Gene Expression Profiling with Missing Data." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1226090856.
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Nascimento, Helvia. "Caracterização da expressão genica de celulas tumorais de pacientes com adenocarcinoma esporadico do colon." [s.n.], 2007. http://repositorio.unicamp.br/jspui/handle/REPOSIP/310956.
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Orientador: Carmen Silvia Passos Lima, Fernando Ferreira Costa<br>Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas<br>Made available in DSpace on 2018-08-12T11:53:50Z (GMT). No. of bitstreams: 1
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Previous issue date: 2007<br>Resumo: Os mecanismos moleculares envolvidos na origem do adenocarcinoma de cólon esporádico (ACE) ainda não estão completamente elucidados. Recentemente, o método da análise seriada da expressão gênica (SAGE) foi descrito como eficaz para identificar a expressão total de genes de tipos celulares diversos, mas esta análise não foi realizada em células epiteliais purificadas do ACE moderadamente diferenciado. Nós caracterizamos pelo método SAGE a expressão gênica total de células epiteliais neoplásicas do cólon de um paciente com ACE moderadamente diferenciado (SAGE CC) e de células epiteliais normais do cólon de um paciente com megacólon chagásico (SAGE CN). Foram geradas, após o seqüenciamento automático, 44.004 e 43.570 tags totais das bibliotecas SAGE CC e SAGE CN, representando 16.484 e 13.479 tags únicas, respectivamente. Na comparação entre as bibliotecas, 171 transcritos diferencialmente expressos foram identificados (P< 0,001; expressão diferencial = 5), incluindo 10% de transcritos que podem representar genes não descritos. As expressões de 10 genes diferencialmente expressos foram quantificadas pela reação em cadeia da polimerase em tempo real (qPCR) na amostra de células epiteliais neoplásicas (SAGE CC), com o intuito de
validar os resultados obtidos pelo SAGE, e, posteriormente, em amostras de células epiteliais de outros cinco pacientes com o mesmo tipo de doença. As expressões foram concordantes em 80% dos genes (CEACAM6, KLK6, LYZ, PFN1, S100A8, S100A9, VIL2 e ZFHX1B) e discordantes nos demais 20% (PLA1A e ZNF277). As expressões dos genes de interesse, quantificadas pelos dois métodos, foram similares na amostra SAGE CC e nas amostras dos demais pacientes com a doença. Foram observadas expressões anormais de genes envolvidos com a proliferação e diferenciação celular e com a resposta ao stress em células epiteliais neoplásicas. Foram também visualizadas expressões anormais de genes não relacionados com a doença e de genes ainda não identificados. Em conjunto, os nossos resultados podem contribuir para a identificação de genes relacionados com a origem ou a progressão do ACE moderadamente diferenciado e, ainda, para a descoberta de agentes terapêuticos específicos que controlem a proliferação anormal das células neoplásicas.<br>Abstract: The molecular mechanisms involved in sporadic colon adenocarcinoma (SCA) are still not completely elucidated. Recently, the serial analysis of gene expression (SAGE) method has allowed the global analysis of genes expressed in diverse cellular types but there are no studies in purified epithelial cells of SCA moderately differenciated. We have characterized through SAGE the global gene expression of neoplastic epithelial cells from a SCA moderately differenciated patient (SAGE CC) and normal epithelial cells from a megacolon patient (SAGE CN). After automatic sequencing, a total of 44.004 tags from SAGE CC and 43.570 tags from SAGE CN profiles were generated, representing 16.484 and 13.479 unique tags, respectively. Comparing both profiles, 171 differentially expressed transcripts were identified (P< 0.001; fold = 5), including 10.0% that may represent novel transcripts. The expression of 10 selected genes was further investigated by realtime polymerase chain reaction (qPCR) in the SCA moderately differenciated epithelial cells sample (SAGE CC), with the purpose of to validate the results obtained by the SAGE method, and also in five epithelial cells samples from the same type of SCA patients. Similar expressions were seen in 80% (CEACAM6, KLK6, LYZ, PFN1, S100A8, S100A9, VIL2 e ZFHX1B) and discordant expressions were seen in 20% (PLA1A e ZNF277) of analysed genes. On SAGE CC sample and samples of the SCA patients, all genes presented similar expressions measured by both methods. We observed abnormal expression of genes involved with cell proliferation and differentiation, and with response to stress in neoplastic epithelial cells. Also, were found abnormal expressions of genes not related with the disease and not identified genes. Together, our results may contribute for the identification of genes involved in the origin or progression of SCA moderately differenciated, as well as for the discovery of new therapeutical agents, with specific action on abnormal proliferation of the neoplastic cells.<br>Doutorado<br>Ciencias Basicas<br>Doutor em Clínica Médica
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McKinney, Eoin Fergal. "Gene expression profiling in systemic vasculitis and systemic lupus erythematosus." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609786.
