Orientador: Marco Antonio Zanini / Resumo: Introdução: meningiomas são os tumores intracranianos mais comuns, correspondendo a 36% dos casos. A Organização Mundial de Saúde (OMS) classifica estes tumores em três graus histológicos: benigno (grau I), atípico (grau II) e anaplásico ou maligno (grau III), sendo que quanto maior o grau, maior a agressividade. Apesar da maior parte das lesões serem benignas, o comprometimento de estruturas na base de crânio e do parênquima cerebral, com taxas de recidiva mais altas em tumores grau II e III, tornam desafiador o tratamento de meningiomas ainda nos dias atuais. A compreensão das alterações moleculares em meningiomas podem contribuir para a identificação de marcadores de agressividade e possíveis novos alvos terapêuticos. A técnica Nanostring é realizada através de contagem digital e atualmente considerada a técnica de larga escala mais sensível. Até o momento, não foram identificados trabalhos em meningiomas utilizando Nanostring. Objetivo: avaliar o perfil de expressão gênica e suas principais vias de meningiomas através da técnica de Nanostring. Pacientes e métodos: foram avaliadas as expressões de aproximadamente 800 genes, através do Kit PanCancer Nanostring, em 17 meningiomas (6 benignos, 6 atípicos e 5 malignos) e 6 aracnóides controle. Os resultados obtidos foram analisados através de ferramentas de bioinformática (R Statistics, Cytoscape e bases de dados online DAVID e COSMIC). Os resultados obtidos foram tabulados em forma de heatmaps e analisados através de plataf... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Introduction: Meningiomas are the most common intracranial tumors and corresponding to 36% of all cases. The World Health Organization (WHO) classifies these tumors into three histological grades: benign (grade I), atypical (grade II) and anaplastic or malignant (grade III), and the higher the degree, the greater the aggressiveness. Although most lesions are benign, compromised structures at the skull base and cerebral parenchyma, with higher relapse rates in grade II and III tumors, make the treatment of meningiomas challenging, even in these days. The understanding of the molecular alterations in meningiomas can contribute to the identification of aggressive markers and possible new therapeutic targets. The Nanostring technique is performed through digital counting and is currently considered the most sensitive large-scale technique. To date, no work on meningiomas has been identified using Nanostring. Objetive: to evaluate the gene expression profile and its main pathways in meningiomas by Nanostring technique. Patients and methods: Approximately 800 genes were evaluated by the PanCancer Nanostring Kit in 17 meningiomas (6 benign, 6 atypical and 5 malignant) and 6 control arachnoids. The results were analyzed through bioinformatics tools (R Statistics, Cytoscape and DAVID and COSMIC online databases). The results were tabulated in heatmaps and analyzed through online database platforms for identification of pathways and networks between different tumor degrees. Results an... (Complete abstract click electronic access below) / Doutor

