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1
Li, Yan 1978 July 15. "Gene expression array simulator." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/87263.
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Thesis (M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, June 2002.<br>"May 10, 2002.<br>Includes bibliographical references (leaf 141).<br>by Yan Li.<br>M.Eng.
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Mapiye, Darlington S. "Normalization and statistical methods for crossplatform expression array analysis." University of the Western Cape, 2012. http://hdl.handle.net/11394/4586.
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>Magister Scientiae - MSc<br>A large volume of gene expression data exists in public repositories like the NCBI’s Gene Expression Omnibus (GEO) and the EBI’s ArrayExpress and a significant opportunity to re-use data in various combinations for novel in-silico analyses that would otherwise be too costly to perform or for which the equivalent sample numbers would be difficult to collects exists. For example, combining and re-analysing large numbers of data sets from the same cancer type would increase statistical power, while the effects of individual study-specific variability is weakened, which would result in more reliable gene expression signatures. Similarly, as the number of normal control samples associated with various cancer datasets are often limiting, datasets can be combined to establish a reliable baseline for accurate differential expression analysis. However, combining different microarray studies is hampered by the fact that different studies use different analysis techniques, microarray platforms and experimental protocols. We have developed and optimised a method which transforms gene expression measurements from continuous to discrete data points by grouping similarly expressed genes into quantiles on a per-sample basis. After cross mapping each probe on each chip to the gene it represents, thereby enabling us to integrate experiments based on genes they have in common across different platforms. We optimised the quantile discretization method on previously published prostate cancer datasets produced on two different array technologies and then applied it to a larger breast cancer dataset of 411 samples from 8 microarray platforms. Statistical analysis of the breast cancer datasets identified 1371 differentially expressed genes. Cluster, gene set enrichment and pathway analysis identified functional groups that were previously described in breast cancer and we also identified a novel module of genes encoding ribosomal proteins that have not been previously reported, but whose overall functions have been implicated in cancer development and progression. The former indicates that our integration method does not destroy the statistical signal in the original data, while the latter is strong evidence that the increased sample size increases the chances of finding novel gene expression signatures. Such signatures are also robust to inter-population variation, and show promise for translational applications like tumour grading, disease subtype classification, informing treatment selection and molecular prognostics.
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Lundén, Karl. "Heterobasidion - conifer pathosystem : heterologous array analysis and transcriptional shift from saprotrophic to necrotrophic growth /." Uppsala : Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, 2010. http://epsilon.slu.se/201019.pdf.
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4
Norouzi, Masoud. "Development of an RNA array to Protein array (RAPA) platform and its application to gene expression analysis of synthetic riboregulators." Thesis, University of Portsmouth, 2018. https://researchportal.port.ac.uk/portal/en/theses/development-of-an-rna-array-to-protein-array-rapa-platform-and-its-application-to-gene-expression-analysis-of-synthetic-riboregulators(5867a39c-55a4-410a-8e5a-53c347b8a81a).html.
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5
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;
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Araujo, Tânia Kawasaki de 1985. "Utilização da técnica de Open Array para investigação de genes associados a fendas labiopalatais em amostra da população brasileira." [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/313118.
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Orientador: Vera Lúcia Gil da Silva Lopes<br>Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas<br>Made available in DSpace on 2018-08-27T00:02:24Z (GMT). No. of bitstreams: 1
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Previous issue date: 2015<br>Resumo: A fenda de labiopalatal (FLP) isolada é o defeito craniofacial mais comum em humanos. O objetivo deste estudo foi avaliar associações entre 39 genes e a etiologia de FLP isolada em uma amostra da população brasileira. Este estudo de associação do tipo caso-controle foi desenhado com um poder estatístico de 81,29% por meio de regressão logística. O grupo de casos foi composto por 182 pacientes com FLP isolada registrados na Base Brasileira de Dados Clínicos e Familiais de Fendas Orofaciais Típicas. O grupo controle foi formado por 355 indivíduos saudáveis, sem história de fendas orais em três gerações. Toda a amostra foi genotipada por meio do sistema OpenArray®TaqManTM para 253 polimorfismos de nucleotídeo único (SNPs) em 39 genes, incluindo dois genes que, recentemente, haviam sido descritos por este grupo de pesquisa. A seleção de SNPs foi feita com o programa SNPbrowser 4.0 (Applied Biosystems) para verificar o número e a localização dos SNPs apropriados para explorar a associação de cada gene com FLP isolada. A análise de associação foi realizada por meio de regressão logística e regressão stepwise. Os resultados foram corrigidos para múltiplos testes (correção de Bonferroni). Vinte e quatro SNPs em 16 genes foram significativamente associados com a etiologia da FLP isolada, incluindo MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 e TCBE3. A análise de regressão stepwise revelou que 11 genes contribuiram em 15,5% do fenótipo de FLP isolada nessa amostra. Este é o primeiro estudo a associar os genes KIF7 e TCEB3 à FLP isolada<br>Abstract: Nonsyndromic cleft lip and palate (NSCLP) is the most common craniofacial birth defect. The aim of this study was to evaluate associations between 39 genes and the etiology of NSCLP in a Brazilian population. This case-control association study was designed with 81.29% statistical power according to logistic regression. The case group was composed of 182 patients with NSCLP enrolled in the Brazilian Database on Orofacial Clefts. The controls included 355 healthy individuals with no history of oral clefting in the past three generations. All samples were genotyped by TaqMan®OpenArrayTM system for 253 single nucleotide polymorphisms (SNPs) in 39 genes, including two that had recently been associated with this process. The SNPs selection was made by SNPbrowser 4.0 (Applied Biosystems) in order to establish the best SNPs to explor the association between each gene and NSCLP. The association analysis was performed using logistic regression and stepwise regression. The results were corrected for multiple testing (Bonferroni correction). Twenty-four SNPs in 16 genes were significantly associated with the etiology of NSCLP, including MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 and TCBE3. Stepwise regression analysis revealed that 11 genes contributed to 15.5% of the phenotype of NSCLP in the sample. This is the first study to associate KIF7 and TCEB3 with NSCLP<br>Doutorado<br>Ciencias Biomedicas<br>Doutora em Ciências Médicas
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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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8
Sandgren, Johanna. "Array-based Genomic and Epigenomic Studies in Healthy Individuals and Endocrine Tumours." Doctoral thesis, Uppsala universitet, Institutionen för kirurgiska vetenskaper, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129533.
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The human genome is a dynamic structure, recently recognized to present with significant large-scale structural variation. DNA-copy number changes represent one common type of such variation and is found both between individuals and within the somatic cells of the same individual, especially in disease states like cancer. Apart from DNA-rearrangements, epigenomic changes are increasingly acknowledged as important events in the maintenance of genomic integrity. In this thesis, different array-based methods have been applied for global genomic and epigenomic profiling of both normal and cancer cells. In paper I, a genomic microarray was established and used to determine DNA-copy number variants (CNVs) in a cohort of 76 healthy individuals from three ethnic populations. We identified 315 CNV regions that in total encompassed ~3,5% of the genome. In paper II, the array was utilized to discover CNVs within several differentiated tissues from the same subject. Six variants were identified providing evidence for somatic mosaicism. In paper III and IV we studied pheochromocytomas and paragangliomas, rare endocrine tumours that most often present as benign and sporadic with unclear genetic/epigenetic cause. Genome-wide DNA-copy number analysis of 53 benign and malignant samples in paper III revealed numerous common and novel chromosomal regions of losses and gains. High frequencies of relatively small overlapping regions of deletions were detected on chromosome 1p arm, encompassing several candidate tumour suppressor genes. In paper IV, an epigenomic map for two histone modifications associated with silent (H3K27me3) or active (H3K4me3) gene transcription, was generated for one malignant pheochromocytoma. Integrated analysis of global histone methylation, copy number alterations and gene expression data aided in the identification of candidate tumour genes. In conclusion, the performed studies have contributed to gain knowledge of CNVs in healthy individuals, and identified regions and genes which are likely associated with the development and progression of pheochromocytoma/paraganglioma.
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Dumas, Laura Jane. "Gene copy number variation in human and primate evolution /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008. http://proquest.umi.com/pqdweb?did=1545571861&sid=1&Fmt=6&clientId=18952&RQT=309&VName=PQD.
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Thesis (Ph.D. in Human Medical Genetics) -- University of Colorado Denver, 2008.<br>Typescript. Includes bibliographical references (leaves 98-112). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;
10
Tong, Lily. "Probing the function of RNase E family using biochemical techniques and gene array technology." Thesis, University of Leeds, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414514.
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11
Fouriki, Angeliki. "Oscillating magnet array-based nanomagnetic gene transfection of mammalian cells relevant to regenerative medicine." Thesis, Keele University, 2017. http://eprints.keele.ac.uk/4280/.
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Successful gene therapy depends upon specific gene delivery into the cells and tissues of interest. Nanomagnetic gene transfection is a relatively new gene delivery technique that has attempted to meet that need and has been effectively used with both viral and non-viralvector systems. It uses magnetic nanoparticles (MNPs) in assisting and directing specific delivery of reporter or therapeutic genes on a single cell basis, in the presence of an externally introduced oscillating magnet. The novelty of the lateral oscillation further stimulates endocytosis of MNP:plasmid complexes with improved in vitro transfection efficiency compared to the static magnet application and other non-viral gene delivery approaches. This work’s purpose was to contribute in the optimisation of this tool for safe and efficient gene delivery, and to investigate the applicability of the method in a wider range of cell types used for regenerative medicine purposes, improving transfection efficiency and duration. Novel transfection experiments using commercially available MNPs coupled to a reporter gene, demonstrated higher levels of transfection efficiency (differing among cell types) and cell viability (80-94%), at the lowest reagent concentrations across all posttransfected cell types, compared with the most widely used cationic lipids (Lipofectamine) and/or electroporation. In particular, using human lung mucoepidermoid carcinoma cells (NCI-H292), the magnetic field requirements for transfection were evaluated; using human osteosarcoma fibroblasts (MG-63), a nanomagnetic transfection protocol at shorter transfection times (30 min) was established for increased transfection efficiency (53% oscillating and 49% static magnet, 7% at 30 min and 24% at 6 hr Lipofectamine, and 21% electroporation); using mouse embryonic fibroblasts (NIH-3T3), the 30 min-protocol was applied further (25% oscillating and 22% static magnet, 2% at 30 min and 22% at 6 hr Lipofectamine); using human mesenchymal stem cells (hMSCs), the ability of the method to transfect primary cells and to retain key markers for multipotency was demonstrated; using human embryonic stem cells (hESCs), the transfection capability in additional types of primary cells was shown, along with indications of retention of key markers for pluripotency and differentiation, although further work is required to confirm this finding. Nanomagnetic gene transfection shows promising results for in vitro and in vivo non-viral gene delivery and biomedical engineering applications. Data from this study could to be used for MNP drug delivery strategies, ultimately for clinical translation.
