Toward a Global Proteome

If mapping the entire human proteome isn't challenge enough, consider this: The Human Proteome Organization, created this past year, aims to coordinate the efforts of the many public and private groups moving into the proteomic field.1 HUPO president Samir Hanash hopes an April 29 meeting at the National Institutes of Health will solidify plans and collaborations to characterize all blood serum proteins, create a library of antibodies to every human protein, and put the data collected in a user

By Brendan Maher | April 15, 2002

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If mapping the entire human proteome isn't challenge enough, consider this: The Human Proteome Organization, created this past year, aims to coordinate the efforts of the many public and private groups moving into the proteomic field.¹ HUPO president Samir Hanash hopes an April 29 meeting at the National Institutes of Health will solidify plans and collaborations to characterize all blood serum proteins, create a library of antibodies to every human protein, and put the data collected in a user friendly database.

"We don't want to say that we will do the whole proteome in the next 18 months," says Hanash, a professor of pediatrics and communicable diseases at the University of Michigan. "That's impossible. But at the same time, it's not true that there's nothing you can do."

Industry groups have lofty aspirations as well as proprietary concerns. Myriad Proteomics proclaimed last year it would complete a map of every human protein-protein interaction by 2004.² Information-based biotechs are increasingly steering into pharmaceutical development making it imperative for them to patent newly generated data, a practice that might not mesh with the HUPO vision.

Complex Project, Complex Issues

HUPO hopes to succeed where many say the Human Genome Organization (HUGO) failed—in bringing together private and public interests. "HUPO has a shot of doing that if you recruit the right people and you show the right vision," says Leroy Hood, president and director of the Institute for Systems Biology in Seattle, who participated in early genomic efforts.

Some HUPO members say they hope the organization will foster collaboration and education programs and set standards, but not oversee or fund projects. "We don't want to come across as the organization that's driving proteomics and you're either in or you're out," says Emanuel F. Petricoin, codirector of the Food and Drug Administration-National Cancer Institute Clinical Proteomics Program. Nevertheless, he says, data must be shared. "If you're going to want to be included, then you're going to have to offer full data access," he says.

Some HUPO members from biotech companies say the rules should accommodate proprietary interests. Pierre Legrain, vice president of science and technologies at Hybrigenics, a Paris-based proteomics company and a member of HUPO's committee on informatics, says, "I think we would be very pleased to see people working with some of our data as soon as we've made patent applications." Patented data would be made available for research, Legrain says, but not for commercial applications.

Big pharmaceuticals, on the other hand, have long supported the creation of free immediate-access databases. "Traditionally, companies like Merck & Co. have had the attitude that they like the basic information to be out there," says Matthias Mann, professor of bioinformatics, University of Southern Denmark and chair of the HUPO informatics committee. Petricoin, HUPO treasurer, says concessions may have to be made: "It's what makes proteomics daunting."

A Consortium of Coalescence

Samir Hanash

Guidelines have yet to be hammered out, but North American, European, and especially Pacific Rim members are clamoring for them to be done quickly, Hanash says. HUPO, in its invitation to the late April meeting, has outlined five initiatives for discussion: Informatics, the plasma proteome, an antibody consortium, the nomination of cell types for full proteomic investigation, and the development of new technologies. Hanash says members hope these initiatives will catch the notice of NIH program administrators. The plasma proteome and antibody consortium are pilot projects that will determine the feasibility of comprehensive human proteomics studies. These projects may also deliver short-term rewards that Hanash says may help keep interest alive." Plasma would be an important joint project because it's relevant to so many activities," he says.

Many in basic research would welcome an antibody initiative. "Whenever ... we find 10 proteins involved in something, we have to send off for 20 peptides and 20 rabbits to be immunized," Mann says. "For all we know, 23 other labs may do the same thing ... that's clearly a duplication of effort." Hood says the effort to please all sides might be the hardest part. "How are you going to get strong-willed people that are going in a lot of different directions to see in what I would call an integrated vision?"

Brendan A. Maher can be contacted at bmaher@the-scientist.com

References
1. D. Steinberg, "Is a human proteome project next?" The Scientist, 15[7]:1 April 2, 2001.

2. D. Steinberg, "Industry group to map proteome," The Scientist, 15[8]:13 Apr. 16, 2001.