Submitted by ISMAEL AUGUSTO SILVA LOMBARDI null (ismaelmedunesp12@yahoo.com.br) on 2017-04-03T00:57:14Z No. of bitstreams: 1 TESE DOUTORADO PDF FINAL.pdf: 5669373 bytes, checksum: ceeebbb9394f6e1d069e27707d066cf8 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-04-11T17:53:40Z (GMT) No. of bitstreams: 1 lombardi_ias_dr_bot.pdf: 5669373 bytes, checksum: ceeebbb9394f6e1d069e27707d066cf8 (MD5) / Made available in DSpace on 2017-04-11T17:53:40Z (GMT). No. of bitstreams: 1 lombardi_ias_dr_bot.pdf: 5669373 bytes, checksum: ceeebbb9394f6e1d069e27707d066cf8 (MD5) Previous issue date: 2017-02-23 / Introdução: meningiomas são os tumores intracranianos mais comuns, correspondendo a 36% dos casos. A Organização Mundial de Saúde (OMS) classifica estes tumores em três graus histológicos: benigno (grau I), atípico (grau II) e anaplásico ou maligno (grau III), sendo que quanto maior o grau, maior a agressividade. Apesar da maior parte das lesões serem benignas, o comprometimento de estruturas na base de crânio e do parênquima cerebral, com taxas de recidiva mais altas em tumores grau II e III, tornam desafiador o tratamento de meningiomas ainda nos dias atuais. A compreensão das alterações moleculares em meningiomas podem contribuir para a identificação de marcadores de agressividade e possíveis novos alvos terapêuticos. A técnica Nanostring é realizada através de contagem digital e atualmente considerada a técnica de larga escala mais sensível. Até o momento, não foram identificados trabalhos em meningiomas utilizando Nanostring. Objetivo: avaliar o perfil de expressão gênica e suas principais vias de meningiomas através da técnica de Nanostring. Pacientes e métodos: foram avaliadas as expressões de aproximadamente 800 genes, através do Kit PanCancer Nanostring, em 17 meningiomas (6 benignos, 6 atípicos e 5 malignos) e 6 aracnóides controle. Os resultados obtidos foram analisados através de ferramentas de bioinformática (R Statistics, Cytoscape e bases de dados online DAVID e COSMIC). Os resultados obtidos foram tabulados em forma de heatmaps e analisados através de plataformas de base de dados online para identificação de vias e redes entre os diferentes graus tumorais Resultados e discussão: os meningiomas benignos e atípicos mostraram similaridade entre seus perfis de expressão e vias significativas, sugerindo que os tumores grau II podem se originar da transformação de tumores benignos. A via de ciclo celular tem componentes hiperregulados nos três graus de tumores, em número maior nas lesões grau II e III. Reguladores desta via elevados, como TP53 e BAX, podem contribuir para balancear seus efeitos mitogênicos, principalmente nos tumores benignos e atípicos. Conclusão: meningiomas benignos e atípicos apresentam similaridades em seus perfis de expressão e vias significativas e sugerindo que lesões grau II podem decorrer da transformação de tumores benignos. A via ciclo celular pode estar associada à agressividade em meningiomas, sendo maior o número de seus componentes hiperexpressos conforme maior o grau histológico dos tumores. Estudos futuros com maior número de tumores são necessários para comprovar os achados deste estudo. / Introduction: Meningiomas are the most common intracranial tumors and corresponding to 36% of all cases. The World Health Organization (WHO) classifies these tumors into three histological grades: benign (grade I), atypical (grade II) and anaplastic or malignant (grade III), and the higher the degree, the greater the aggressiveness. Although most lesions are benign, compromised structures at the skull base and cerebral parenchyma, with higher relapse rates in grade II and III tumors, make the treatment of meningiomas challenging, even in these days. The understanding of the molecular alterations in meningiomas can contribute to the identification of aggressive markers and possible new therapeutic targets. The Nanostring technique is performed through digital counting and is currently considered the most sensitive large-scale technique. To date, no work on meningiomas has been identified using Nanostring. Objetive: to evaluate the gene expression profile and its main pathways in meningiomas by Nanostring technique. Patients and methods: Approximately 800 genes were evaluated by the PanCancer Nanostring Kit in 17 meningiomas (6 benign, 6 atypical and 5 malignant) and 6 control arachnoids. The results were analyzed through bioinformatics tools (R Statistics, Cytoscape and DAVID and COSMIC online databases). The results were tabulated in heatmaps and analyzed through online database platforms for identification of pathways and networks between different tumor degrees. Results and discussion: benign and atypical meningiomas showed similarity between their expression profiles and significant pathways, suggesting that grade II tumors can originate from the transformation of benign tumors. The cell cycle pathway has components that are hyperregulated in the three tumor grades, which are higher in grade II and III lesions. Regulators of this elevated pathway, such as TP53 and BAX, may contribute to balance their mitogenic effects, especially in benign and atypical tumors. Conclusion: benign and atypical meningiomas present similarities in their expression profiles and significant pathways and suggesting that grade II lesions may result from the transformation of benign tumors. The cell cycle pathway may be associated with aggression in meningiomas, with a higher number of hyperexpressed components as the histological grade of the tumors increases. Further studies with a greater number of tumors are needed to confirm the findings of this study.