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Qin, Li-Xuan. "The clustering of regression models method with applications in gene expression data /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9591.
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Goh, Xin Yi. "Integrative analysis of array comparative genomic hybridisation and microarray gene expression profiles in oesophageal adenocarcinoma." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609976.
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14
Marincevic, Millaray. "Array-based Characterization of Chronic Lymphocytic Leukemia : - with Focus on Subsets Carrying Stereotyped B-cell Receptors." Doctoral thesis, Uppsala universitet, Institutionen för genetik och patologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-132895.
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In chronic lymphocytic leukemia (CLL), the presence of multiple subsets expressing ‘stereotyped’ B-cell receptors (BCRs) has implicated antigen(s) in leukemogenesis. These stereotyped subsets display similar immunoglobulin (IG) gene usage, almost identical complementarity determining region 3’s and may share clinical features. For instance, subsets #1 (IGHV1/5/7/IGKV1-39) and #2 (IGHV3-21/IGLV3-21) have inferior outcome compared to non-subset patients, whereas subset #4 (IGHV4-34/IGKV2-30) display a favourable prognosis. The aim of this thesis was to investigate genomic aberrations, gene expression patterns and methylation profiles in stereotyped subsets and compare epigenetic profiles in CLL and mantle cell lymphoma (MCL). In paper I, we investigated genomic aberrations in subsets #2, #4 and #16 and in non-stereotyped samples (n=101) using high-density 250K SNP arrays. Subset #2 and non-subset #2 IGHV3-21 cases displayed a higher frequency of aberrations than subset #4 cases. The high incidence of del(11q) in both subset #2/non-subset #2 may reflect the adverse survival reported for IGHV3-21 patients. In contrast, the lower frequency of genetic events and lack of poor-prognostic aberrations in subset #4 may partially explain their indolent disease. In paper II, we analysed the global RNA expression in subset #4, #16 and non-subset IGHV4-34 CLL patients (n=25). Subsets #4 and 16 showed distinct gene expression profiles, where genes involved in cell regulatory pathways were significantly lower expressed in subset #4, in line with their low-proliferative disease. In paper III, a genome-wide methylation array was applied to investigate methylation profiles in subsets #1, #2 and #4 (n=39). We identified differential methylation patterns for all subsets and found affected genes to be involved in e.g. apoptosis and therapy resistance. When performing functional annotation, a clear enrichment of genes involved in adaptive immunity was observed. These genes were preferentially methylated in subset #1 when compared to either subset #2 or #4, possibly due to different antigen responses. In paper IV, the genome-wide methylation profiles for 30 CLL and 20 MCL patients were investigated. Distinct methylation profiles were observed, where MCL displayed a more homogeneous profile. Homeobox transcription factor genes showed a higher degree of methylation in MCL, while apoptosis-related genes and proliferation-associated genes were methylated in CLL. In summary, this thesis demonstrates that stereotyped CLL subsets display differences in gene expression profiles, genetic aberrations and methylation patterns, underscoring the functional relevance of subgrouping according to BCR stereotypy. The distinct methylation profiles of CLL and MCL suggests that different epigenetic mechanisms are involved in the pathogenesis of these B-cell malignancies.
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Fält, Susann. "Analysis of global gene expression in complex biological systems using microarray technology /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-612-3/.
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Kardooni, Hoda. "Epigenetic silencing of gene expression in paediatric malignant astrocytoma." Thesis, University of Wolverhampton, 2015. http://hdl.handle.net/2436/615001.
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Brain tumours account for the most frequent type of solid tumours among children. Despite advances in surgery and chemotherapy, brain tumours are still the main cause of cancer deaths in children. Furthermore, little is known about DNA methylation changes in paediatric astrocytoma. Recent investigations suggest that many tumours are initiated not only by genetic abnormalities, but also caused by epigenetic changes. DNA methylation is a key epigenetic mechanism that controls the regulation of gene expression. Interestingly, unlike DNA mutations, epigenetic abnormalities are reversible. The reversibility of epigenetic abnormalities upon pharmacological unmasking has prompted interest in developing epigenetic therapy with the crucial goal of restoring the expression of aberrantly silenced genes. The focus of this study was to utilise a combination of different microarray strategies to develop an integrative candidate gene approach to identify several novel frequently methylated genes in a cohort of paediatric HGA (High grade glioma) samples. In addition, to investigate the potential of therapeutic efficacy of a DNA methyltransferase inhibitor, 5-Aza-dC in paediatric HGA. There were 147 genes commonly identified to be potentially methylated in IN699 cells using the two different array strategies integration; re-expression array and Illumina Infinium Human Methylation 450k array. Furthermore, using two complementary microarray strategies including methylation 450k array and expression array, this work identified 55 genes that were both methylated and under-expressed in these HGA cultures. Following validation with CoBRA and RT-PCR coupled with the response of hypermethylated promoters to the demethylating agent 5-Aza-dC, six novel genes (CXCL14, PRR5L, ELTD1, ITGA2, KRT8 and NTM) that are frequently silenced in paediatric astrocytoma were identified. This study suggests that re-expression of ii CXCL14 inhibited the colony formation and cell growth and reduces the migration rate significantly in IN699 short term culture and likely have functional significance in the development of paediatric HGA and an excellent candidate gene for further analysis. In parallel, the efficacy of 5-Aza-dC treatment was examined in paediatric HGA aiming to introduce this epigenetic therapy as a potential mechanism in management of this tumours. This study demonstrated that, relatively low dose of 5-Aza-dC sharply reduced the colony formation and inhibited proliferation and not through the apoptotic effect. It is likely that this reduction in proliferation without cell death is due to using relatively low doses that do not acutely kill cells, thus, allow the sustained alterations in both gene expression patterns and appearance of a new phenotype to emerge. Taken together, this work contributes to a more detailed understanding of the effect of epigenetic silencing on paediatric HGA. This investigation also demonstrated the use of epigenetic drug, 5-aza-dC to reverse the gene silencing for the potential treatment of paediatric HGA.
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Urbich, Carmen. "Identifizierung neuer Schubspannungs-regulierter Gene mittels "Atlas cDNA Expression Array" Bedeutung für die Funktion von Endothelzellen /." [S.l.] : [s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=961909625.
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Xue-Franzén, Yongtao. "DNA microarray approaches to understanding the regulation and evolution of gene expression networks." Stockholm : Huddinge : Karolinska institutet ; Södertörns högskola, 2009. http://diss.kib.ki.se/2009/978-91-7409-554-8/.
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Wylie, Christi J. "Distinct Transcriptomes Define Rostral and Caudal 5HT Neurons." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1266002785.
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Mellick, Albert S. Jr, and n/a. "Tissue Specific Gene Expression Patterning and Carcinogenesis." Griffith University. School of Health Science, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20041102.114313.