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Granberg, Fredrik. "Global Profiling of Host Cell Gene Expression During Adenovirus Infection." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7221.
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McKethan, Brandon Lee Dickstein Rebecca. "Gene expression profiling of the nip mutant in Medicago truncatula." [Denton, Tex.] : University of North Texas, 2007. http://digital.library.unt.edu/permalink/meta-dc-3940.
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Baken, Kirsten Annika. "Immunotoxicogenomics gene expression profiling as a tool to study immunotoxicity /." [Maastricht] : Maastricht : Universitaire Pers Maastricht ; University Library, Universiteit Maastricht [host], 2007. http://arno.unimaas.nl/show.cgi?fid=9329.
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Will, Malcolm B. "Gene expression profiling of mesenchymal stem cells aged in vitro." Thesis, University of Glasgow, 2010. http://theses.gla.ac.uk/1964/.
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Mesenchymal Stem Cells (MSC’s) have shown promise as a cell-based therapy for myocardial repair. However, MSC’s have a finite replicative lifespan and lose proliferative and differentiation capacity during expansion in vitro. Therefore, understanding the molecular mechanisms that regulate ageing and senescence of MSC’s should enhance our ability to use these cells in cell-based approaches and give insight into mechanisms of tissue ageing. We established MSC cultures from the sternal bone marrow of eight donors undergoing coronary artery bypass surgery. After thirty population doublings (nine passages) MSC’s displayed morphological abnormalities, expression of senescence associated β-galactosidase, telomere erosion and decreased adipogenic and osteogenic differentiation capacity. Using serial analysis of gene expression (SAGE) we identified 243 known genes differentially expressed between MSC’s at passages two and nine. Analysis of known direct interactions between genes revealed a regulatory signaling network centered on down-regulation of the transcription factor, activator protein 1 (AP-1). Transcriptional changes in MSC’s at passage nine included genes associated with inflammation, regulation of cell cycle, metabolism and extracellular matrix re-modelling. The validation studies corroborated the SAGE results and eighteen genes were identified as differentially expressed in late passage MSC’s from multiple donors. Furthermore, caveolin 1, cyclin D1, tissue plasminogen activator and olfactomedin-like 3 were able to discriminate MSC’s of different culture age. In addition, we show evidence that the p38 MAPK signalling pathway contributes to the decline in proliferation and differentiation of MSC’s during expansion and is critical for the maintenance of genomic stability. The results provide further evidence that MSC’s senesce prematurely in response to undefined culture stresses. Our studies have provided novel markers that identify MSC ageing in vitro and suggest that identifying factors that activate p38 MAPK signalling should enhance our ability to use MSC’s in cell-based therapies.
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Romero, Claudia. "CELLULAR IMMUNE RESPONSE AND GENE EXPRESSION PROFILING IN CROHN'S DISE." Doctoral diss., University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2704.