Probiotics/prebiotic supplementation represents a viable option for addressing systemic inflammation and chronic disease risk resulting from excessive body weight. The purpose of this feasibility study was to determine if 90-d of supplementation with prebiotic and probiotic could alter mRNA responsible for inflammation and subsequently metabolic health in weight stable overweight adults. Participants were advised to not change their diet or exercise habits during the study. All protocols were approved by the University IRB and participants gave written informed consent. Participants were randomly assigned to either placebo (N=7; rice flour) or combined (N=8) prebiotic (PreticX® Xylooligosaccharide; 0.8 g/d; ADIP) and probiotic (MegaDuo® Bacillus subtilis HU58 and Bacillus coagulans SC-208; 3 Billion CFU/d) and measurements were made at baseline, 30, 60, and 90-d. Whole body DXA scans (GE iDXA®) and blood 574-plex mRNA analysis (Nanostring®) were used to generate primary outcomes. Compared to placebo, supplementation was associated with a 36% reduction in visceral adipose tissue (p = 0.001). Supplement resulted in significant, differential expression of 15 mRNA associated with adipose tissue inflammation, systemic inflammation, and/or chronic disease risk. The key findings support that 90-d prebiotic/probiotic supplementation may be associated with an improved metabolic health, reduced adipose tissue inflammation, reduced systemic inflammation, and reduced chronic disease risk. Collectively these findings demonstrate the potential of a prebiotic/probiotic supplement to impact metabolic health risk independent of weight loss in free-living individuals.

As infestações por Rhipicephalus microplus, conhecido como o carrapato do boi, causam enormes prejuízos econômicos na produção de gado na região tropical e países subtropicais em todo o mundo. O método atual de controle do ectoparasito depende exclusivamente de produtos tóxicos como os acaricidas, que deixam resíduos no meio ambiente e seu uso contínuo tem provocado o aparecimento de carrapatos resistentes, sendo, portanto, de pouca eficácia. O grupo de pesquisa em carrapatos da FMRP-USP tria antígenos candidatos que foram testados em vacinação experimental feita em bovinos, utilizando formulação antigênica multicomponente. Baseando-se nos resultados do transcriptoma de leucócitos do sangue periférico de bovinos vacinados, que identificou genes diferencialmente expressos, cuja expressão é afetada pelas infestações e a partir do transcriptoma da pele de bovinos da raça Nelore e Holandês, o presente estudo tem objetivo avaliar, através da técnica Nanostring, genes que possam ser empregados em testes para identificar bovinos geneticamente resistentes ao carrapato e comparar com os dados já obtidos dos transcriptomas de sangue periférico e de pele. Foi analisada a expressão gênica de leucócitos de sangue periférico de vacas da raça holandesa pouco e muito infestada, e da raça nelore durante períodos de baixa e alta infestação natural por carrapatos. Os dados obtidos mostraram que a infestação modulou um número maior de genes nos holandeses muito infestados do que nas outras raças. De acordo com a análise funcional realizada dos genes diferencialmente expressos (DEGs) encontrados pode-se observar uma possível relação do perfil de expressão gênica dos holandeses com a imunidade inata, ao passo que o perfil de expressão gênica encontrado na raça nelore pode estar relacionado tanto com a imunidade inata quanto a imunidade adaptativa. Dessa forma, avaliando o perfil de resistência e suscetibilidade, este trabalho sugere que os genes CXCL6, S100A8 (Calgranulina A) TYRP1, IgM, ELANE, CCL19, PDGFRL, VCAM1, NOX1 e CEBPE, podem ser possíveis assinaturas gênicas relacionadas a resistência ou suscetibilidade / Infestations with the cattle tick, Rhipicephalus microplus, cause huge economic losses in cattle production in tropical and subtropical countries worldwide. Control of ticks and tick-borne diseases of livestock depends almost exclusively of chemical control, such as use of acaricides, which leads to environmental concerns and due to their continued use, has generated resistance mechanisms in ticks, presenting steadily decreasing efficiency in controlling tick infestations. The research group of ticks of FMRP-USP selects new antigens that were tested in an experimental immunization, using a multicomponent antigen formulation. Based on the transcriptome results from peripheral blood leukocytes from vaccinated cattle, which identified genes whose expression is affected by infestations, and from the skin transcriptome of Nelore and Holstein bovine, the aim of this project is evaluate, by Nanostring technology, genes that may be used in tests to identify genetically resistant cattle to bovine tick and compare with the data already obtained from peripheral blood transcriptome and skin transcriptome. Gene expression was analyzed in peripheral blood of Holstein (much infested or less infested), and Nelore during periods of low and high natural infestation of ticks. The results showed that a greater number of genes were modulated in Holstein than the other breeds. According to the functional analysis of differentially expressed genes (DEGs) it can be observed a possible correlation from Holsteins profile with innate immunity, while the gene expression profile found in Nelore can be related both with the innate and adaptive immunity. Thus, evaluating the resistance and susceptibility profile, this work suggests that genes CXCL6, S100A8 (Calgranulin A) TYRP1, IgM, ELANE, CCL19, PDGFRL, VCAM1, NOX1 and CEBPE may be possible gene signatures related to resistance or susceptibility.

