BioWorld International Correspondent
LONDON - The proteins involved in one of the most important cellular pathways that can lead to human disease have been mapped in their entirety by researchers at Cellzome AG.
Using the same methods as they used for their previous study, which mapped the proteins of the yeast Saccharomyces cerevisiae, the team identified all the proteins interacting within a key pathway leading to inflammation.
The pathway begins with the pro-inflammatory cytokine tumor necrosis factor-alpha (TNF-alpha) stimulating its receptor on the cell surface and ends in the nucleus with activation of the transcription factor NF-kappaB, which turns on the transcription of many genes encoding proteins with roles in inflammation.
Numerous drug targets for diseases such as rheumatoid arthritis are likely to be identified as a result of the work. Researchers also will be able to discern where in the pathway known drugs work and which drugs are specific to the pathway.
Giulio Superti-Furga, senior vice president for biology at Cellzome, of Heidelberg, Germany, told BioWorld International: "This was a very satisfactory exercise. We have elucidated the entire pathway. We have recapitulated, in one go, almost everything that humankind has done toward understanding this pathway during the past 20 years."
Although parts of the pathway were known before, Superti-Furga said no one had previously managed such a comprehensive analysis of it. "We now know who speaks to whom, all the way from the cell membrane to the cell nucleus," he said.
One reason for publishing the paper was to establish the company's method as a means of dissecting protein pathways that are important in human diseases. "After we did our important study on yeast, everyone asked us if we could do it for humans," Superti-Furga said.
The team's paper is in the Jan. 25, 2004, Nature Cell Biology and is titled "A physical and functional map of the human TNF-alpha/NF-kappaB signal transduction pathway."
Cellzome, which has registered intellectual property rights over the reported work, has embarked on studying other human disease pathways. One of its projects has examined the pathway involved in processing amyloid-precursor protein, a reaction that is thought to play an important role in the onset of Alzheimer's disease. The company is looking for partners to work with them on as many as 25 specific disease pathways.
Superti-Furga and his colleagues aimed to understand all the interactions with the proteins that play a role in the TNF-alpha/NF-kappaB pathway. Proteins form complexes, which may contain tens of proteins, and those act sequentially to form "pathways."
"We took a functional proteomics approach, using TAP-mass spectrometry, which essentially allows you to fish' for the complexes that are built around the known elements of the pathway," Superti-Furga said. "We can then take these known elements, which are rather like signposts, and isolate them under physiological conditions, to identify the proteins associated with them."
As a result of the work, the team was able to identify 75 percent of all the proteins that have been implicated in the pathway. They also identified many proteins not previously known to be involved. The team carried out tests on many of those to confirm their involvement in the pathway. "We showed that 10 of these proteins were rate-limiting and essential to the operation of the pathway," Superti-Furga said.
The approach allows drug discovery teams to move from anecdotal research to a systems-based approach, he said.
"It means you now have a full complement of players, you know how they are hierarchically related to each other, and you also have data on which elements are essential for the process," he said.
"The next step," Superti-Furga said, "is to take chemicals that are of interest in that pathway, immobilize them, and, again with mass spectrometry, see what they bind to. You can identify chemical entities - these may even be known drugs - that are acting as anti-inflammatory agents, but where their mechanism of action is not understood, and find out which part of the pathway it works on. And you can take your own compound that you have screened against this pathway and obtain virtually a full understanding of the mechanism of its action, the drug's target and the way its target is causing its effect in the wider context."