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Despite the chronic debate in the etiology of crohn's disease (cd), a debilitating inflammatory bowel disease (ibd) closely related to ulcerative colitis (uc), an emerging interest in a possible mycobacterial role has been marked. Granuloma and pathologic manifestations in cd resemble aspects found in tuberculosis, leprosy and paratuberculosis. The latter, a chronic enteritis in cattle, goat, sheep and primates, which is similar to human enteritis, also known as cd, is caused by a fastidious, slow growing mycobacterium avium subspecies paratuberculosis (map). Due to the similarities between cd and paratuberculosis, a mycobacterial cause in cd has been proposed. Recent discovery of a possible association between nod2/card15 mutations and risk of cd added support to microorganism-host interactions. In this study, a possible mycobacterial role in cd etiology has been evaluated by investigating the presence of map dna, the state of the cellular immune response and microarray gene expression profiling in peripheral blood and surgical tissue from cd, uc and healthy control subjects. Nested pcr detected map dna in tissue from 10/12(83%) cd patients compared to 1/6(17%) non-ibd subjects. Fluorescence in situ hybridization (fish) with the aid of confocal scanning laser microscopy (cslm) detected map dna in 8/12(67%) cd subjects compared to 0/6(0%) in non-ibd subjects. The detection of map dna by either technique in tissue from cd subjects is significant compared to non-ibd subjects (p < 0.05). Map dna was also detected in both inflamed and non-inflamed tissue from patients with cd suggesting map infiltration in human tissue. Correlation of possible map presence and the function of polymorphonuclear leukocytes (pmn) and peripheral blood mononuclear cells (pbmc) in 19 cd patients and 12 controls have been evaluated. Pmn phagocytosis of viable fitc-map was suppressed in 13/19(68%) cd patients compared to 0/12(0%) in healthy controls (p<0.05). Pbmc phagocytosis of viable fitc-map was suppressed in 5/19(26%) of cd patients compared to 0/12(0%) of healthy controls (p<0.05). The proliferative response of pbmc with t-cell majority from cd and controls subjects was evaluated against pha, candida albicans, pwm and map ppd. Dysfunctional proliferative response against pha was found in 8/19(42%) cd patients compared to 1/12(8.3%) in controls suggesting possible t-cell anergy. Pbmc from 11 cd subjects reacted normally to pha, 7/11(64%) reacted strongly to map ppd suggesting previous exposure to mycobacteria, and 3/11(27%) did not react with map ppd suggesting lack of pre-exposure to mycobacteria. From the seven mycobacterial pre-exposed samples, 6/7(86%) showed a normal ability to recall antigens by activated macrophages when exposed to c. Albicans, and all 7 samples had a normal pwm response. Finally, microarray-chip technology was employed to identify the expression profile of genes that have a role in the immune response of cd patients. Rna was isolated from fresh buffy coats from 8 healthy controls, 2 cd, and 1 uc patients. Chips with an estimated of 30,000 human genes were hybridized to cdna from these samples. We found that 17% of the total number of genes was differentially expressed. Over 200 genes were involved in the immune response, 7 genes where common to both forms of ibd (uc and cd), and 8 genes were found to be either downregulated in cd and upregulated in uc or viceversa. The ifngr1 gene, which encodes the ligand-binding chain of the ifn-gamma receptor, was found to be downregulated in 2/2(100%) of cd patients, but not in uc patients. It is known that defects in ifngr1 are a cause of atypical mycobacterial infection and bcg infection. Patients suffering from this deficiency have an immunologic defect predisposing them to infection with mycobacteria. This correlates with the proposed theory as map being the causative agent of cd. Furthermore, the results indicate a host susceptibility requirement for the establishment of mycobacterial infection in cd patients. Further characterization of ifngr1 using real-time pcr is underway. Collectively, detection of map dna in the majority of cd tissue and the alteration in pmn and pbmc to respond efficiently to map may be related to the fact that mycobacterial pathogens infect phagocytic cells of susceptible hosts and consequently the immune response is dysregulated. Furthermore, the fact that a gene linked to mycobacterial susceptibility was found to be downregulated in cd patients only, strengthens the mycobacterial etiology of cd. In general, the data suggest a possible role for a bacterial pathogen in cd pathogenesis.<br>Ph.D.<br>Other<br>Burnett College of Biomedical Sciences<br>Biomolecular Sciences: Ph.D.