As infestações por Rhipicephalus microplus, conhecido como o carrapato do boi, causam enormes prejuízos econômicos na produção de gado na região tropical e países subtropicais em todo o mundo. O método atual de controle do ectoparasito depende exclusivamente de produtos tóxicos como os acaricidas, que deixam resíduos no meio ambiente e seu uso contínuo tem provocado o aparecimento de carrapatos resistentes, sendo, portanto, de pouca eficácia. O grupo de pesquisa em carrapatos da FMRP-USP tria antígenos candidatos que foram testados em vacinação experimental feita em bovinos, utilizando formulação antigênica multicomponente. Baseando-se nos resultados do transcriptoma de leucócitos do sangue periférico de bovinos vacinados, que identificou genes diferencialmente expressos, cuja expressão é afetada pelas infestações e a partir do transcriptoma da pele de bovinos da raça Nelore e Holandês, o presente estudo tem objetivo avaliar, através da técnica Nanostring, genes que possam ser empregados em testes para identificar bovinos geneticamente resistentes ao carrapato e comparar com os dados já obtidos dos transcriptomas de sangue periférico e de pele. Foi analisada a expressão gênica de leucócitos de sangue periférico de vacas da raça holandesa pouco e muito infestada, e da raça nelore durante períodos de baixa e alta infestação natural por carrapatos. Os dados obtidos mostraram que a infestação modulou um número maior de genes nos holandeses muito infestados do que nas outras raças. De acordo com a análise funcional realizada dos genes diferencialmente expressos (DEGs) encontrados pode-se observar uma possível relação do perfil de expressão gênica dos holandeses com a imunidade inata, ao passo que o perfil de expressão gênica encontrado na raça nelore pode estar relacionado tanto com a imunidade inata quanto a imunidade adaptativa. Dessa forma, avaliando o perfil de resistência e suscetibilidade, este trabalho sugere que os genes CXCL6, S100A8 (Calgranulina A) TYRP1, IgM, ELANE, CCL19, PDGFRL, VCAM1, NOX1 e CEBPE, podem ser possíveis assinaturas gênicas relacionadas a resistência ou suscetibilidade / Infestations with the cattle tick, Rhipicephalus microplus, cause huge economic losses in cattle production in tropical and subtropical countries worldwide. Control of ticks and tick-borne diseases of livestock depends almost exclusively of chemical control, such as use of acaricides, which leads to environmental concerns and due to their continued use, has generated resistance mechanisms in ticks, presenting steadily decreasing efficiency in controlling tick infestations. The research group of ticks of FMRP-USP selects new antigens that were tested in an experimental immunization, using a multicomponent antigen formulation. Based on the transcriptome results from peripheral blood leukocytes from vaccinated cattle, which identified genes whose expression is affected by infestations, and from the skin transcriptome of Nelore and Holstein bovine, the aim of this project is evaluate, by Nanostring technology, genes that may be used in tests to identify genetically resistant cattle to bovine tick and compare with the data already obtained from peripheral blood transcriptome and skin transcriptome. Gene expression was analyzed in peripheral blood of Holstein (much infested or less infested), and Nelore during periods of low and high natural infestation of ticks. The results showed that a greater number of genes were modulated in Holstein than the other breeds. According to the functional analysis of differentially expressed genes (DEGs) it can be observed a possible correlation from Holsteins profile with innate immunity, while the gene expression profile found in Nelore can be related both with the innate and adaptive immunity. Thus, evaluating the resistance and susceptibility profile, this work suggests that genes CXCL6, S100A8 (Calgranulin A) TYRP1, IgM, ELANE, CCL19, PDGFRL, VCAM1, NOX1 and CEBPE may be possible gene signatures related to resistance or susceptibility.

