By Martha Downs
Small Times Correspondent
Aug. 20, 2001 — The prospect of making sense out of the human genome has spawned a dizzying array of tiny tools. A blizzard of press releases and scientific reports touts a series of high-throughput methods that would make Henry Ford proud.
The latest, announced recently by scientists at Yale
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| Thousands of protein samples are spotted on a nickel-coated slide in figure A. Figure B is an enlarged image of one of the blocks. This protein chip promises to help scientists make sense of the human genome by speeding up analysis of proteins, which carry out genetic instructions. |
One of the scientists, Michael Snyder, is so excited by the breakthrough’s commercial possibilities that he’s co-founding a company to manufacture and market the proteome chip — Protometrix Inc., to be based in Guilford, Conn.
The acting president of Protometrix, Michael Sherman, said the company plans to play an important role in the emerging field of functional proteomics, or the study of what proteins really do.
Basically, here’s the science behind the company:
Knowing the identity of genes is only the first step in understanding how an organism functions — or how it fails. DNA doesn’t act alone. Even as the U.S. government’s Human Genome Project and the private Institute for Genomic Research in Rockville, Md., raced to complete their own maps of the human genome, scientists cautioned that they would need to know which genes were actually expressed and which proteins produced to have any hope of fulfilling the promises made on behalf of this vast endeavor.
If DNA is the playbook for making life, then RNA is like the quarterback. RNA passes instructions to the real players: proteins, which get things done in the body. Most diseases are caused by proteins that are underproduced, overproduced or just don’t work right. Most drugs are proteins, too. So, knowing which instructions get passed out is important, but it doesn’t tell you which players really get tackled and who gets their hands on the ball.
Based on the instructions carried in about 30,000 genes, the human body produces at least 100,000 proteins. Right now, medical science can assign functions to only about one fifth of them. That’s a little like trying to follow a football game where sixteen of the players are invisible.
Gene expression microarrays, known as gene chips or DNA chips, let scientists listen in on the quarterback’s huddle. Using gene chips, researchers can tell what instructions are being passed out to the players.
Proteome chips, on the other hand, are more like an announcer’s play-by-play. Once the cellular machinery receives instructions from the DNA, proteome chips will be able to tell researchers which proteins were produced in what forms and which other molecules they bind.
Gene chips consist of glass slides, spotted with neat rows of nanoliter-sized dots of genetic material. Analogous to a DNA chip, Snyder’s proteome chip carries thousands of nanoliter-sized dots of proteins, primed to react with any compound the researchers choose.
A new variation even bears a thin layer of silicone elastomer, dubbed the ProtoWell, perforated with thousands of tiny reaction wells, to better control each interaction. The chip lets researchers examine 6,000 interactions in the same time it used to take to look at just a handful.
Sherman, the company’s acting president, said Protometrix will play three roles in the industry:
- First, laboratory researchers could buy targeted chips with up to a few thousand proteins for their own research.
- Second, Protometrix would provide screening services, using chips with up to 100,000 compounds that require sophisticated robotics to run.
- Third, they anticipate that the software and information resources they are developing will be valuable to researchers at academic labs, pharmaceutical companies and biotech firms.
Backed by the venture capital firms of Collinson Howe & Lennox and Orbimed, Protometrix is setting up independent research and development facilities this month in Guilford. After a complete analysis of the yeast proteome, the company plans to move onto the much larger human proteome, as well as analyzing protein function in infectious bacteria and fungi. Snyder said he hopes to complete a human proteome chip within three years.
Of course, Protometrix isn’t the only player on this field. Several biotech companies, including Ciphergen Biosystems Inc. of Freemont, Calif., Molecular Staging Inc. of New Haven, Conn., and Large Scale Biology Corp., based in Vacaville, Calif., have developed protein chips that detect a targeted set of proteins by using antibodies.
So far, though, Snyder’s lab is the first to put nearly all the proteins from an organism onto one piece of glass or plastic. Snyder’s approach is more useful for examining protein interactions, while antibodies are better at detecting which proteins are there.
A similar method is used to make both gene chips and proteome chips. Researchers isolate or synthesize thousands of stretches of DNA or proteins. Then they spot these “probes” onto a slide, in very precise rows, resulting in many thousands of tiny spots precisely aligned across the surface of one microscope slide. With the help of genetically engineered florescent tags, every spot that binds with a partner will light up.
These methods for DNA and RNA detection have been perfected at companies like Affymetrix of Santa Clara, Calif., Nanogen Inc. in San Diego and Caliper Technologies Corp. in Mountain View, Calif., but a similar method of high-throughput detection for proteins has eluded researchers until now.
One of the first tasks Protometrix will tackle with the new chip is to find out which of the 5,800 yeast proteins bind to one another. That information alone won’t determine each protein’s function, but it will narrow the possibilities considerably.
“I find it terribly exciting,” said Harvard Medical School biochemist Stuart Schreiber, “It’s a real glimpse of what we’re going to be able to do with proteomes in the future.” Schreiber published a proof-of-concept paper this spring in the journal Science, in which he described laying down many copies of three proteins on the same chip and demonstrating that they reacted reliably with known partners.
COMPANY’S SYSTEM FOCUSES THE SEARCH
If the information produced by gene chip and protein chip technology seems daunting, that’s because it is. “In my mind, there’s no such thing as too much information,” Snyder said. He may be right, but sometimes it helps to know where to look first.
One way to focus the search for gene functions is to watch what mutant organisms do under a wide range of conditions.
Gene chips vary genetic information under one set of ideal conditions. A new system put out by Biolog Inc., of Hayward, Calif., allows researchers to examine simultaneously the way one type of cell functions under thousands of different environments.
The technique can integrate functions like cell growth, nutrition and stress by measuring cellular respiration. Taking one simple measure under many different circumstances gives the researchers clues to what a gene does, telling them where to focus more effort.
A single gene can affect a huge number of processes, but it’s hard to sort out which of them really matter, said Barry Bochner, Biolog chairman and vice president for research and development. Doing the same comparison using gene expression arrays, a geneticist might see that 300 RNAs have gone up, most by a little, a few by a lot, and 200 others have gone down. The researcher won’t necessarily know which of those are important. “Because we’re measuring at the cellular level, if we see a change, we know the cell has noticed it,” Bochner said.
Biolog is beginning to produce the arrays in a floppy disk-sized microcard format that uses tiny channels allowing only one-way flow. A technician can inoculate a whole card, containing more than 300 wells, with one push of a syringe, but the device is still large enough that the results can be read visually. That’s an advantage for small research labs and for NASA, which contracted Biolog to develop tests to monitor the microbial population of space-going hydroponic gardens.
For now, the arrays are optimized to grow bacteria and fungi. Paradigm Genetics, in Research Triangle Park, N.C., has used them to zero in on gene function in the rice blast fungus, a major crop disease. Knowing which genes are crucial to the fungus’ survival and ability to infect plants brings them one step closer to a strategy for defeating it.