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Building bridges: Trading up from basic
science
A $300,000 investment in collecting gene
expression data grew into a $140-million international collaboration
This is the story of how the Stem Cell Network built a bridge
to the future of stem cell research.
It started with a $300,000 investment that brought together
25 Canadian scientists who rolled up their sleeves and created
StemBase, the largest stem cell gene expression database in
the world. The original investment burgeoned into the $12-million
Gene Expression Project that, in turn, became the foundation
for the $140-million International Regulome Consortium (the
bridge), a Canadian-led initiative that will unite the world's
leading stem cell scientists to create a comprehensive understanding
of the genetic circuits that regulate life.
| Gene expression demystified
Gene expression is the process that converts the
coded information in a gene into the molecules
that allow a cell to operate. Scientists need
this information to identify and isolate stem
cells, understand how they function and discover
how they may be used – for instance, to
repair tissues damaged by diseases such as muscular
dystrophy, blindness and Parkinson's.
"Think of the human genome as a big sheet
of plywood with 25,000 light bulbs on it,"
explains Rudnicki. "Each light bulb corresponds
to a cell connected to a dimmer switch. Different
cell types have different patterns of light and
different levels of brightness. At the International
Regulome Consortium, we are turning over that
piece of plywood, looking at the wires and trying
to understand the circuitry."
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"The Gene Expression Project started in 2002,"
says William Read, who managed the project through to its
successful conclusion in the spring of 2006. "If the
Stem Cell Network hadn't stepped up with the seed money, none
of this would have got off the ground."
Ultimately, the Network contributed $1 million, an 11-to-1
ratio of matching funds from four federal and provincial agencies:
the Canada Foundation for Innovation, the Ontario Innovation
Trust, the Ontario Research and Development Challenge Fund
and Genome Canada.
StemBase is a key end product of the project. It is internationally
recognized as an authoritative source of gene expression information
and ranks as the world's seventh-largest contributor
to the U.S. National Center for Biological Information's
GEO database, the most comprehensive pool of gene expression
data in existence.
"And it's extensive." adds Miguel Andrade, Network
bioinformatician. "StemBase includes more than 600 samples
of stem cell gene expression."
The database is now available to commercial users whose annual
fees help to maintain it.
The project led to the creation of a team (building the database
involved 22 highly qualified people, including four post-doctoral
fellows) that will help establish the International Regulome
Consortium.
"The linkage is the people," says Read. "The
project team will be the core of the international effort."
Michael Rudnicki, the Stem Cell Network's Scientific
Director, describes the international effort arising from
the Gene Expression Project as potentially revolutionizing
the understanding of how cells function at the genomic level
and helping to develop novel therapies in regenerative medicine.
"This is the third generation of the human genome project,"
explains Dr. Rudnicki, who also leads the International
Regulome Consortium. "The first generation was discovering
the sequence of the human genome. The second generation was
annotating it, understanding where the different genes are.
This third generation will allow us to understand how genes
function."
Already $65 million of international funding is in place.
The work will be done by 37 investigators at 18 institutions
in seven countries.
"It's out of the gates," says Rudnicki. "We've
had five international workshops to consider everything from
technological approaches to bioinformatic standards. There
has been tremendous support and enthusiasm internationally
for working on this."
In Canada, applications have been submitted for $35 million
of funding for infrastructure from agencies such as the Canada
Foundation for Innovation. Rudnicki is optimistic.
"Only a country like Canada could broker something like
this," he declares. "It speaks to our capacity to
bring people together."
And to the Network's ability to build bridges to the future.
www.stemcellnetwork.ca
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