By Jim Shrine

Quark Biotech Inc. is applying its gene discovery technology treatments for stroke, in a $19 million collaboration with Fujisawa Pharmaceutical Co.

The deal is Quark¿s second major collaboration with a Japanese partner in the past six months. Last fall, the San Ramon, Calif.-based company signed a deal with Sankyo Co. Ltd., of Tokyo, to study gene responses and identify drug candidates for Type II diabetes. The $19 million deal with Osaka-based Fujisawa includes research and milestone components, said Rami Skaliter, Quark¿s vice president of research and development. There also is a royalty element and a provision in which Quark could get some marketing rights in the U.S. and Europe, he said.

¿The main focus is to sort out the genes and find those that are important, and the cause of the pathology,¿ Skaliter said of the company¿s approach. ¿Specifically [in this case], we¿re looking for genes with neuroprotective activity. This is a new area for us.¿

Privately held Quark¿s main research facilities are in the Weizmann Science Park, in Nes-Ziona, Israel. It also has facilities in the San Francisco and Chicago areas. The company was founded in 1994.

In Cancer Deal With Perkin-Elmer

Quark¿s technologies are designed to focus on and identify small numbers of critical genes that are targets for the specific area being researched. The technologies include differential expression profiling that uses DNA chips and RNA probes, and functional profiling, as well as bioinformatic algorithms and statistical correlation analysis. The company said the methods combine to allow for the discovery of the critical genes involved in a pathology and a ¿filtering¿ system that isolates only those suitable for drug development.

¿We have streamlined our technologies to really get to the bottom-line genes, the ones that have the major impact on the pathology itself,¿ Skaliter said. ¿Another thing that distinguishes us is the way we have integrated the technologies. Many companies have isolated or different technologies, but none has the width of our technology platform.¿

The company said its differential expression profiling detects minor changes in the pattern and abundance of gene and protein expression in diseased tissue, which results in detailed information regarding the regulation of the differentially expressed gene and the localization of the protein encoded by it.

The high-throughput functional profiling is based on a knockout technique to expose genes responsible for the particular phenotype.

Quark also has a collaboration with Perkin-Elmer Corp., of Norwalk, Conn., in which the companies are developing a diagnostic for the ATM gene, which may relate to predisposition to certain cancers, Skaliter said. A product is in early clinical testing, he added.