Scientists develop free web service for joint analysis of gene and metabolism work

The joint research team from Russia, USA, Canada, and Germany has developed a new web service called GAM (Genes And Metabolites) for the comprehensive study of biological processes in cells, the St. Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) said on Friday. The program identifies relations between changes in metabolism and genes, enabling for example a better understanding of functioning immune system cells or tumor. New insights gained by means of the new service could be applied to develop autoimmune diseases and cancer drugs.

"Our service is a great help for many biologists and immunologists dealing with the influence of metabolism on clinical changes. In previous studies, we have shown the high performance of the developed algorithm and confirmed the results of the program analysis experimentally. A large number of research groups asked us for the help, thus Alexey Sergushichev fr om ITMO University in Saint Petersburg, Russia has created a web service so as scientists from all over the world could easily apply the program by themselves," said project supervisor Maxim Artyomov, assistant professor at Washington University in St. Louis.

The GAM software compares the original data on metabolite concentrations and gene expression with databases providing description of most biological processes in a standard state. Then a network diagram is created, wh ere nodes represent the substances and edges are the pathways of their transformations during chemical reactions. For each node, the program defines the weight as an indicator of the metabolite significance in the overall process, depending on the deviation of the concentration from the norm. Thus, cell processes can be identified through the joint analysis of two states: reference (normal) one and the perturbed state influenced by an external factor.
Study of autoimmune and oncologic diseases

The GAM-service could be applied to study autoimmune pathologies involving the deactivation of the immune system while attacking healthy tissues. Such kind of imbalance in immune system function is determined both by metabolism, and by the (expression) of genes.

"Metabolic pathways incorporate enzymes catalyzing chemical reactions. The reactions cannot go without essential enzymes encoded by specific genes. Using our web service, one can analyze changes not only in metabolite concentrations, but also in gene expression. Thus, one could understand the mechanisms of cellular processes and identify key reactions in the course of various autoimmune diseases. In the future, it will assist the development of immune system regulators, for example, immune suppressors for the effective treatment of such pathologies as diabetes mellitus type I or chronic hepatitis B, which are caused by the immune system disorders," said Sergushichev.

The new development could be also useful for biologists and pharmacologists studying processes, which occur within cancer cells. Using the GAM service, one could construct an entire map of metabolic pathways in such cells and reveal mechanisms of tumor growth. In the previous study, the scientists by means of newly created algorithm have shown the inhibition of certain metabolic processes in cancer cells to be able to slowdown the tumor growth.

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