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.

Thesis (Ph. D.)--West Virginia University, 2001. / Title from document title page. Document formatted into pages; contains x, 152 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 119-149).

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HER2 overexpression in breast cancer tumors predicts lower overall survival. Because of the aggressive nature of HER2 tumors and the association with metastatic disease, the HER2 receptor holds great promise as a therapeutic target in metastatic breast cancer. We are developing small molecule inhibitors that bind to the ATP binding site of the tyrosine kinase domain in order to inhibit tyrosine auto-phosphorylation. This process controls biological pathways that mediate the cell growth. In normal cells this process is highly controlled. We are targeting the modification of the side chain of the hydroxy methyl group of 2-Hydroxy methyl-5,8-dimethoxy-1,4-naphthaquinone. These compounds should inhibit the tyrosine kinase cascade of reactions thereby suppressing the overexpression of HER2 shutting down the tumor growth. The synthesis and characterization of a series of substituted naphthaquinone analogs with different increasing chain lengths will be reported.

Thesis (doctoral)--Lund University, 1997. / Added t.p. with thesis statement inserted. Includes bibliographical references.

Thesis (doctoral)--Lund University, 1997. / Added t.p. with thesis statement inserted. Includes bibliographical references.

Thesis (Ph.D.)--University of Melbourne, The Walter and Eliza Hall Institute of Medical Research, The Division of Immunology and the Division of Molecular Medicine, Dept. of Medical Biology, Faculty of Medicine and Dentistry, 2009. / Typescript. Includes bibliographical references (p. 133-165)

