<p>The array-based form of comparative genomic hybridization (array-CGH) is a new methodology that has shown to be of significant importance. This thesis focuses on the development of array-CGH with the aim to define candidate regions/genes on chromosome 22 in a wide spectrum of cancer-related conditions. In <b>paper I</b>, we developed and applied the first comprehensive genomic microarray, representing human chromosome 22, for analysis of DNA copy number. Using this array-based approach, we identified gene copy number alterations, including heterozygous/homozygous deletions, amplifications, IGLV/IGLC locus instability and the breakpoints of imbalanced translocation, in several 22q-associated disorders. In <b>paper II</b>, we applied the same array to perform DNA copy number profiling of a series of ovarian carcinoma. cDNA arrays were also used in this study to correlate gene expression levels with DNA-copy number. In the course of this analysis, we determined a small 3.5 Mb candidate 22q telomeric region and suggested a number of specific candidate genes. <b>Paper III</b> described the comprehensive and high-resolution analysis of chromosome 22 in a large set of various stage breast cancers. Multiple distinct patterns of genetic aberrations were observed. The smallest identified candidate locus was 220 kb in size and mapped to a gene-rich region in the vicinity of telomere of 22q. Intriguing result of this study was the detection of high frequency (26.6%) of intra-tumoral clonal variation in gene copy number profiles, which should be viewed as a high number, considering that we study in detail only a single human chromosome. In <b>paper IV</b>, we profiled a series of 28 Wilms tumor samples using 22q-array in order to assess specific regions affected with DNA dosage-alterations. The distribution of aberrations defined a complex amplifier genotype and delimited two tumor suppressor/oncogene candidate loci. These results open up for several avenues for continued research of these tumor forms. These findings also demonstrate the power of array-CGH in the precise determination of minute DNA copy number alterations and strengthen the notion that further studies, preferentially in the context of the entire human genome, are needed.</p>

<p>Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder with the clinical hallmark of bilateral vestibular schwannomas (VS). Patients affected by a severe NF2 phenotype also presents with peripheral schwannomas, meningiomas and ependymomas. The closely related disorder schwannomatosis also displays multiple schwannomas, but never VS. Mutation screening of the <i>NF2</i> gene in the above mentioned tumors did not identify mutations in numerous of cases. We analyzed the DNA sequence covering the <i>NF2</i> locus in order to identify evolutionarily conserved non-genic sequences (CNGs) with unknown regulatory function (paper I). The aim was to analyze CNGs for mutations in DNA derived from patients affected by NF2 associated tumors. During mutation analysis of the coding part of <i>NF2</i> and within the CNGs defined in paper I, were mutations detected in 39% of sporadic meningiomas (paper II). Two candidate regions were identified on 22q using array-CGH. Methylation profiling did not identify methylation of the <i>NF2</i> promoter in these tumors. Sporadic schwannomas were profiled for CNV using a 22q genomic array in the search for putative gene(s) that in addition to <i>NF2</i> could be involved in the development of schwannoma and/or schwannomatosis (paper III). The predominant aberration identified was monosomy 22. Terminal and interstitial deletions encompassing the <i>NF2</i> gene were detected in tumor DNA and eight loci affected by CNV in constitutional DNA. Some of these CNVs are unlikely to be phenotypically neutral, considering their size and gene content. Two schwannomatosis candidate regions were identified on 22q using array-CGH (paper IV). These regions were further characterized by a PCR-product based array with higher resolution. Rearrangements of the immunoglobulin lambda (<i>IGL</i>) locus detected were restricted to schwannomatosis patients. In the second candidate region spanning <i>GSTT1</i> and <i>CABIN1</i> genes, was frequent copy number polymorphism at the <i>GSTT1</i> locus identified. We further describe missense mutations in the <i>CABIN1 </i>gene, making this gene a plausible candidate which may contribute to the pathogenesis of these disorders. </p>