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Despite significant advances in diagnosis and treatment, breast cancer remains the leading cause of cancer-related deaths in Australian women. Colorectal cancer is the second most common cancer in both males and females; after prostate and breast cancer, respectively, and excluding non-melanocytic skin cancer. Both breast cancer and colorectal cancer follow a common progressive course of illness; presenting (at least initially) with benign symptoms that can be treated by ablation (or removal) of the affected area. Cancer progression is associated with breakdown of tissue barriers (such as basement membranes), leading to the spread of cancer cells (via the vasculature or lymphatic system), and the establishment of secondary metastatic disease at green-field sites. Secondary tumours presenting in the lungs, ovaries, liver, bone, or brain are associated with chronic-debilitating symptoms that are difficult to treat, and will result in death. In the case of breast and colon cancer, effective early therapeutic intervention does have a significant impact upon patient survival. Tumour progression in breast and colon carcinomas is characterised by invasion of the surrounding stroma, and the acquisition of stromal characteristics, by previously epithelial cells. This progression is associated with the expression of extracellular proteases (ECPs) and increased motility. The process of mesenchymal transformation that tumour cells undergo is also referred to as the epithelial to mesenchymal transition (EMT). In general terms the aim of the study, presented in this thesis, was to investigate gene expression in cancer biology; and to characterise changes in breast cancer and colon cancer, with a focus on those genes, and gene products that may play a role in metastasis, including a family of ECPs, the matrix metalloproteinases (MMPs). In our laboratory, we have applied methods in microdissection, differential display polymerase chain reaction amplification (DD-PCR), and array hybridisation analysis to identify gene expression patterns in late stage archival formalin fixed paraffin embedded (FFPE) breast tumour biopsies that may be indicative of the EMT; or the response to the surrounding stroma/interstitium to the presence of the tumour.' The quality of nucleic acid obtainable from FFPE material presents a considerable challenge for gene expression studies. In order to identify tissue specific gene expression patterns, DD-PCR products, amplified from message obtained following segregation of tumour tissue from surrounding stroma, was hybridised to arrayed cDNA libraries created from stromal tumours, or sarcomas. In this way, 21 known genes, or expressed sequence tags (ESTs), were identified. These included the cytoskeletal element and EMT marker, vimentin, the mammary developmental factor and, signal transducer and activator of transcription (STAT)-3, and the cargo selection protein (TIP47). Seventeen genes showed differential expression in either the tumour, or stromal fractions. When applied to transformed breast cancer cell lines (MDA-MB-435 & T47D) DD-array analysis revealed a further 17 genes that were differentially regulated in invasive cells, compared with those displaying a less invasive phenotype. Six of the ESTs identified by DD-PCR array analysis, had no known (or predicted) function. For example, bcaf-2 was identified as the 3'-end of a putative open reading frame (ORF) localised to chromosome 6, while bcaf-10 showed homology with a known ORF. In order to analyse the expression of these bcafs further, a stromal cell culture model, representative of the original osteosarcoma cDNA libraries from which they were obtained, was used. In this model, CD14' (or adherent) peripheral blood mononuclear cells (PBMCs) treated with macrophage colony stimulating factor (M-CSF), can be allowed to differentiate into macrophage-like (ML) cells; while cells treated with M-CSF, and the receptor activator of NF-KB ligand (RANKL) will differentiate into multinucleate osteoclast-like (OCL) multinucleate giant cells. Uniquely, the stromal EST, bcaf-2 was expressed only by RANKL-treated (or OCL) cells. bcaf-2 and other ESTs, identified by DD-PCR analysis (and recently published) are the subject of on going research in our laboratory. The role of RANKL in mammary gland development and bone metastasis suggested that the identification of a RANKL-regulated stromal factor in breast tissue (bcaf-2) was not an artefact. RANKL is a membrane-bound, member of the tumour necrosis factor (TNF)-a cytokine super family. In order to test the hypothesis that RANKL might act as an inflammatory cytokine to regulate clinically significant stromal gene expression in the breast, we employed quantitative real time PCR analysis to examine the relative levels of selected members of a group of metal dependent ECPs, the matrix metalloproteinases (MMPs). RNA was extracted from ML cells and OCL cells, as well as RANK positive breast cancer cell lines (T47D, MDA-MB-435 & MCF-7). When the relative levels of protease mRNA were compared we demonstrated a significant (>20- fold) specific increase in collagenase (collagenase 2lMMP-8 and collagenase 3lMMP-13), and the tissue inhibitor of MMP (TIMP)-2 expression in M-CSF and RANKL treated PBMCs cells. When the assay was applied to RANKL treated breast cancer cell lines (MCF-7, T47D & MDAMB- 231), minor (40-fold) but potentially significant alterations in stromal protease gene expression were observed. The changes observed did not however, support the hypothesis that RANKL might act as an inflammatory cytokine to induce significant alterations in ECP expression in breast cancer cells. To investigate the role of RANKL as a driver of EMT in aberrant breast epithelium, total message (mRNNcDNA) from T47D, MCF-7, MDA-MB-231 cells, and message from the same cell lines treated with RANKL were compared by comparative fluorescent cDNA microarray analysis. Of the 1,700 targets available on the arrays, this study identified 160 that were differentially expressed in RANKL treated cells. The results suggest that RANKL may promote rather than suppress a mammary epithelial phenotype in breast cancer. In fact a putative mesenchymal to epithelial transition (MET) was observed following microscopic analysis, and this finding is the subject of on going research in our laboratory. Sporadic structural alterations in certain mitogenic factors represent important early events in cancer progression, while inherited mutations govern familial susceptibility to disease. In colon cancer, a close link exists between Winglessllnt (WNT) signalling, disease pathology, and the expression of MMPs. To examine the relationship between protease expression and structural genetic alterations in this EMT-linked signalling pathway, and others, we applied combined QPCR analysis of MMP expression and PCR-Single Strand Conformation Analysis (SSCA) to 26 colonic tumours, and patient-matched normal colonic mucosa. In this study, significant correlations between the expression of ECPs, and a key mediator of WNT signalling (p-catenin) were identified. While tumours possessing specific functional mutations in K-Ras, were found to group with phenotypic clustering based on protease gene expression. This result may be due to an interruption of normal interactions between RasIRaf signalling and transforming growth factor (TGF) P signalling, via Sma- and Mad- related protein (SMAD) signalling. These results demonstrate that the already identified link between mutations in kinase signalling, and aspects of gross colon tumour morphology (such as dysplasia) may be due to aberrant MMP expression patterning. The final aim of this research was to utilise methods developed in microdissection and specific Q-PCR analysis, to identify whether tumour-stroma differences in MMP gene expression might be used as markers of disease pathology. Total RNA from tumour, and biopsy-matched adjacent stromal tissue were segregated from 35 FFPE archival breast tumour biopsies. Comparison with stroma identified specific associations between TIMP-2 expression in the stroma and lymph node involvement, as well as stromelysin-3 (MMP-I I ) and TIMP-I expression and calcification of the tumour. Furthermore, a significant correlation was identified in the pattern of gelatinase (gelatinase AIMMP-2 & gelatinaseB1MMP-9) expression; while no significant correlation was identified in tumour-stroma MMP gene expression differences, and tumour grade, or hormone receptor status. These results suggest that coordinated changes within the tumour, and proximal stromal tissues (rather than tissue specific changes per se), regulate pathologically significant changes in breast carcinogenesis. In conclusion, this thesis describes the use of novel techniques in specific and global gene expression analysis that permitted examination of stromal gene expression changes in epithelial tumour progression. Microdissection facilitated localisation of expression to particular tissues, while cell culture models provided material with which to optimise and demonstrate the efficacy of techniques used (where tumour material itself was not abundant). Furthermore, we have identified significant and specific correlations between general stromal protease gene expression changes, a putative mammary epithelial differentiation factor (RANKL), alterations in growth factor signalling, and epithelial tumour pathology in the breast and colon. The combination of techniques developed in this study may assist in improvement of categorisation of tumours in clinical pathology. Specifically, the development of novel grading systems that link underlying molecular genetic changes with changes in tumour pathology. These processes may assist to improve diagnosis and provide more effective patient/tumour-specific drug therapies.
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Mellick, Albert S. Jr. "Tissue Specific Gene Expression Patterning and Carcinogenesis." Thesis, Griffith University, 2004. http://hdl.handle.net/10072/365189.
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Despite significant advances in diagnosis and treatment, breast cancer remains the leading cause of cancer-related deaths in Australian women. Colorectal cancer is the second most common cancer in both males and females; after prostate and breast cancer, respectively, and excluding non-melanocytic skin cancer. Both breast cancer and colorectal cancer follow a common progressive course of illness; presenting (at least initially) with benign symptoms that can be treated by ablation (or removal) of the affected area. Cancer progression is associated with breakdown of tissue barriers (such as basement membranes), leading to the spread of cancer cells (via the vasculature or lymphatic system), and the establishment of secondary metastatic disease at green-field sites. Secondary tumours presenting in the lungs, ovaries, liver, bone, or brain are associated with chronic-debilitating symptoms that are difficult to treat, and will result in death. In the case of breast and colon cancer, effective early therapeutic intervention does have a significant impact upon patient survival. Tumour progression in breast and colon carcinomas is characterised by invasion of the surrounding stroma, and the acquisition of stromal characteristics, by previously epithelial cells. This progression is associated with the expression of extracellular proteases (ECPs) and increased motility. The process of mesenchymal transformation that tumour cells undergo is also referred to as the epithelial to mesenchymal transition (EMT). In general terms the aim of the study, presented in this thesis, was to investigate gene expression in cancer biology; and to characterise changes in breast cancer and colon cancer, with a focus on those genes, and gene products that may play a role in metastasis, including a family of ECPs, the matrix metalloproteinases (MMPs). In our laboratory, we have applied methods in microdissection, differential display polymerase chain reaction amplification (DD-PCR), and array hybridisation analysis to identify gene expression patterns in late stage archival formalin fixed paraffin embedded (FFPE) breast tumour biopsies that may be indicative of the EMT; or the response to the surrounding stroma/interstitium to the presence of the tumour.' The quality of nucleic acid obtainable from FFPE material presents a considerable challenge for gene expression studies. In order to identify tissue specific gene expression patterns, DD-PCR products, amplified from message obtained following segregation of tumour tissue from surrounding stroma, was hybridised to arrayed cDNA libraries created from stromal tumours, or sarcomas. In this way, 21 known genes, or expressed sequence tags (ESTs), were identified. These included the cytoskeletal element and EMT marker, vimentin, the mammary developmental factor and, signal transducer and activator of transcription (STAT)-3, and the cargo selection protein (TIP47). Seventeen genes showed differential expression in either the tumour, or stromal fractions. When applied to transformed breast cancer cell lines (MDA-MB-435 & T47D) DD-array analysis revealed a further 17 genes that were differentially regulated in invasive cells, compared with those displaying