48 research outputs found
Reverse engineering of Ewing Sarcoma regulatory network uncovers PAX7 and RUNX3 as master regulators associated with good prognosis
Ewing Sarcoma (ES) is a rare malignant tumor occurring most frequently in adolescents and young adults. The ES hallmark is a chromosomal translocation between the chromosomes 11 and 22 that results in an aberrant transcription factor (TF) through the fusion of genes from the FET and ETS families, commonly EWSR1 and FLI1. The regulatory mechanisms behind the ES transcriptional alterations remain poorly understood. Here, we reconstruct the ES regulatory network using public available transcriptional data. Seven TFs were identified as potential MRs and clustered into two groups: one composed by PAX7 and RUNX3, and another composed by ARNT2, CREB3L1, GLI3, MEF2C, and PBX3. The MRs within each cluster act as reciprocal agonists regarding the regulation of shared genes, regulon activity, and implications in clinical outcome, while the clusters counteract each other. The regulons of all the seven MRs were differentially methylated. PAX7 and RUNX3 regulon activity were associated with good prognosis while ARNT2, CREB3L1, GLI3, and PBX3 were associated with bad prognosis. PAX7 and RUNX3 appear as highly expressed in ES biopsies and ES cell lines. This work contributes to the understanding of the ES regulome, identifying candidate MRs, analyzing their methilome and pointing to potential prognostic factors
Differential Evolutionary Constraints in the Evolution of Chemoreceptors: A Murine and Human Case Study
Chemoreception is among the most important sensory modalities in animals. Organisms use the ability to perceive chemical compounds in all major ecological activities. Recent studies have allowed the characterization of chemoreceptor gene families. These genes present strikingly high variability in copy numbers and pseudogenization degrees among different species, but the mechanisms underlying their evolution are not fully understood. We have analyzed the functional networks of these genes, their orthologs distribution, and performed phylogenetic analyses in order to investigate their evolutionary dynamics. We have modeled the chemosensory networks and compared the evolutionary constraints of their genes in Mus musculus, Homo sapiens, and Rattus norvegicus. We have observed significant differences regarding the constraints on the orthologous groups and network topologies of chemoreceptors and signal transduction machinery. Our findings suggest that chemosensory receptor genes are less constrained than their signal transducing machinery, resulting in greater receptor diversity and conservation of information processing pathways. More importantly, we have observed significant differences among the receptors themselves, suggesting that olfactory and bitter taste receptors are more conserved than vomeronasal receptors
Reverse engineering the neuroblastoma regulatory network uncovers MAX as one of the master regulators of tumor progression
Neuroblastoma is the most common extracranial tumor and a major cause of infant cancer mortality worldwide. Despite its importance, little is known about its molecular mechanisms. A striking feature of this tumor is its clinical heterogeneity. Possible outcomes range from aggressive invasion to other tissues, causing patient death, to spontaneous disease regression or differentiation into benign ganglioneuromas. Several efforts have been made in order to find tumor progression markers. In this work, we have reconstructed the neuroblastoma regulatory network using an information-theoretic approach in order to find genes involved in tumor progression and that could be used as outcome predictors or as therapeutic targets. We have queried the reconstructed neuroblastoma regulatory network using an aggressive neuroblastoma metastasis gene signature in order to find its master regulators (MRs). MRs expression profiles were then investigated in other neuroblastoma datasets so as to detect possible clinical significance. Our analysis pointed MAX as one of the MRs of neuroblastoma progression. We have found that higher MAX expression correlated with favorable patient outcomes. We have also found that MAX