Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity.

Glioblastoma Multiforme is a brain tumor distinguished by its aggressiveness. We suggested that this aggressiveness leads single-cell RNA-sequence data (scRNA-seq) to span a representative portion of the cancer attractors domain. This conjecture allowed us to interpret the scRNA-seq heterogeneity as reflecting a representative trajectory within the attractor's domain. We considered factors such as genomic instability to characterize the cancer dynamics through stochastic fixed points. The fixed points were derived from centroids obtained through various clustering methods to verify our method sensitivity. This methodological foundation is based upon sample and time average equivalence, assigning an interpretative value to the data cluster centroids and supporting parameters estimation. We used stochastic simulations to reproduce the dynamics, and our results showed an alignment between experimental and simulated dataset centroids. We also computed the Waddington landscape, which provided a visual framework for validating the centroids and standard deviations as characterizations of cancer attractors. Additionally, we examined the stability and transitions between attractors and revealed a potential interplay between subtypes. These transitions might be related to cancer recurrence and progression, connecting the molecular mechanisms of cancer heterogeneity with statistical properties of gene expression dynamics. Our work advances the modeling of gene expression dynamics and paves the way for personalized therapeutic interventions.

A Strategy Utilizing Protein-Protein Interaction Hubs for the Treatment of Cancer Diseases.

We describe a strategy for the development of a rational approach of neoplastic disease therapy based on the demonstration that scale-free networks are susceptible to specific attacks directed against its connective hubs. This strategy involves the (i) selection of up-regulated hubs of connectivity in the tumors interactome, (ii) drug repurposing of these hubs, (iii) RNA silencing of non-druggable hubs, (iv) in vitro hub validation, (v) tumor-on-a-chip, (vi) in vivo validation, and (vii) clinical trial. Hubs are protein targets that are assessed as targets for rational therapy of cancer in the context of personalized oncology. We confirmed the existence of a negative correlation between malignant cell aggressivity and the target number needed for specific drugs or RNA interference (RNAi) to maximize the benefit to the patient's overall survival. Interestingly, we found that some additional proteins not generally targeted by drug treatments might justify the addition of inhibitors designed against them in order to improve therapeutic outcomes. However, many proteins are not druggable, or the available pharmacopeia for these targets is limited, which justifies a therapy based on encapsulated RNAi.

An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851.

BACKGROUND: Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behaviour and provide novel ways to identify potential therapeutic targets and develop new drugs. Gene regulatory networks (GRN) are examples of in silico representation of interaction between regulatory genes and their targets. OBJECTIVES: In this work, we update the MDR P. aeruginosa CCBH4851 GRN reconstruction and analyse and discuss its structural properties. METHODS: We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process. FINDINGS: Our result is a GRN with a greater number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa. MAIN CONCLUSIONS: Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.

A method for in silico exploration of potential glioblastoma multiforme attractors using single-cell RNA sequencing.

We presented a method to find potential cancer attractors using single-cell RNA sequencing (scRNA-seq) data. We tested our method in a Glioblastoma Multiforme (GBM) dataset, an aggressive brain tumor presenting high heterogeneity. Using the cancer attractor concept, we argued that the GBM's underlying dynamics could partially explain the observed heterogeneity, with the dataset covering a representative region around the attractor. Exploratory data analysis revealed promising GBM's cellular clusters within a 3-dimensional marker space. We approximated the clusters' centroid as stable states and each cluster covariance matrix as defining confidence regions. To investigate the presence of attractors inside the confidence regions, we constructed a GBM gene regulatory network, defined a model for the dynamics, and prepared a framework for parameter estimation. An exploration of hyperparameter space allowed us to sample time series intending to simulate myriad variations of the tumor microenvironment. We obtained different densities of stable states across gene expression space and parameters displaying multistability across different clusters. Although we used our methodological approach in studying GBM, we would like to highlight its generality to other types of cancer. Therefore, this report contributes to an advance in the simulation of cancer dynamics and opens avenues to investigate potential therapeutic targets.

Data-Driven Modeling of Breast Cancer Tumors Using Boolean Networks.

