Caracterização in silico do modelo de interação de genes da auto-renovação das células tronco e sinalização por cálcio em metástases de melanoma humano

Melanoma é um câncer de pele muito suscetível à ocorrência de metástases e, por isso, é considerado uma neoplasia maligna agressiva. Até hoje, mais de 90% das causas de morte por câncer são atribuídas à ocorrência de metástases. Acredita-se, ainda, que especificamente um subconjunto de células da população de um tecido tumoral é capaz de semear e repopular o seu tumor de origem. Estudos evidenciam que essas células “iniciadoras” de tumores comumente possuem características semelhantes às de células tronco, tais como poder de auto-renovação e capacidade de dar origem a células progenitoras ou diferenciadas, o que lhes rendeu o nome de células tronco tumorais (CTTs). Existem evidencias de que a via de sinalização do íon cálcio tem papel fundamental em uma série ampla de processos biológicos, dentre os quais estão o comprometimento celular na diferenciação de células tronco. Sendo assim, nós questionamos no presente estudo a influência da via de sinalização do Ca2+ na regulação da pluripotência de células tronco dentro de um contexto de neoplasia maligna. Para isso, nós criamos uma rede in silico (“STEMCa”) de interação proteína-proteína para modelar a integração de ambas as vias (sinalização por Ca2+ e regulação de pluripotência de células tronco). Após, nós avaliamos a expressão dos genes que codificam as proteínas desse modelo, utilizando um repositório público de microarranjos. Para os dados de expressão, foram utilizadas apenas amostras clínicas de melanomas metastáticos (tendo tumores primários como controle) de três conjuntos independentes de amostras de pacientes. Por fim, utilizamos ferramentas de biologia de sistemas para inferir potenciais candidatos a alvos terapêuticos e/ou marcadores de metástase. Nossa análise de expressão diferencial indica que, em ao menos um dos conjuntos de amostras de pacientes, 51% dos genes do modelo construído (151 de um total de 294 genes) encontram-se consistentemente desregulados (valor de p corrigido <0.05) em metástases de melanoma quando são comparados com amostras de tumor primário, sugerindo que, de fato, as vias avaliadas têm expressão aberrante. Além disso, nossos cálculos topológicos em cima do modelo proposto apontam GNAQ, GSK3B, GSTP1, MAPK3, PPP1CC, PRKACA, e SMAD4 como potenciais candidatos a serem estudados para intervenções terapêuticas ou como biomarcadores.Melanoma is a skin cancer with high incidence to develop metastasis and, therefore, it is considered to be an aggressive malignant neoplasm. To date, more than 90% of cancer-related causes of death are still attributed to the occurrence of metastasis. It has been postulated that a subset of cells within the tumor tissue is solely capable of seeding and restore the whole tumoral tissue. A number of studies have reported that these tumor-initiating cells also named as cancer stem cells (CSCs) commonly display stem-like properties, such as self-renewal and also potency (i.e. they are able to give rise to progenitor or differentiated cells). Calcium ion (Ca2+) signaling pathway plays a fundamental role on a broad series of biological processes, and its role in stem cell fate and commitment to differentiation has additionally been proposed. Hence, one could speculate whether Ca2+ signaling pathway and stem cell pluripotency regulation crosstalk may influence the metastatic transformation of melanoma cancer cells. In order to find evidence for this role, we build an in silico protein-protein interaction network (“STEMCa”) to model the integration of both pathways (Ca2+ signaling and stem cell pluripotency regulation). Thereafter, we evaluated the expression pattern of the genes coding for the proteins within the “STEMCa” model by utilizing three publicly available microarray datasets from human patients found in Gene Expression Omnibus (GEO). For our analysis, we compared data from clinical samples of melanomas metastasis with primary tumors (controls). Finally, we used systems biology tools to identify putative therapeutic targets in silico and/or candidate biomarkers for melanoma metastasis. Our analysis revealed that the expression profile of the genes within our “STEMCa” model is consistently deregulated, with 151 out of 294 of its members (51%) displaying significant changes of expression (corrected p-value <0.05) in at least one of the datasets of melanoma metastases, when compared with primary biopsy tumors. This suggests that the integrated pathways comprising our network are aberrant in gene expression. In addition, topological measurements of “STEMCa” model point towards GNAQ, GSK3B, GSTP1, MAPK3, PPP1CC, PRKACA, and SMAD4 as optimal candidates in silico to be further studied as potentially good therapeutic targets or biomarkers

