Orientador: Alan Roger dos Santos Silva / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-27T16:02:08Z (GMT). No. of bitstreams: 1 Neves-Silva_Rodrigo_D.pdf: 4907287 bytes, checksum: 38719ff902e5d495d2cea840229a01b1 (MD5) Previous issue date: 2015 / Resumo: Tumores odontogênicos (TOs) são neoplasias originadas do órgão de desenvolvimento dentário ou de seus remanescentes. Neste contexto, o ameloblastoma é um dos TOs mais relevantes devido a sua elevada frequência e alto potencial de agressividade clínica. O presente estudo se propôs a realizar uma análise clinicopatológica retrospectiva de ameloblastomas e, posteriormente, validar o uso da técnica do tissue microarray (TMA) para a análise imunoistoquímica de ameloblastomas. Material e métodos: O estudo clinicopatológico se baseou numa amostra de 869 TOs, oriundos de dois centros de Patologia Oral brasileiros, sendo 177 (20,36%) casos de ameloblastomas, dos quais foram selecionados 40 (22,59%) casos representativos de ameloblastomas multicísticos que foram distribuídos em dois blocos do TMA montados em triplicata contendo cilindros de 1.0mm e 2.0mm (Sakura Co., Tokyo, Japan). A validação da análise imunoistoquímica foi realizada para proteínas expressas em citoplasma (citoqueratina 14, citoqueratina 19 e Bcl-2) e em núcleo (Ki-67); analisada por meio semiquantitativo e também por microscopia óptica digital (Aperio Scanscope CS® Slide Scanner; Aperio Technologies Inc.; Vista, CA; USA) e quantificada por meio dos algoritmos PixelCount® e NuclearV9® (Aperio Technologies Inc.; Vista, CA; USA). Resultados: Os 40 casos de ameloblastoma multicístico afetaram predominantemente pacientes do gênero masculino (62,5%), a média de idade no momento do diagnóstico foi de 39,92 anos (variando de 15 a 71 anos), a maioria (92,5%) dos casos ocorreu na região posterior da mandíbula. A concordância obtida para a expressão imunoistoquímica entre os diferentes diâmetros do TMA e os cortes convencionais mostrou melhores resultados para os cilindros de 2.0mm montados em triplicata nas análises digital e semiquantitativa. Em conclusão, o presente estudo demonstrou originalmente que a técnica do TMA pode ser usada com rigor científico para estudos baseados na análise imunoistoquímica de marcadores de citoplasma e núcleo celular em ameloblastomas multicísticos / Abstract: Odontogenic tumors (OTs) are neoplasms originating from the tooth developing apparatus or its remnants. In this context, ameloblastoma is one of the most relevant OTs due to its high frequency and clinical potential of aggressiveness. The present study performed a retrospective, clinicopathological analysis of ameloblastomas and subsequently validated the use of the tissue microarray (TMA) for immunohistochemical analysis of ameloblastomas. Materials and methods: The clinicopathologic study was based on a sample of 869 OTs from two Brazilian Oral Pathology Centers. Of these, 177 (20.36%) cases were ameloblastomas, of which 40 (22.59%) cases of multicystic ameloblastomas were selected and divided into two TMA blocks mounted in triplicate containing cores of 1.0mm and 2.0mm (Sakura Co., Tokyo, Japan). The validation of the immunohistochemical analysis was performed for proteins expressed in the cytoplasm (cytokeratin 14, cytokeratin 19, and Bcl-2) and nuclei (Ki-67), analyzed in a semiquantitative way as well as by digital optical microscopy (Aperio Scanscope CS® Slide Scanner; Aperio Technologies Inc., Vista, CA, USA), and quantified by PixelCount® and NuclearV9® algorithms (Aperio Technologies Inc., Vista, CA, USA). Results: Forty cases of ameloblastoma affected predominantly male patients (n=25; 62.5%). The mean age at diagnosis was 39.92 years (ranging from 15 to 71 years), and the majority (92.5%) of the cases occurred in the posterior mandible. The concordance obtained for the immunohistochemical expression in different TMA core diameters and whole sections showed best results for 2.0mm TMA assembled in triplicates both for semiquantitative and digital analyses. In conclusion, this study originally demonstrated that the TMA technique could be used with scientific rigor in studies based on immunohistochemical analysis of cytoplasmic and nuclear markers in multicystic ameloblastomas / Doutorado / Estomatologia / Doutor em Estomatopatologia

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In this dissertation, first we consider the problem of testing homogeneity and order in a contaminated normal model, when the data is correlated under some known covariance structure. To address this problem, we developed a moment based homogeneity and order test, and design weights for test statistics to increase power for homogeneity test. We applied our test to microarray about Down’s syndrome. This dissertation also studies a singular Bayesian information criterion (sBIC) for a bivariate hierarchical mixture model with varying weights, and develops a new data dependent information criterion (sFLIC).We apply our model and criteria to birth- weight and gestational age data for the same model, whose purposes are to select model complexity from data.

