Scientific sleuthing

On the southern edge of the main campus, the university's health sciences complex throbs with a feverish energy: a swarm of students and staff come and go, patients and their visitors spill out on to the sidewalks, emergency vehicles scurry to and fro, construction cranes scar the skyline as creations of concrete, and steel and glass rise up to replace the tired structures of brick and wood that once claimed the ground.

From the steps of Athabasca Hall, basking lazily in the record-breaking heat of an early July day, the impassioned war on disease seems far away. But inside this building, the university's first home on campus and now part of the computing science complex, is the nerve centre of a project that could conceivably have a greater impact on the practice of medicine than anything else ever done on the University of Alberta. Or almost anywhere else, for that matter.

The initiative is called the Human Metabolome Project, and the idea behind it is extremely simple: to make it possible to identify the biochemical fingerprints of disease. Analogous to the marks left by loops and whorls of skin would be the signature traces of metabolites - those small molecules that result from the biochemical modification of chemical compounds in living organisms and cells - identified using nuclear magnetic resonance (NMR) spectroscopy.

To this end, the Human Metabolome Project has undertaken the identification, quantification, cataloguing and storage of all metabolites that can potentially be found in human tissues and biofluids (blood, urine, tears, etc.) at concentrations greater than one micromolar (a millionth part of a litre).

To date more than 800 metabolites have been identified, and it's expected that by the end of 2006 a total of 1,400 such compounds will have been characterized, quantified and archived into databases accessible through the Internet. In addition, pure samples of each metabolite will be preserved by storing them in freezers at a temperature of -80º C.

The motivating force behind the Human Metabolome Project is a U of A scientist whose relentless curiosity isn't confined by traditional disciplinary boundaries. As an undergraduate at the U of A, Wishart majored in physics. After earning two graduate degrees at Yale - in molecular biophysics and biochemistry - he returned to the U of A as a postdoctoral fellow wit-h the Protein Engineering Network of Centres of Excellence.

When he was ready for a continuing faculty position, despite lucrative offers from numerous suitors at other institutions, he decided to stay in his hometown and accept an appointment in the U of A Faculty of Pharmacy and Pharmaceutical Sciences, where he currently holds the Bristol Myers Squibb Chair in Peptide Metabolism.

He accepted his academic staff position a dozen years ago - not a long time by some measures, but ample time for Wishart, who now has joint appointments in the Departments of Computing Sciences and Biological Sciences, to establish himself as one of the university's premier scholars.

Wishart was only four years into his new academic posting when his current project took wing, and he has no difficulty recalling the seminal moment to which the Human Metabolome Project owes its existence. It occurred as Wishart was preparing to deliver a guest lecture about how NMR spectroscopy could be used to diagnose or monitor disease. He was scanning some of the more obscure literature on the subject when his attention was suddenly galvanized.

"Something just jumped off the page at me," he said. The object of his interest was an illustration showing how markedly the NMR spectrum generated from the blood of someone suffering from Fanconi's Syndrome (a rare kidney disorder) differed from that of a non-sufferer.

"It was immediately obvious how different it was," said Wishart, who was struck so forcibly by the illustration because a close relative of his had just been diagnosed with that very syndrome - but only after a decade of "bizarre tests and treatments."

"That got the wheels turning," said Wishart, who began thinking about the exciting opportunities for using NMR spectroscopy, with which he was extremely familiar, for disease diagnosis and monitoring. Ironically, the resulting Human Metabolome Project owes as much to what Wishart, with his broad and extensive scientific background, didn't know as to what he did.

"In our naivety of how it was supposed to be done, we started dealing with spectra differently," he said. While other labs interested in the NMR spectra of biofluids were looking at the spectra simply as amorphous shapes to be compared one to another, Wishart took his lab in another direction. "Our concept was, 'let's figure out what every single peak represents' - we didn't know that you weren't supposed to do it that way."

To enable his approach, Wishart devised some novel techniques that led to two patents and a spin-off company named Chenomx Inc., which exploits those techniques to develop software for NMR analysis of complex mixtures for broad application in life science technologies.

Once Wishart had the tools in place to dissect the spectra, identifying the compounds present and their quantity, he was faced with filling a massive void: there simply wasn't a good library of all the small molecules that might be encountered in human biological fluids or cells. "It was like trying to put together a jigsaw puzzle with pieces missing," he said. "The analogy would be a puzzle of 1,000 pieces missing 800."

The Human Metabolome Project is the attempt to find all those missing pieces and finally put the puzzle together into a coherent image. In many ways, it parallels the Human Genome Project, which was completed in a sort of first draft form in 2001 and finalized in 2003. That project was tasked with determining the sequence of all of the genes and all of the chromosomes in a human cell. That took about 12 years to complete and cost almost a billion dollars.

While the Human Metabolome project, which was launched in 2005, is a much more modest undertaking - its budget is nowhere near a billion dollars - it has the potential to change the way medicine is done. Testing for small molecules - in blood and urine particularly - is already an important part of medicine, but currently doctors rely on a small set of tests that focus on less than two dozen molecules.