expression and protein levels were increased during neuroblastoma SH-SY5Y cells differentiation. We propose that MAX is involved in neuroblastoma progression, possibly increasing cell differentiation by means of regulating the availability of MYC:MAX heterodimers. This mechanism is consistent with the results found in our SH-SY5Y differentiation protocol, suggesting that MAX has a more central role in these cells differentiation than previously reported. Overexpression of MAX has been identified as anti-tumorigenic in other works, but, to our knowledge, this is the first time that the link between the expression of this gene and malignancy was verified under physiological conditions
Systems Biology-Based Analysis Indicates Global Transcriptional Impairment in Lead-Treated Human Neural Progenitor Cells
Lead poisoning effects are wide and include nervous system impairment, peculiarly during development, leading to neural damage. Lead interaction with calcium and zinc-containing metalloproteins broadly affects cellular metabolism since these proteins are related to intracellular ion balance, activation of signaling transduction cascades, and gene expression regulation. In spite of lead being recognized as a neurotoxin, there are gaps in knowledge about the global effect of lead in modulating the transcription of entire cellular systems in neural cells. In order to investigate the effects of lead poisoning in a systemic perspective, we applied the transcriptogram methodology in an RNA-seq dataset of human embryonic-derived neural progenitor cells (ES-NP cells) treated with 30 µM lead acetate for 26 days. We observed early downregulation of several cellular systems involved with cell differentiation, such as cytoskeleton organization, RNA, and protein biosynthesis. The downregulated cellular systems presented big and tightly connected networks. For long treatment times (12 to 26 days), it was possible to observe a massive impairment in cell transcription profile. Taking the enriched terms together, we observed interference in all layers of gene expression regulation, from chromatin remodeling to vesicle transport. Considering that ES-NP cells are progenitor cells that can originate other neural cell types, our results suggest that lead-induced gene expression disturbance might impair cells’ ability to differentiate, therefore influencing ES-NP cells’ fate
Turnera subulata Anti-Inflammatory Properties in Lipopolysaccharide-Stimulated RAW 264.7 Macrophages
In South America, particularly in the Northeastern regions of Brazil, Turnera subulata leaf extract is used as an alternative traditional medicine approach for several types of chronic diseases, such as diabetes, hypertension, chronic pain, and general inflammation. Despite its widespread use, little is known about the medicinal properties of the plants of this genus. In this study, we evaluate the antioxidant and anti-inflammatory of T. subulata leaf extract in an in vitro model of inflammation, using lipopolysaccharide-stimulated RAW-264.7 macrophage cell line. We observed that cotreatment with T. subulata leaf extract was able to reduce the oxidative stress in cells due to inflammatory response. More importantly, we observed that the leaf extract was able to directly modulate inflammatory response by altering activity of members of the mitogen-activated protein kinase pathways. Our results demonstrate for the first time that T. subulata have antioxidant and anti-inflammatory properties, which warrant further investigation of the medicinal potential of this species.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140112/1/jmf.2016.0047.pd
Antioxidant and Anti-Inflammatory Properties of Anacardium occidentale