a less invasive phenotype. Six of the ESTs identified by DD-PCR array analysis, had no known (or predicted) function. For example, bcaf-2 was identified as the 3'-end of a putative open reading frame (ORF) localised to chromosome 6, while bcaf-10 showed homology with a known ORF. In order to analyse the expression of these bcafs further, a stromal cell culture model, representative of the original osteosarcoma cDNA libraries from which they were obtained, was used. In this model, CD14' (or adherent) peripheral blood mononuclear cells (PBMCs) treated with macrophage colony stimulating factor (M-CSF), can be allowed to differentiate into macrophage-like (ML) cells; while cells treated with M-CSF, and the receptor activator of NF-KB ligand (RANKL) will differentiate into multinucleate osteoclast-like (OCL) multinucleate giant cells. Uniquely, the stromal EST, bcaf-2 was expressed only by RANKL-treated (or OCL) cells. bcaf-2 and other ESTs, identified by DD-PCR analysis (and recently published) are the subject of on going research in our laboratory. The role of RANKL in mammary gland development and bone metastasis suggested that the identification of a RANKL-regulated stromal factor in breast tissue (bcaf-2) was not an artefact. RANKL is a membrane-bound, member of the tumour necrosis factor (TNF)-a cytokine super family. In order to test the hypothesis that RANKL might act as an inflammatory cytokine to regulate clinically significant stromal gene expression in the breast, we employed quantitative real time PCR analysis to examine the relative levels of selected members of a group of metal dependent ECPs, the matrix metalloproteinases (MMPs). RNA was extracted from ML cells and OCL cells, as well as RANK positive breast cancer cell lines (T47D, MDA-MB-435 & MCF-7). When the relative levels of protease mRNA were compared we demonstrated a significant (>20- fold) specific increase in collagenase (collagenase 2lMMP-8 and collagenase 3lMMP-13), and the tissue inhibitor of MMP (TIMP)-2 expression in M-CSF and RANKL treated PBMCs cells. When the assay was applied to RANKL treated breast cancer cell lines (MCF-7, T47D & MDAMB- 231), minor (40-fold) but potentially significant alterations in stromal protease gene expression were observed. The changes observed did not however, support the hypothesis that RANKL might act as an inflammatory cytokine to induce significant alterations in ECP expression in breast cancer cells. To investigate the role of RANKL as a driver of EMT in aberrant breast epithelium, total message (mRNNcDNA) from T47D, MCF-7, MDA-MB-231 cells, and message from the same cell lines treated with RANKL were compared by comparative fluorescent cDNA microarray analysis. Of the 1,700 targets available on the arrays, this study identified 160 that were differentially expressed in RANKL treated cells. The results suggest that RANKL may promote rather than suppress a mammary epithelial phenotype in breast cancer. In fact a putative mesenchymal to epithelial transition (MET) was observed following microscopic analysis, and this finding is the subject of on going research in our laboratory. Sporadic structural alterations in certain mitogenic factors represent important early events in cancer progression, while inherited mutations govern familial susceptibility to disease. In colon cancer, a close link exists between Winglessllnt (WNT) signalling, disease pathology, and the expression of MMPs. To examine the relationship between protease expression and structural genetic alterations in this EMT-linked signalling pathway, and others, we applied combined QPCR
analysis of MMP expression and PCR-Single Strand Conformation Analysis (SSCA) to 26 colonic tumours, and patient-matched normal colonic mucosa. In this study, significant correlations between the expression of ECPs, and a key mediator of WNT signalling (p-catenin) were identified. While tumours possessing specific functional mutations in K-Ras, were found to group with phenotypic clustering based on protease gene expression. This result may be due to an interruption of normal interactions between RasIRaf signalling and transforming growth factor (TGF) P signalling, via Sma- and Mad- related protein (SMAD) signalling. These results demonstrate that the already identified link between mutations in kinase signalling, and aspects of gross colon tumour morphology (such as dysplasia) may be due to aberrant MMP expression patterning. The final aim of this research was to utilise methods developed in microdissection and specific Q-PCR analysis, to identify whether tumour-stroma differences in MMP gene expression might be used as markers of disease pathology. Total RNA from tumour, and biopsy-matched adjacent stromal tissue were segregated from 35 FFPE archival breast tumour biopsies. Comparison with stroma identified specific associations between TIMP-2 expression in the stroma and lymph node involvement, as well as stromelysin-3 (MMP-I I ) and TIMP-I expression and calcification of the tumour. Furthermore, a significant correlation was identified in the pattern of gelatinase (gelatinase AIMMP-2 & gelatinaseB1MMP-9) expression; while no significant correlation was identified in tumour-stroma MMP gene expression differences, and tumour grade, or hormone receptor status. These results suggest that coordinated changes within the tumour, and proximal stromal tissues (rather than tissue specific changes per se), regulate pathologically significant changes in breast carcinogenesis. In conclusion, this thesis describes the use of novel techniques in specific and global gene expression analysis that permitted examination of stromal gene expression changes in epithelial tumour progression. Microdissection facilitated localisation of expression to particular tissues, while cell culture models provided material with which to optimise and demonstrate the efficacy of techniques used (where tumour material itself was not abundant). Furthermore, we have identified significant and specific correlations between general stromal protease gene expression changes, a putative mammary epithelial differentiation factor (RANKL), alterations in growth factor signalling, and epithelial tumour pathology in the breast and colon. The combination of techniques developed in this study may assist in improvement of categorisation of tumours in clinical pathology. Specifically, the development of novel grading systems that link underlying molecular genetic changes with changes in tumour pathology. These processes may assist to improve diagnosis and provide more effective patient/tumour-specific drug therapies.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>School of Health Sciences<br>Faculty of Health Sciences<br>Full Text
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Dimassi, Sarra. "Identification de gènes responsables d'épilepsies de l'enfant." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1114.
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L'épilepsie est une affection neurologique chronique qui se définit par la répétition de crises épileptiques, signe de l'hyperactivité paroxystique d'un groupe de neurones corticaux. Ces dernières années, plusieurs gènes responsables d'épilepsies monogéniques ont été mis en évidence. Notre travail avait pour objectif l'identification d'anomalies génétiques responsables ou favorisants certaines formes d'épilepsies de l'enfant. Ce travail est composé de quatre études complémentaires. La première était l'exploration pangénomique d'une cohorte de 47 patients porteurs d'épilepsie à paroxysme rolandique (EPR) par CGH array, à la recherche de variations de nombre de copies (CNV) récurrentes. Nous avons ainsi pu mettre en évidence plusieurs CNVs emportant des gènes impliqués dans l'épilepsie, dont PRRT2 et GRIN2A. La deuxième reposait sur la même approche appliquée à une cohorte de 8 patients tunisiens présentant des spasmes infantiles. Elle a permis d'identifier une délétion 9q34.3 emportant le gène EHMT1, responsable du syndrome de Kleefstra et une duplication 15q13.1, région impliquée dans des troubles du neurodéveloppement. Pour la troisième étude, nous avons comparé deux techniques de capture pour séquençage à haut débit d'un panel de gènes impliqués dans les épilepsies de l'enfant, à partir des échantillons de 24 patients épileptiques. Cette approche nous a permis de mettre au point un logiciel d'analyse de couverture, que nous avons nommé DeCovA. Lors de la dernière étude, nous avons appliqué une stratégie de séquençage d'exome en trio pour explorer 10 patients porteurs des spasmes infantiles. Nous avons ainsi pu mettre en évidence des variants pathogènes de novo chez quatre patients,impliquant les gènes KCNQ2, SCN1A, NR2F1 et ALG13. Nos résultats confirment ainsi la place importante de la génétique et l'intérêt majeur des nouvelles technologies dans l'exploration étiologique des épilepsies de l'enfant<br>Epilepsy is a chronic neurological disorder characterized by repeated epileptic seizures, a sign of cortical neurons paroxysmal hyperactivity. In recent years, several monogenic genes involved in epilepsy have been identified. The aim of our work is to identify new genetic abnormalities responsible for childhood epilepsies. This work is divided into four complementary studies. First, we searched copy number variation (CNV) by pangenomic exploration of a cohort of 47 patients with Rolandic epilepsy (RE) using CGH array. We identified several CNVs carrying genes involved in epilepsy, including PRRT2 and GRIN2A (genes). Secondly, the same approach was applied to a cohort of 8 Tunisian patients with infantile spasms. It allowed the identification of a 9q34.3 deletion includingEHMT1, implicated in Kleefstra syndrome and a 15q13.1 duplication, known to be involved in neurodevelopment disorders. For the third study, we compared two library-building methods for a gene-targeted panel for the diagnosis of Monogenic childhood epilepsies, in a cohort of 24 epileptic patients. This approach allowed us to develop a coverage analysis software, which we named DeCovA. In the last study, we used a trio-based exome-sequencing approach to look for de novo mutations in 10 patients with infantile spasms. We found de novo pathogenic variants in four patients, involving KCNQ2, SCN1A, NR2F1, and ALG13. Our results confirm the increasing role of genetics and the major interest of new technologies in the etiological exploration of childhood epilepsy
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Mehta, Shaveta. "Biomarkers of anti-angiogenic therapy in breast cancer." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:8b3869e3-fd60-450c-b165-0fe773681613.
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The hunt for biomarkers for anti-VEGF agent bevacizumab is ongoing since last decade with no success. Identifying robust biomarkers for stratifying patients and for monitoring response is important for the future use of bevacizumab in breast cancer. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) analysis and genome wide gene expression analysis are two promising approaches to understand the molecular mechanisms and search for biomarker of anti-angiogenic therapy. Firstly, with the retrospective pilot study, a close link between DCE-MRI findings and the molecular mechanisms assisting cancer survival and metastasis was established. Secondly, the prospective window of opportunity study conducted using single cycle of bevacizumab given before neoadjuvant chemotherapy and by performing detailed pharmacodynamic analyses with DCE-MRI and gene expression before and two weeks after bevacizumab had shown a wide variation in responses to bevacizmab both at genomic and imaging level. A close link between changes in DCE-MRI and the changes in gene expression profile was further established suggesting DCE-MRI has potential to serve as non-invasive biomarkers of antiangiogenic therapy. Tumours with high baseline values of forward transfer constant K<sup>trans</sup> showed the maximum response as assessed by DCE-MRI after bevacizumab. By performing biopsy after single cycle of bevacizumab, the changes in genes related to immune response, metabolism and cell signalling were observed that gives a useful insight into mechanisms governing response and resistance to bevacizumab. Also the certain gene expression changes observed with post bevacizumab biopsies, such as down regulation of endothelial cell specific molecule-1 (ESM1), cyclin E1 (CCNE1) and up regulation of pyruvate dehydrogenase kinase 1 (PDK1), cyclic GMP-inhibited phosphodiesterase B (PDE3B) could be helpful in decision-making about future therapy with bevacizumab at an early stage. This study has suggested that using bevacizumab in combination with other targeted agents could overcome resistance.
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Holst, Martin Ingo. "Identifikation und Charakterisierung differenziell exprimierter Gene in einer Mausmutanten mit prolongierter Engrailed-2 Expression mithilfe der Array-Technologie." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=985081120.
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Suzuki, Keli Tieko. "Investigação molecular por sequenciamento do gene CBP em portadores da síndrome de Rubinstein-Taybi." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/5/5141/tde-24052012-154642/.