Notch signaling plays a key role in development, tissue homeostasis, and cancer. High expression levels of Notch signaling components are associated with aggressive disease and poor patient prognosis in breast cancer. Mesenchymal‐epithelial transition factor (MET) is a receptor tyrosine kinase with an established prognostic significance correlating with poor disease outcome in breast cancer patients as a result of high metastatic rate. We performed expression array analysis to identify candidate Notch target genes; we identified and validated MET as a target of NOTCH1 signaling in breast cancer. We found that NOTCH1 knockdown significantly reduces MET promoter activity, as well as expression levels of MET transcript and protein. The mechanism of NOTCH1 regulation of MET expression will be the focus of future work. To further identify candidate target genes of NOTCH1 signaling, we generated and validated a NOTCH1 antibody for use in chromatin immunoprecipitation experiments.

Notch signaling plays a key role in development, tissue homeostasis, and cancer. High expression levels of Notch signaling components are associated with aggressive disease and poor patient prognosis in breast cancer. Mesenchymal‐epithelial transition factor (MET) is a receptor tyrosine kinase with an established prognostic significance correlating with poor disease outcome in breast cancer patients as a result of high metastatic rate. We performed expression array analysis to identify candidate Notch target genes; we identified and validated MET as a target of NOTCH1 signaling in breast cancer. We found that NOTCH1 knockdown significantly reduces MET promoter activity, as well as expression levels of MET transcript and protein. The mechanism of NOTCH1 regulation of MET expression will be the focus of future work. To further identify candidate target genes of NOTCH1 signaling, we generated and validated a NOTCH1 antibody for use in chromatin immunoprecipitation experiments.

Aberrant DNA synthesis and maintenance have been implicated in numerous human diseases. I describe here a novel strategy for systematically identifying budding yeast mutants with elevated levels of DNA damage foci, which represent hubs of DNA damage and repair. A previous study manually scored foci in single mutants but was limited in its ability to survey many conditions in large populations. I developed an automated and statistically robust method for identifying aberrant foci phenotypes by combining synthetic genetic array (SGA) and high-content screening (HCS) methodology. Using this approach, I scored thousands of essential and non-essential gene mutants subjected to environmental and genetic perturbations, including the DNA damaging agent, phleomycin, and deletions of DNA repair genes, SGS1 and YKU80. Collectively, I identified a functionally enriched set of 367 mutants that had increased frequencies of DNA damage foci and established SGA-HCS as a powerful tool for investigating the yeast DNA damage response.

Aberrant DNA synthesis and maintenance have been implicated in numerous human diseases. I describe here a novel strategy for systematically identifying budding yeast mutants with elevated levels of DNA damage foci, which represent hubs of DNA damage and repair. A previous study manually scored foci in single mutants but was limited in its ability to survey many conditions in large populations. I developed an automated and statistically robust method for identifying aberrant foci phenotypes by combining synthetic genetic array (SGA) and high-content screening (HCS) methodology. Using this approach, I scored thousands of essential and non-essential gene mutants subjected to environmental and genetic perturbations, including the DNA damaging agent, phleomycin, and deletions of DNA repair genes, SGS1 and YKU80. Collectively, I identified a functionally enriched set of 367 mutants that had increased frequencies of DNA damage foci and established SGA-HCS as a powerful tool for investigating the yeast DNA damage response.

