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

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

Estudo da evolução dos receptores químicos nos organismos Mus musculus, Homo sapiens e Rattus norvegicus através de ferramentas de Biologia de Sistemas

A quimiorrecepção (QR) é uma modalidade sensorial muito importante em todos os ani-mais. Estudos recentes permitiram a identificação das famílias de genes QR, divididas em receptores olfatórios (OL), vomeronasais (VN), gustatórios (TS) e de traços de aminas (TAAR). Utilizando dados do Gene Ontology Project (GO), nós conseguimos determinar os genes envolvidos em cada modalidade sensorial química nos organismos Mus musculus, Homo sapiens e Rattus norvegicus. Os GO IDs utilizados foram 0004984 e 0007608, 0050909 e 0008527, 0016503 e 0019236, respectivamente, para os receptores OL, TS e VN (os TAAR foram retirados das análises por falta de dados disponíveis). Adquirimos os parâmetros das redes funcionais formadas pelas proteínas codificadas por esses genes atra-vés do banco de dados STRING-DB e Biomart. Os critérios utilizados para nossas análises foram conectividade [k(i)], clusterização [c(i)] e índice estimado de plasticidade (EPI) des-ses receptores. Dividimos o conjunto de dados em proteínas envolvidas diretamente na QR e proteínas envolvidas na transdução do sinal e posteriores cascatas químicas, denomina-dos de Grupo dos Receptores (GR) e dos Acessórios (GA). Comparando as médias de EPIs do GR e GA através de ANOVA simples e teste Tuckey, foi observado que as médias do GR eram significativamente maiores que as do GA (p<0,001). Esses testes foram repetidos em cada subgrupo receptor com seu respectivo subgrupo acessório e foram observados os mesmos resultados gerais, além de ser encontrado nos três organismos uma similaridade entre os OL e TS2, VN e TS1 (p<0,05). Foi analisada a entropia da distribuição dos valores de k(i) e c(i) e foi encontrado que estes eram significativamente maiores (p<0,001) no GA. Isso se reflete na distribuição de forma mais uniforme desses valores no GA e de forma mais concentrada no GR. Os resultados sugerem que a seleção natural é menos estringente nos receptores do que no maquinário de transdução de sinal, permitindo uma variação mais dinâmica desses. Essa capacidade é muito importante para a adaptação dos organismos aos diversos nichos ecológicos em que estão inseridos. Estes dados estão em acordo com os atuais modelos propostos para a evolução dos receptores químicos.Chemoreception (CR) is a very important sensory modality in all animals. Recent studies allowed the characterization of.CR gene families, divided in olfactory receptors (OL), vo-meronasal (VN), gustatory (TS) and trace amine (TAAR). Using data gathered from The Gene Ontology Project (GO), we were able to amass the genes associated with each type of sensory perception. The GO ID’s used for this work were 0004984 and 0007608, 0050909 and 0008527, 0016503 and 0019236, for olfactory, gustatory and vomeronasal ontology groups, respectively. We sorted these genes in groups by receptor modality, with one fur-ther division of the Taste Group into the Taste-1 and Taste-2 receptors groups. We ac-quired the network parameters of the proteins translated from these genes groups using data from STRING Database. We used as criterions for our analysis the connectivity and clusterization indexes (i.e. k(i) and c(i), respectively). Also used in our analysis was the Evolutionary Plasticity Index (EPI). We subsequently divided the whole dataset into two more groups: those of proteins directly involved in the chemical binding of the stimuli, named Receptor Group (RG); and those involved into signal transduction and further chemical pathways, named Accessory Group (AG). We compared the mean EPIs of all the RGs and AGs using One-Way ANOVA and Tukey test and found that the AGs’ means were significantly lower than the RGs’ (p<0,001). We also found that the OL and TS2, VN and TS1 EPI means where similar in all three organisms (p<0,05). We compared the over-all distribution of the c(i) and k(i) on and observed that all of the RGs presented very low values, whereas the AGs presented a more uniform distribution. The sole exception in this analysis was the Olfactory RGs’ c(i), which all have a more extreme oriented distribution, with proteins with very high and very low values, but no intermediary ones. Also with ANOVA, we observed that the Entropy of AGs’ k(i) distribution was significantly higher than the RGs’ (p<0,05). Our findings suggest that the evolutionary plasticity in the RGs is higher than that on the AGs. This means that the selective pressures among the chemore-ceptors are weaker than that on the transduction machinery, resulting in a greater diversity for these receptors. Put together, these results support the Birth-and-Death Evolution model proposed for chemosensory receptors