Network-Based Identification of Altered Stem Cell Pluripotency and Calcium Signaling Pathways in Metastatic Melanoma

Malignancy of cancer has been linked to distinct subsets of stem-like cells, the so-called cancer stem cells (CSCs), which persist during treatment and seem to lead to drug-resistant recurrence. Metastatic spread of cancer cells is one of the hallmarks of malignancy and contributes to most human melanoma-related deaths. Recently, overlapping groups of proteins and pathways were shown to regulate stem cell migration and cancer metastasis, raising the question of whether genes/proteins involved in stem cell pluripotency may have important implications when applied to the biology of cancer metastasis. Furthermore, it is well known that ion channels and receptors, particularly those responsible for calcium (Ca2+) signal generation, are critical in determining the cellular fate of stem cells (SCs). In the present study, we searched for evidence of altered stem cell pluripotency and Ca2+ signaling-related genes in the context of melanoma metastasis. We did this by using network analysis of gene expression in tissue biopsies from three different independent datasets of patients. First, we created an in silico network model (“STEMCa” interactome) showing the landscape of interactions between stem cell pluripotency and Ca2+ signaling-related genes/proteins, and demonstrated that around 51% (151 out of 294) of the genes within this model displayed significant changes of expression (False Discovery Rate (FDR), corrected p-value </p

Focussed microarray analysis of apoptosis in periodontitis and its potential pharmacological targeting by carvacrol

AbstractObjectiveThe objective of this study was to perform a landscape analysis of apoptosis-related genes/proteins and to study the differential gene expression by analysing array data from periodontitis patients and, second, to evaluate the anti-apoptotic effects of carvacrol, a monoterpenoid phenol, in vitro.DesignA gene/protein interaction network model ‘APOP’ was developed by using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) version 9.05. Differential gene expression was determined by using the limma package from R and false discovery rate (FDR). With ViaComplex software, gene expression was plotted over the network. The anti-apoptotic effect of carvacrol was tested on sorbitol-treated HaCaT cells, by using a commercial kit for caspase-3 activity.ResultsThe ‘APOP’ model characterised the landscape of interactions between apoptosis-related genes/proteins in silico. Forty-nine out of 70 genes from this model, such as CSF2RB, NFKBIE, ENDOG, CASP10 and CASP3, were differentially expressed (corrected p-value<0.05) in periodontitis samples when compared to those of healthy controls. In addition, carvacrol (0.43%) was able to inhibit the pro-apoptotic effects induced by sorbitol (0.3M), as seen by the reduction in caspase-3 activity on HaCaT cells.ConclusionOur results suggest that caspase-3 can be a target protein to inhibit periodontitis-associated apoptosis of epithelial cells and that carvacrol has therapeutic potential as an anti-apoptotic agent

The combined strategy for iron uptake is not exclusive to domesticated rice

Iron (Fe) is an essential micronutrient that is frequently inaccessible to plants. Rice (Oryza sativa L.) plants employ the Combined Strategy for Fe uptake, which is composed by all features of Strategy II, common to all Poaceae species, and some features of Strategy I, common to non-Poaceae species. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe defciency in O. sativa and its wild progenitor O. rufpogon. We identifed 622 and 2,017 diferentially expressed genes in O. sativa and O. rufpogon, respectively. Among the genes up-regulated in both species, we found Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2. In order to evaluate the conservation of these Strategies among other Poaceae, we identifed the orthologs of these genes in nine species from the Oryza genus, maize and sorghum, and evaluated their expression profle in response to low Fe condition. Our results indicate that the Combined Strategy is not specifc to O. sativa as previously proposed, but also present in species of the Oryza genus closely related to domesticated rice, and originated around the same time the AA genome lineage within Oryza diversifed. Therefore, adaptation to Fe2+ acquisition via IRT1 in fooded soils precedes O. sativa domestication

Third brazilian consensus for autoantIbodies screening in HEp-2 Cells : historical perspectve, quality control and clinical associatons