La bio-informatique est un champ pluridisciplinaire qui utilise la biologie, l’informatique, la physique et les mathématiques pour résoudre des problèmes posés par la biologie. L’une des thématiques de la bio-informatique est l’analyse des séquences génomiques et la prédiction de gènes d’ARN non codants. Les ARN non codants sont des molécules d’ARN qui sont transcrites mais pas traduites en protéine et qui ont une fonction dans la cellule. Trouver des gènes d’ARN non codants par des techniques de biochimie et de biologie moléculaire est assez difficile et relativement coûteux. Ainsi, la prédiction des gènes d’ARNnc par des méthodes bio-informatiques est un enjeu important. Cette recherche décrit un travail d’analyse informatique pour chercher des nouveaux ARNnc chez le pathogène Candida albicans et d’une validation expérimentale. Nous avons utilisé comme stratégie une analyse informatique combinant plusieurs logiciels d’identification d’ARNnc. Nous avons validé un sous-ensemble des prédictions informatiques avec une expérience de puces à ADN couvrant 1979 régions du génome. Grace à cette expérience nous avons identifié 62 nouveaux transcrits chez Candida albicans. Ce travail aussi permit le développement d’une méthode d’analyse pour des puces à ADN de type tiling array. Ce travail présente également une tentation d’améliorer de la prédiction d’ARNnc avec une méthode se basant sur la recherche de motifs d’ARN dans les séquences. / Bioinformatics is a multidisciplinary field that uses biology, computer science, physics and mathematics to solve problems in biology. One of the topics of bioinformatics is the analysis of genomic sequences and prediction of genes from non-coding RNA (ncRNA). The non-coding RNAs are RNA molecules that are transcribed but not translated into protein and have a function in the cell. The use of biochemistry and molecular biology techniques in order to find non-coding RNA genes is rather difficult and relatively expensive. Thus, the prediction of genes by bioinformatics methods is an important issue. This research describes a computer analysis to search for new ncRNA in the pathogen Candida albicans and an experimental validation. The strategy used was to combine several algorithms and to validate a subset of computer predictions with a microarray experience covering 1979 regions of the genome. We have identified 62 new transcripts in Candida albicans. We have also developed an analytical method for tiling array and attempted to improve the prediction of ncRNAs this with a method based on the search of RNA motifs in the sequences.

O melanoma cutâneo é a neoplasia de pele de maior mortalidade e grande imprevisibilidade na sua evolução. Na doença disseminada, as opções terapêuticas são pouco eficazes. A pesquisa de novos marcadores tumorais permite a melhor compreensão da patogênese do melanoma e possibilita a descoberta de alvos moleculares. A proteína Dermicidina (DCD) foi identificada entre os 9 genes de uma assinatura gênica de predição de diagnóstico clínico do melanoma humano, porém vários autores divergem sobre o papel desta na doença e os mecanismos moleculares pelos quais a DCD atua nos tumores permanecem incertos. O presente estudo teve como objetivo investigar o papel da DCD na tumorigênese do melanoma maligno e correlacionar sua expressão com dados clínicos, demográficos e patológicos dos pacientes. Através da técnica de imuno-histoquímica em lâminas de TMAs (tissue-microarray), o padrão de expressão de DCD foi analisado em tecido tumoral de duas coortes de pacientes, a primeira com 53 casos tratados no Hospital A.C. Camargo, predominantemente caucasianos, e a segunda com 48 casos, todos asiáticos, obtidos comercialmente da empresa IMGENEX. A análise in situ da Dermicidina mostrou que a proteína está expressa de forma heterogênea nas células tumorais, e pode ocorrer tanto em tumores amelanocíticos como melanocíticos. Em melanomas primários, a expressão de DCD foi mais frequente em tumores localizados nas regiões do tronco e membros superiores, já nas metástases, a proteína foi detectada predominantemente em células em transito nos linfonodos (69,23% dos casos). Analisando os resultados dos 101 pacientes das duas coortes em conjunto, pelo método de Kaplan-Meier, foi confirmado que nos indivíduos com tumores DCD-negativo, a taxa