On the Fast Track in Functional Proteomics
Linking of technologies sets pace for researchers
By A.J.S. Rayl [The Scientist]
Researchers in Canada and Denmark are employing mass spectrometry,
three-dimensional tissue biology, and supercomputing to blaze a trail in
functional proteomics research. In the process, they're putting their company,
MDS Proteomics Inc., on the fast track in the latest race to develop new drug
targets and eventually better treatments for all kinds of diseases. By using this
combination of technologies, MDS Proteomics is accelerating the process of
identifying, analyzing, and understanding the myriad structures, interactions,
and pathways of proteins.
"This integrated approach is critical to developing a new generation of drugs to treat
disease," says Matthias Mann, scientific founder of MDS Proteomics and chief
proteomics officer. Medical Data Services (MDS) Inc., an international health and life
sciences company based in Toronto, launched MDS Proteomics in 2000 following the
purchase of Protana, a Danish proteomics company. It is currently expanding its
headquarters, and research facilities are under development in Charlottesville, Va., and
Boston.
MDS Proteomics uses a "one-two-three, punch" approach in its research:
The process begins with growing three-dimensional cells in a state-of-the-art
optimized suspension culture device.
Researchers then use highly sensitive mass spectrometry to analyze the
protein activity in the cells.
A highly sophisticated bioinformatics system crunches the huge amounts of data
generated so that protein 'pictures' emerge in a new, more revealing way.
From Gel to BioReactor
Although researchers had been investigating gel-purified proteins, this past January
MDS Proteomics hired a young cellular biologist from Odense University, Jorge Sans
Burns, who brought with him the notion of using three-dimensional tissue biology to
grow the cells. Burns had learned about the optimized tissue culture suspension device,
now known as the BioReactor, by reading the current literature in cell biology. NASA
scientists developed this rotating wall vessel in the mid-1980s to give the space
agency's biologists a way to research the genetic impact of microgravity on astronauts.
The BioReactor has since been shown to produce three-dimensional tissue.1,2
"The idea struck me that sample handling is a key issue," says Burns, now a senior
research scientist at MDS Proteomics lab in Odense. "It's an overworn phrase, but
'garbage in, garbage out.' If we want to have something that is representative of what is
going wrong inside a patient, we need to be very careful about how we handle that
sample, especially in the context of proteomes, because they're highly context
dependent. They'll be changing very rapidly, contrary to the genome, which is more
stable." As a result, how the tissue is handled is of "prime importance" in the end result
and "whether it means anything in terms of what's going on inside the patient," says
Burns, who earned his cellular pathology degree at the University of Bristol, studying
under Sir Michael Anthony Epstein of Epstein-Barr virus fame. 3
Burns points out that conventional, gel-purified methods can be problematic, and
"they may introduce artifacts" because the cells are trying to grow on a piece of plastic.
Beyond that, he adds: "Since we are 3-D organisms with tissues, it seemed to make a
lot of sense to approach this from that angle for the simple reason that the BioReactor
system of three-dimensional tissue modeling appears to be a way to create the proteins
in a more 'relevant' way to people." Upon suggesting the company employ BioReactors
to grow the cells, Burns got an almost immediate 'thumbs-up.' MDS Proteomics has
since purchased enough BioReactors "to conduct the first stage of experiments and to
look at a number of things in parallel."
Burns is now looking to collect information in the BioReactors that is "more
representative" of how given cells would behave inside the patient rather than cells
grown in other, conventional cultures. Although the BioReactor is still relatively new, "a
technology that's still to be explored ... its potential still to be realized," Burns notes that
the BioReactor is "a valid tool" for getting closer to an in vivo like situation. "If nothing
else, it is a cost-effective way of growing large numbers of cells," he says. "That's the
least it does."
Burns has already found that "the cells are behaving [in a way] they don't in other
culture systems, more tissue-like, more as if they were in the human body." Therefore, in
addition to allowing the company to scale-up its approach and enabling these
researchers to acquire more relevant data on specific diseases, the BioReactors, he
suggests, will also help them "tackle some of the issues related to the complexity of
tissue organization." Such insights should help open the door to determine the use of
certain proteins as diagnostic markers. "To express the cells in a more tissue-like
manner is, I feel, one step toward being able to express the targets in the right sort of
way," comments Burns.
From BioReactor to Mass Spectrometer
Once the cells emerge from the BioReactor, they are analyzed in Mann's laboratories,
which house a large number of highly customized mass spectrometers. "We are using
mass spectrometry to analyze very small amounts of proteins, as well as protein-protein
interactions," explains Mann. Mass spectrometry, of course, has long been used for
chemical and elemental analyses, but during the last decade, it has been successfully
redefined to identify and characterize proteins, and Mann is recognized as one of the
leading pioneers of its use in functional proteomics.4
"We are trying to study the function of the proteins and one of those things is to see
what a protein interacts with and how it interacts with other proteins, and we are [looking
to] do that on a large scale," he elaborates. "We can fuse a cancer gene, for example, to
tag and then transvect it, [resulting] in interacting proteins, which we then analyze. So,
with mass spectrometry, we have a way of seeing interacting proteins and thereby, we
can determine the function of a specific gene," he explains.
Given the revelation in February that the human genome consists of fewer than
expected genes, one of the major take-home points is that human complexity lies in the
proteins genes produce. "To quote my managing director [for Europe], Ole Vorm: 'The
human genome data is water on the treadmill of proteomics,'" says Burns. "That there
are fewer genes than we had believed puts much more onus on the proteome; there
must be significantly more differences based on the proteomes."