In tropical America, principally in Northeastern Brazil, the leaf extract of Anacardium occidentale is traditionally used for treatment of different diseases. However, chemical and biological properties and activities of Anacardium occidentale are poorly investigated and known. Here, we evaluated the antioxidant and anti-inflammatory activities “in vitro” of leaf extract from Anacardium occidentale. Our results show that leaf extract exhibits antioxidant activity when used to treat RAW 264.7 macrophage cells. Antioxidant effects were observed by decrease in oxidative damage in macrophage cells treated with 0.5 µg/mL and 5 µg/mL of leaf extract. Moreover, leaf extract reversed oxidative damage and inflammatory parameters induced in LPS-stimulated RAW 264.7 macrophage cells. Leaf extract at 0.5 µg/mL and 5 µg/mL was able to inhibit release of TNF-α and IL-1β in LPS-stimulated cells. Taken together, our results indicate antioxidant and anti-inflammatory effects of leaf extract from Anacardium occidentale and reveal the positive effects that intake of these products can mediate in biological system
Aumento da atividade da MMP-2 induzido por tratamento com retinol e ácido retinóico em células de Sertoli cultivadas
EspĂ©cies reativas de oxigĂŞnio (ROS) tĂŞm sido descritas como potenciais causadoras de doenças como aterosclerose, artrite e câncer. Falhas na regulação das metaloproteinases de matriz (MMP), uma famĂlia de proteases que degradam matriz extracelular, parecem estar intimamente relacionadas com essas mesmas doenças. AlĂ©m disso, autores sugerem uma relação entre a atividade das MMPs e ROS. Em trabalhos anteriores, nosso grupo de pesquisa demonstrou que o tratamento com retinol 7 ÎĽM foi capaz de induzir mudanças no metabolismo de cĂ©lulas de Sertoli cultivadas, como o aumento da atividade de enzimas antioxidantes, aumento do dano oxidativo a biomolĂ©culas, ativação de ERK1/2 MAPK, alteração do ciclo celular e transformação prĂ©-neoplásica, ligando o tratamento com retinol ao estresse oxidativo. No presente trabalho, nĂłs utilizamos a tĂ©cnica de zimografia para verificar a atividade da MMP-2 em cĂ©lulas de Sertoli tratadas com retinol e ácido retinĂłico. NĂłs encontramos que tanto o tratamento por 24 horas com retinol 7 ÎĽM, quanto o tratamento por 24 horas com ácido retinĂłico 1 nM, aumentaram a atividade da MMP-2 em cĂ©lulas de Sertoli cultivadas. O cotratamento com diferentes antioxidantes reverteu o aumento da atividade da MMP-2 induzido por retinol, mas nĂŁo por ácido retinĂłico. AlĂ©m disso, o tratamento com retinol, mas nĂŁo com ácido retinĂłico, foi capaz de aumentar a produção de ROS quantificada pela oxidação de DCFH-DA. NĂłs encontramos tambĂ©m que tanto o tratamento com retinol quanto com ácido retinĂłico foram capazes de aumentar a fosforilação de ERK1/2. Entretanto, somente o aumento da atividade da MMP-2 induzido por tratamento com retinol foi inibido por co-tratamento com UO126, um potente inibidor de fosforização de ERK1/2. Nossos resultados sugerem que o aumento da atividade da MMP-2 induzido por retinol, mas nĂŁo por ácido retinĂłico, está relacionado com a fosforilação de ERK1/2 e com a geração de ERO.Reactive oxygen species (ROS) have been hypothesized to play a causative role in numerous diseases such as atherosclerosis, arthritis and cancer. Failures in the regulation of the matrix metalloproteinases (MMP), a family of extracellular matrixdegrading proteases, appear to be intimately involved in these diseases. In addition, authors suggest a relationship between MPP activity and ROS. In early reports our research group has demonstrated that 7 ÎĽM retinol was able to induce changes in Sertoli cell metabolism, such as up-regulation of antioxidant enzyme activities, increase in oxidative damage to biomolecules, activation of ERK1/2 MAPK, cell-cycle alteration and pre-neoplasic transformation, linking retinol treatment and oxidative stress. Here, we verify the MMP activity in cultured Sertoli cells treated with vitamin A using gelatin zymography. We found that both retinol (7 ÎĽM by 24 hours) and retinoic acid (1 nM by 24 hours) treatments induces MMP-2 activity in cultured Sertoli cells. Antioxidants cotreatment reversed retinol-induced but not retinoic acid-induced MMP-2 activity. Moreover, retinol but not retinoic acid treatment increased ROS production quantified by DCFH-DA oxidation. We found that both retinol and retinoic acid treatment induced ERK1/2 phosphorylation. However, only retinol-increased MMP-2 activity was inhibited by UO126, a potent ERK1/2 phosphorylation inhibitor. Our results suggested that the increase on MMP- 2 activity induced by retinol, but not by retinoic acid, was related to ERK1/2 phosphorylation and ROS production
