Features - March 18, 2009
DNA on the Loose: Next-Gen Blood Tests Tap Free-Floating
Genetic Material
Tests using floating nucleic acids could diagnose disease, monitor pregnancy and weed
out "mad" cows
By Barbara Juncosa
Free-floating messages in the bloodstream could soon provide a unique window into the body.
Researchers worldwide are racing to decipher circulating genetic material for better ways to diagnose
disease, monitor pregnancy, and even improve food safety.
Circulating DNA and RNA--temporary gene copies that act as blueprints for protein production--was first
discovered in 1948. Researchers still do not fully understand how the free-floating genetic fragments
(chemically referred to as nucleic acids) survive outside the protective barriers of cells, but recent
technological advances now allow scientists to comb through these tiny messages for clues about human
health.
Traditional genetic screens, such as paternity tests and criminal profiling, utilize the abundant DNA stored
in the nuclei of circulating blood cells. Although these tests shed light on a person's genetic inheritance,
they do not provide insights on the current health of specific tissues and organs--information that could
potentially be gleaned from the free nucleic acids.
Debate about the exact origins of circulating DNA and RNA continues, but dead cells from all areas of the
body certainly contribute to the pool with new evidence mounting that living cells also release nucleic
acids, perhaps enabling cell-to-cell communication over vast distances in the body, says Asif Butt, senior
research fellow at King's College London.
Even healthy patients have circulating DNA and RNA, says Michael Fleischhacker, a molecular biologist
at Charité-Universitätsmedizin Berlin hospital, but individuals with chronic disease such as cancer,
inflammatory bowel disease and systemic lupus typically harbor increased levels of these messages in
their blood. Simply monitoring the overall concentrations of nucleic acids in circulation, however, does not
provide sufficient information about any one condition, prompting scientists to hunt for genetic targets
specific to particular diseases.
Cancer researchers, for example, are seeking out patterns of chemical modifications and mutations
detectable in the circulating gene fragments that are unique to malignancies. This approach could allow
physicians to profile tumors without invasive sampling, says David Hoon, a molecular oncologist at the
John Wayne Cancer Center Institute in Santa Monica, Calif.
The long-term goal is to identify genetic guides that can point physicians to a tumor's location as well as
patterns that are characteristic of its stage to determine and monitor treatment and disease progression in
patients, says Brian Durie, an oncologist at the CedarsSinai Medical Center's Samuel Oschin
Comprehensive Cancer Institute in Los Angeles.
Fleischhacker cautions, however, that preparing these tests for routine cancer screening is likely to take a
few years, because today's sensitive techniques can also detect rare mutations in healthy people that are
of no clinical consequence.
Perhaps the most successful application of testing circulating DNA to date has been in the area of
prenatal care. In the late 1990s researchers first recognized that fetal DNA could be detected in the
mother's blood, albeit at very low levels, opening the door for noninvasive testing during pregnancy.
Traditional methods for examining fetal DNA, such as amniocentesis, require removing a sample of
amniotic fluid surrounding the baby, increasing the risk of miscarriage, says Diana Bianchi, professor of
pediatrics at Tufts University School of Medicine in Boston. Analysis of the mother's blood, on the other
hand, could allow physicians to safely monitor the fetus and mother throughout the pregnancy.
In the U.S. and Europe, blood tests have already been approved for the diagnosis of rhesus D
incompatibility--a condition in which a mother produces antibodies against her fetus due to the absence
of the blood factor in her own body. Gender screening is also performed in Europe for families at high risk
of passing on genetic disorders linked to the X chromosome. Bianchi says blood tests for Down's
syndrome could be available in the near future.
Beyond cancer and prenatal testing, circulating nucleic acids could help physicians track a broad range of
diseases, including stroke, heart attack and complications from diabetes. Butt's team has already
identified several genetic markers important for diagnosing (and potentially predicting) diabetic
retinopathy--damage to the eye's retina. Currently, only annual comprehensive eye tests can detect the
condition, which is a leading cause of blindness in adults in the U.S., according to the National Eye
Institute in Bethesda, Md.
Even the safety of animals stands to get a boost from testing circulating DNA. Researchers last month
announced that chronic wasting disease in elk and bovine spongiform encephalopathy (mad cow
disease) in cattle could be diagnosed up to six months before symptoms show up.
The only way to confirm a case of these diseases right now is to examine an animal's brain postmortem,
says study leader Christoph Sensen, director of the Sun Center of Excellence for Visual Genomics at the
University of Calgary in Alberta. But by comparing the circulating DNA profiles of sick and healthy
animals, Sensen's team was able to identify disease-specific genetic patterns for diagnostic use in live
animals. Providing a cheap method for testing all livestock in slaughterhouses, Sensen says, will be
important for certifying the safety of meat exports and preventing future disease transmission to humans.
Although blood has been the primary focus for work on circulating nucleic acids, some researchers are
now looking to test other bodily fluids. Urine is a particularly attractive candidate as it could provide an
alternative source for testing circulating DNA and RNA in the developing world where drawing blood can
be impractical, notes Timothy Block, co-founder of the Hepatitis B Foundation and a virologist at the
Drexel University College of Medicine in Philadelphia.
With such broad applications, King's College's Butt agrees that the future of this technology is bright, but
cautions that commercial partners will be key for developing clinical tests in the coming years.
Howard Urnovitz, CEO of Chronix Biomedical, Inc., in San Jose, Calif., is already looking for companies in
the diagnostic field to help commercialize his company's bioinformatic approach to computationally mining
thousands of sequenced circulating DNA fragments from healthy volunteers and patients for diagnosing
and tracking specific diseases, including multiple myeloma (a cancer of disease-fighting plasma cells that
is incurable but treatable), breast cancer and multiple sclerosis.
Despite the pressing need for identifying and validating new disease markers, Peter Gahan, a cell
biologist at King's College, is optimistic. "Funding was virtually nonexistent five to 10 years ago," Gahan
says, but "we are already beginning to get markers that could enter into predictive medicine."