Neurofibromatosis type-2 (NF2) is an autosomal dominant disorder with the clinical hallmark of bilateral eighth cranial nerve schwannomas. However, the diagnostic criterion is complicated by the presence of a variable phenotype, with the severe form presenting with additional tumors such as peripheral schwannoma, meningioma and ependymoma. We constructed a microarray spanning 11Mb of 22q, encompassing the NF2 gene, to detect deletions in schwannoma. Forty seven patients were analyzed and heterozygous deletions were detected in 45% of tumors. Using this array-based approach, we also detected genetic heterogeneity in a number of samples studied. Despite the high sensitivity and the comprehensive series of studied schwannomas, no homozygous deletions affecting the NF2 gene were detected <b>(paper I)</b>. In order to detect more subtle deletions within the NF2 locus, a higher-resolution gene-specific array was developed, for the detection of disease-causing<b> </b>deletions using a PCR-based non-redundant strategy. This novel approach for array construction significantly increased the reliability and resolution of deletion-detection within the NF2 locus <b>(paper II)</b>. To further expand the coverage of the 11 Mb microarray, we constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number. This 22q array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb <b>(paper III)</b>. Using this array, we analyzed sporadic and familial schwannomatosis samples, which revealed two commonly deleted regions within the immunoglobulin lambda locus and the GSTT1/CABIN1 locus. These regions were further characterized using higher-resolution non-redundant arrays, bioinformatic tools, positional cloning and mutational screening. Missense mutations were detected in the CABIN1 gene, which may contribute to the pathogenesis of schwannomatosis and therefore requires further study <b>(paper IV)</b>. Meningioma is the second most common NF2-associated tumor and loss of 1p has been previously established as a major genetic factor for disease initiation/progression and also correlates with increased morbidity. We analyzed 82 meningiomas using a chromosome 1 tiling-path genomic microarray. The distribution of aberrations detected supports the existence of at least four regions on chromosome 1, which are important for meningioma tumorigenesis <b>(paper V)</b>.

The array-based form of comparative genomic hybridization (array-CGH) is a new methodology that has shown to be of significant importance. This thesis focuses on the development of array-CGH with the aim to define candidate regions/genes on chromosome 22 in a wide spectrum of cancer-related conditions. In <b>paper I</b>, we developed and applied the first comprehensive genomic microarray, representing human chromosome 22, for analysis of DNA copy number. Using this array-based approach, we identified gene copy number alterations, including heterozygous/homozygous deletions, amplifications, IGLV/IGLC locus instability and the breakpoints of imbalanced translocation, in several 22q-associated disorders. In <b>paper II</b>, we applied the same array to perform DNA copy number profiling of a series of ovarian carcinoma. cDNA arrays were also used in this study to correlate gene expression levels with DNA-copy number. In the course of this analysis, we determined a small 3.5 Mb candidate 22q telomeric region and suggested a number of specific candidate genes. <b>Paper III</b> described the comprehensive and high-resolution analysis of chromosome 22 in a large set of various stage breast cancers. Multiple distinct patterns of genetic aberrations were observed. The smallest identified candidate locus was 220 kb in size and mapped to a gene-rich region in the vicinity of telomere of 22q. Intriguing result of this study was the detection of high frequency (26.6%) of intra-tumoral clonal variation in gene copy number profiles, which should be viewed as a high number, considering that we study in detail only a single human chromosome. In <b>paper IV</b>, we profiled a series of 28 Wilms tumor samples using 22q-array in order to assess specific regions affected with DNA dosage-alterations. The distribution of aberrations defined a complex amplifier genotype and delimited two tumor suppressor/oncogene candidate loci. These results open up for several avenues for continued research of these tumor forms. These findings also demonstrate the power of array-CGH in the precise determination of minute DNA copy number alterations and strengthen the notion that further studies, preferentially in the context of the entire human genome, are needed.

Neurofibromatosis type 2 (NF2) is an autosomal dominant disorder with the clinical hallmark of bilateral vestibular schwannomas (VS). Patients affected by a severe NF2 phenotype also presents with peripheral schwannomas, meningiomas and ependymomas. The closely related disorder schwannomatosis also displays multiple schwannomas, but never VS. Mutation screening of the NF2 gene in the above mentioned tumors did not identify mutations in numerous of cases. We analyzed the DNA sequence covering the NF2 locus in order to identify evolutionarily conserved non-genic sequences (CNGs) with unknown regulatory function (paper I). The aim was to analyze CNGs for mutations in DNA derived from patients affected by NF2 associated tumors. During mutation analysis of the coding part of NF2 and within the CNGs defined in paper I, were mutations detected in 39% of sporadic meningiomas (paper II). Two candidate regions were identified on 22q using array-CGH. Methylation profiling did not identify methylation of the NF2 promoter in these tumors. Sporadic schwannomas were profiled for CNV using a 22q genomic array in the search for putative gene(s) that in addition to NF2 could be involved in the development of schwannoma and/or schwannomatosis (paper III). The predominant aberration identified was monosomy 22. Terminal and interstitial deletions encompassing the NF2 gene were detected in tumor DNA and eight loci affected by CNV in constitutional DNA. Some of these CNVs are unlikely to be phenotypically neutral, considering their size and gene content. Two schwannomatosis candidate regions were identified on 22q using array-CGH (paper IV). These regions were further characterized by a PCR-product based array with higher resolution. Rearrangements of the immunoglobulin lambda (IGL) locus detected were restricted to schwannomatosis patients. In the second candidate region spanning GSTT1 and CABIN1 genes, was frequent copy number polymorphism at the GSTT1 locus identified. We further describe missense mutations in the CABIN1 gene, making this gene a plausible candidate which may contribute to the pathogenesis of these disorders.