Cancer is a genomic disease involving various intertwined pathways with complex cross-communication links. Conceptually, this complex interconnected system forms a network, which allows one to model the dynamic behavior of the elements that characterize it to describe the entire system's development in its various evolutionary stages of carcinogenesis. Knowing the activation or inhibition status of the genes that make up the network during its temporal evolution is necessary for the rational intervention on the critical factors for controlling the system's dynamic evolution. In this report, we proposed a methodology for building data-driven boolean networks that model breast cancer tumors. We defined the network components and topology based on gene expression data from RNA-seq of breast cancer cell lines. We used a Boolean logic formalism to describe the network dynamics. The combination of single-cell RNA-seq and interactome data enabled us to study the dynamics of malignant subnetworks of up-regulated genes. First, we used the same Boolean function construction scheme for each network node, based on canalyzing functions. Using single-cell breast cancer datasets from The Cancer Genome Atlas, we applied a binarization algorithm. The binarized version of scRNA-seq data allowed identifying attractors specific to patients and critical genes related to each breast cancer subtype. The model proposed in this report may serve as a basis for a methodology to detect critical genes involved in malignant attractor stability, whose inhibition could have potential applications in cancer theranostics.

Mining in Twitter for adverse events from malaria drugs: the case of doxycycline. / O uso do Twitter como minerador de eventos adversos de medicamentos de combate à malária: o caso da doxiciclina.

During the post-marketing period, when medicines are used by large population contingents and for longer periods, unexpected adverse events (AE) can occur, potentially altering the drug's risk-benefit ratio enough to demand regulatory action. AE are health problems that can occur during treatment with a pharmaceutical product, which in the drug's post-marketing period can require a significant increase in health care and result in unnecessary and often fatal harm to patients. Therefore, a key objective for the health system is to identify AE as soon as possible in the post-marketing period. Some countries have pharmacovigilance systems responsible for collecting voluntary reports of post-marketing AE, but studies have shown that social networks can be used to obtain more and faster reports. The current project's main objective is to build a totally automated system using Twitter as a source to detect both new and previously known AE and conduct the statistical analysis of the resulting data. A system was thus built to collect, process, analyze, and assess tweets in search of AE, comparing them to U.S. Food and Drug Administration (FDA) data and the reference standard. The results allowed detecting new and existing AE related to the drug doxycycline, showing that Twitter can be useful in pharmacovigilance when employed jointly with other data sources.

Durante o período de pós-comercialização, quando medicamentos são usados por grandes populações e por períodos de tempo maiores, eventos adversos (EA) inesperados podem ocorrer, o que pode alterar a relação risco-benefício dos medicamentos o suficiente para exigir uma ação regulatória. Eventos adversos são agravos à saúde que podem surgir durante o tratamento com um produto farmacêutico, os quais, no período de pós-comercialização do medicamento, podem requerer um aumento significativo de cuidados de saúde e resultar em danos desnecessários aos pacientes, muitas vezes fatais. Portanto, o quanto antes, a descoberta de EA no período de pós-comercialização é um objetivo principal do sistema de saúde. Alguns países possuem sistemas de vigilância farmacológica responsáveis pela coleta de relatórios voluntários de EA na pós-comercialização, mas estudos já demonstraram que, com a utilização de redes sociais, pode-se conseguir um número maior e mais rápido de relatórios. O objetivo principal deste projeto é construir um sistema totalmente automatizado que utilize o Twitter como fonte para encontrar EA novos e já conhecidos e fazer a análise estatística dos dados obtidos. Para isso, foi construído um sistema que coleta, processa, analisa e avalia tweets em busca de EA, comparando-os com dados da Agência Americana de Controle de Alimentos e Medicamentos (FDA) e do padrão de referência construído. Nos resultados obtidos, conseguimos encontrar EA novos e já existentes relacionados ao medicamento doxiciclina, o que demonstra que o Twitter, quando utilizado em conjunto com outras fontes de dados, pode ser útil para a farmacovigilância.