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A Síndrome de Rubinstein-Taybi (RTSs) é uma doença rara de herança autossômica dominante, caracterizada por dismorfismos craniofaciais, polegares e háluces alargados, deficiência intelectual e de crescimento. RTSs tem sido associada com mutações no gene CREBBP (CBP) e mutações menos frequentes no gene EP300 que foram descritas em oito indivíduos. CBP e p300 possuem alta homologia e são extremamente importantes em várias vias de sinalização, principalmente como coativadores de transcrição e na acetilação das histonas. Nosso estudo baseou-se na análise de alterações moleculares por sequenciamento direto do CBP, FISH e array-CGH em 20 pacientes com RTSs. Dos 20 pacientes avaliados por sequenciamento direto foram identificadas oito alterações moleculares, dentre estas, seis são alterações moleculares novas as quais não foram descritas na literatura, são elas: i) duas deleções (p.M747fs STOP830 e p.G1011fs STOP1021) ii) duas alterações do tipo nonsense (p.Arg1341X, p.Arg1498X) iii) três do tipo missense (p.Arg1907Trp, p.Leu604Pro e p.His1291Arg). Também identificamos um polimorfismo de único nucleotídeo (SNP) (rs115594471/ c.5874CT). Dois pacientes apresentaram deleção do gene CBP em um dos alelos, identificado pelo método array-CGH. Outro, apresentou uma translocação aparentemente equilibrada t(2;16), cuja análise subsequente com FISH revelou uma quebra na região do CBP. Neste trabalho, a taxa de detecção de alteração molecular no CBP por sequenciamento direto foi de 40% (08/20). Porém, a taxa de detecção das alterações moleculares no CBP foi de 55% (11/20), considerando a combinação das diferentes técnicas utilizadas (FISH, sequenciamento direto e array-CGH). Não houve correlação genótipo-fenótipo, exceto por uma maior frequência da presença de epicanto nos pacientes com alteração no CBP. Os resultados obtidos neste trabalho servem como o diagnóstico molecular para os pacientes com RTSs atendidos no Ambulatório do Laboratório de investigação Médica 001 (ALIM 001) do Instituto da Criança - FMUSP, contribuindo para uma melhor orientação médica, como também para realização do aconselhamento genético às famílias<br>Rubinstein-Taybi syndrome (RTSs) is a rare autosomal dominant disease characterized by craniofacial dysmorphisms, broad thumbs and toes, mental and growth deficiency. RTS has been associated with CREBBP (CBP) gene mutations and less frequently with mutations in EP300 gene, which have been reported in eight individuals. CBP and p300 have high homology and are extremely important in many signaling pathways especially as transcriptional coactivators and histone acetylation. Our study was based on the alteration analysis by direct sequencing of the CBP, by FISH and array-CGH in 20 RTSs patients. We identified eight molecular alterations in 20 RTSs patients evaluated by direct sequencing: i) two deletions (p.M747fs STOP830 and p.G1011fs STOP1021) ii) two nonsense alterations (p.Arg1341X and p.Arg1498X) iii) Three missense alteration (p.Arg1907Trp, p.Leu604Pro and p.His1291Arg). Single-nucleotide polymorphism were also identified (rs115594471 / c.5874CT), and six of these are new molecular alterations, not described in literature. Two RTSs patients studied had CBP gene deletion in one allele, identified by array-CGH method. Other patient, presented with apparent balanced translocation t(2;16) in which the subsequent analysis using FISH, showed a break in region of CBP. In this work, the rate of detection of molecular alteration in CBP by direct sequencing in RTSs patient was 40.0% (08/20). However, the rate of detection of molecular alteration in CBP was 55.0% (11/20), considering the combination of different techniques (FISH, direct sequencing and array-CGH. No significant correlation could be established in this study between the different types of mutations and genotype-phenotype of RTSs patients, except a higher frequency of the presence of epicanthus in the RTS patients with alteration in the CBP. The results of this study serve as a molecular diagnosis for RTSs patients treated at the Ambulatory of the Medical Investigation Laboratory 001 (ALIM 001) of the Instituto da Criança - FMUSP, and this contributes to better clinical management, such as making an appropriate genetic counseling for families
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Levy, Mark. "The role of dietary zinc and CuZnSOD gene expression in response to oxidative stress in the lung and brain." The Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=osu1054069625.
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Michael, Bindhu. "Human T lymphotropic virus type 1 (HTLV-1) accessory protein p30(II) modulates cellular and viral gene expression." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1088784889.
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Thesis (Ph. D.)--Ohio State University, 2004.<br>Title from first page of PDF file. Document formatted into pages; contains xvii, 250 p.; also includes graphics (some col.) Includes bibliographical references (p. 207-250). Available online via OhioLINK's ETD Center
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Wennmalm, Kristian. "Analytical strategies for identifying relevant phenotypes in microarray data /." Stockholm, 2007. http://diss.kib.ki.se/2007/978-91-7357-401-3/.
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Delgado, Verdugo Alberto. "Genetic Aspects of Endocrine Tumorigenesis : A Hunt for the Endocrine Neoplasia Gene." Doctoral thesis, Uppsala universitet, Endokrinkirurgi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-224111.
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Endocrine tumors arise from endocrine glands. Most endocrine tumors are benign but malignant variants exist. Several endocrine neoplasms display loss of parts of chromosome 11 or 18, produce hormones and responds poorly to conventional chemotherapeutics. The multiple endocrine neoplasia syndromes are mainly confined to endocrine tumors. This opens the question if there exists a single or several endocrine tumor genes. The aim of the study was to describe genetic derangements in endocrine tumors. Paper I: Investigation of mutational status of SDHAF2 in parathyroid tumors. SDHAF2 is located in the proximity of 11q13, a region that frequently displays loss in parathyroid tumors. We established that mutations in SDHAF2 are infrequent in parathyroid tumors. Paper II: Study of SDHAF2 gene expression in a cohort of benign pheochromocytomas (PCC) (n=40) and malignant PCC (n=10). We discovered a subset of benign PCC (28/40) and all malignant PCC (10/10) with significantly lower SDHAF2 expression. Benign PCC with low SDHAF2 expression and malignant tumors consistently expressing low levels of SDHAF2 were methylated in the promoter region. SDHAF2 expression was restored in vitro after treatment with 5- aza-2-deoxycytidine. Paper III: HumanMethylation27 array (Illumina) covering 27578 CpG sites spanning over 14495 genes were analyzed in a discovery cohort of 10 primary small neuroendocrine tumors (SI-NETs) with matched metastases. 2697 genes showed different methylation pattern between the primary tumor and its metastasis. We identified several hypermethylated genes in key regions. Unsupervised clustering of the tumors identified three distinct clusters, one with a highly malignant behavior. Paper IV: Loss of chromosome 18 is the most frequent genetic aberration in SI-NETs. DNA from SI-NETs were subjected to whole exome capture sequencing and high resolution SNP array. Genomic profiling revealed loss of chromosome 18 in 5 out of 7 SI-NETs. No tumor-specific somatic mutation on chromosome 18 was identified which suggests involvement of other mechanisms than point mutations in SI-NET tumorigenesis. Paper V: The cost for diagnostic genetic screening of common susceptibility genes in PCC is expensive and labor intensive. Three PCC from three patients with no known family history were chosen for exome capture sequencing. We identified three variants in known candidate genes. We suggest that exome-capture sequencing is a quick and cost-effective tool.
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Wagner, Brandie D. "Permutation based microarray gene selection methods with covarience adjustment applicable to complex diseases /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2007.
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Thesis (Ph.D. in Analytic Health Sciences) -- University of Colorado Denver, 2007.<br>Typescript. Includes bibliographical references (leaves 57-60). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;
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Zhou, Chuan. "A Bayesian model for curve clustering with application to gene expression data analysis /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/9576.
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Lewis, Tyler E. "Investigation of Parameters Affecting the Nanoinjection of HeLa 229 Cancer Cells." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5526.
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The ability to deliver sequences of DNA and other molecular loads across the membrane of a cell and into its nucleus is an area of interest in the medical community. One of its many applications is that of gene therapy. In contrast to other forms of treatment, gene therapy seeks to treat diseases at the cellular level. The success of these treatments depends on the technologies for cell transfection that are available. Physical methods are sometimes able to overcome poor efficiencies of chemical methods and the safety concerns of viral methods, but are usually impractical due to the limited number of cells that are able to be transfected at a time, isolation, and immobilization of the cells. Nanoinjection is capable of using millions of small lances in an array to inject hundreds of thousands of cells simultaneously with relatively high efficiencies and viabilities. The solid nature of the lances also allows them to be smaller than their hollow-needle counterparts, which results in higher cell viability. Propidium Iodide (PI), a dye whose fluorescence increases greatly when bound to nucleic acids, was used as an injection molecule for testing the efficacy of the nanoinjection process on HeLa 229 cancer cells in a portion of the experiments, with a GFP plasmid of DNA being used in the rest. After injection, flow cytometry was used to detect the concentration of PI or the expression of the GFP in the injected cells. Since PI cannot normally penetrate the membrane of living cells, those found with high concentrations of PI were either successfully injected or dead, which can be determined by the flow cytometry. Investigation of the parameters that affect the efficiency of the nanoinjection process will help improve it for further research. Some of these parameters that were investigated include the force of injection, the material used for the lances (silicon versus carbon nanotubes), and the injection speed of the lance arrays. An injection device capable of small changes in deflection was designed to ensure accurate increments in force for testing, as well as a pulsed current control injection system. Results for injections of varying forces indicate a slow rise in PI uptake from 0 to 1.8 Newtons where it reaches a maximum uptake of 4.11 when normalized to the PI uptake of the positive controls. The PI uptake then remains relatively level as the force continues to increase, averaging an uptake of approximately 3.1. The slow rise is likely due to more of the cells being punctured as the force increases until most have been punctured and the PI uptake levels off. The viability of the injected cells was close to that of the controls with no clear trend. A comparison of lance arrays made from silicon and carbon nanotubes using DNA as the molecular load shows little difference between materials. Different injection speeds tested show that only 1-5% of the cells in the injection process are lost for speeds in the range of 0.08-0.16 mm/sec, whereas 49-69% of the cells are lost using speeds between 0.6-3 mm/sec.
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Finnell, Jordan Grant. "Anthrax, Matrix Biology, and Angiogenesis: Capillary Morphogenesis Gene 2 Mediates Activity and Uptake of Type IV Collagen-Derived Anti-Angiogenic Peptides." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6849.
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Capillary Morphogenesis Gene 2 (CMG2) is a type I transmembrane, integrin-like receptor. It was originally identified as one of several genes upregulated during capillary formation. It was subsequently identified as one of two physiological anthrax toxin receptors, where CMG2 serves as a cell-surface receptor for anthrax toxin and mediates entry of the toxin into cells via clathrin-dependent endocytosis. Additionally, loss-of-function mutations in CMG2 cause the genetic disorder hyaline fibromatosis syndrome (HFS), where the core symptom is dysregulation of extracellular matrix homeostasis (ECM), including excessive accumulation of proteinaceous hyaline material; HFS clearly indicates that CMG2 plays an essential function in ECM homeostasis and repair. Most often, these situational roles have been evaluated as separate intellectual and experimental entities; consequently, whereas details have emerged for each respective situational role, there has been little attempt to synthesize knowledge from each situational role in order to model a holistic map of CMG2 function and mechanism of action in normal physiology.The work presented in this thesis is an example of such a synthesis. Interactions between CMG2 and type IV collagen (Col IV) were evaluated, to better understand this putative interaction and its effect on CMG2 function in angiogenesis. Using an overlapping library peptide array of the Col IV α1 and α2 chains, it was found that CMG2-binding peptides were enriched within the NC1 domains. This finding was corroborated via another epitope mapping peptide array, where we found a major epitope for CMG2-binding within the α2 NC1 domain (canstatin). Identification of CMG2 interactions with Col IV NC1 domains (including canstatin) was both surprising and intriguing, as these domains are potent endogenous inhibitors of angiogenesis. To further evaluate the physiological relevance of interactions with Col IV NC1 domains, a canstatin-derived peptide from the original array was synthesized and used for further studies. This peptide (here known as S16) binds with high affinity (KD = 440 ± 160 nM) to the extracellular, ligand-binding CMG2 vWA domain; specificity was confirmed through competition studies with anthrax toxin PA, and through demonstration of divalent cation-dependent binding. CMG2 was found to be the relevant endothelial receptor for S16. CMG2 in fact mediates endocytic uptake of peptide S16, as demonstrated by flow cytometry, and colocalization studies. S16 further inhibits migration of endothelial cells. These findings demonstrate that CMG2 is a functional receptor for Col IV NC1 domain fragments. CMG2 may exert a pro-angiogenic effect through endocytosis and clearance of anti-angiogenic NC1 domain fragments. Additionally, this is the first demonstration of CMG2-mediated uptake of an endogenous matrix fragment, and suggests a mechanism by which CMG2 regulates ECM and basement membrane homeostasis, thereby establishing a functional connection between the receptor's role in matrix biology and angiogenesis.
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Nair, Amrithraj Muraleedharan. "Studies of retroviral vectors for in utero gene transfer and investigation of calcium-mediated gene regulation by Human T-lymphotropic virus type-1." The Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=osu1088785797.
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Wu, Ling. "Functional Characterization of SCN5A, The Cardiac Sodium Channel Gene Associated With Cardiac Arrhythmias and Sudden Death." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1206732295.
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Libby, Eric. "Investigations into the design and dissection of genetic networks." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103265.
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The sequencing of the human genome revealed that the number of genes does not explain why humans are different from other organisms like mice and dogs. Instead, it is how genes interact with each other and the environment that separates us from other organisms. This motivates the study of genetic networks and, consequently, my research. My work delves into the roles that simple genetic networks play in a cell and explores the biotechnological aspects of how to uncover such genes and their interactions in experimental models.<br>Cells must respond to the extracellular environment to contract, migrate, and live. Cells, however, are subject to stochastic fluctuations in protein concentrations. I investigate how cells make important decisions such as gene transcription based on noisy measurements of the extracellular environment. I propose that genetic networks perform Bayesian inference as a way to consider the probabilistic nature of these measurements and make the best decision. With mathematical models, I show that allosteric repressors and activators can correctly infer the state of the environment despite fluctuating concentrations of molecules. Viewing transcriptional networks as inference modules explains previous experimental data. I also discover that the particular inference problem determines whether repressors or activators are better.<br>Next, I explore the genetic underpinnings of two canine models of atrial fibrillation: atrial tachypacing and ventricular tachypacing. Using Affymetrix microarrays, I find that the genetic signatures of these two models are significantly different both in magnitude and in class of genes expressed. The ventricular tachypacing model has thousands of transcripts differentially expressed with little overlap between 24 hours and 2 weeks, suggesting independent mechanisms. The atrial tachypacing model demonstrates an adaptation as the number of genes found changed decreases with increasing time to the point that no genes are changed at 6 weeks. I use higher level analysis to find that extracellular matrix components are among the most changed in ventricular tachypacing and that genes like connective tissue growth factor may be responsible.<br>Finally, I generalize the main problem of microarray analysis into an evaluation problem of choosing between two competing options based on the scores of many independent judges. In this context, I rediscover the voting paradox and compare two different solutions to this problem: the sum rule and the majority rule. I find that the accuracy of a decision depends on the distribution of the judges' scores. Narrow distributions are better solved with a sum rule, while broad distributions prefer a majority rule. This finding motivates a new algorithm for microarray analysis which outperforms popular existing algorithms on a sample data set and the canine data set examined earlier. A cost analysis reveals that the optimal number of judges depends on the ratio of the cost of a wrong decision to the cost of a judge.
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Suryo, Rahmanto Yohan. "THE PHYSIOLOGICAL AND PATHOPHYSIOLOGICAL ROLES OF MELANOTRANSFERRIN." Thesis, The University of Sydney, 2007. http://hdl.handle.net/2123/2439.
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Melanotransferrin or melanoma tumour antigen p97 (MTf) is a transferrin homologue that is found predominantly bound to the cell membrane via a glycosylphosphatidylinositol anchor. The molecule is a member of the transferrin super-family that binds iron through a single high affinity iron(III)-binding site. Melanotransferrin was originally identified at high levels in melanoma cells and other tumours, but at lower levels in normal tissues. Since its discovery, the function of MTf has remained intriguing, particularly regarding its role in cancer cell iron transport. In fact, considering the crucial role of iron in many metabolic pathways e.g., DNA and haem synthesis, it is important to understand the function of melanotransferrin in the transport of this vital nutrient. Melanotransferrin has also been implicated in diverse physiological processes, such as plasminogen activation, angiogenesis, cell migration and eosinophil differentiation. Despite these previous findings, the exact biological and molecular function(s) of MTf remain elusive. Therefore, it was important to investigate the function of this molecule in order to clarify its role in biology. To define the roles of MTf, six models were developed during this investigation. These included: the first MTf knockout (MTf -/-) mouse; down-regulation of MTf expression by post-transcriptional gene silencing (PTGS) in SK-Mel-28 and SK-Mel-2 melanoma cells; hyper-expression of MTf expression in SK-N-MC neuroepithelioma cells and LMTK- fibroblasts cells; and a MTf transgenic mouse (MTf Tg) with MTf hyperexpression. The MTf -/- mouse was generated through targeted disruption of the MTf gene. These animals were viable, fertile and developed normally, with no morphological or histological abnormalities. Assessment of Fe indices, tissue Fe levels, haematology and serum chemistry parameters demonstrated no differences between MTf -/- and wild-type (MTf +/+) littermates, suggesting MTf was not essential for Fe metabolism. However, microarray analysis showed differential expression of molecules involved in proliferation such as myocyte enhancer factor 2a (Mef2a), transcription factor 4 (Tcf4), glutaminase (Gls) and apolipoprotein d (Apod) in MTf -/- mice compared with MTf +/+ littermates. Considering the role of MTf in melanoma cells, PTGS was used to down-regulate MTf mRNA and protein levels by >90% and >80%, respectively. This resulted in inhibition of cellular proliferation and migration. As found in MTf -/- mice, melanoma cells with suppressed MTf expression demonstrated up-regulation of MEF2A and TCF4 in comparison with parental cells. Furthermore, injection of melanoma cells with decreased MTf expression into nude mice resulted in a marked reduction of tumour initiation and growth. This strongly suggested a role for MTf in proliferation and tumourigenesis. To further understand the function of MTf, a whole-genome microarray analysis was utilised to examine the gene expression profile of five models of modulated MTf expression. These included two stably transfected MTf hyper-expression models (i.e., SK-N-MC neuroepithelioma and LMTK- fibroblasts) and one cell type with downregulated MTf expression (i.e., SK-Mel-28 melanoma). These findings were then compared with alterations in gene expression identified using the MTf -/- mouse. In addition, the changes identified from the microarray data were also assessed in another model of MTf down-regulation in SK-Mel-2 melanoma cells. In the cell line models, MTf hyper-expression led to increased proliferation, while MTf down-regulation resulted in decreased proliferation. Across all five models of MTf down- and upregulation, three genes were identified as commonly modulated by MTf. These included ATP-binding cassette sub-family B member 5 (Abcb5), whose change in expression mirrored MTf down- or up-regulation. In addition, thiamine triphosphatase (Thtpa) and Tcf4 were inversely expressed relative to MTf levels across all five models. The products of these three genes are involved in membrane transport, thiamine phosphorylation and proliferation/survival, respectively. Hence, this study identifies novel molecular targets directly or indirectly regulated by MTf and the potential pathways involved in its function, including modulation of proliferation. To further understand the function of MTf, transgenic mice bearing the MTf gene under the control of the human ubiquitin-c promoter were generated and characterised. In MTf Tg mice, MTf mRNA and protein levels were hyper-expressed in a variety of tissues compared with control mice. Similar to the MTf -/- mice, these animals exhibited no gross morphological, histological, nor Fe status changes when compared with wild-type littermates. The MTf Tg mice were also born in accordance with classical Mendelian ratios. However, haematological data suggested that hyper-expression of MTf leads to a mild, but significant decrease in erythrocyte count. In conclusion, the investigations described within this thesis clearly demonstrate no essential role for MTf in Fe metabolism both in vitro and in vivo. In addition, this study generates novel in vitro and in vivo models for further investigating MTf function. Significantly, the work presented has identified novel role(s) for MTf in cell proliferation, migration and melanoma tumourigenesis.
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Suryo, Rahmanto Yohan. "THE PHYSIOLOGICAL AND PATHOPHYSIOLOGICAL ROLES OF MELANOTRANSFERRIN." Faculty Medicine, Department of Pathology, 2007. http://hdl.handle.net/2123/2439.
