BORNHEIM, Germany ¿ A consortium of proteome researchers from academia and biotech companies in Germany received a three-year, EUR10.8 million (US$9.5 million) granted by the German Research Ministry.
The money is expected to fuel development of new methods in proteome analysis on the level of protein detection and separation and related bioinformatics, Josef Kellermann, of Martinsried-based Max Planck Institute for Biochemistry, told BioWorld International. He is one of the coordinators of the consortium.
The consortium¿s work includes a clinical program led by Wilex AG, of Munich, related to clinical trials involving renal cell carcinoma patients treated with Wilex¿s G250-antibody. The clinical program includes researchers from the University Hospital of Mainz, Germany.
¿We analyze the proteomes of tumor tissue resected from patients taking part in the trials,¿ Wilex CEO Olaf Wilhelm said. From there the researchers want to identify proteins that allow predictions of an individual patient¿s response to Wilex therapies.
Wilex expects to obtain first rights for drugs based on disease markers and new cancer targets developed in this program.
The consortium aims at developing methods that ¿can be applied on cell systems as well as on tissues,¿ Kellermann said.
Wilhelm said, ¿It¿s a challenge just doing proteome analysis of defined cell lines. But doing proteomics on tissue samples taken from individual patients is even more sophisticated.¿
Therefore, methods of sample preparation and processing, proteome analysis and the underlying bioinformatics must be validated thoroughly, he explained. The consortium is developing such methods and technology in parallel with the clinical program.
The consortium said it plans to develop methods of sample preparation using tissue from mouse models, which are being provided by GSF (National Research Center for Environment and Health), of Neuherberg, Kellermann said.
In addition, researchers from Munich University and Martinsried-based companies TopLab AG and Biomax Informatics AG aim to develop new technologies. These include mass spectroscopy and chromatography for analysis of proteomes.
Currently, such proteome analysis is done mainly by 2-dimensional gel electrophoresis, which separates proteins by charge and molecular weight. After electrophoresis the gels show characteristic samples of spots caused by stained proteins.
Definiens AG, of Munich, develops image-processing software to speed up automated evaluation of 2-D gels. ¿Our contribution is to provide a new high-throughput image analysis tool, which is able to handle [spot samples on gels resulting from] experiments designed on many different treatments,¿ Definiens¿ director of bioinformatics, Michael Alvers, said. Definiens was founded in 1995. It has its roots in remote sensing.