de sobrevida foi de 65,54% em 60 meses, e de 62,86% em 130 meses. Já indivíduos com tumor DCD-positivo tiveram sobrevida de 43,33% em 5 anos, e 28,12% em 130 meses, sendo a diferença significante entre os grupos (p=0,0229). A taxa de óbito dos pacientes com tumor DCD-positivo foi mais elevada, 56%, quando comparada à taxa dos indivíduos com tumor DCDnegativo, 33,33% (p=0,0281). Também foi encontrada uma tendência de tumores expressando DCD se relacionarem a pacientes com idade superior a 50 anos (p=0,1057). Em uma consulta de 4 estudos diferentes que reuniram os dados de sequenciamento de DNA de tumores de 515 pacientes, observamos que o gene DCD, em melanomas, não se encontra predominantemente amplificado, mas sim mutado. A substituição E43K foi a alteração mais frequente, correspondendo a 70% dos casos com mutação no gene. Ao relacionarmos os casos disponíveis de mutação em DCD com os genes BRAF, NRAS, MITF, CDKN2A e ERBB4, encontrou-se uma associação com a mutação BRAF V600E nos casos em que ocorria a mutação DCD E43K. Por ter alta frequência em melanomas (variando entre 45 e 54%), e ser um indicador de pior prognóstico para a neoplasia, a expressão de DCD pode ser considerada um potencial biomarcador / Cutaneous melanoma is the skin neoplasia with the highest mortality rate and great unpredictability in its evolution. In disseminated disease, the treatment options are little effective. The research for new tumor markers allows a better understanding of the pathogenesis of melanoma and enables the discovery of molecular targets. The Dermcidin protein (DCD) was identified among the nine genes of a gene signature predicting clinical diagnosis of human melanoma, although many authors differ on its role in the disease and the molecular mechanisms by which DCD acts in tumors remain unclear. The present study aimed to investigate the role of DCD in the tumorigenesis of malignant melanoma and to correlate its expression with clinical, demographic and pathologic data of patients. Using the technique of immunohistochemistry in TMA slides (tissue microarray), the expression pattern of DCD was analyzed in tumoral tissue of two cohorts of patients, the first with 53 cases treated in hospital AC Camargo, predominantly caucasians, and the second with 48 cases, all Asians, commercially obtained from IMGENEX company. The in situ analysis of Dermcidin showed that the protein is expressed in a heterogeneous manner in tumor cells, and can occur in non-melanocytic as well as in melanocytic tumors. In the primary melanoma, DCD expression was more seen in tumors located in the regions of torso and upper limbs. In the metastases, the protein was found predominantly in cells in transit in the lymph nodes (69.23% of cases). Analyzing the 101 patients of the two cohorts together, by the Kaplan-Meier method, it was confirmed that patients with DCD-negative, the survival rate was 65.54% in 60 months, and 62.86% in 130 months, while the group of patients with DCD-positive tumor had 43.33% in 5 years, and 22.12% in 130 months, knowing that a difference between the groups was significative (p=0.0229). The death rate of patients with DCD-positive tumor was higher, 56%, when compared with the death rate of individuals with DCD-negative tumor, 33.33% (p=0.0281). It was also found a trend of tumors expressing DCD related to patients older than 50 years (p=0.1057). In a search of 4 different studies grouping the DNA sequencing tumor of 515 patients we observed that the DCD gene, in melanoma, is not predominantly amplified, but mutated. The E43K substitution was the most frequent alteration, corresponding to 70% of cases of gene mutation. When comparing the available cases of mutations in DCD with the genes BRAF, NRAS, MITF, CDKN2A, ERBB4, we found an association with the BRAF V600E mutation in cases where occurred the DCD E43K. By having high frequency in melanomas (ranging between 45 and 54%) and being an indicator of poor prognosis for the neoplasia, DCD expression can be considered as a potential biomarker

