Oxysterol metabolism and regulation presented as a SBGN diagram

Abstract

In the post genomic era, the understanding of the wealth of data provided by high throughput technologies has required a new perspective on cell metabolism, which is then shifted from a reductionist view of the past to a holistic and quantitative approach. Indeed, a major challenge biologists are facing is to integrate the large datasets available. To tackle it, a novel area of biology called System Biology has been settled. Further, despite diagrams and cartoons have been extensively used in biology to explain cellular phenomenon, to date there are no standard notations recognized by all scientific communities. Now, as the necessity to manage this richness of data has become as pressing as ever, a standard language needs to be defined. For this purpose the System Biology Graphic Notation (SBGN) has been proposed as a good answer to this issue. Its remarkable simplicity and consistency makes possible to be easily understood by biologists and also to be processed by machines, in order to make simulations and predictions. Cholesterol is a well-studied subject as it is an essential component of cellular membranes and a starting point for the biosynthesis of steroid hormones and Vitamin D. Additionally, its oxidation leads to a class of compounds named oxysterols which carry out diverse, valuable functions: they occur as bile acid intermediates, as cholesterol transporters and they are also deemed to have a role in regulating cholesterol homeostasis. In this thesis a representation of oxysterols metabolic pathways is proposed, using the SBGN notation. To validate the interaction showed an extensive literature research and database mining has been performed. Furthermore, a discussion of their involvement in several major human diseases is presented.