Desenvolvimento de ferramentas de bioinformática para o estudo evolutivo de sistemas bioquĂmicos
O crescente corpo de informações gerado pelo desenvolvimento de tĂ©cnicas de altodesempenho, como sequenciamento de DNA em larga escala, tĂ©cnicas de microarranjo de DNA, hibridização de proteĂnas, etc., tem evidenciado uma intrincada relação entre os diversos personagens que compõe os sistemas biolĂłgicos. Alguns dos sistemas bioquĂmicos presentes em organismos modernos surgiram há bilhões de anos e estavam presentes em organismos primitivos, ao passo que determinados sistemas sĂŁo mais recentes e especĂficos de alguns grupos taxonĂ´micos. O entendimento das relações entre os diferentes personagens dos sistemas biolĂłgicos apresenta-se como fundamental para a compreensĂŁo da vida e a avaliação dos aspectos evolutivos que permearam a constituição dos sistemas bioquĂmicos e suas intrincadas inter-relações pode auxiliar sobremaneira no estudo da biologia. Diversas teorias encontram-se bem estabelecidas no estudo evolutivo em nĂvel de espĂ©cies e populações. Da mesma maneira, há um extenso acervo bibliográfico acerca da evolução de genes individuais. Entretanto, o surgimento, estabelecimento e evolução dos sistemas bioquĂmicos permanecem escassamente estudados. Na presente tese, partimos da análise de dois sistemas bioquĂmicos, o sistema de apoptose e o sistema de estabilidade genĂ´mica, os quais sĂŁo bastante associados em mamĂferos. Apesar da Ăntima relação entre esses sistemas, eles foram originados em momentos diferentes da evolução. Buscamos reconstruir o cenário evolutivo que uniu os sistemas de apoptose e estabilidade genĂ´mica, onde encontramos uma relação direta entre ancestralidade, essencialidade e clusterização. Os resultados tambĂ©m sugerem uma relação inversa entre essas trĂŞs caracterĂsticas e plasticidade. A análise de plasticidade efetuada na rede de apoptose e estabilidade genĂ´mica foi ampliada para 4850 famĂlias de proteĂnas em 55 eucariotos, apresentando basicamente os mesmos resultados, indicando um mecanismo geral de evolução do genoma. Subsequentemente, propusemos um modelo matemático de crescimento do genoma onde a novidade genĂ©tica surge por duplicação de genes muito conectados e pouco clusterizados. A rede artificial obtida mimetiza diversos aspectos topolĂłgicos das redes biolĂłgicas conhecidas. Os resultados analisados em conjunto sugerem um mecanismo geral de evolução do genoma, onde a novidade genĂ©tica surge na porção mais plástica do genoma, basicamente por duplicação gĂŞnica. Essa duplicação ocorre prioritariamente nos hubs intermodulares.The increasing body of information generated by high-throughput techniques, such as DNA sequencing, genome-wide microarray, and two-hybrid system, has unveiled an intricate relationship among different components of biological systems. Some of the biological systems found in modern organisms have their origins billion years ago and were present in primitive organisms. On the other hand, some biological systems are more recent and specifically related to some taxa. The characterization of the relationships involving the different components of biological systems is crucial to the understanding of life. Additionally, the evaluation of evolutionary aspects which work in biochemical systems construction, modeling their intricate relationship, could help improve biological research field. Several theories are well-established in evolutionary research of species and population. Likewise, there is plenty of bibliography concerning individual gene evolution. However, there is paucity of data concerning the origin, establishment, and evolution of entire biological systems. In the present thesis, we start by analyzing two biochemistry systems: apoptosis and genome stability. These systems are considerably associated in mammals. Despite its entangled functioning, each system has emerged in different points of evolution. We reconstructed the evolutionary scenario which entangled both systems. We found a direct relationship among ancestrality, essentiality, and clustering. Our results also suggest an inverse relationship of these three proprieties with plasticity. The same plasticity analysis used in apoptosis and genome stability systems was amplified to 4850 gene families in 55 eukaryotes, showing basically the same results. It suggests a general mechanism of genome evolution. We then propose a genome growth model where genetic novelty arrives through gene duplication of highly connected but not so clustered genes. The resulting artificial network reproduces several known topological aspects of biological networks. The results, when simultaneously analyzed, suggest general genome evolution mechanisms, where the genetic novelty arrives in more plastic area of the genome, basically by gene duplication. That duplication occurs mainly in intermodular hubs