The RAS-MAPK syndromes are a group of clinically and genetically related disorders, characterized by cardiac defects, facial dysmorphism, cutaneous abnormalities and neurocognitive impairment. The pathogenesis is dysregulation of the RAS-MAPK pathway, and several genes within the pathway are involved. The present thesis aimed at identifying genetic causes in three of the RAS-MAPK syndromes - Noonan syndrome (NS), cardio-facio-cutaneous syndrome (CFC) and Neurofibromatosis-Noonan syndrome (NFNS) - and at correlating genotype with phenotype. A mutation analysis of six genes associated with the RAS-MAPK syndromes in NS and CFC patients revealed mutations in 10/31 patients. The results suggested more complex genetic overlap and genetic heterogeneity among these syndromes than previously believed. Subsequently, gene dosage imbalances of seven RAS-MAPK-syndrome-related genes were investigated in mutation-negative patients. A multiplex ligation-dependent probe amplification strategy was developed that excluded copy number changes of these genes as a common mechanism in NS. Genetic causes of clinical variability in NS were investigated where an atypical and severe NS patient was described. In addition, multiple café-au-lait (CAL) spots affected the patient and four otherwise healthy family members. Molecular analysis of four candidate genes revealed a previously described de novo PTPN11 mutation and an inherited NF1 variant in the patient. Neither of them explained the CAL spots trait, which consequently represented a distinct entity. The results suggested that the atypical and severe phenotype in the patient could be a consequence of an additive effect. Finally, a family displaying NFNS was investigated clinically and molecularly revealing a novel mutation in the GAP-domain of NF1. Furthermore, the results suggested that other RAS-MAPK-syndrome-related genes are not involved in NFNS. A proposal of prioritizing the GAP-domain of NF1 in NFNS was presented. Conclusively, these studies contribute to further understanding of the RAS-MAPK syndromes and facilitate the diagnostic process and future prognosis prediction.

Homeostasis is an indispensable phenomenon in the maintenance of living organisms. Genetic defects which disrupt negative feedback processes can impact homeostatic regulation, potentially resulting in disease. To uncover the molecular mechanisms governing these and other diseases potentially related to defective homeostasis, I used the Drosophila neuromuscular junction as a model system. I characterized two potential mechanisms that regulate homeostasis within the nervous system. First, in Drosophila larval motor neurons, ligand activation of Drosophila metabotropic glutamate receptor A (DmGluRA) mediates a Phosphoinositide 3-kinase (PI3K)-dependent downregulation of neuronal activity, but the mechanism by which mGluR activates PI3K remains incompletely understood. Here, I identified Ca 2+ /Calmodulin-dependant protein kinase II (CaMKII) and the Focal adhesion kinase (DFak) as critical intermediates in the DmGluRA-dependent activation of PI3K at Drosophila motor nerve terminals. I found that transgene-induced CaMKII inhibition or the DFak CG1 null mutation each block the ability of glutamate application to activate PI3K in larval motor nerve terminals, whereas transgene-induced CaMKII activation increases PI3K activity in motor nerve terminals in a DFak-dependent manner, even in the absence of glutamate application. I conclude that the activation of PI3K by DmGluRA is mediated by CaMKII and DFak. Second, I observed that Push, a putative E3-ubiquitin ligase and Ca 2+ /Calmodulin binding protein, regulates both neurotransmitter release and retrograde signaling in the Drosophila neuromuscular junction. I found that RNAi-mediated Push inhibition in the neuron increases but, in the muscle decreases, neurotransmitter release. Similar results were obtained from RNAi knock down of PLCβ and IP3R, which mediates Ca 2+ release from the endoplasmic reticulum. I conclude that Push mediation of the ubiquitin proteasome system may be important in the regulation of PLCβ/IP3R-mediated intracellular Ca 2+ release, and that this Ca 2+ release in the neuron inhibits neurotransmitter release, but in the muscle activates neurotransmitter release via a retrograde signal.

