Integración de la Bioinformática en la caracterización Clínica y Genómica de Retinitis Pigmentosa, Síndrome de Noonan y Síndrome de Retraso Mental Martin-Probs, en un mismo individuo. Reporte de un Caso / Integration of Bioinformatics in the Clinical and Genomic Characterization of Retinitis Pigmentosa, Noonan Syndrome and Martin-Probs Mental Retardation Syndrome, in the Same Individual. Case report

Introducción: El avance en las técnicas bioinformáticas ha permitido realizar acercamientos y mejoras en los diagnósticos clínicos, correlacionando genotipo ­ fenotipo y permitiendo el acercamiento a una terapia personalizada. Objetivo: Realizar mediante técnicas bioinformáticas, la caracterización molecular y de expresión génica de una paciente con manifestaciones clínicas (dismorfias, retraso en el desarrollo) de una enfermedad compleja (poligénica). Materiales y métodos: Se realizó la secuenciación de exoma completo a partir de una muestra de sangre periférica. Se analizaron los datos obtenidos mediante análisis in-sílico, utilizando programas como SIFT, Mutation Tester, UMD y Provean, para determinar la significancia clínica de variantes encontradas; además se usó programa GeneMania para determinar las interacciones génicas. Resultados:Se encontraron 3 variantes en los genes SEMA4A, PTPN11 y RAB40A, asociados a Retinitis pigmentosa 35, Síndrome de Noonan y Sindrome de retraso mental Martin-Probs, respectivamente; encontrando según los softwares predictores, en el primer caso un significado clínico aparentemente benigno, y en los dos últimos genes un significado clínico patogénico. El análisis de redes génicas reveló alteraciones en funciones biológicas como la señalización mediada por fosfatidilinositol, respuesta al factor del crecimiento fibroblástico, vía de señalización de neutrofina y la morfogénesis de vasos sanguíneo que permitieron explicar gran parte de la sintomatología observada. Conclusión: El análisis personalizado de las patologías complejas mediante el uso de la clínica, herramientas genómicas y bioinformaticas han permitido un avance significativo en las técnicas para el procesamiento y análisis de datos, beneficiando los estudios científicos que permiten el acercamiento a un correcto diagnóstico y adecuada consejería genética.

Introduction: Advances in bioinformatics techniques have allowed approaches and improvements in clinical diagnoses, correlating genotype - phenotype and allowing the approach to personalized therapy. Objective: In order to perform the molecular characterization and gene expression in a patient with complex clinical manifestations through bioinformatics techniques, complete exome sequencing was performed by a peripheral blood sample to a woman with facial dysmorphisms and developmental disorders. Material and methods: We analyzed the data obtained by in-silico analysis, using programs such as SIFT, Mutation Tester, UMD and Provean, to determine the clinical significance of the found variants and GeneMania program was used to determine gene interactions. Results: 3 variants were found in the genes SEMA4A, PTPN11 and RAB40A, associated with Retinitis pigmentosa 35, Noonan Syndrome and Mental Retardation Syndrome Martin-Probs, respectively; according to the predictive softwares, in the first case an apparently benign clinical meaning, and in the last two genes a clinical pathogenic meaning. The analysis of gene networks revealed alterations in biological functions such as signaling mediated by phosphatidylinositol, response to the fibroblastic growth factor, neutrophin signaling pathway and blood vessel morphogenesis that allowed us to explain a large part of the observed symptomatology. Conclusion: The personalized analysis of complex pathologies through the use of clinical, genomic and bioinformatic tools has allowed a significant advance in techniques for processing and analyzing data, benefiting scientific studies that allow the approach to a correct diagnosis and adequate genetic counseling.

Genes related to maintenance of autophagy and successful aging / Genes relacionados à manutenção da autofagia e envelhecimento bem-sucedido

ABSTRACT Considering aging as a phenomenon in which there is a decline in essential processes for cell survival, we investigated the autophagic and proteasome pathways in three different groups: young, older and oldest old male adults. The expression profile of autophagic pathway-related genes was carried out in peripheral blood, and the proteasome quantification was performed in plasma. No significant changes were found in plasma proteasome concentrations or in correlations between proteasome concentrations and ages. However, some autophagy- and/or apoptosis-related genes were differentially expressed. In addition, the network and enrichment analysis showed an interaction between four of the five differentially expressed genes and an association of these genes with the transcriptional process. Considering that the oldest old individuals maintained both the expression of genes linked to the autophagic machinery, and the proteasome levels, when compared with the older group, we concluded that these factors could be considered crucial for successful aging.