INTRODUÇÃO: O crescimento e a progressão de diversos tipos de tumores dependem da angiogênese, isto é, a formação de novos vasos sanguíneos. Fatores da família do VEGF (VEGF-A, VEGF-C, Flk-1/KDR) são potentes mediadores da angiogênese e níveis elevados destes fatores podem ser detectados em vários tumores humanos. Outras proteínas como NDRG1, osteonectina, HIF-1 e galectina-3 encontram-se associadas, de modo indireto, à angiogênese. MÉTODOS: O objetivo deste estudo foi analisar a expressão imunoistoquímica de NDRG1, osteonectina, VEGF-A, VEGF-C, Flk-1/KDR, HIF-1 e galectina-3 em 265 lesões benignas e malignas da tireóide por tissue microarray (TMA), incluindo tireóide normal, bócio, adenoma folicular, carcinoma papilífero, carcinoma folicular e metástases de carcinoma papilífero e folicular da tireóide. Lâminas em diferentes níveis do bloco de TMA foram submetidas à reação imunoistoquímica utilizando-se anticorpos específicos contra NDRG1, osteonectina, VEGF-A, VEGF-C, Flk-1/KDR, HIF-1, galectina-3. Foi realizada uma avaliação semiquantitativa da expressão destas proteínas, analisando-se a intensidade de coloração e a porcentagem de células positivas para cada marcador. RESULTADOS: De um modo geral, a expressão de NDRG1, osteonectina, VEGF-A, VEGF-C, Flk-1/KDR, HIF-1 e galectina-3 foi maior nos carcinomas de tireóide em relação ao bócio e adenoma folicular. Dentre as proteínas estudadas, a galectina-3 foi aquela que apresentou melhor acurácia diagnóstica na distinção entre lesões benignas e malignas da tireóide, com uma sensibilidade 64,1% e especificidade de 94,4%. Nos carcinomas de tireóide, a expressão de NDRG1, VEGF-A, VEGF-C e HIF-1 apresentou correlação estatística significativa com estádio TNM mais avançado e alto risco pelo método AMES. A análise multivariada revelou que a idade 45 anos, o tamanho tumoral maior do que 4,0 cm, o estádio IV do TNM e a perda de expressão de galectina-3 foram fatores que contribuíram para a recorrência ou óbito em pacientes com carcinoma de tireóide. CONCLUSÕES: Nos carcinomas de tireóide, a expressão de NDRG1, VEGF-A, VEGF-C, HIF-1 se correlacionou com tumores mais avançados. Com exceção da galectina-3, nenhuma das proteínas estudadas apresentou impacto na sobrevida dos pacientes com carcinoma de tireóide. Nestes pacientes, a perda de expressão de galectina-3 foi um fator de risco para recorrência ou óbito. / INTRODUCTION: The growth and progression of different types of tumors depend on angiogenesis, i.e., the formation of new blood vessels. Members of the VEGF family (VEGF-A, VEGF-C, Flk-1/KDR) are potent mediators of angiogenesis and elevated levels of these factors can be detected in various human tumors. Other proteins such as NDRG1, osteonectin, HIF-1 and galectin-3 are indirectly associated with angiogenesis. METHODS: The objective of this study was to investigate the immunohistochemical expression of NDRG1, osteonectin, VEGF-A, VEGF-C, Flk-1/KDR, HIF-1 and galectin-3 in 265 benign and malignant thyroid lesions by tissue microarray (TMA), including normal thyroid, goiter, follicular adenoma, papillary carcinoma, follicular carcinoma, and papillary and follicular thyroid carcinoma metastases. Slides obtained from different levels of the TMA block were submitted to immunohistochemistry using specific antibodies against NDRG1, osteonectin, VEGF-A, VEGF-C, Flk-1/KDR, HIF-1, and galectin-3. The expression of these proteins was analyzed semiquantitatively, evaluating the intensity of staining and the percentage of positive cells for each marker. RESULTS: In general, the expression of NDRG1, osteonectin, VEGF-A, VEGF-C, Flk-1/KDR, HIF-1 and galectin-3 was higher in thyroid carcinomas when compared to goiter and follicular adenoma. Among the proteins studied, galectin-3 presented the best diagnostic accuracy in the distinction between benign and malignant thyroid lesions, with a sensitivity of 64.1% and specificity of 94.4%. In thyroid carcinomas, the expression of NDRG1, VEGF-A, VEGF-C and HIF-1 was significantly correlated with a more advanced TNM stage and AMES high risk. Multivariate analysis revealed that age 45 years, tumor size > 4.0 cm, TNM stage IV and loss of expression of galectin-3 were associated with recurrence or death in patients with thyroid carcinoma. CONCLUSIONS: In thyroid carcinomas, the expression of NDRG1, VEGF-A, VEGF-C and HIF-1 is correlated with more advanced tumors. Except for galectin-3, none of the proteins studied had an impact on the survival of patients with thyroid carcinoma. In these patients, loss of expression of galectin-3 was a risk factor for recurrence or death.