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Durrant, Wendy E. "Gene expression profiling of the Cf-9 dependent defence response." Thesis, University of East Anglia, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323392.
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Menon, Suraj. "Integration and biological interpretation of microarry gene expression profiling data." Thesis, Cardiff University, 2009. http://orca.cf.ac.uk/55858/.
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Many different strategies have been developed for the analysis of microarray data and these have a significant influence on the level and quality of knowledge that may be achieved from a microarray-based experiment. Two such strategies are explored in this thesis. Part A of this thesis describes explorations of a resource-efficient strategy that could allow for large-scale integration of microarray data in an unsupervised fashion. For this purpose, comparisons were carried out between a series of genelists manually extracted from the literature, representing a disparate set of microarray experiments. Initial results were highly unexpected, and are likely to have been caused by violations of the assumptions of the hypergeometric test used for assessing comparisons. Statistical modelling was found to successfully simulate these results however the estimated net effect of these violations was found to be considerable. These findings strongly caution against the comparison of microarray experiments using their genelists. Part B then describes the development of Gene Set Discovery (GSD), a novel methodology to perform threshold-free gene set analysis of microarray datasets without requiring sample class information. This was achieved by deriving a novel metric that allows for the selection of those gene sets that exhibit significant discrimination between samples. GSD was implemented on four microarray datasets and the results were found to be biologically plausible and/or in agreement with prior analyses of these datasets. These findings suggested that GSD could be a potentially useful tool for biological theme discovery in microarray datasets, particularly in studies of cancer where sample classification is problematic. Also described is a related methodology for extraction of informative genes from within selected gene sets, and a scheme for visualization of results in an integrated format.
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McKethan, Brandon Lee. "Gene Expression Profiling of the nip Mutant in Medicago truncatula." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3940/.
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The study of root nodule symbiosis between nitrogen-fixing bacteria and leguminous plant species is important because of the ability to supplement fixed nitrogen fertilizers and increase plant growth in poor soils. Our group has isolated a mutant called nip in the model legume Medicago truncatula that is defective in nodule symbiosis. The nip mutant (numerous infections with polyphenolics) becomes infected by Sinorhizobium meliloti but then accumulates polyphenolic defense compounds in the nodule and fails to progress to a stage where nitrogen fixation can occur. Analysis of the transcriptome of nip roots prior to inoculation with rhizobia was undertaken using Affymetric Medicago Genome Array microarrays. The total RNA of 5-day old uninoculated seedlings was analyzed in triplicate to screen for the NIP gene based on downregulated transcript levels in the mutant as compared to wild type. Further microarray data was generated from 10 days post inoculation (dpi) nip and wild type plants. Analysis of the most highly downregulated transcripts revealed that the NIP gene was not identifiable based on transcript level. Putative gene function was assigned to transcripts with altered expression patterns in order to characterize the nip mutation phenotypically as inferred from the transcriptome. Functional analysis revealed a large number of chaperone proteins were highly expressed in the nip mutant, indicating high stress in the mutant prior to infection by rhizobia. Additionally, a database containing the information regarding the nip expression profile at both 0 days post inoculation (dpi) and 10 dpi were created for screening of candidate genes as predicted from sequence in the genomic region containing NIP.
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Jacobsen, Mette Dorph. "Analysis of Candida albicans gene expression using single cell profiling." Thesis, University of Aberdeen, 2005. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU193586.