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Doctor of Philosophy(PhD)<br>Melanotransferrin or melanoma tumour antigen p97 (MTf) is a transferrin homologue that is found predominantly bound to the cell membrane via a glycosylphosphatidylinositol anchor. The molecule is a member of the transferrin super-family that binds iron through a single high affinity iron(III)-binding site. Melanotransferrin was originally identified at high levels in melanoma cells and other tumours, but at lower levels in normal tissues. Since its discovery, the function of MTf has remained intriguing, particularly regarding its role in cancer cell iron transport. In fact, considering the crucial role of iron in many metabolic pathways e.g., DNA and haem synthesis, it is important to understand the function of melanotransferrin in the transport of this vital nutrient. Melanotransferrin has also been implicated in diverse physiological processes, such as plasminogen activation, angiogenesis, cell migration and eosinophil differentiation. Despite these previous findings, the exact biological and molecular function(s) of MTf remain elusive. Therefore, it was important to investigate the function of this molecule in order to clarify its role in biology. To define the roles of MTf, six models were developed during this investigation. These included: the first MTf knockout (MTf -/-) mouse; down-regulation of MTf expression by post-transcriptional gene silencing (PTGS) in SK-Mel-28 and SK-Mel-2 melanoma cells; hyper-expression of MTf expression in SK-N-MC neuroepithelioma cells and LMTK- fibroblasts cells; and a MTf transgenic mouse (MTf Tg) with MTf hyperexpression. The MTf -/- mouse was generated through targeted disruption of the MTf gene. These animals were viable, fertile and developed normally, with no morphological or histological abnormalities. Assessment of Fe indices, tissue Fe levels, haematology and serum chemistry parameters demonstrated no differences between MTf -/- and wild-type (MTf +/+) littermates, suggesting MTf was not essential for Fe metabolism. However, microarray analysis showed differential expression of molecules involved in proliferation such as myocyte enhancer factor 2a (Mef2a), transcription factor 4 (Tcf4), glutaminase (Gls) and apolipoprotein d (Apod) in MTf -/- mice compared with MTf +/+ littermates. Considering the role of MTf in melanoma cells, PTGS was used to down-regulate MTf mRNA and protein levels by >90% and >80%, respectively. This resulted in inhibition of cellular proliferation and migration. As found in MTf -/- mice, melanoma cells with suppressed MTf expression demonstrated up-regulation of MEF2A and TCF4 in comparison with parental cells. Furthermore, injection of melanoma cells with decreased MTf expression into nude mice resulted in a marked reduction of tumour initiation and growth. This strongly suggested a role for MTf in proliferation and tumourigenesis. To further understand the function of MTf, a whole-genome microarray analysis was utilised to examine the gene expression profile of five models of modulated MTf expression. These included two stably transfected MTf hyper-expression models (i.e., SK-N-MC neuroepithelioma and LMTK- fibroblasts) and one cell type with downregulated MTf expression (i.e., SK-Mel-28 melanoma). These findings were then compared with alterations in gene expression identified using the MTf -/- mouse. In addition, the changes identified from the microarray data were also assessed in another model of MTf down-regulation in SK-Mel-2 melanoma cells. In the cell line models, MTf hyper-expression led to increased proliferation, while MTf down-regulation resulted in decreased proliferation. Across all five models of MTf down- and upregulation, three genes were identified as commonly modulated by MTf. These included ATP-binding cassette sub-family B member 5 (Abcb5), whose change in expression mirrored MTf down- or up-regulation. In addition, thiamine triphosphatase (Thtpa) and Tcf4 were inversely expressed relative to MTf levels across all five models. The products of these three genes are involved in membrane transport, thiamine phosphorylation and proliferation/survival, respectively. Hence, this study identifies novel molecular targets directly or indirectly regulated by MTf and the potential pathways involved in its function, including modulation of proliferation. To further understand the function of MTf, transgenic mice bearing the MTf gene under the control of the human ubiquitin-c promoter were generated and characterised. In MTf Tg mice, MTf mRNA and protein levels were hyper-expressed in a variety of tissues compared with control mice. Similar to the MTf -/- mice, these animals exhibited no gross morphological, histological, nor Fe status changes when compared with wild-type littermates. The MTf Tg mice were also born in accordance with classical Mendelian ratios. However, haematological data suggested that hyper-expression of MTf leads to a mild, but significant decrease in erythrocyte count. In conclusion, the investigations described within this thesis clearly demonstrate no essential role for MTf in Fe metabolism both in vitro and in vivo. In addition, this study generates novel in vitro and in vivo models for further investigating MTf function. Significantly, the work presented has identified novel role(s) for MTf in cell proliferation, migration and melanoma tumourigenesis.
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de, Sousa Emma Louise. "The use of novel xenografting methods to reveal differential gene expression between breast cancer at primary and metastatic sites." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:20c957a8-68c7-43f1-b0f6-722ae71dfb5a.
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In developed countries, breast cancer is the commonest malignancy among women. Understanding the mechanisms involved in breast cancer progression and the influence of the microenvironment on cancer cell proliferation, results in better treatments. This study aimed to optimise breast cancer xenograft rates using a novel chamber developed for tissue engineering purposes. The established tumours were subjected to enzyme digestion, creating a single cell suspension, which was then injected into immunocompromised mice at primary, metastatic and intra-cardiac sites. The resulting tumours in the mammary fat pad (MFP) and bone were compared using species-specific reverse-transcription polymerase chain reaction (RT-PCR) and cDNA microarray, to examine the influence of the microenvironment on gene expression. The achieved xenograft graft rates of 25% were similar to those previously reported. The matrix metalloproteinase family of enzymes (MMPs) degrade extracellular matrix, influencing invasion and migration of malignant cells. RT-PCR results showed that the majority of the MMPs expressed in the cancers were stromal rather than tumour in origin. MT1-MMP, MMP-2 and MMP-11 had significantly higher expression levels in the MFP than in the bone, but MMP-9 was expressed more in the bone than MFP. There was also an up-regulation of stromal production of MT1-MMP and MMP-13 in the MFP in the presence of tumour. This may have significance when considering which MMPs are the most appropriate targets for inhibition during cancer treatment. The most significant of the differentially expressed genes on microarray analysis were trefoil factor 1 (TFF1) and insulin growth-factor binding protein 3 (IGFBP-3), both expressed significantly more in tumours from the MFP than the bone. The thesis presented demonstrates some of the complexities of tumour-stromal interactions and supports Paget’s seed-soil theory, confirming in several ways the variation in gene expression in breast cancer between primary and metastatic sites.
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Morice-Picard, Fanny. "Etude clinique et génétique de l’albinisme oculocutané : développement d’outils de diagnostic moléculaire et recherche de nouveaux gènes." Thesis, Bordeaux 2, 2013. http://www.theses.fr/2013BOR22101/document.
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Notre travail s’est intéressé à l’albinisme oculocutané en étudiant ses aspects clinico- moléculaires. Malgré l’analyse approfondie des gènes connus d’albinisme oculocutané, 15 % des patients restent sans mutation identifiée indiquant que les mutations sont situées dans des régions géniques non analysées par les techniques classiques de diagnostic moléculaire, ou qu’il existe d’autres gènes d’albinisme oculocutané. Nous avons établi une base de données clinico- biologiques décrivant les caractéristiques de plus de 400 patients analysés. Des outils de diagnostic moléculaire ont été développés à la recherche de mutations situées dans les introns et les régions régulatrices et de réarrangements géniques. Différentes stratégies ont également été utilisées pour rechercher des gènes candidats. La puce à façon a permis l’identification de grands réarrangements dans les gènes TYR, OCA2 et SLC45A2 et un réarrangement complexe du gène OCA2 chez 2 patients non apparentés. L'analyse de gènes candidats nous a permis d'identifier, chez 5 patients non apparentés présentant un albinisme oculocutané non syndromique, des mutations dans le gène SLC24A5, très récemment associé à l’AOC6. Le séquençage d’exome de 6 patients a mis en évidence des gènes candidats pour lesquels des analyses complémentaires sont poursuivies afin de confirmer leur implication dans la pathogenèse de l’AOC.Les résultats de ce travail permettent de redéfinir les aspects cliniques et moléculaires de l’AOC, d’identifier de nouveaux mécanismes moléculaires à l’origine de l’AOC ainsi que des gènes candidats dont la fonction dans le développement pigmentaire reste à élucider. L’identification de nouveaux gènes impliqués dans l’AOC pourrait permettre de mieux comprendre et de mieux prendre en charge les patients avec un AOC<br>Our work focused on oculocutaneous albinism (OCA) by studying its clinical and molecular aspects. Despite a thorough analysis of the known genes involved in oculocutaneous albinism, 15% of patients remain without diagnostic at the molecular level indicating that mutations are located in unexplored regions and are undetected by standard techniques or that other genes are involved in albinism. We established a clinicomolecular database describing more than 400 patients and developped molecular tools in order to improve molecular diagnostic including a custom high resolution array-CGH dedicated to the four OCA genes (TYR, OCA2, TYRP1 and SLC45A2). We also used different strategies to identify new genes. Array-CGH allows us to detect large deletion in TYR, OCA2 and SLC45A2 and a complexe rearrangement in OCA2 in 2 unrelated patients. We identified, in 5 patients presenting with a non syndromic OCA, mutations in SLC24A5, recently associated with OCA6. Exome sequencing of 6 different patients allows us to identify candidate genes, for which further studies are required to confirm their involvement in OCA pathogenesis. The results of this work allowed us to delineate clinical and genetics aspects of more than 400 OCA patients and to identify new molecular mechanisms leading to OCA and candidates genes for which exact nature of their functions has to be understood. Giving the complexity of pigmentary system development and its regulation, identification of new genes leading to OCA could help to better understand OCA and take care of patients
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Landes, Nico. "Vitamin E : elucidation of the mechanism of side chain degradation and gene regulatory functions." Phd thesis, [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=975679473.
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Larsson, Ola. "Transcriptome studies of cell-fate and aging /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-296-9/.
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Hodges, Emily Carol. "High resolution genomic tools for the discovery of protein function in mammalian cells /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-775-8/.
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Marshall, Jean-Claude. "Transcriptional and genetic profiling of human uveal melanoma from an immunosuppressed rabbit model." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103272.
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Uveal melanoma is the most common primary intraocular malignant tumour in adults. Despite improvements in the diagnosis and treatment of the primary tumour, patients continue to have the same mortality rate as several decades ago, reflecting our poor understanding of the mechanisms behind the formation of metastases in this disease. The purpose of this study was therefore to characterize an animal model of uveal melanoma and use this model to study the transcriptional changes that cells undergo from culture to intraocular tumour, to circulation and finally to the formation of a metastatic nodule.<br>Using microarrays we identified 314 changes in transcript abundance between the intraocular tumour and metastatic lesions. Principal Components Analysis was used to cluster these transcripts into four distinct groups. A further 61 gene transcripts showed statistically significant changes between re-cultured cells isolated from the model, with the circulating malignant cells representing an intermediate step between cells isolated from intraocular tumours and metastatic lesions. We have produced a detailed analysis of the molecular changes that take place as human uveal melanoma cells evolve from a primary tumour to metastasis in an animal model, including the decrease in expression of specific melanoma markers. These changes were verified using quantitative real time polymerase chain reaction and three different functional assays.<br>In addition we sought to describe the genetic changes that are present in these cells. Using comparative genomic hybridization arrays we were able to successfully describe the deletions and amplifications that are present in genomic DNA extracted from paraffin embedded sections of the primary tumour. This represents the first time that archival tissue has successfully been used for this sort of analysis in uveal melanoma. We identified several genomic amplifications and deletions including an area of amplification of Wnt2, which is involved in beta-catenin regulation and C-Met, which plays a role in tumour cell homing to the liver in patients.<br>To the best of our knowledge, this is the first time that a detailed genetic analysis has been carried out on the progression of uveal melanoma from intraocular tumour, to circulation, to the formation of metastases.