Orientadores: João Palermo Neto, Antonio Armario Garcia / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-21T19:54:17Z (GMT). No. of bitstreams: 1 Queiroz_JuliadeSouza_D.pdf: 6420413 bytes, checksum: 5de0fbd4bbb6451ff5729cbdc2fc74ce (MD5) Previous issue date: 2012 / Resumo: A exposição do organismo a estressores psicossociais e ambientais altera de forma significativa o funcionamento do sistema imune. Os efeitos do estresse sobre a resposta imune têm sido atribuídos, principalmente, à ativação do eixo hipotálamo-pituitária-adrenal (HPA) com consequente aumento nos níveis de ACTH e glicocorticóides e à ativação do sistema nervoso autônomo simpático (SNAS), com liberação de catecolaminas. Nos últimos anos, a alga Chlorella vulgaris (CV) tem despertado o interesse da comunidade científica pelos seus efeitos moduladores sobre as defesas do hospedeiro imunossuprimido. Em estudos anteriores mostramos que o restabelecimento da geração de granulócitos-macrófagos nos órgãos hematopoéticos e a ativação das funções efetoras de fagócitos e linfócitos são cruciais na expressão da atividade imunomoduladora da alga. No entanto, nada se sabe sobre os efeitos da CV no sistema nervoso central em situações de estresse. Sendo assim, neste trabalho realizamos estudos pioneiros com relação ao efeito do tratamento com a alga sobre: 1) a ativação neuronal (c-fos) no córtex pré-frontal, septum lateral, núcleo da Rafe e lócus coeruleus; 2) a ativação do eixo HPA através da expressão do gen de hnCRF na região parvocelular do núcleo paraventricular do hipotálamo, mpdPVN, liberação de ACTH e de corticosterona e, 3) avaliação indireta da atividade do SNAS através dos níveis de glicose no plasma de animais estressados. Considerando-se a medula óssea ser o sítio de origem das células pluripotenciais das quais se originam as células do sistema hematopoético, e que este sistema é totalmente vulnerável ao controle neuroendócrino, avaliamos os efeitos do tratamento com CV sobre a hematopoese de animais estressados através dos 4) crescimento e diferenciação de precursores para granulócitos e macrófagos (CFU-GM); 5) presença de fatores estimuladores da formação de colônias do soro (colony stimulating activity - CSA); 6) quantificação de populações de células maduras e imaturas e 7) morte celular na população de células tronco. A regulação da produção de células hematopoéticas pelas células do estroma da medula óssea em camundongos estressados foi avaliada pela técnica de cultura líquida de longa duração de células da medula óssea (LTBMC), que consiste em um modelo ex vivo para o estudo das interações entre as células progenitoras hematopoéticas e as células do estroma. Nela avaliamos 8) o CFU-GM, níveis de IL-1? / IL-6 e quantificamos uma população madura e uma imatura. Nossos resultados mostraram que a aplicação do estressor produziu um aumento na expressão de c-fos em todas as áreas cerebrais avaliadas, assim como na expressão do gen de hnCRF na região mpdPVN. Os níveis de ACTH e corticosterona também estavam aumentados após o estresse, assim como os níveis de glicose. Na medula óssea observamos que a aplicação do estressor reduziu o número de CFU-GM, e aumentou os níveis de CSA no plasma. Houve um aumento na morte celular e redução no número de precursores hematopoéticos e de células maduras. Na LTBMC, um prejuízo na atividade funcional do estroma medular foi observado através: da redução do CFU-GM, dos níveis de IL-1? / IL-6 e do número de células imaturas e maduras. O aumento na expressão de c-fos após o estresse foi prevenida pelo tratamento com CV em todas as áreas avaliadas, com exceção da região magnocelular do PVN. O resultado mais acentuado do tratamento com CV foi observado na redução da expressão de c-fos no núcleo da Rafe e do gen para hnCRF no mpdPVN, que se encontrou em níveis semelhantes aos observados no grupo controle após o estresse. Todas as alterações hematopoéticas causadas pelo estresse foram prevenidas pelo tratamento com CV. Tomados em seu conjunto, nossos resultados mostraram que o efeito protetor da hematopoese pode ser devido a uma prevenção na ativação neuronal de áreas cerebrais relacionadas à decodificação do estressor do tipo emocional, reduzindo a amplitude de ativação do eixo HPA e do SNAS / Abstract: The exposition of the organism to psychosocial and environmental stressful stimuli alters the functioning of the immune system in a significant way. The effects of stress on the immune response are mainly attributed to the activation of the hypothalamic-pituitary axis (HPA) with consequent increment on ACTH and glucocorticoids levels and, to the activation of the autonomic nervous system, with the incremented levels of cathecholamines. In the last years, increasing interests about the algae Chlorella vulgaris (CV) has been demonstrated by the scientific community, due to its modulatory effects on the defenses of the immunosuppressed host. In previous studies we demonstrated that the reestablishment of the generation of granulocytes and macrophages in bone marrow and, the activation of effectors functions of phagocytes and lymphocytes, are crucial features about the immunomodulatory activity from the algae. However, nothing is known about the activity of CV in the central nervous system. Thus, pioneer investigation was made in this work about the effect of treatment with the CV on: 1) neuronal activation (c-fos) in pre-frontal cortex, lateral septum, Rafe nucleus and locus coeruleus; 2) activation of the HPA axis by analysis of expression of the gen to hnCRF in the parvocelular region from the paraventricular nucleus of the hypothalamus -mpdPVN and the release of ACTH and corticosterone) and, 3) glucose levels, as an indirect indicator of autonomic nervous system activity. Considering that the bone marrow is the site of origin from pluripotent cells from which all cells from the hematopoietic system are originated, and also that this system is vulnerable to the neuroendocrine control, we evaluated the effects of the treatment with CV on the hematopoiesis of stressed animals through 4) growing and differentiation of precursors to granulocytes and macrophages (CFU-GM); 5) colony stimulating activity from the serum (CSA); 6) quantification of population of mature and immature populations and 7) cell death. The interaction between stromal cells and hematopoietic progenitors in stressed mice was evaluated by the technique of long term bone marrow culture (LTBMC). In the culture we evaluated 8) the CFU-GM, levels of IL-1? / IL-6 and quantification of mature and immature population. The application of the stressor produced an increase in the expression of c-fos in all brain areas evaluated and in the expression of the gen to hnCRF in mpdPVN. Increased levels of ACTH, corticosterone and glucose found in stressed animals corroborate these findings. Reduced numbers of CFU-GM in the bone marrow and increase in plasma CSA, increased cell death in stem cell population (LSK) and decreased numbers of hematopoietic precursors and of mature cells was also observed in stressed group. In LTBMC we observed impairment on the functional activity from medullar stroma, which was observed by reduction of: CFU-GM, IL-1? / IL-6 levels and number of immature and mature cells. Treatment with CV partially prevented increase in c-fos activation caused by stress in the brain except in the magnocelular region from PVN. The more accentuated result from treatment with CV of stressed animals was observed in the expression of c-fos in the Raphe nucleus and in the expression of the gen to hnCRF in mpdPVN, where levels were similar to that observed in control group. All hematopoietic alterations observed after stress were prevented by the treatment with CV. Taken together, our results demonstrate that the protective effect of the treatment with CV on hematopoiesis of stressed animals may be due to a prevention of the neuronal activation in areas related to the decodification of the emotional stressful stimuli, reducing the amplitude of HPA axis and autonomic nervous system activity / Doutorado / Farmacologia / Doutora em Farmacologia