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Candida albicans is an important fungal pathogen of humans and shows great flexibility in adapting to diverse host niches, which present different ambient pH values, changes in O2 concentrations, various different substrates for metabolism and host defence mechanisms. Knowledge on how these environmental stimuli are sensed by the fungal cells is limited. Here, a bioinformatics approach was employed to search for putative receptors in the C. albicans genome. However, no obvious novel receptor candidates were identified that might function in environmental sensing in C. albicans. Using a GFP-based reporter system gene expression in C. albicans on the single cell level was monitored. To examine responses to ambient pH, the PHR1 and PHR2 promoters, which are regulated in an inverse pH-dependent manner, were used to construct C. albicans strains that could function as pH biosensors in vitro and in vivo. The two strains were used as indicators of ambient pH under various in vitro conditions as well as in ex vivo and in vivo models of infections. In the mouse model of systemic candidiasis the ambient pH in infected kidney tissue appeared to show local variation. The fatty acid beta-oxidation in C. albicans was also examined. Three strains were constructed containing GFP fusions with the promoters of beta-oxidation genes FAA21, POX4 and POT11. The regulation of the three promoters was first studied in vitro and later in different infection models. When introduced into the mouse model of systemic candidiasis differential expression of POX4 and POT11 was observed despite being co-regulated in vitro under the range of conditions examined. Hence, POX4 and POT11 may respond to additional as yet undefined stimuli that are relevant in vivo. Nevertheless, the data indicate that the lipid beta-oxidation is active in some fungal cells growing in the mouse kidney.
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Kan, Takatsugu. "Gene expression profiling in human esophageal cancers using cDNA microarray." Kyoto University, 2003. http://hdl.handle.net/2433/148738.
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Bury, Joanna J. "Gene expression profiling of peripheral tissues in amyotrophic lateral sclerosis." Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/10101/.
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Background: Amyotrophic Lateral Sclerosis, in which cortical and spinal motor neurons degenerate, is a late onset neurodegenerative condition that accounts for ~1 in 400 UK deaths, typically within 3-5 years from the initial manifestations of disease. It forms part of a broad spectrum of clinically, genetically as well as pathologically heterogeneous disorders that include behavioural variant frontotemporal lobar degeneration (bvFTLD). A large intronic hexanucleotide G4C2 repeat expansion of >30 copies was recently identified, in 2011, in the previously uncharacterised chromosome 9 open reading frame 72 (C9ORF72) gene which is now thought to explain up to 43% of familial ALS (~20-30% of familial FTLD) and around 7% of sporadic cases. Rationale & Hypothesis: The principle aim of the PhD was to perform gene expression profiling of peripheral tissues in ALS. In the first instance whole blood was trialled. However, this proved unreliable, owing to the shear abundance of erythrocyte derived alpha and beta haemoglobin transcripts that are contained within the sample and the variability in the efficiency of its removal using the Ambion® GLOBINClear or NuGEN Ovation® WB reduction strategies. Instead disease related changes in transcription/alternative splicing were detected in a large bank (n=820) of patient and control lymphoblastoid cell lines (LCL’s) with the main purpose of: 1) elucidating further the mechanism(s) of neurotoxicity associated with the C9ORF72 G4C2 repeat expansion and, 2) establishing within this specific genetic subtype, modifiers of a fast (<2yrs) versus slow (≥4yrs) disease progression in order to identify potential new areas of therapeutic research. Methodology: Biotinylated, sense-strand cDNA targets of ~40 -70nt were hybridized onto Human Exon 1.0ST GeneChip® Arrays. A GC-RMA normalisation procedure was carried out in Partek® Genomics Suite and differentially expressed or alternatively spliced transcripts were detected at the 5% significance level (p<0.05) with a fold-change threshold of ≥ ±1.20 applied. Findings: Overall a marginal increase in gene transcription was observed with respect to C9ORF72 (59.3%, n=650/1,096) and nonC9ORF72-related_SALS patients (63.9%, n=1,148/1,796) compared to neurologically healthy controls. DAVID enriched gene ontology terms included translation, which was specific to carriers of the G4C2 repeat, in addition to RNA processing, DNA metabolism, RNP complex biogenesis and the cell cycle which reflect more common features of the broader ALS phenotype. A number of key validation targets, including several RNA binding partners of the G4C2 repeat (FUS, RPL22, NUDT2, PURA, EIF4H and HNRNPA0/F) were subsequently confirmed in a qRT-PCR assay. Isoform A/B specific transcripts of the C9ORF72 gene, itself, were found not to be differentially expressed across the LCL’s in the ECACC discovery and replication cohorts. Conclusions: Whether pathogenicity of the G4C2 expanded allele arises as a consequence of haploinsufficiency or through an aberrant gain of function mechanism has yet to be determined; although emerging evidence favours a role of RNA toxicity. In light of this model, an up-regulation in the expression of C9ORF72 binding partners and other, RNA processing & splicing related transcripts fits with the hypothesis that the cells are attempting to compensate for the sequestration of these proteins into toxic RNA foci in the cytoplasm which leads to disruption of their normal physiological function. Small sample sizes meant limited conclusions could be drawn from the analysis of C9ORF72 specific modifiers of survival in ALS. Clinical data points towards a possible effect of gender which is supported in the literature but other factors such as correlations with expansion length would need to be considered in conducting future work.