O III Consenso Brasileiro para Pesquisa de Autoanticorpos em Células HEp-2 (FAN) objetivou discutir estratégias para controlar a qualidade do ensaio, promover a atualização das associações clínicas dos diversos padrões e avaliar as difculdades de implantação do II Consenso ocorrido no ano de 2002. Métodos: Nos dias 13 e 14 de abril de 2007 participaram do encontro em Goiânia pesquisadores e especialistas de diversos centros universitários e laboratórios clínicos de diferentes regiões do Brasil, com o propósito de discutir e aprovar as recomendações que visam a melhores padronização, interpretação e utilização do ensaio pelos clínicos. Foram convidados como ouvintes representantes comerciais de diferentes empresas produtoras de insumos para realização do teste de FAN. Resultados e conclusão: Dada a heterogeneidade de microscópios e reagentes disponíveis no mercado, o III Consenso enfatizou a necessidade do controle de qualidade em ensaios de imunofuorescência indireta. Foram também feitas algumas adequações na terminologia utilizada para classifcar os diferentes padrões. Finalmente, foi realizada uma atualização das associações clínicas com fnalidade de facilitar cada vez mais o melhor uso do ensaio pelos clínicos. _________________________________________________________________________________ ABSTRACTThe Third Brazilian Consensus for Autoantibodies Screening in HEp-2 Cells (ANA) had as purpose the evaluation of diffculties in the accomplishment of the 2nd Consensus recommendations that took place in the year of 2002, the discussion of strategies for quality control of the assay and the discussion of an update of the clinical associations of the several immunofuorescent patterns. Methods: Several ANA experts from university centers and private laboratories in different areas in Brazil joined the workshop in Goiânia on 2007 April 13 and 14 with the purpose of discussing and approving the recommendations for standardization, interpretation and use of the test by physicians. Commercial representatives of different ANA slide brands were also invited as listeners to the workshop. Results and conclusion: The 3rd ANA Consensus emphasized the need for quality control in indirect immunofuorescent assays since there is a considerable heterogeneity of available microscopes and reagents. It also promoted adaptations in the previously approved terminology used to classify the different patterns and fnally updated the clinical associations of the several patterns with the purpose of providing guidance for interpretation of the assay by clinical pathologists and assistant physicians

Third Brazilian consensus for autoantibodies screening in HEp-2 cells (ANA) : recommendations for standardization of autoantibodies screening trial in HEp-2 cells, quality control and clinical associations

Objetivo: O 3º Consenso Brasileiro para pesquisa de autoanticorpos em Células HEp-2 (FAN) teve como propósito avaliar as dificuldades de implantação do 2º Consenso ocorrido no ano de 2002, discutir estratégias para controlar a qualidade do ensaio e promover a atualização das associações clínicas dos diversos padrões. Métodos: Participaram do encontro em Goiânia nos dias 13 e 14 de abril de 2008 pesquisadores e especialistas de diversos centros universitários e laboratórios clínicos de diferentes regiões do Brasil, com o propósito de discutir e aprovar as recomendações que visam à melhor padronização, interpretação e utilização do ensaio pelos clínicos. Representantes comerciais de diferentes empresas produtoras de insumos para realização do teste de FAN foram convidados como ouvintes. Resultados e Conclusões: O 3º Consenso enfatizou a necessidade do controle de qualidade em imunofluorescência dada a heterogeneidade de microscópios e reagentes disponíveis no mercado, promoveu adequações na terminologia utilizada para classificar os diferentes padrões e, finalmente, atualizou as associações clínicas com finalidade de facilitar cada vez mais o melhor uso do ensaio pelos clínicos. ________________________________________________________________________________ ABSTRACTObjective: The Third Brazilian Consensus for autoantibodies Screening in HEp-2 cells had as purpose the evaluation of difficulties in the accomplishment of the 2nd Consensus recommendations that took place in the year of 2002, the discussion of strategies for quality control of the assay and the promotion of an update of the clinical associations of the several immunofluorescent patterns. Methods: Several ANA experts from university centers and private laboratories in different areas in Brazil joined the workshop in Goiânia on 2008 April 13 and 14 with the purpose of discussing and approving the recommendations for standardization, interpretation and use of the test by physicians. Commercial representatives of different ANA slide brands were also invited as listeners to the workshop. Results and Conclusions: The 3rd Consensus emphasized the need for quality control in indirect immunofluorescent since there is a considerable heterogeneity of available microscopes and reagents. It also promoted adaptations in the previously approved terminology used to classify the different patterns and finally updated the clinical associations of the several patterns with the purpose of providing guidance for interpretation of the assay by clinical pathologists and assistant physicians