Indiana University-Purdue University Indianapolis (IUPUI) / ABSTRACT Yue Wang Neurofibromin, nerve growth factor and Ras: their roles in controlling the excitability of mouse sensory neurons Neurofibromin, the product of the Nf1 gene, is a guanosine triphosphatase activating protein (GAP) for p21ras (Ras) that accelerates the conversion of active Ras-GTP to inactive Ras-GDP. It is likely that sensory neurons with reduced levels of neurofibromin have augmented Ras-GTP activity. In a mouse model with a heterozygous mutation of the Nf1 gene (Nf1+/-), the patch-clamp recording technique is used to investigate the role of neurofibromin in controlling the state of neuronal excitability. Sensory neurons isolated from adult Nf1+/- mice generate more APs in response to a ramp of depolarizing current compared to Nf1+/+ mice. In order to elucidate whether the activation of Ras underlies this augmented excitability, sensory neurons are exposed to nerve growth factor (NGF) that activates Ras. In Nf1+/+ neurons, exposure to NGF increases the production of APs. To examine whether activation of Ras contributes to the NGF-induced sensitization in Nf1+/+ neurons, an antibody that neutralizes Ras activity is internally perfused into neurons. The NGF-mediated augmentation of excitability is suppressed by the Ras-blocking antibody in Nf1+/+ neurons, suggesting the NGF-induced sensitization in Nf1+/+ neurons depends on the activation of Ras. Surprisingly, the excitability of Nf1+/- neurons is not altered by the blocking antibody, suggesting that this enhanced excitability may depend on previous activation of downstream effectors of Ras. To determine the mechanism giving rise to augmented excitability of Nf1+/- neurons, isolated membrane currents are examined. Consistent with the enhanced excitability of Nf1+/- neurons, the peak current density of tetrodotoxin-resistant (TTX-R) and TTX-sensitive (TTX-S) sodium currents (INa) are significantly larger than in Nf1+/+ neurons. Although the voltage for half-maximal activation (V0.5) is not different, there is a significant depolarizing shift in the V0.5 for steady-state inactivation of INa in Nf1+/- neurons. In summary, these results demonstrate that the enhanced production of APs in Nf1+/- neurons results from a larger current amplitude and a depolarized voltage dependence of steady-state inactivation of INa that leads to more sodium channels being available for the subsequent firing of APs. My investigation supports the idea that regulation of channels by the Ras cascade is an important determinant of neuronal excitability. Grant D. Nicol, Ph.D, Chair

Background: Development of brain metastases in advanced melanoma patients is a frequent event that limits patients’ quality of life and survival. Despite recent insights into melanoma genetics, systematic analyses of genetic alterations in melanoma brain metastasis formation are lacking. Moreover, whether brain metastases harbor distinct genetic alterations beyond those observed at different anatomic sites of the same patient remains unknown. Experimental Design and Results: In our study, 54 intracranial and 18 corresponding extracranial melanoma metastases were analyzed for mutations using targeted next generation sequencing of 29 recurrently mutated driver genes in melanoma. In 11 of 16 paired samples, we detected nucleotide modifications in brain metastases that were absent in matched metastases at extracranial sites. Moreover, we identified novel genetic variants in ARID1A, ARID2, SMARCA4 and BAP1, genes that have not been linked to brain metastases before; albeit most frequent mutations were found in ARID1A, ARID2 and BRAF. Conclusion: Our data provide new insights into the genetic landscape of intracranial melanoma metastases supporting a branched evolution model of metastasis formation.