Busca de novos alvos terapêuticos no tratamento de neuroblastoma utilizando ferramentas de biologia de sistemas

Neuroblastoma é um tumor do sistema nervoso periférico e uma das principais causas de mortalidade infantil por câncer no Brasil e no mundo. A característica marcante desses tumores é sua heterogeneidade clínica – as apresentações variam desde formas benignas e tratáveis até variantes extremamente agressivas, que levam o paciente a óbito em poucos meses. A fim de determinar as melhores estratégias para o tratamento desse câncer, um grande número de pesquisadores tem procurado por novos biomarcadores e alvos terapêuticos. Atualmente, o melhor marcador biológico para a progressão de neuroblastoma é a amplificação do gene MYCN, que ocorre na maioria dos casos mais agressivos. Entretanto, esse marcador não é capaz de discriminar entre todos os tipos de pacientes, demonstrando a necessidade de encontrarmos outros marcadores. Neste trabalho, reconstruímos a rede de regulação gênica de neuroblastoma utilizando ferramentas de bioinformática e biologia de sistemas a fim de buscar novos biomarcadores e alvos terapêuticos para esta doença. Através dessa rede, analisamos uma assinatura de genes diferentemente expressos em metástases agressivas, buscando fatores de transcrição que pudessem estar envolvidos na progressão tumoral. Através dessa análise, observamos que MAX é um dos reguladores mestres do processo, e variações em sua expressão estavam correlacionadas com o desfecho de pacientes, sugerindo seu potencial como biomarcador. Além disso, também observamos o aumento do conteúdo de MAX em células de linhagem de neuroblastoma humano durante um protocolo de diferenciação experimental, sugerindo que essa proteína tem um papel muito mais central no controle do balanço entre proliferação e diferenciação do que previamente descrito.Neuroblastoma is a peripheral nervous system tumor and one of the main causes of children cancer mortality in Brazil and in the rest of the world. The hallmark of these tumors is their clinical heterogeneity – presentations vary from benign and treatable to extremely aggressive variants, the latter leading the patient to death in just a few months. In order to come up with the best strategies for treatment and management of this cancer, a great number of researchers have been searching for novel biomarkers and therapeutic targets. To this date, the best neuroblastoma biomarker is the amplification of MYCN oncogene, which occurs in the majority of aggressive cases. However, this biomarker alone does not suffice to discriminate among all patients types, illustrating the need for finding other biomarkers. In this work, we reverse engineered the neuroblastoma gene regulatory network using systems biology and bioinformatics tools in order to find novel biomarkers and therapeutic targets. Using this network, we analyzed an aggressive metastasis gene signature to find transcription factors that could be involved in tumor progression. Through this analysis, we observed that MAX was a master regulator of this process, and that changes in its expression were associated with patient survival, suggesting its role as potential biomarker. Additionally, we observed that MAX content was increased in human neuroblastoma cell lines undergoing experimental differentiation. These results suggest that this protein has a much more central role in regulating the balance between proliferation and differentiation than previously described

Antioxidant and anti-inflammatory properties of Anacardium occidentale leaf extract

In tropical America, principally inNortheastern Brazil, the leaf extract of Anacardiumoccidentale 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 g/mL and 5 g/mL of leaf extract.Moreover, leaf extract reversed oxidative damage and inflammatory parameters induced in LPS-stimulated RAW264.7 macrophage cells. Leaf extract at 0.5 g/mL and 5 g/mL was able to inhibit release of TNF- and IL-1 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