The Islet Regulome Browser, developed by IGTP scientists, brings genomic data to life for diabetes researchers
The paper "Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes" published in Nature Genetics on Friday is the result of work carried out by an International team that includes Dr Lorenzo Pasquali and Mireia Ramos-Rodríguez of the Endocrine Regulatory Genomics Research Group at the Germans Trias i Pujol Research Institute and the Josep Carreras Leukaemia Research Institute. Pasquali's group has provided their tool, the Islet Regulome Browser, which allows non-bioinformaticians to visualize and use all the data collected in this study. The work brings personalized medicine for type 2 diabetes a little closer.
Type 2 diabetes affects more than 400 million people worldwide and is an important public health issue in most of the world. People with type 2 diabetes cannot control the levels of available sugar in their blood, thus needing medication to keep normal blood sugar levels and are at very high risk of deadly complications. Sugar levels in the blood are controlled by tissues in the pancreas called the "islets of Langerhans, which is made up of specialized cells." Failure of these cells is key to the development of type 2 diabetes. To find out more about the risk of developing type 2 diabetes and mechanisms of the disease an international team of researchers are examining the genome of the cells that make up the islets of Langerhans.
"Data is very difficult to handle and interpret," Pasquali tells us. "Modern research generates huge amounts of data, but you need technological tools to integrate it and specialised knowledge to interpret it." The group's Islet Regulome Browser is specifically designed to access and display data obtained from islets of Langerhans, including the genetic and genomic structural information that is relevant for type 2 diabetes. For this paper, the group included the data from the research and implemented new visualizations that make it accessible for diabetes researchers all over the world who wish to consult it.
Given the large amount of information about the DNA structure and the genetic code of cells available, it is difficult for doctors and researchers who are not trained in specialized biological computing skills, or bioinformatics, to interpret and use such data. It is publicly available, but usually in unprocessed, difficult to use formats. This is where the Islet Regulome Browser, developed by Pasquali's team comes in. A professional can use the on-line web at www.isletregulome.com to explore the genome through an interactive webpage interface. The browser converts complex data into plots, graphics and tables, which are much easier to consult and download for researchers and health professionals working on diabetes. The graphics present the information about genetic code, variants associated with diabetes, 3D chromatin structure and interactions in a clear and visual way.
In this new study, published in Nature Genetics, a team of scientists lead by Jorge Ferrer (Centro de Regulacio Genomica, Ciberdem, and Imperial College) created a tridimensional map of the genome in the cells composing the islets of Langerhans. The map shows how regions of the genome with DNA variants associated with type 2 diabetes, far from any gene in conventional, linear maps, are actually in physical contact with genes that play an important role in insulin-producing cells, which may be dysfunctional in type 2 diabetes . These studies, therefore, allow the identification of genes that underlie the onset of type 2 diabetes. Knowledge of the genetic variations in these areas will provide information on who is susceptible to developing diabetes. The Islet Regulome Browser will make this process quicker and easier.