Durante el período de poscomercialización, cuando grandes poblaciones consumen medicamentos durante períodos más prolongados de tiempo, se pueden producir eventos adversos (EA) inesperados, lo que puede alterar la relación riesgo-beneficio de los medicamentos. Esta situación es suficiente para exigir una acción regulatoria. Los EA son agravios a la salud que pueden surgir durante el tratamiento con un producto farmacéutico, los cuales, durante el período de poscomercialización del medicamento, pueden requerir un aumento significativo de cuidados de salud y resultar en lesiones innecesarias para los pacientes, muchas veces fatales. Por lo tanto, el hallazgo anticipado de EA durante el período de poscomercialización es un objetivo primordial del sistema de salud. Algunos países cuentan con sistemas de vigilancia farmacológica, responsables de la recogida de informes voluntarios de EA durante la poscomercialización, pero algunos estudios ya demostraron que, con la utilización de las redes sociales, se puede conseguir un número de informes mayor y más rápido. El objetivo principal de este proyecto es construir un sistema totalmente automatizado que utilice Twitter como fuente para encontrar nuevos EA y ya conocidos, además de realizar un análisis estadístico de los datos obtenidos. Para tal fin, se construyó un sistema que recoge, procesa, analiza y evalúa tweets en búsqueda de eventos adversos, comparándolos con datos de la Agencia Americana de Control de Alimentos y Medicamentos (FDA) y del estándar de referencia construido. En los resultados obtenidos, conseguimos encontrar nuevos eventos adversos y ya existentes, relacionados con el medicamento doxiciclina, lo que demuestra que Twitter, cuando es utilizado junto a otras fuentes de datos, puede ser útil para la farmacovigilancia.

An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851

BACKGROUND Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behaviour and provide novel ways to identify potential therapeutic targets and develop new drugs. Gene regulatory networks (GRN) are examples of in silico representation of interaction between regulatory genes and their targets. OBJECTIVES In this work, we update the MDR P. aeruginosa CCBH4851 GRN reconstruction and analyse and discuss its structural properties. METHODS We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process. FINDINGS Our result is a GRN with a greater number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa. MAIN CONCLUSIONS Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.

O uso do Twitter como minerador de eventos adversos de medicamentos de combate à malária: o caso da doxiciclina / El uso de Twitter como localizador de eventos adversos con medicamentos de combate a la malaria: el caso de la doxiciclina / Mining in Twitter for adverse events from malaria drugs: the case of doxycycline

Durante o período de pós-comercialização, quando medicamentos são usados por grandes populações e por períodos de tempo maiores, eventos adversos (EA) inesperados podem ocorrer, o que pode alterar a relação risco-benefício dos medicamentos o suficiente para exigir uma ação regulatória. Eventos adversos são agravos à saúde que podem surgir durante o tratamento com um produto farmacêutico, os quais, no período de pós-comercialização do medicamento, podem requerer um aumento significativo de cuidados de saúde e resultar em danos desnecessários aos pacientes, muitas vezes fatais. Portanto, o quanto antes, a descoberta de EA no período de pós-comercialização é um objetivo principal do sistema de saúde. Alguns países possuem sistemas de vigilância farmacológica responsáveis pela coleta de relatórios voluntários de EA na pós-comercialização, mas estudos já demonstraram que, com a utilização de redes sociais, pode-se conseguir um número maior e mais rápido de relatórios. O objetivo principal deste projeto é construir um sistema totalmente automatizado que utilize o Twitter como fonte para encontrar EA novos e já conhecidos e fazer a análise estatística dos dados obtidos. Para isso, foi construído um sistema que coleta, processa, analisa e avalia tweets em busca de EA, comparando-os com dados da Agência Americana de Controle de Alimentos e Medicamentos (FDA) e do padrão de referência construído. Nos resultados obtidos, conseguimos encontrar EA novos e já existentes relacionados ao medicamento doxiciclina, o que demonstra que o Twitter, quando utilizado em conjunto com outras fontes de dados, pode ser útil para a farmacovigilância.

Durante el período de poscomercialización, cuando grandes poblaciones consumen medicamentos durante períodos más prolongados de tiempo, se pueden producir eventos adversos (EA) inesperados, lo que puede alterar la relación riesgo-beneficio de los medicamentos. Esta situación es suficiente para exigir una acción regulatoria. Los EA son agravios a la salud que pueden surgir durante el tratamiento con un producto farmacéutico, los cuales, durante el período de poscomercialización del medicamento, pueden requerir un aumento significativo de cuidados de salud y resultar en lesiones innecesarias para los pacientes, muchas veces fatales. Por lo tanto, el hallazgo anticipado de EA durante el período de poscomercialización es un objetivo primordial del sistema de salud. Algunos países cuentan con sistemas de vigilancia farmacológica, responsables de la recogida de informes voluntarios de EA durante la poscomercialización, pero algunos estudios ya demostraron que, con la utilización de las redes sociales, se puede conseguir un número de informes mayor y más rápido. El objetivo principal de este proyecto es construir un sistema totalmente automatizado que utilice Twitter como fuente para encontrar nuevos EA y ya conocidos, además de realizar un análisis estadístico de los datos obtenidos. Para tal fin, se construyó un sistema que recoge, procesa, analiza y evalúa tweets en búsqueda de eventos adversos, comparándolos con datos de la Agencia Americana de Control de Alimentos y Medicamentos (FDA) y del estándar de referencia construido. En los resultados obtenidos, conseguimos encontrar nuevos eventos adversos y ya existentes, relacionados con el medicamento doxiciclina, lo que demuestra que Twitter, cuando es utilizado junto a otras fuentes de datos, puede ser útil para la farmacovigilancia.