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Foerster, Susann. "Gene expression profiling of human lymph node-positive gastric adenocarcinomas." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2011. http://dx.doi.org/10.18452/16259.
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In dieser Arbeit wurden Genexpressionsprofile diffuser und intestinaler Magenadenokarzinome mittels Microarray-Technik erstellt. Der intestinale Typ konnte als stark proliferierender Tumor mit signifikanter Überexpression von zellzyklusrelevanten Genen definiert werden, während der diffuse Typ als stark stromaabhängig mit signifikanter Überexpression von Genen der extrazellulären Matrix hervortrat. Thrombospondin 4 (THBS4) wurde dabei als das am stärksten differentiell exprimierte Gen identifiziert, wobei seine mRNA in diffusen Tumoren eminent überexprimiert wird. Immunhistochemische Studien bestätigten diese starke Überexpression auf Proteinebene und zeigten, dass THBS4 eine übermäßig angereicherte extrazelluläre Komponente des Tumorstromas ist. Kolokalisierungsstudien zeigten zudem, dass THBS4-positive Zellen auch positiv für Vimentin und Smooth muscle actin (alpha) sind. Diese Ergebnisse belegen, dass THBS4 von Tumor-assoziierten Fibroblasten (TAF) exprimiert wird. Dies konnte durch zusätzliche in vitro Experimente bestätigt werden, die aufzeigten, dass TAF von diffusen Tumoren eine stärkere THBS4-mRNA Expression aufweisen als normale Fibroblasten des Magens. Abschließend konnten in vitro Kokultur-Studien aufdecken, dass die THBS4-Expression in Fibroblasten durch Tumorzellen diffuser Magentumore transkriptionell stimuliert wird. Metastasenbefall regionaler Lymphknoten (N+) ist bei den meisten Magenadenokarzinomdiagnosen bereits vorhanden. Dieser ist der stärkste derzeit verfügbare Parameter zur Abschätzung der Prognose, reicht aber für eine eindeutige Vorhersage nicht aus. Um ergänzende molekulare Prognoseindikatoren zu identifizieren, wurden aus den Microarray-Daten Gene, deren Expression mit dem klinischen Verlauf von N+ Patienten korreliert, extrahiert. Einige dieser Gene, z.B. RAN binding protein 17 und ras-related associated with diabetes, konnten mittels quantitativer real-time PCR als Marker für verkürztes progressionsfreies Überleben validiert werden.<br>In this work, gene expression profiles of diffuse and intestinal-type gastric adenocarcinomas were established using the microarray technique. The intestinal type was identified to be a highly proliferative entity with significant overexpression of cell cycle-relevant genes, whereas the diffuse type was proven to be strongly stroma-dependent with significant overexpression of extracellular matrix genes. Thrombospondin 4 (THBS4) was identified as the gene most differentially expressed between the two types with vast mRNA overexpression in diffuse-type tumors. Immunohistochemical studies proved overexpression on protein level and elucidated that THBS4 is a heavily accumulated extracellular constituent of the tumor stroma. Colocalization studies uncovered that THBS4-positive cells are also positive for vimentin and alpha-smooth muscle actin. These data signify that THBS4 is expressed by subpopulations of cancer-associated fibroblasts (CAFs). This was further evidenced by in vitro experiments demonstrating that THBS4 mRNA expression is increased in CAFs of diffuse-type tumors compared to normal gastric fibroblasts. Finally, in vitro coculture studies revealed that transcriptional THBS4 expression in fibroblasts is stimulated by diffuse-type gastric tumor cells. Metastatic involvement of regional lymph nodes (N+) usually accompanies diagnosis of gastric adenocarcinoma and is currently considered the most important parameter for assessment of prognosis. However, estimation of prognosis based on this parameter alone is not sufficiently reliable. In order to identify additional molecular prognosis markers, genes whose expression correlates with clinical outcome of N+ patients were extracted from the microarray data. Via quantitative real-time PCR, several genes, e.g. RAN binding protein 17 and ras-related associated with diabetes, were successfully validated to allow an expression-based stratification of patients with respect to disease-free survival.
