Computer chips tweaked to aid disease research

Stanford researchers have collaborated with Intel to study the autoimmune disease lupus using short pieces of a disease-associated protein on silicon chips much like those found in computers.

Though primarily designed for research, the technique holds promise to improve diagnosis of multiple diseases and to quickly determine the most effective drug for a particular patient. Its ability to help researchers understand how proteins interact in the body also could help speed drug development, according to a Stanford article.

"When I see patients in the clinic right now, I may know they have arthritis, but I don't know which of the 20 or 30 types of the disease they have," said associate professor of medicine Paul (P.J.) Utz, M.D. Finding out can take days or weeks. "Now we can measure thousands of protein interactions at a time, integrate this information to diagnose the disease and even determine how severe it may be. We may soon be able to do this routinely while the patient is still in the physician's office."

Intel developed the chips, which the researchers call Intel arrays, using short segments of biological proteins, called peptides, on silicon wafers. The Stanford researchers then used the chip to analyze thousands of protein interactions simultaneously. The researchers previously used a similar technique with proteins arrayed on glass. Silicon is much less sticky to proteins than glass, allowing researchers to skip some steps meant to account for that. Silicon also allows the peptides to be placed closer together and does not fluoresce, making detection easier.

In the study, the researchers looked at nearly 9,000 combinations on the chip. They were able to identify patients with lupus who expressed high levels of antibodies against a particular protein or histone called 2B--those likely to require more intensive therapy, according to the abstract in Nature Medicine.

Other research is looking at protein interactions to help prevent drug side effects. Mount Sinai and the University of California, San Francisco have created computer models to predict adverse events.

Meanwhile, the Pentagon's research arm, the Defense Advanced Research Projects Agency (DARPA), recently awarded $17.8 million in grants in search of a 10-fold reduction in time and cost to create new medicines and materials. The creation of synthetic protein structures for research to speed development of new vaccines was among that call to action.

To learn more:
- here's the Stanford article
- read the abstract

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