Introdução: A Neurofibromatose tipo 1 (NF1) é uma doença genética autossômica dominante causada por mutação no gene NF1 (17q11.2; proteína neurofibromina). A incidência é de aproximadamente 1:3500 recém-nascidos e o diagnóstico clínico é possível na maioria dos casos. Alguns estudos sugeriram que pacientes com NF1 são mais suscetíveis a apresentar deficiência de vitamina D quando comparados à população geral. Objetivo: Determinar os níveis de 25(OH)D em indivíduos com NF1 e em controles saudáveis. Nos pacientes com NF1 nos também avaliamos o fenótipo clínico e analisamos polimorfismos comuns do gene VDR (BsmI e FokI) para avaliar se estavam correlacionados com os níveis de 25(OH)D. Métodos: Estudo de caso-controle que incluiu 45 pacientes com NF1 do Sul do Brasil e 45 controles saudáveis pareados por idade, sexo e tipo de pele de acordo com a classificação de Fitzpatrick. Resultados e Conclusões: Setenta e sete vírgula oito por cento dos 90 sujeitos de pesquisa apresentaram níveis de 25(OH)D abaixo de 30ng/ml. Deficiência de 25(OH)D (<20ng/mL) foi observada em 28 (31,1%) e insuficiência (de 20 a 30ng/mL) em 42 (46,6%). Deficiência ou insuficiência de 25(OH)D não foi mais frequente em pacientes com NF1 do que em controles (p=0,074). Nos não observamos qualquer associação entre os polimorfismos do gene VDR e os níveis de vitamina D sugerindo que o fenótipo da insuficiência ou deficiência bioquímica de 25(OH)D nos pacientes estudados não está associado com essas variantes genéticas. / Introduction: Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder caused by mutations in the NF1 gene (17q11.2, neurofibromin). The estimated incidence is approximately 1:3500 newborns and clinical diagnosis is possible in the majority cases. A few studies suggest that patients with NF1 are more likely to have vitamin D deficiency when compared to the general population. Objectives: The goal of the study was to determine the levels of 25-OH-vitamin D [25(OH)D] in individuals with NF1 and disease-unaffected controls. In NF1 patients we also assessed clinical phenotype and analyzed common VDR gene polymorphisms (BsmI and FokI) to verify whether they were associated with lower vitamin D levels. Methods: Case-control study that included 45 NF1 patients from Southern Brazil and 45 healthy controls matched by sex, skin type and age to the cases. Results and conclusions: Overall, 70 (77.8%) of the individuals studied had levels of 25(OH)D below 30ng/ml: vitamin D deficiency was observed in 28 (31.1%) and vitamin D insufficiency in 42 (46.6%) subjects. 25(OH)D deficiency or insufficiency were not more frequent in NF1 patients than in controls (p=0,074). We did not observe an association of VDR gene polymorphisms and vitamin D levels suggesting that the insufficient or deficient biochemical phenotypes in the patients studied here are not associated with these genetic variants.

