Proteomics: Beyond the Genome

IBM and MDS are building a giant database devoted to protein interactions. Here's a chat with the developer, who sees it as the next big thing in medicine

Now that the fanfare over completion of the map of human genes has died down, the hard work of making sense of the genome begins. Much of that work will revolve around what genes produce -- proteins. Proteomics, the study of interactions between proteins, is the key to understanding how our bodies stay healthy. Drug researchers consider a comprehensive catalogue of proteomics as the next Holy Grail in the genomic field.

This new research frontier has caught the attention of IBM (IBM ) and Toronto (Canada) life-sciences company MDS Inc. Through their joint venture, called Blueprint Worldwide, the companies have set up a free database of proteomics information in the hope of setting the standard for tracking such data.

The database picks up where the government-funded Human Genome Project's GenBank genomics database leaves off. A consortium of government institutes -- including the National Institutes of Health's National Center for Biotechnology Information, and the European Bioinformatics Institute -- have given the Blueprint database their stamp of approval.

The venture aims to be the "definitive, worldwide source" on proteomics data, according to MDS Proteomics. It will cost nothing for researchers to access, but MDS Proteomics will offer consulting services to drug companies and other researchers, who want a hand in making sense of the info, while IBM will use the venture to showcase its computers' abilities to crunch life-sciences data. "There is not a world standard for protein interactions," says Frank Gleeson, president and chief executive officer of MDS Proteomics. "Without such standards, the pace of scientific understanding is slowed down."

Genomics researchers, both private and public, have already been gathering and analyzing protein information. Though there are many databases and other resources available, Gleeson expects Blueprint's database will be widely used, since, like the Human Genome Project's database, it's a free resource. The company aims to eventually make money from developing proteomics-derived drugs.

In an interview with Amy Tsao, who covers biotechnology for BusinessWeek Online, Gleeson explained the importance of proteomics in the quest to develop better drugs. What follows are are edited excerpts from their conversation:

Q: Why is proteomics so important?


By understanding what proteins do and how they work together to achieve cellular function, we can get a better picture of how to intervene in disease, which occurs when proteins go wrong.

Q: How is genomics different from proteomics?


This is a continuum. Genomics doesn't neatly stop at some place and proteomics conveniently begin at another place.... The field of study devoted to identifying genes, discovering genes, and determining gene sequences has been labeled genomics. The field of understanding the functions of those genes, their correlation with a disease, [is] functional genomics.

To fully understand the variance of a gene, the number of proteins that any particular gene makes, the cell cycle under which genes make proteins, how they interact with one another, [that is] proteomics. Proteins are almost always targets for antibodies or small-molecule therapeutics, so proteomics is much closer to the disease state -- to where you want to be to treat disease more effectively.

Q: What is the state of the field?


It's an emerging field and it will stand on the shoulders of the gene-sequencing information. Now that we have genetic databases as a backdrop, we can build on that to start to understand what genes do, what proteins do, how disease occurs, and the molecular basis of disease.

Because of the wealth of data we already have and advances in super-computing, we anticipate proteomics will grow very rapidly. We would anticipate that building data sets of proteomic information, while much greater than genomic information data sets, will likely take less time because we have the foundation in place.

Q: What's the time frame to have a complete protein database?


Over the next five to 10 years, we believe the scientific world will advance the understanding of molecular function dramatically, so that our understanding of [the] disease process 10 years from now will be radically increased over what it is today. That's the practical embodiment of proteomics.

Q: Who are the big corporate players in proteomics now?


MDS is a world leader in functional proteomics -- in other words, rapidly determining the function of proteins. Others in the space include Myriad Proteomics (MYGN ), Britain's Oxford Glycosciences, Geneva Proteomics. Of course, Celera Genomics (CRA ) shouldn't be left off the list.

Q: When will we see proteomics-derived drugs in the marketplace?


I think we've already seen proteomics-based products enter the market, and in the next decade, we will see many, many more.

One might say a recent drug launched by Novartis (NVS ) -- Gleevac for leukemia -- is in some ways an indication...of what the future will hold for developing drugs that are very [specifically targeted]. The targets are very well understood and well characterized because of a refined understanding of the proteins involved in the disease...and the pathways that are affected.

Edited by Patricia O'Connell

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