Using Pharmacogenomic Databases for Discovering Patient-Target Genes and Small Molecule Candidates to Cancer Therapy.

With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics. We briefly explain how to submit a query to cancer genome databases to predict which genes are significantly altered across several types of cancers using CBioPortal. Moreover, we describe how to identify clinically available drugs and potential small molecules for gene targeting using CellMiner. We also show how to generate a gene signature and compare gene expression profiles to investigate the complex biology behind drug response using Connectivity Map. Furthermore, we discuss on-going challenges, limitations and new directions to integrate molecular, biological and epidemiological information from oncogenomics platforms to create hypothesis-driven projects. Finally, we discuss the use of Patient-Derived Xenografts models (PDXs) for drug profiling in vivo assay. These platforms and approaches are a rational way to predict patient-targeted therapy response and to develop clinically relevant small molecules drugs.

Geographical Distribution of Access to Healthcare in Patients Diagnosed with Hypospadias / Distribución geográfica del acceso a la asistencia sanitaria en pacientes con diagnóstico de hipospadias

Objective Hypospadias is a congenital disease of unknown etiology involving multiple epigenetic, genetic, and endocrinological factors. It is a highly incapacitating condition. Its surgical management is one of the most frequent surgical procedures done by pediatric urologists. Furthermore, the geographical distribution and healthcare access is limited in Colombia. The Colombian Ministry of Health has consolidated a nationwide registry called Integrated Social Protection Information System (SISPRO, in the Spanish acronym) to collect comprehensive information on the use and frequency of resources associated with health care in Colombia. The aim of the present study was to analyze the number of cases reported between 2014 and 2018 and the geographical distribution of access to healthcare of patients with hypospadias in Colombia. Methods An observational, retrospective study of hypospadias in Colombia, 2014­ 2018, was performed using data extracted from the Individual Health Records System (RIPS) in SISPRO. Satscan, version 9.6 was used to perform a distribution analysis of the georeferenced population using a Poisson model. To visualize the results, the software projected the result onto a Google Earth map. Results Between January 2014 and December 2018, a total of 8,990 cases of hypospadias were evaluated in Colombia. The geographical distribution in the national territory has areas with high evaluation rates. On average, the departments in which the majority of cases were evaluated during the study period were Bogotá, D.C., Antioquia, and Valle del Cauca (2,196, 1,818 and 1,151 cases, respectively). The statistical analysis of the space exploration (►Fig. 1) identified the area with the highest concentration of cases (red) and the areas in which the lowest number of patients was evaluated (blue). The geographical distribution showed increasing trends in areas near the center of the country, especially in the cities of Bogotá, Cali, Ibagué, and Pereira. Conclusion There is a greater concentration of cases evaluated in the center of the country, where the cities with better access to subspecialized medical care are located. This highlights inequalities in health services and the opportunity for surgical care among regions of the country. If we consider that the prevalence rates of hypospadias remain stable, 87% of the patients with hypospadias will not be evaluated by a subspecialist.

Objetivo Hipospadias es una enfermedad congénita de etiología desconocida que involucra múltiples factores epigenéticos, genéticos y endocrinológicos. Es una condición sumamente incapacitante. Su manejo quirúrgico es uno de los procedimientos quirúrgicos más frecuentes realizados por urólogos pediátricos. Además, la distribución geográfica y el acceso a la atención médica son limitados en Colombia. El Ministerio de Salud de Colombia ha consolidado un registro a nivel nacional denominado Sistema Integrado de Información de Protección Social (SISPRO) para recopilar información integral sobre el uso y frecuencia de los recursos asociados a la atención de la salud en Colombia. El objetivo del presente estudio fue analizar el número de casos notificados entre 2014 y 2018 y la distribución geográfica del acceso a la atención médica por los pacientes con hipospadias en Colombia. Métodos Se realizó un estudio observacional y retrospectivo de hipospadias en Colombia, 2014-2018, utilizando datos extraídos del Sistema de Registros Sanitarios Individuales (RIPS) en SISPRO. Se usó Satscan, versión 9.6 para realizar un análisis de distribución de la población georreferenciada usando un modelo de Poisson. Para visualizar los resultados, el software proyectó el resultado en un mapa de Google Earth. Resultados Entre enero de 2014 y diciembre de 2018, se evaluaron un total de 8.990 casos de hipospadias en Colombia. La distribución geográfica en el territorio nacional tiene áreas con mayor concentración de la atención de pacientes con hipospadias, al igual que áreas sin atención de esta condicion. En promedio, los departamentos donde se evaluaron la mayoría de los casos durante el período de estudio fueron Bogotá, D.C., Antioquia, y Valle del Cauca (439.2, 363.6, y 230.2, respectivamente). El análisis estadístico de la exploración espacial ([Figura 1]) identificó el área con la mayor concentración de casos (rojo) y las áreas donde se evaluó el menor número de pacientes (azul). La distribución geográfica mostró tendencias crecientes en áreas cercanas al centro del país, especialmente en las ciudades de Bogotá, Cali, Ibagué y Pereira. Conclusiones Existe una mayor concentración de casos evaluados en el centro del país, donde se encuentran las ciudades con un mejor acceso a atención médica subespecializada. Esto pone de relieve las desigualdades en el acceso a los servicios de salud y la oportunidad de atención quirúrgica entre las regiones del país. Si consideramos que las tasas de prevalencia de hipospadias permanecen estables, aproximadamente el 87% de los pacientes con hipospadias no serán evaluados por un subespecialista.

Advances in the integration of optical and mass spectrometry molecular imaging technologies: from omics data to molecular signature discovery.

Many molecular mechanisms in complex biological processes of diseases cannot be fully understood without direct visualization. In the last decades, advances in imaging principles and technologies have expanded our ability to capture and analyze the morphology of tissues and cells' components on conventional widefield optical and fluorescence microscopies and their derivatives confocal and multiphoton fluorescence laser-scanning microscopes, as well as transmission electron microscopes. Innovative imaging technologies are now emerging for constructing fine structural features, precise localization and the dynamic interplay of single and macromolecular assemblies that drive cell growth, differentiation and cell death as well as stromal and chromatin remodeling within many cellular context. The newer super-resolution microscopies capture images with unprecedented sensitivity and clarity allowing the exploration of interactions between individual molecules with a distance resolution as low as 20 nm. But these techniques are not robust enough to quantitate molecules on a genome-wide scale. Mass spectrometry imaging is a high-throughput chemical imaging technique for the identification, quantitation and distribution of proteins, lipids and chemical metabolites at picomol level within a single-cell and complex multicellular tissue. Here we provide an overview on imaging instrumentations and computational platforms to store, data mining, analyze and retrieving genomic, proteomic and immunohistochemistry digital image information which are available for multilevel academic-private collaborations. The expansion of these data sets will lead to a merge picture from it we will retrieve knowledge for more rational-design systems to basic and clinical research in near future.