RESUMO Considerando o envelhecimento como um fenômeno em que há um declínio nos processos essenciais a sobrevivência celular, investigamos as vias autofágica e proteassômica em três grupos: jovens, idosos e longevos. O perfil de expressão dos genes relacionados à via autofágica foi analisado em sangue periférico, e a quantificação do proteassoma realizada em plasma. Não foram encontradas alterações significativas nas concentrações plasmáticas de proteassoma ou na correlação entre as concentrações de proteassoma e as idades. No entanto, alguns genes relacionados a autofagia e / ou apoptose foram expressos diferencialmente. Além disso, as análises de rede e de enriquecimento mostraram uma interação entre quatro dos cinco genes diferencialmente expressos e a associação desses ao processo transcricional. Considerando que os indivíduos longevos mantiveram tanto a expressão de genes ligados à maquinaria autofágica, quanto os níveis de proteassoma quando comparados aos idosos, concluímos que esses fatores poderiam ser considerados cruciais para o envelhecimento bem-sucedido.

“Preventing transform when sickness”——Regulating pre-metastasis niche to prevent tumor metastasis / 中草药

Metastasis is the leading cause of cancer-related death. Pre-metastatic niche formation is the contributing factor of tumor metastasis. Traditional Chinese medicine (TCM) has a curative effect on metastasis and cancer recurrence in clinic. Modern pharmacological studies have shown that China meteria medica (CMM) can inhibit tumor metastasis by affecting tumor secretion, preventing recruitment of immune suppressive cells, and influencing anti-inflammatory polarization of matrix components in certain tissues. The regulation of CMM has the characteristics of multi-target, minor effect, and bidirection, It may play a integrate role with multi-factor and minor effect in regulating tumor-related gene expression or gene-gene combination by influencing regulating tumor-related functional gene networks. This is consistent with the research strategy of taking signal transduction dynamic network as drug target. Therefore, the prevention and treatment of pre-metastatic niche formation via TCM is an effective research strategy. This review summarizes the current research progress on regulating pre-metastasis niche by CMM, and provides a theoretical basis for the future research of TCM to prevent tumor metastasis.

Gene networks as a tool to understand transcriptional regulation

Gene regulatory networks, or simply gene networks (GNs), have shown to be a promising approach that the bioinformatics community has been developing for studying regulatory mechanisms in biological systems. GNs are built from the genome-wide high-throughput gene expression data that are often available from DNA microarray experiments. Conceptually, GNs are (un)directed graphs, where the nodes correspond to the genes and a link between a pair of genes denotes a regulatory interaction that occurs at transcriptional level. In the present study, we had two objectives: 1) to develop a framework for GN reconstruction based on a Bayesian network model that captures direct interactions between genes through nonparametric regression with B-splines, and 2) to demonstrate the potential of GNs in the analysis of expression data of a real biological system, the yeast pheromone response pathway. Our framework also included a number of search schemes to learn the network. We present an intuitive notion of GN theory as well as the detailed mathematical foundations of the model. A comprehensive analysis of the consistency of the model when tested with biological data was done through the analysis of the GNs inferred for the yeast pheromone pathway. Our results agree fairly well with what was expected based on the literature, and we developed some hypotheses about this system. Using this analysis, we intended to provide a guide on how GNs can be effectively used to study transcriptional regulation. We also discussed the limitations of GNs and the future direction of network analysis for genomic data. The software is available upon request.

Progress in Gene Logic Networks / 生物化学与生物物理进展

As tremendous genomic data avalanches, exploring biological mechanism by data analysis and theory methods has become important for theoretical biology research. This method is significant for the study of complex gene functions and gene networks. Bowers used higher order logic relationships to decipher protein network organization, which is a systemic method called logic analysis of phylogenetic profiles (LAPP). LAPP is a data modeling and different from traditional computational methods. This computational approach identifies logic relationships of the elements (or components) in complex networks through the logic analysis of their expression data. The method can be used to infer functional relationships of two associated proteins to one another. It is important for discovering the new function mechanism of the protein. The clusters of orthologous groups (COGs) involved in a gene network usually are large groups and therefore LAPP is also an approach for complex gene logic networks. After the establishment of the gene logic network, it is convenient for the regulation of gene through the network. The method can used in many fields, such as species evolution, oncologic diagnosis and so on. LAPP was systematically described and analyzed and recent developments in methodologies and applications were highlighted. Some opinions of them were also given.