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Dibra, Harpreet Kaur. "Determination of an interaction between the DNA repair proteins MLH1 and sMBD4 and aspirin regulation of DNA repair gene and protein expression in colorectal cancer." Thesis, University of Wolverhampton, 2010. http://hdl.handle.net/2436/109190.
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The base excision repair protein, MBD4 (also known as MED1) is known to be transcriptionally coupled to a mismatch repair protein MLH1. To date the significance of this coupling has not been elucidated and the significance of MBD4 within the mismatch repair system and apoptotic pathway is still being understood. Recently a novel alternatively spliced form of MBD4 has been identified and termed sMBD4. To date the significance of sMBD4 is unknown. MBD4 and sMBD4 share a common glycosylase domain and this is the domain through which MBD4 is reported to interact with MLH1. It was the aim of this study to determine if sMBD4 was also a binding partner of MLH1 to help elucidate a potential role of sMBD4 and to further characterise the binding domain between MLH1 and MBD4. Recombinant proteins were utilised in binding assays however, a specific protein – protein interaction could not be determined. Regular aspirin intake is associated with a reduction in the incidence of colorectal cancer. Aspirin has been shown to be cytotoxic to colorectal cancer cells in vitro. The molecular basis for this cytotoxicity is controversial, with a number of competing hypotheses in circulation. One suggestion is that the protective effect is related to the induction of DNA mismatch repair (MMR) proteins in DNA MMR proficient cells. As MBD4 has previously been suggested to be coupled to MLH1 expression by a post‐translational mechanism the cytotoxicy of aspirin in relation to MBD4 expression was examined. This study reports that aspirin does not up‐regulate MBD4 gene transcription in vitro in the DNA mismatch repair proficient/p53 mutant colorectal cancer cell line SW480. However, MBD4 gene transcription was up‐regulated upon treatment with the aspirin precursor, salicylic acid. The suggested involvement of the DNA repair proteins in the mechanism of action of aspirin promoted the investigation into the expression of DNA damage signalling pathways genes upon aspirin exposure. This study utilised a commercially available PCR array to analyse the expression of 84 DNA damage signalling genes in the SW480 colorectal cancer cell line upon aspirin treatment. It is reported that treatment of the SW480 cell line with aspirin caused changes in mRNA expression of several key genes involved in DNA damage signalling including a significant down‐regulation in expression of the genes encoding ATR, BRCA1 and MAPK12 and increases in the expression of XRCC3 and GADD45α genes. Regulation of these genes could potentially have profound effects on colorectal cancer cells and may play a role in the observed chemo‐protective effect of aspirin in vivo.Further to this, protein expression was analysed to determine if correlation could be established with the changes in mRNA expression observed. Although a correlation was not seen between transcript and protein levels of ATR, BRCA1 and GADD45α, an increase in XRCC3 protein expression upon aspirin treatment in SW480 cells was observed by immunoblotting, immunofluorescence and immunohistochemical analysis. This study indicates that alterations in gene expression seen in microarray studies need to be verified at the protein level. Furthermore, this study reports the novel discovery of XRCC3 gene and protein expression being susceptible to exposure to the non‐steroidal anti‐inflammatory drug, aspirin.
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Desai, Neil Bipinchandra. "Molecular Characterization of Ductal Carcinoma In Situ: Pilot Studies." Yale University, 2010. http://ymtdl.med.yale.edu/theses/available/etd-03242010-174328/.
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Ductal carcinoma in situ (DCIS); is thought directly to precede invasive breast cancer (IBC). Screening mammography has driven the incidence of this key precursor lesion to >65,000 cases per year. However, little is known about the factors controlling the natural history or risk for recurrence following treatment of a particular patients DCIS. Though the heterogeneity of the disease is well established, no histologic or demographic criteria have been able to stratify DCIS for treatment. We hypothesize that at initial diagnosis there exist biologically distinct subsets of DCIS with associated prognoses that may be recognized by molecular markers. Molecular approaches have been limited by technical design issues related to the types of tissue available for analysis, namely degraded formalin-fixed paraffin embedded (FFPE) specimens and small core biopsy samples. However, new technologies promise to overcome these issues. In the first phase of our investigation, we aimed a) to pilot feasibility studies on the use of FFPE DCIS for molecular analyses including gene expression microarray and b) to pilot feasibility study of selective, high throughput sequencing through the use of "exon capture" on small input material that simulated expected DCIS core biopsy amounts. The results of this work offer specific technical guidelines for the molecular study of DCIS. Moreover, they have enabled the initiation of the second phase of this study, which aims to assess molecular profiles of DCIS recurrence and progression.
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Wise, Ingrid. "Epigenetic modifications in essential hypertension." Thesis, Federation University of Australia, 2018. http://researchonline.federation.edu.au/vital/access/HandleResolver/1959.17/165633.
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Background: Hypertension (HTN) is a complex, multifactorial, quantitative trait under polygenic control that affects more than one billion people globally. Despite advances in our understanding of the pathophysiology of HTN and the implementation of more effective treatment and prevention strategies, HTN remains one of the world’s great public health problems. The accepted inference from genome-wide association studies (GWAS) is that the genetic code lays the foundation for transcriptomic changes and in turn physiological change. On the other side of the coin, environmental factors (smoking, diet, chemical exposure) can in turn affect DNA itself in genes relevant to blood pressure (BP). Variation in epigenetic forms of modification may thus explain additional phenotypic variation in BP and provide new clues to the physiological processes influencing its regulation. DNA methylation is one of these epigenetic mechanisms responsible for changes to gene expression, activated by interaction with environmental triggers. DNA methylation is a reversible epigenetic modifier of specific dinucleotide sites called CpGs, which consists of a transfer of a methyl group derived from S-adenosyl-L-methionine to position five of a cytosine ring, forming 5mC. Pathophysiologically, the kidney is known as the key organ of BP regulation and one of the most important contributors to HTN. According to the hypothesis put forward by Guyton, over 40 years ago, the control of BP in the steady-state and longer-term is critically dependent on renal mechanisms. In fact, almost all monogenic forms of HTN are driven by rare mutations in genes involved in salt handling in the distal nephron. It is therefore crucial to understand kidney DNA methylation changes that may drive gene expression in kidney and lead to HTN. Hypothesis: The central hypothesis underpinning this PhD thesis is that alterations in kidney specific DNA methylation plays a fundamental role in modulating gene expression changes involved in the regulation of BP and pathophysiology of EH. Aims: This PhD thesis focuses on characterising the role of DNA methylation in the hypertensive kidney using array and RNA-sequencing methods. Three major aims are addressed: • Aim 1: To characterise blood and kidney global DNA methylation dynamics and its functional role in the hypertensive population (Chapter 3). • Aim 2: To determine the role of genome-wide, loci specific DNA methylation in the hypertensive human kidney (Chapter 4). • Aim 3: To understand the relationship between DNA methylation and differential expression of genes associated with BP and HTN in the human kidney (Chapter 5). Results: In Aim 1 global DNA methylation changes were characterised in peripheral blood leukocyte and kidney DNA of the hypertensive (HT) population using he ELISA method. We found no association between HTN diagnosis and global methylation percentage in either peripheral blood leukocytes or kidney DNA. However, a negative correlation was found between global methylation and diastolic blood pressure (DBP), yet this relationship was not evident after adjustment for the effect of antihypertensive medication. Furthermore, we investigated the sensitivity of ELISA-based global methylation detection by calculating the percentage of global methylation in kidney using array based methods; the results were similar, demonstrating no association between HTN diagnosis and median kidney methylation<br>Doctor of Philosophy
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Liu, Yanling. "Electric DNA chips for determination of pathogenic microorganisms." Doctoral thesis, Stockholm : Bioteknologi, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-9187.
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Rostami, Elham. "Traumatic brain injury in humans and animal models." Doctoral thesis, Stockholm : Reproprint AB, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212088.
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So, Austin Pierre. "Universal Sequence Tag Array (U-STAR) platform : strategies towards the development of a universal platform for the absolute quantification of gene expression on a global scale." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/5580.
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The advent of technologies specifically designed to capture glimpses of gene expression on
a systems-wide scale has led to a revolution in our understanding of cellular dynamics, identifying
the contributions and interactions of families of genes involved in cell development, dysfunction,
and death. Broadly classified into count-based “digital” or signal-based “analogue” approaches,
these technologies have permitted “portraits” of the transcriptome to be generated through
comparative measurements of gene expression, enabling, for example, the generation of qualitative
models of disease. However, truly predictive models of cellular function that can enhance our
ability to discover new pharmaceuticals, detect and monitor disease, evaluate treatments, and
ultimately, predict and prevent illness, require platforms that can provide detailed and accurate
measurements of transcript abundances on an absolute scale. Unfortunately, inherent limitations
preclude these technologies from providing this level of quantitative information.
This thesis examines design issues associated with a popular digital approach to
transcriptomics, serial analysis of gene expression (SAGE), that diminish us utility as a tool for
absolute transcriptomics. Careful analysis of the processing steps involved in converting the
starting mRNA population into short sequence tags (SST5) and subsequently into a format
amenable to interrogation via sequencing technology reveals the introduction of strong biases and
artifacts that limit reproducible abundance measurements in SAGE to transcripts present within
the highest 2 orders of magnitude in the original sample. As a large number of steps are involved
in formatting SSTs for analysis via sequencing, an alternative strategy is presented that utilizes a
microarray-based analogue approach for the interrogation of SSTs. Termed the Universal
Sequence Tag Array (U-STAR) platform, this platform is able to provide accurate quantitative
measurements over a 3-decade range of transcript abundances by obviating sources of bias
associated with both SAGE and DNA microarray technologies and eliminating the requirement
for material amplification. The SAGE-like utilization of STARtags also endows this technology
with the potential to be used as a universal platform, eliminating costs associated with custom
microarray construction, and minimizing those associated with the preparation and large-scale
sequencing of SAGE libraries. Considerations for future development are also discussed for the USTAR
platform.