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Carlén, Lina. "Characterization of psoriasis lesions by protein expression profiling /." Stockholm : Karolinska institutet, 2006. http://diss.kib.ki.se/2006/91-7140-808-8/.
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Boräng, Stina. "Subtracted Approaches to Gene Expression Analysis in Atherosclerosis." Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3684.
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<p>Gene expression analysis has evolved as an extensive toolfor elucidation of various biological and molecular eventsoccurring in different organisms. A variety of techniques andsoftware tools have been developed to enable easier and morerapid means of exploring the genetic information. A moreeffective approach than exploring the whole content of genesexpressed under certain conditions is to study fingerprintassays or to use subtracted cDNA libraries to identify onlydifferentially expressed genes.</p><p>The objective for the work in this thesis has been toexplore differentially expressed genes in atherosclerosis. Thiswas done by applying and modifying a protocol for thesubtractive approach RDA (Representational Difference Analysis)in different model systems.</p><p>Initially, the molecular effects of an anti-atheroscleroticdrug candidate were elucidated. In addition, two alternativeapproaches to identify differentially expressed genes obtainedafter iterative rounds of RDA subtraction cycles wereevaluated. This revealed that in most cases, the shotgunapproach in which the obtained gene fragments are clonedwithout any prior selection has clear advantages compared tothe more commonly used selection strategy, whereby distinctbands are excised after gel electrophoresis.</p><p>A key process in the atherosclerotic plaque initiation isthe phenotypic change of macrophages into foam cells, which canbe triggered in a model system by using macrophages exposed tooxidised LDL. To investigate the genes expressed in thisprocess, the RDA technique was combined with microarrayanalysis, which allows for selectivity and sensitivity throughRDA, as well as rapid high-throughput analysis usingmicroarrays. The combination of these techniques enablessignificant differences in gene expression to be detected, evenfor weakly expressed genes and the results to be reliablyvalidated in a high throughput manner.</p><p>Finally, investigation of the focal nature ofatherosclerotic lesions and gene expression profiling werestudied using in vivo aortic tissues from ApoE-/- and LDLR -/-mice. The study was based on a comparison between localisationsthat are likely, and others that are unlikely, to developatherosclerotic plaques, and the RDA technique was employed toexplore differential gene expression.</p><p><b>Keywords:</b>Representational Difference Analysis,atherosclerosis, gene expression profiling</p>
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Bjork, Kathe Elizabeth. "Robust identification of differential gene expression and discrimination /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.
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Thesis (Ph.D. in Biostatistics) -- University of Colorado at Denver and Health Sciences Center, 2006.<br>Typescript. Includes bibliographical references (leaves 237-239). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;