Aumento da atividade da MMP-2 induzido por tratamento com retinol e ácido retinóico em células de Sertoli cultivadas
EspĂ©cies reativas de oxigĂŞnio (ROS) tĂŞm sido descritas como potenciais causadoras de doenças como aterosclerose, artrite e câncer. Falhas na regulação das metaloproteinases de matriz (MMP), uma famĂlia de proteases que degradam matriz extracelular, parecem estar intimamente relacionadas com essas mesmas doenças. AlĂ©m disso, autores sugerem uma relação entre a atividade das MMPs e ROS. Em trabalhos anteriores, nosso grupo de pesquisa demonstrou que o tratamento com retinol 7 ÎĽM foi capaz de induzir mudanças no metabolismo de cĂ©lulas de Sertoli cultivadas, como o aumento da atividade de enzimas antioxidantes, aumento do dano oxidativo a biomolĂ©culas, ativação de ERK1/2 MAPK, alteração do ciclo celular e transformação prĂ©-neoplásica, ligando o tratamento com retinol ao estresse oxidativo. No presente trabalho, nĂłs utilizamos a tĂ©cnica de zimografia para verificar a atividade da MMP-2 em cĂ©lulas de Sertoli tratadas com retinol e ácido retinĂłico. NĂłs encontramos que tanto o tratamento por 24 horas com retinol 7 ÎĽM, quanto o tratamento por 24 horas com ácido retinĂłico 1 nM, aumentaram a atividade da MMP-2 em cĂ©lulas de Sertoli cultivadas. O cotratamento com diferentes antioxidantes reverteu o aumento da atividade da MMP-2 induzido por retinol, mas nĂŁo por ácido retinĂłico. AlĂ©m disso, o tratamento com retinol, mas nĂŁo com ácido retinĂłico, foi capaz de aumentar a produção de ROS quantificada pela oxidação de DCFH-DA. NĂłs encontramos tambĂ©m que tanto o tratamento com retinol quanto com ácido retinĂłico foram capazes de aumentar a fosforilação de ERK1/2. Entretanto, somente o aumento da atividade da MMP-2 induzido por tratamento com retinol foi inibido por co-tratamento com UO126, um potente inibidor de fosforização de ERK1/2. Nossos resultados sugerem que o aumento da atividade da MMP-2 induzido por retinol, mas nĂŁo por ácido retinĂłico, está relacionado com a fosforilação de ERK1/2 e com a geração de ERO.Reactive oxygen species (ROS) have been hypothesized to play a causative role in numerous diseases such as atherosclerosis, arthritis and cancer. Failures in the regulation of the matrix metalloproteinases (MMP), a family of extracellular matrixdegrading proteases, appear to be intimately involved in these diseases. In addition, authors suggest a relationship between MPP activity and ROS. In early reports our research group has demonstrated that 7 ÎĽM retinol was able to induce changes in Sertoli cell metabolism, such as up-regulation of antioxidant enzyme activities, increase in oxidative damage to biomolecules, activation of ERK1/2 MAPK, cell-cycle alteration and pre-neoplasic transformation, linking retinol treatment and oxidative stress. Here, we verify the MMP activity in cultured Sertoli cells treated with vitamin A using gelatin zymography. We found that both retinol (7 ÎĽM by 24 hours) and retinoic acid (1 nM by 24 hours) treatments induces MMP-2 activity in cultured Sertoli cells. Antioxidants cotreatment reversed retinol-induced but not retinoic acid-induced MMP-2 activity. Moreover, retinol but not retinoic acid treatment increased ROS production quantified by DCFH-DA oxidation. We found that both retinol and retinoic acid treatment induced ERK1/2 phosphorylation. However, only retinol-increased MMP-2 activity was inhibited by UO126, a potent ERK1/2 phosphorylation inhibitor. Our results suggested that the increase on MMP- 2 activity induced by retinol, but not by retinoic acid, was related to ERK1/2 phosphorylation and ROS production