Definições para a padronização da pesquisa de auto-anticorpos contra constituintes do núcleo (FAN HEp-2), nucléolo, citoplasma e aparelho mitótico e suas associações clínicas

OBJECTIVE: The Second Brazilian Consensus on Antinuclear Antibodies (ANA) in HEp-2 Cells approved and extended the decision trees developed during the First Brazilian Consensus in order to also offer information about mixed patterns of fluorescence. METHODS: Since this test elicits reactions not only to nuclear autoimmune antigens but also to different cell compartments, new denominations for the test were approved. Results and CONCLUSIONS: These new denominations encompass variations on the autoantibody testing against the nucleus (ANA HEp-2), nucleolus, cytoplasm, and mitotic apparatus issue. Furthermore, major clinical associations were described for each immunofluorescent pattern, facilitating the interpretation of laboratory results in the clinical practice.OBJETIVO: O Segundo Consenso Brasileiro de Fator Antinuclear (FAN) em Células HEp-2 ratificou os algoritmos de decisão para leitura dos padrões do FAN na imunofluorescência indireta vistos na primeira edição do Consenso Brasileiro, adicionando ainda um novo algoritmo relacionado com os padrões mistos. MÉTODOS: Tendo em vista a habilidade do teste em detectar autoantígenos nos distintos compartimentos celulares, e não apenas no núcleo, propõe-se novas denominações para este exame laboratorial. RESULTADOS E CONCLUSÕES: Como novas denominações algumas sugestões foram igualmente aceitas, dentro do tema pesquisa de auto-anticorpos contra constituintes do núcleo (FAN HEp-2), nucléolo, citoplasma e aparelho mitótico. Foram abordadas as principais relevâncias clínicas com os padrões de FAN descritos, facilitando o melhor uso do ensaio pelo médico.FMUSPUNIFESPBio-Rad Laboratório BrasilHospital Geral de GoiâniaBiomédicaUniversidade Federal de UberlândiaUFMG HCPUCRS HCNew Life Produtos HospitalaresUniversidade Católica de GoiásFMUSP HC Laboratório CentralPatologista ClínicaFMUSP HCFrischmann Aisengart Unidad InmunologíaUniversidade Católica de Goiás Laboratório de Auto-ImunidadeExame Medicina LaboratorialFMUFG HC Laboratório de Imuno-Reumatologia e HLALab. Santa LuziaMedivax/BionHSPE/SPUniversidade Católica de Goiás Laboratório da Área de SaúdeFarmacêutica-BioquímicaUniv. Fed. Mato GrossoFMUFG Serviço de ReumatologiaHospital Durand Unidad InmunologíaLaboratório ClínicoUFRGS HCPA Serviço de ReumatologiaUERJ FCMUFMG FMHospital Universitário de Brasília Laboratório de ReumatologiaUNIFESPSciEL