During the post-marketing period, when medicines are used by large population contingents and for longer periods, unexpected adverse events (AE) can occur, potentially altering the drug's risk-benefit ratio enough to demand regulatory action. AE are health problems that can occur during treatment with a pharmaceutical product, which in the drug's post-marketing period can require a significant increase in health care and result in unnecessary and often fatal harm to patients. Therefore, a key objective for the health system is to identify AE as soon as possible in the post-marketing period. Some countries have pharmacovigilance systems responsible for collecting voluntary reports of post-marketing AE, but studies have shown that social networks can be used to obtain more and faster reports. The current project's main objective is to build a totally automated system using Twitter as a source to detect both new and previously known AE and conduct the statistical analysis of the resulting data. A system was thus built to collect, process, analyze, and assess tweets in search of AE, comparing them to U.S. Food and Drug Administration (FDA) data and the reference standard. The results allowed detecting new and existing AE related to the drug doxycycline, showing that Twitter can be useful in pharmacovigilance when employed jointly with other data sources.

Big Data e Nuvens Computacionais: Aplicações em Saúde Pública e Genômica / Big data and cloud computing: Applications in Public Health and Genomics / Big Data y Cloud Computing: Aplicaciones en Salud Pública y Genómica

Big Data é um termo utilizado para descrever conjuntos de dados cuja captura, armazenamento, distribuição e análise requerem métodos e tecnologias avançadas devido a qualquer combinação de seu tamanho (volume), a frequência de atualização (velocidade) e diversidade (heterogeneidade). Este artigo apresenta uma revisão bibliográfica sobre aplicações de Big Data em saúde pública e em genômica. São descritos diversos exemplos, e alguns desafios tecnológicos relacionados com a análise destes dados são identificados. Também é discutida a utilização de nuvens computacionais no processamento de Big Data. No nosso ponto de vista, a nuvem computacional é uma plataforma adequada para o processamento de grandes volumes de dados, e pode ser usada também em diversas aplicações relacionadas à saúde pública e genômica. Diversos trabalhos disponíveis na literatura e citados neste artigo corroboram esta visão.

Big Data is a term used to describe data sets whose capture, storage, distribution and analysis require advanced methods and technologies due to any combination of its size (volume), the update frequency (speed) and diversity (heterogeneity). This paper presents a literature review of Big Data applications in public health and genomics. Several examples are described, and some technological challenges related to the analysis of these data are identified. The use of computational clouds for Big Data processing is also discussed in this paper. In our view, the cloud is an appropriate platform for the processing of large volumes of data, and it can be used in several applications related to public health and genomics. Several studies available in the literature and cited in this paper corroborate this view.

Big Data es un término usado para describir conjuntos de datos cuya captura, almacenamiento, distribución y análisis requieren métodos y tecnologías avanzadas, debido a una combinación de su tamaño (volumen), la frecuencia de actualización (velocidad) y la diversidad (heterogeneidad). Este artículo presenta una revisión de la literatura de aplicaciones Big Data en la salud pública y la genómica. Se describen varios ejemplos, y algunos de los desafíos tecnológicos relacionados con el análisis de estos datos se identifica. También discute es el uso de nubes computacionales en el procesamiento de grandes volúmenes de datos. En nuestra opinión, la plataforma de computación en la nube es adecuado para el procesamiento de grandes volúmenes de datos, y también puede ser utilizado en diversas aplicaciones relacionadas con la salud pública y la genómica. Varios estudios disponibles en la literatura y citados en este artículo corroboran esta opinión.