Nanostring technology provides a new method to measure gene expressions. It's more sensitive than microarrays and able to do more gene measurements than RT-PCR with similar sensitivity. This system produces counts for each target gene and tabulates them. Counts can be normalized by using an Excel macro or nSolver before analysis. Both methods rely on data normalization prior to statistical analysis to identify differentially expressed genes. Alternatively, we propose to model gene expressions as a function of positive controls and reference gene measurements. Simulations and examples are used to compare this model with Nanostring normalization methods. The results show that our model is more stable, efficient, and able to control false positive proportions. In addition, we also derive asymptotic properties of a normalized test of control versus treatment.

No description available.

Cervical cancer is the third most common cancer among women worldwide, and the fourth leading cause of cancer mortality. Despite significant declines in the incidence and mortality rates of cervical cancer in Canada, it remains the 4th most common cancer in women aged 20-29 years. In order to gain novel insights into cervical cancer tumourigenesis and clinical outcome, we investigated and characterized the alterations in microRNA (miRNA) expression in this disease. Firstly, we performed global miRNA expression profiling of cervical cancer cell lines (n=3), and patient specimens (n=79). From this analysis, we identified miR-196b to be significantly down-regulated in cervical cancer, and characterized its role in regulating the HOXB7~VEGF axis. The global miRNA expression data also led to the development of a candidate 9-miRNA signature that was prognostic for disease-free survival in patients with cervical cancer, although we were unable to validate this signature in an independent cohort. This report describes important considerations concerning the development and validation of microRNA signatures for cervical cancer. Our investigations also led us to a comparison of three methods for measuring miRNA abundance: the TaqMan Low Density Array, the NanoString nCounter assay, and single-well quantitative real-time PCR. Our findings demonstrated limited concordance between the TLDA and NanoString platforms, although each platform correlated well with PCR, which is considered the gold standard for nucleic acid quantification. Furthermore, we examined biases created by amplification protocols for microarray studies. Our analysis demonstrated that performing a correction using the LTR-method (linear transformation of replicates) could help mitigate, but not completely eliminate such biases. Overall, this report presents insights into the role of miRNAs in cervical cancer, as well as an evaluation of technical considerations concerning miRNA and mRNA expression profiling studies.

Cervical cancer is the third most common cancer among women worldwide, and the fourth leading cause of cancer mortality. Despite significant declines in the incidence and mortality rates of cervical cancer in Canada, it remains the 4th most common cancer in women aged 20-29 years. In order to gain novel insights into cervical cancer tumourigenesis and clinical outcome, we investigated and characterized the alterations in microRNA (miRNA) expression in this disease. Firstly, we performed global miRNA expression profiling of cervical cancer cell lines (n=3), and patient specimens (n=79). From this analysis, we identified miR-196b to be significantly down-regulated in cervical cancer, and characterized its role in regulating the HOXB7~VEGF axis. The global miRNA expression data also led to the development of a candidate 9-miRNA signature that was prognostic for disease-free survival in patients with cervical cancer, although we were unable to validate this signature in an independent cohort. This report describes important considerations concerning the development and validation of microRNA signatures for cervical cancer. Our investigations also led us to a comparison of three methods for measuring miRNA abundance: the TaqMan Low Density Array, the NanoString nCounter assay, and single-well quantitative real-time PCR. Our findings demonstrated limited concordance between the TLDA and NanoString platforms, although each platform correlated well with PCR, which is considered the gold standard for nucleic acid quantification. Furthermore, we examined biases created by amplification protocols for microarray studies. Our analysis demonstrated that performing a correction using the LTR-method (linear transformation of replicates) could help mitigate, but not completely eliminate such biases. Overall, this report presents insights into the role of miRNAs in cervical cancer, as well as an evaluation of technical considerations concerning miRNA and mRNA expression profiling studies.

No description available.