"There may be several hundred thousand proteins made from these 35,000 genes,"
Mann adds, reiterating what Francis S. Collins and J. Craig Venter said at the recent
American Association for the Advancement of Science annual meeting in San Francisco.
"Because the genes can make different proteins ..., the proteins will be much more
diverse than the genes we will be studying; therefore, the numbers will be several-fold
higher," Mann continues. "It's not like you measure the sequence once and you're done.
You have to measure in all kinds of environments, so you may end up with orders of
magnitude more data than the Human Genome Project."
Computational Steps
Consequently, MDS Proteomics is generating considerably more data than either the
public or private human genome projects. Uncovering the multitudes of protein
interaction requires substantial bioinformatics and supercomputing capabilities. To
address that issue, the company formed a strategic alliance with IBM, which recently
launched its Life Science Initiative, and is providing the firm with its primary computer
infrastructure in Odense and at the company's corporate headquarters in Toronto. "We
now have very large computers that allow us to search this huge amount of data that
we're generating," says Mann. Actually, the systems in Odense and Toronto together
form one of the largest Linux clusters in the world.
The company may be young, but its scientists, notes Burns, "are some of the most
cited mass spectrometry and proteomics scientists and have published some 60
papers in Cell, Science, and Nature, among other journals." With remarkable speed,
MDS Proteomics has become, in fact, one of the largest functional proteomics
ventures--now employing some 225 people (60 scientists), according to Mann--deep
into conducting functional proteomics research.
Although the company's first functional proteomics facility was established in Odense,
MDS is rapidly expanding. In addition to a Toronto facility established in conjunction with
Anthony Pawson's laboratory at the Samuel Lunenfeld Research Institute at the Mount
Sinai Hospital--Pawson is a fellow of the Royal Societies of London and Canada and is
also an MDS Proteomics founder--the company just opened a 50,000-square-foot
state-of-the-art laboratory in its headquarters for analyzing protein interaction pathways,
producing data for its proprietary BIND database to select and validate targets for its
partners. In the soon-to-open Boston division, scientists will focus on high-throughout
screening, structural biology and drug design, medicinal chemistry, and protein
identification, while in Virginia, they will specialize in the analysis of complex mixtures of
proteins to identify novel membrane bound receptor proteins as targets fro therapeutic
drugs.
Mass spectrometry has provided "the big change" over the last decade, says the
German-born and -raised Mann, who earned his chemical engineering degree from Yale
University and also has a background in mathematics, physics, and biotechnology. "In
terms of general biology, we now have the ability to take apart the cell and look into the
different compartments, really look in and know what proteins are there, what they look
like, whether they look differently in one compartment than they do in another, what their
phosphorylation stages are, and whether they're turned on and when they are turned
off."5
"This [research] just was not possible previously, because we didn't have the
throughput and the sensitivities, and so it had to be studied indirectly before," he
continues. "The promise of proteomics is to study the proteins directly at the cellular level
so they're not only in the genetic screen or only in the computer, but [where] you can
study them directly. Now, for the first time, because of the advances in the analysis
methods, we can do that. Mass spectrometry allows for analyses of hundreds of proteins
very sensitively."
The simplified notion of one gene, one protein, one function is disappearing fast,
Mann says. "We are learning that a protein can have quite a different function depending
on where it's located in the cell." The implications of that knowledge may well be
enlightening beyond the imagination. Both Mann and Burns are reluctant to specify
exactly what diseases they are currently researching, but Mann does offer this: "We do
have quite a focused medical interest in this for various forms of cancer, among other
things."
"The proteome paves the path for the genome," says Burns. "If one can find the right
targets, then one would be in a better position to find the right treatments, and we're on
that road now. We're in a phase now where we have to address more complex
questions, and having tools like we've never had before helps us enormously with the
process of identifying proteins and then understanding more about how the human
genome functions as it does, in states of health and disease."
If the BioReactor lives up to its promises, as these researchers expect it will,
three-dimensional biology will aid in rendering "a truer answer--meaning that the
changes you see, for example, in cancer vs. noncancer--would hopefully be more
reflective of the tissue stage rather than being a culture effect," says Mann. "Mass
spectrometry is quite proven now," he adds.6 "We have already generated a lot of data
that we have put through the supercomputers, and hopefully with the BioReactors we
can do a lot more." MDS Proteomics is venturing that use of the BioReactor, combined
with the capability of mass spectrometry analyses and the
supercomputing/bioinformatics capacity of the company to sort through and review the
endless streams of data will, in turn, offer up a sum result that is far greater than its
technological parts. This approach will fill "one of the critical holes," Mann concludes, on
the road to the next generation of drug targets and advanced treatments for various
diseases.
A.J.S. Rayl (ajsrayl@loop.com) is a contributing editor for The Scientist.
References
1. T.J. Goodwin et al., "Three-dimensional culture of a mixed mullerian tumor of the ovary: expression
of in vivo characteristics," In Vitro Cellular and Developmental Biology, 33:366-74, 1997.
2. T.J. Goodwin et al., "Coculture of normal human small intestine cells in a rotating-wall vessel
culture system," Proceedings of the Society for Experimental Biology and Medicine, 202, 1993.
3. M.A. Epstein et al., "Virus particles in cultured lymphoblasts from Burkitts lymphoma," Lancet, 1:702,
1964.
4. J.B. Fenn et al., "Electrospray ionization for mass-spectrometry of large biomolecules," Science,
246:64-71, 1989.
5. A. Pandey, M. Mann, "Proteomics to study genes and genomes," Nature, 405: 837-46, 2000.
6. W. Blackstock, M. Mann, editors, "Proteomics: A Trends Guide," Trends In Biological Sciences,
Elsevier, Summer 2000.
the-scientist.com |
