1- Scientific context and project objectives

The project involves equipping Inserm Unit 484 with an information system intended to set up a “Promotology” platform with the aim of studying the regulating sequences of genes. Such a platform would enable gene regulations to be analysed in different cell contexts and therefore gene targets to be sought in different diseases. The unit would use this platform to develop a cancer prevention strategy, eventually in view of developing new therapies. The procedure is as follows: - construct transcript regulation models in promoting sequences of over-expressed genes in the cancer cell, identify co-regulated genes by screening biological resource centres, - analyse the expression of genes identified through a comparison with data obtained from biochips. The expression of genes identified in silico would subsequently be confirmed by molecular biology technology, such as quantitative RT-PCR, Western blotting and RNA interference.

2- Project description

Several biological resource centres need to be consulted to construct regulation models. Using a query system and filtering tools, relevant information only is extracted and saved in the information system. After acquiring this information, it is transferred via a pre-established processing chain. All of the data is then compared with information from other biological and bioinformatics experiments. This process is carried out according to different protocols described by specific sets of parameters which implement statistical methods and inter-database screening tools. The project involves developing several modules, including: a database for saving parameters, protocols and the results of analyses carried out on the platform. A gene expression database from DNA chips. The base model will be imported as much as possible from standard models of the regional biomedical information system so as to keep the structures the same. A metabolic database for saving metabolic pathways involving the target genes. A software platform for handling and processing data. With this, it will be possible to send complex queries to the information system. It will contain all data processing in particular. These tools exist or are based on known algorithms. They have already been tested and validated by the scientific community and/or manufacturers and, as such, setting them up is not an innovation in itself. However, their simultaneous use within an information system is not yet possible. A data management platform to manage data flow between the various structures of the information system.

3- Expected results

This information system is being developed as part of a policy to enhance basic knowledge of how cells work so as to use and transfer this knowledge in the medical field for the development of new therapies. It seems increasingly clear that one of the future methods of diagnosis and therapy is tied in with the development of transcriptome technologies which should shed light on and identify the causes of cancer through gene expression studies. The information system is designed to acquire and process multiple data rapidly as well as to facilitate data distribution. In addition, this platform, which is unique in Auvergne, will make it easier to share biomedical techniques and skills and to forge links between teams working on the same subject, at different levels of technological transfer and processing. More generally, in the context of point 7.2 of the document describing the ex programme E-nnovegne and more precisely the creation of a biomedical resource centre, this programme is part of the more extensive medical research platform of the university hospital centre, the Jean Perrin Centre, the Blaise Pascal and Auvergne Universities and the French National Institute for Agricultural Research (INRA), comprising Inserm Units 384 and 484, the Inserm Clinical Investigation Centre (CIC), the Clinical Pharmacology Centre (CPC), the Pain Treatment and Assessment Centre (CETD), the Cancéropole, the National Reference Centre for Leucodystrophy Prevention, the protist biology laboratory, the small animal imagery platform and INRA’s metabolome platform. The purpose is to standardise and professionalise data exchange between the various research bodies, whether they be public or private.

LifeGrid, the regional information system