Introdução: A Neurofibromatose tipo 1 (NF1) é uma doença genética autossômica dominante causada por mutação no gene NF1 (17q11.2; proteína neurofibromina). A incidência é de aproximadamente 1:3500 recém-nascidos e o diagnóstico clínico é possível na maioria dos casos. Alguns estudos sugeriram que pacientes com NF1 são mais suscetíveis a apresentar deficiência de vitamina D quando comparados à população geral. Objetivo: Determinar os níveis de 25(OH)D em indivíduos com NF1 e em controles saudáveis. Nos pacientes com NF1 nos também avaliamos o fenótipo clínico e analisamos polimorfismos comuns do gene VDR (BsmI e FokI) para avaliar se estavam correlacionados com os níveis de 25(OH)D. Métodos: Estudo de caso-controle que incluiu 45 pacientes com NF1 do Sul do Brasil e 45 controles saudáveis pareados por idade, sexo e tipo de pele de acordo com a classificação de Fitzpatrick. Resultados e Conclusões: Setenta e sete vírgula oito por cento dos 90 sujeitos de pesquisa apresentaram níveis de 25(OH)D abaixo de 30ng/ml. Deficiência de 25(OH)D (<20ng/mL) foi observada em 28 (31,1%) e insuficiência (de 20 a 30ng/mL) em 42 (46,6%). Deficiência ou insuficiência de 25(OH)D não foi mais frequente em pacientes com NF1 do que em controles (p=0,074). Nos não observamos qualquer associação entre os polimorfismos do gene VDR e os níveis de vitamina D sugerindo que o fenótipo da insuficiência ou deficiência bioquímica de 25(OH)D nos pacientes estudados não está associado com essas variantes genéticas. / Introduction: Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder caused by mutations in the NF1 gene (17q11.2, neurofibromin). The estimated incidence is approximately 1:3500 newborns and clinical diagnosis is possible in the majority cases. A few studies suggest that patients with NF1 are more likely to have vitamin D deficiency when compared to the general population. Objectives: The goal of the study was to determine the levels of 25-OH-vitamin D [25(OH)D] in individuals with NF1 and disease-unaffected controls. In NF1 patients we also assessed clinical phenotype and analyzed common VDR gene polymorphisms (BsmI and FokI) to verify whether they were associated with lower vitamin D levels. Methods: Case-control study that included 45 NF1 patients from Southern Brazil and 45 healthy controls matched by sex, skin type and age to the cases. Results and conclusions: Overall, 70 (77.8%) of the individuals studied had levels of 25(OH)D below 30ng/ml: vitamin D deficiency was observed in 28 (31.1%) and vitamin D insufficiency in 42 (46.6%) subjects. 25(OH)D deficiency or insufficiency were not more frequent in NF1 patients than in controls (p=0,074). We did not observe an association of VDR gene polymorphisms and vitamin D levels suggesting that the insufficient or deficient biochemical phenotypes in the patients studied here are not associated with these genetic variants.

Introdução: A Neurofibromatose tipo 1 (NF1) é uma doença genética autossômica dominante causada por mutação no gene NF1 (17q11.2; proteína neurofibromina). A incidência é de aproximadamente 1:3500 recém-nascidos e o diagnóstico clínico é possível na maioria dos casos. Alguns estudos sugeriram que pacientes com NF1 são mais suscetíveis a apresentar deficiência de vitamina D quando comparados à população geral. Objetivo: Determinar os níveis de 25(OH)D em indivíduos com NF1 e em controles saudáveis. Nos pacientes com NF1 nos também avaliamos o fenótipo clínico e analisamos polimorfismos comuns do gene VDR (BsmI e FokI) para avaliar se estavam correlacionados com os níveis de 25(OH)D. Métodos: Estudo de caso-controle que incluiu 45 pacientes com NF1 do Sul do Brasil e 45 controles saudáveis pareados por idade, sexo e tipo de pele de acordo com a classificação de Fitzpatrick. Resultados e Conclusões: Setenta e sete vírgula oito por cento dos 90 sujeitos de pesquisa apresentaram níveis de 25(OH)D abaixo de 30ng/ml. Deficiência de 25(OH)D (<20ng/mL) foi observada em 28 (31,1%) e insuficiência (de 20 a 30ng/mL) em 42 (46,6%). Deficiência ou insuficiência de 25(OH)D não foi mais frequente em pacientes com NF1 do que em controles (p=0,074). Nos não observamos qualquer associação entre os polimorfismos do gene VDR e os níveis de vitamina D sugerindo que o fenótipo da insuficiência ou deficiência bioquímica de 25(OH)D nos pacientes estudados não está associado com essas variantes genéticas. / Introduction: Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder caused by mutations in the NF1 gene (17q11.2, neurofibromin). The estimated incidence is approximately 1:3500 newborns and clinical diagnosis is possible in the majority cases. A few studies suggest that patients with NF1 are more likely to have vitamin D deficiency when compared to the general population. Objectives: The goal of the study was to determine the levels of 25-OH-vitamin D [25(OH)D] in individuals with NF1 and disease-unaffected controls. In NF1 patients we also assessed clinical phenotype and analyzed common VDR gene polymorphisms (BsmI and FokI) to verify whether they were associated with lower vitamin D levels. Methods: Case-control study that included 45 NF1 patients from Southern Brazil and 45 healthy controls matched by sex, skin type and age to the cases. Results and conclusions: Overall, 70 (77.8%) of the individuals studied had levels of 25(OH)D below 30ng/ml: vitamin D deficiency was observed in 28 (31.1%) and vitamin D insufficiency in 42 (46.6%) subjects. 25(OH)D deficiency or insufficiency were not more frequent in NF1 patients than in controls (p=0,074). We did not observe an association of VDR gene polymorphisms and vitamin D levels suggesting that the insufficient or deficient biochemical phenotypes in the patients studied here are not associated with these genetic variants.