IV Brazilian Guidelines for autoantibodies on HEp-2 cells

Objective: the Fourth Brazilian Consensus for Autoantibodies Screening in HEp-2 Cells (ANA) was held in Vitoria, Espirito Santo, and aimed to discuss strategies and recommendations about the technique, standardization, interpretation and quality control of the indirect immunofluorescence reaction on HEp-2 cells.Methods: Twenty three ANA experts from university centers and private laboratories in different areas from Brazil discussed and agreed upon recommendations for the fourth edition of the Brazilian Consensus for Autoantibodies Screening in HEp-2 Cells.Results and conclusion: the 4th ANA Consensus included three novel patterns into the existing algorithm (cytoplasmic Rods and Rings, nuclear Quasi-homogeneous, and CENP-F). Emphasis was given to the need of attention in describing the peculiar mixed pattern elicited by anti-DNA topoisomerase I (Scl-70) autoantibodies, comprising nuclear fine specked, nucleolar homogeneous pattern, NOR staining in metaphase plates, and cytoplasmic fine speckled patterns. the group also emphasized the need for continuous quality control in indirect immunofluorescence assays, the establishment of screening dilutions, as well as conjugate titration. An alert was made regarding the heterogeneity of commercial kits in defining patterns and the use of solid phase methodologies to determine the presence of autoantibodies. (C) 2014 Elsevier Editora Ltda. All rights reserved.Objetivo: O IV Consenso Brasileiro para Pesquisa de Autoanticorpos em Células HEp-2 (FAN) realizado em Vitória (ES), no dia 18 de setembro de 2012, objetivou discutir estratégias e recomendações relacionadas ao procedimento técnico, à padronização e à interpretação dos resultados da pesquisa de autoanticorpos em células HEp-2. Métodos: Participaram do evento 23 pesquisadores e especialistas de Universidades e laboratórios brasileiros. Foram abordados diferentes tópicos, discutidos amplamente a fim de se estabelecer recomendações específicas. Resultados e conclusão: O IV Consenso integrou à árvore de decisão o padrão citoplasmático em Anéis e Bastões, o padrão nuclear pontilhado Quasi-homogêneo (QH) e o padrão misto CENP-F. Discutiu-se ainda a necessidade de atenção para a classificação do padrão misto relacionado à presença de anticorpos anti-DNA topoisomerase I (Scl-70), compreendendo os componentes nuclear pontilhado fino, nucleolar homogêneo, NOR na placa metafásica e citoplasmático pontilhado fino. Foram sugeridas diretrizes para o controle de qualidade do teste, diluição de triagem e diluição de esgotamento, e foi emitido alerta quanto à necessidade de atenção em relação à heterogeneidade de substratos disponíveis no mercado e a utilização de metodologias automatizadas para detecção de autoanticorpos.Albert Einstein Medicina DiagnosticaAlka TecnologiaAmaral Costa LaboratorioConselho Federal de BiomedicinaDASAEuroimmun BrasilGrupo FleuryHemagenMedivaxOlimpusPadrao Laboratorio ClinicPontificia Universidade Catolica de Goias - PUC-GoiasSociedade Brasileira de Patologia Clinica e Medicina LaboratorialSociedade Brasileira de ReumatologiaThermo ScientificWama DiagnosticaWerfen Group - Werfen MedicalHermes PardiniConselho Regional de Biomedicina - 3a RegiaoPUC Goias, Goiania, Go, BrazilFleury Med & Saude, São Paulo, BrazilUniversidade Federal de São Paulo UNIFESP, Discipline Rheumatol, São Paulo, BrazilUniv Fed Uberlandia, Hosp Clin, Serv Rheumatol, BR-38400 Uberlandia, MG, BrazilClin Doencas Reumat Porto Alegre, Ctr Diagnost Med & Rheuma, Porto Alegre, RS, BrazilAmaral Costa Med Diagnost, Belem, PA, BrazilUniv São Paulo, Fac Med, Hosp Clin, Lab Invest Med, São Paulo, BrazilUniv São Paulo, Fac Med, Hosp Clin, Lab Cent, São Paulo, BrazilHosp Israelita Albert Einstein, Dept Clin Pathol, São Paulo, BrazilInst Hermes Pardini, Belo Horizonte, MG, BrazilUniv São Paulo, Fac Med, São Paulo, BrazilUniv Fed Minas Gerais, Fac Med, Belo Horizonte, MG, BrazilUniv Catolica Brasilia, Brasilia, DF, BrazilUniv Fed Goias, Fac Med, Goiania, Go, BrazilUniv Sul Santa Catarina UNISUL, Florianopolis, SC, BrazilUniv Vale do Itajai UNIVALE, Florianopolis, SC, BrazilUniv Fed Espirito Santo, Vitoria, ES, BrazilEBMSP, Salvador, BA, BrazilGrp DASA, São Paulo, BrazilEscola Super Ciencias Saude Dist Fed, Brasilia, DF, BrazilLab Sabin, Brasilia, DF, BrazilUniversidade Federal de São Paulo UNIFESP, Discipline Rheumatol, São Paulo, BrazilWeb of Scienc

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio