Aptamers Identify Protein Signatures
Method for screening may provide early warning system
By Ricki Lewis [The Scientist]
A technique not deemed "sexy" enough for commercialization a decade ago may
finally find its niche in proteomics. SomaLogic Inc. of Boulder, Colo. is pioneering
aptamers, which are modified DNA molecules that bind specific proteins in body
fluid samples. Aptamers are initially selected for specific binding activities from
a huge starting pool, then variants are obtained during subsequent rounds of
amplification. The technology builds on the ability of aptamers to bind tenaciously
to proteins. "Single-stranded oligonucleotides can fold into any shape, and behave
like antibodies," explains Larry Gold, SomaLogic founder.
To develop an aptamer screen, the researchers begin with a small amount of a
purified protein from a particular cell type under particular conditions. That protein is
used to select an aptamer from a pool, and the aptamer is eventually incorporated
into an array with others that bind different proteins in that cell type, forming a unique
protein signature. "The idea is that the pathology of tumors and other conditions will
show changes in proteins in the blood, so that simple blood tests can be done
routinely, for early warnings," says Gold, who with Craig Tuerk developed aptamer
technology at the University of Colorado, Boulder, in 1989.1
Gold and Tuerk used an in vitro selection and evolution method called SELEX
(systematic evolution of ligands by exponential enrichment) to investigate RNAs that
bind bacteriophage T4 DNA polymerase. From there, the budding technology wound
its way through a trajectory of biotech companies--to NeXagen in 1991, which soon
merged with another firm to spawn NeXstar Pharmaceuticals. Despite an impressive
patent estate, long-standing prejudices delayed the launch of the technology:
specifically, the lag in commercialization of antibody-based technologies, and Big
Pharma's thirst for orally active compounds. "Aptamers would always have to be
injected and aimed extracellularly, because they do not cross cell membranes. So it
was a limited niche, but one through which many diseases could be approached,"
Gold recalls.
Circa 1997, however, his view broadened. "Four years ago, I finally understood the
potential for research and diagnostics. I took out the Affymetrix chip and added
something to make the reporting more accurate, and wondered if we could provide
high-density arrays of aptamers. If we could make, quickly enough, aptamers with
specificities, we could make proteomics cheap." Then in 1999, Gilead Sciences of
Foster City, Calif., bought NeXstar, and soon after sold an exclusive license for in vitro
diagnostics using aptamer technology back to Gold, who started SomaLogic.
Aptamers are not just oligos--they are modified to resist nuclease digestion, and to
remain in the bloodstream longer, or to be sufficiently stable in serum for diagnostics.
They differ by a variable 30 to 40 base sequence that is nestled between sequences
complementary to PCR primers, which provides the amplification mechanism for the
cycles of evolution and selection.
Used as a diagnostic--or prognostic, since it will yield information before
symptoms arise--arrays of aptamers are bound to a solid support, and a body fluid
sample applied. Unbound protein is washed off, and stains that tag proteins but not
nucleic acids used to generate protein profiles. "At every address in the array, there
will be a billion molecules of each aptamer. Blood or urine is applied, and we collect
some number of proteins at each address," says Gold.
Aptamers have therapeutic potential too because they block receptors and other
protein activities.2 Gilead Sciences has developed an aptamer called NX1838, for
example, that inhibits vascular endothelial growth factor (VEGF). "NX1838 functions as
an antagonist in an angiogenic disease model--excess blood vessels. It inhibits
VEGF activity, binding it tightly, so that the protein cannot bind its receptor," Gold says.
It is currently in clinical trials to treat age-related macular degeneration.
Ricki Lewis (rickilewis@nasw.org) is a contributing editor for The Scientist.
References
1. C. Tuerk and L. Gold. "Systematic evolution of ligands by exponential enrichment: RNA ligands
to bacteriophage T4 DNA polymerase," Science, 249:505-10, 1990.
2. E. N. Brody et al., "The use of aptamers in large arrays for molecular diagnostics," Molecular
Diagnostics, 4:381-8, 1999.
The Scientist 15[7]:14, Apr. 2, 2001
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