"What metabolomics promises, is a list of some 2,500 molecules and the technology to potentially measure maybe 300 or 400 of those all at once," Wishart said. And the testing, he adds, would be much, much faster and much less expensive - costing only pennies and done with a handheld device in the doctor's office. "It will change the way that diagnostic testing is done - and the way that most clinical chemistry is done."

The intention of the Human Metabolome Project is to provide the tools that will enable that change to take place. "What we want to do is provide the Rosetta Stone for the future of metabolomics. We want to say 'These are the compounds that are part of your body. Here's our parts list. Here are the instructions. Here's how they work. Here's how they relate to disease. Here's how they relate to genetics.' "

While the Human Genome Project was a worldwide effort, the Human Metabolome Project is entirely based in Alberta. Other research groups around the world are interested in metabolomics, but what is happening in Alberta is unique. "We planted the flag in the ground first," said Wishart, "and others are letting us finish."

Wishart, who acts as project leader, is one of nine principal investigators involved in the project. In addition to Wishart, seven others come from the University of Alberta - Brian Sykes (Biochemistry), Russ Greiner (Computing Science), Fiona Bamforth (Clinical Chemistry), Derrick Clive (Chemistry), Liang Li (Chemistry), Mike Ellison (Biochemistry) and Tom Marrie (Medicine) - and biochemist Hans Vogel contributes NMR spectroscopy expertise from the University of Calgary.

Another 30 individuals work on various aspects of the project, which has a very small physical footprint - one small office in the south wing of Athabasca Hall, ordinary in every way, is pretty much it - making use of existing facilities and primarily functioning as a virtual entity.

Project manager Lori Querengesser has a particular interest in the bioinformatics tools being developed to facilitate the project. (Bioinformatics is the use of techniques from disciplines such as mathematics, statistics and computer science to solve biological problems.) Among these tools is a program called Biospider, which has been used to search the Internet and bring back any data it finds about metabolites.

According to Wishart, the study of small molecules was where biochemistry began, and as long ago as the beginning of the 20th century people were writing about and describing small molecules. "For the next half century, that's all biochemistry was," he says. However, in the 1970s, molecular biology took over, and with the interest in cloning and similar pursuits, small molecules were largely forgotten.

The first stage of the Human Metabolome Project was largely what Wishart describes as a "backfilling process - searching out what had already been learned about small molecules and entering that information into a database. The project has now moved into its second phase - using clinical samples to measure and identify the compounds present. In some cases these are things that have never been seen or described before.

Because it is necessary to identify everything that could be found in a human body, Wishart and his colleagues have turned their attention to substances that are not naturally ingested, including drugs and food additives. In fact, an offshoot of the Human Metabolome Project is the world's most complete drug database, DrugBank (www.drugbank.ca), which contains detailed information about nearly 4,300 drugs. This includes not only such things as the chemical structure and the molecular weight - and, of course, the NMR spectrum - but also patient information, including possible side effects and contraindications.

"DrugBank was good practice," said Wishart. "We cut our teeth on it. We knew that the information we wanted had to be somewhere. We just had to go out and find it."

Without the support of Genome Canada, the federal agency created in 2001 to serve as Canada's primary funding and information resource for genomics and proteomics, the Human Metabolome Project might never have gotten off the ground. The project was made possible by a $7.5 million grant issued under Genome Canada's Applied Genomics and Proteomics in Human Health funding umbrella.

Although the Human Metabolome Project slightly pushes the envelope of what Genome Canada typically funds, it has generated a great deal of enthusiasm. "This project has the potential to be among the highest profile activities taking place in Alberta universities," said Gijs van Rooijen, the chief scientific officer for Genome Alberta, the organization set up by Genome Canada to oversee genomics infrastructure and research in Alberta. "People around the world are looking carefully at what it is doing, and a number of international efforts are prepared to team up with it."

The initial start-up capital for the Human Metabolome Project came as a result of a funding competition that saw an international scientific review panel consider applications and give the Alberta project one of the highest ratings.

Recently, the Project underwent a mid-term review by internationally respected scientists, and the results were equally as encouraging. "Again, the Project received one of the highest rankings," said Van Rooijen. "It had done all it said it would and more."

Van Rooijen adds that the Human Metabolome Project is building on existing strengths at the U of A and the University of Calgary - strengths in NMR technology, bioinformatics, chemistry, and medical laboratory science. And, he says, the cooperation is building strength upon strength. "Traditionally individual chemists, biologists or computing scientists make individual discoveries. This project brings all the discoveries under the same umbrella and the whole is definitely bigger than the individual parts."

Wishart says that, if all goes well, he and his colleagues should have the first version of the Human Metabolite Database ready for release to the public by the first day of 2007. Researchers will then be able to translate the information it contains - the relationship of the various metabolites to genes and proteins, pathways and disease - to tests that will inform medical practitioners in their offices.

"Everything tells us that knowing this information is what physicians are looking for," said Wishart. "The bottom line is that we will be able to diagnose most diseases better, faster and cheaper."