Genetically Sequencing Healthy Babies Yielded Surprising Results
Today in Melrose, Massachusetts, Cora Stetson is the picture of good health, a bubbly precocious 2-year-old. But Cora has two separate mutations in the gene that produces a critical enzyme called biotinidase and her body produces only 40 percent of the normal levels of that enzyme.
In the last few years, the dream of predicting and preventing diseases through genomics, starting in childhood, is finally within reach.
That's enough to pass conventional newborn (heelstick) screening, but may not be enough for normal brain development, putting baby Cora at risk for seizures and cognitive impairment. But thanks to an experimental study in which Cora's DNA was sequenced after birth, this condition was discovered and she is being treated with a safe and inexpensive vitamin supplement.
Stories like these are beginning to emerge from the BabySeq Project, the first clinical trial in the world to systematically sequence healthy newborn infants. This trial was led by my research group with funding from the National Institutes of Health. While still controversial, it is pointing the way to a future in which adults, or even newborns, can receive comprehensive genetic analysis in order to determine their risk of future disease and enable opportunities to prevent them.
Some believe that medicine is still not ready for genomic population screening, but others feel it is long overdue. After all, the sequencing of the Human Genome Project was completed in 2003, and with this milestone, it became feasible to sequence and interpret the genome of any human being. The costs have come down dramatically since then; an entire human genome can now be sequenced for about $800, although the costs of bioinformatic and medical interpretation can add another $200 to $2000 more, depending upon the number of genes interrogated and the sophistication of the interpretive effort.
Two-year-old Cora Stetson, whose DNA sequencing after birth identified a potentially dangerous genetic mutation in time for her to receive preventive treatment.
(Photo courtesy of Robert Green)
The ability to sequence the human genome yielded extraordinary benefits in scientific discovery, disease diagnosis, and targeted cancer treatment. But the ability of genomes to detect health risks in advance, to actually predict the medical future of an individual, has been mired in controversy and slow to manifest. In particular, the oft-cited vision that healthy infants could be genetically tested at birth in order to predict and prevent the diseases they would encounter, has proven to be far tougher to implement than anyone anticipated.
But in the last few years, the dream of predicting and preventing diseases through genomics, starting in childhood, is finally within reach. Why did it take so long? And what remains to be done?
Great Expectations
Part of the problem was the unrealistic expectations that had been building for years in advance of the genomic science itself. For example, the 1997 film Gattaca portrayed a near future in which the lifetime risk of disease was readily predicted the moment an infant is born. In the fanfare that accompanied the completion of the Human Genome Project, the notion of predicting and preventing future disease in an individual became a powerful meme that was used to inspire investment and public support for genomic research long before the tools were in place to make it happen.
Another part of the problem was the success of state-mandated newborn screening programs that began in the 1960's with biochemical tests of the "heel-stick" for babies with metabolic disorders. These programs have worked beautifully, costing only a few dollars per baby and saving thousands of infants from death and severe cognitive impairment. It seemed only logical that a new technology like genome sequencing would add power and promise to such programs. But instead of embracing the notion of newborn sequencing, newborn screening laboratories have thus far rejected the entire idea as too expensive, too ambiguous, and too threatening to the comfortable constituency that they had built within the public health framework.
"What can you find when you look as deeply as possible into the medical genomes of healthy individuals?"
Creating the Evidence Base for Preventive Genomics
Despite a number of obstacles, there are researchers who are exploring how to achieve the original vision of genomic testing as a tool for disease prediction and prevention. For example, in our NIH-funded MedSeq Project, we were the first to ask the question: "What can you find when you look as deeply as possible into the medical genomes of healthy individuals?"
Most people do not understand that genetic information comes in four separate categories: 1) dominant mutations putting the individual at risk for rare conditions like familial forms of heart disease or cancer, (2) recessive mutations putting the individual's children at risk for rare conditions like cystic fibrosis or PKU, (3) variants across the genome that can be tallied to construct polygenic risk scores for common conditions like heart disease or type 2 diabetes, and (4) variants that can influence drug metabolism or predict drug side effects such as the muscle pain that occasionally occurs with statin use.
The technological and analytical challenges of our study were formidable, because we decided to systematically interrogate over 5000 disease-associated genes and report results in all four categories of genetic information directly to the primary care physicians for each of our volunteers. We enrolled 200 adults and found that everyone who was sequenced had medically relevant polygenic and pharmacogenomic results, over 90 percent carried recessive mutations that could have been important to reproduction, and an extraordinary 14.5 percent carried dominant mutations for rare genetic conditions.
A few years later we launched the BabySeq Project. In this study, we restricted the number of genes to include only those with child/adolescent onset that could benefit medically from early warning, and even so, we found 9.4 percent carried dominant mutations for rare conditions.
At first, our interpretation around the high proportion of apparently healthy individuals with dominant mutations for rare genetic conditions was simple – that these conditions had lower "penetrance" than anticipated; in other words, only a small proportion of those who carried the dominant mutation would get the disease. If this interpretation were to hold, then genetic risk information might be far less useful than we had hoped.
Suddenly the information available in the genome of even an apparently healthy individual is looking more robust, and the prospect of preventive genomics is looking feasible.
But then we circled back with each adult or infant in order to examine and test them for any possible features of the rare disease in question. When we did this, we were surprised to see that in over a quarter of those carrying such mutations, there were already subtle signs of the disease in question that had not even been suspected! Now our interpretation was different. We now believe that genetic risk may be responsible for subclinical disease in a much higher proportion of people than has ever been suspected!
Meanwhile, colleagues of ours have been demonstrating that detailed analysis of polygenic risk scores can identify individuals at high risk for common conditions like heart disease. So adding up the medically relevant results in any given genome, we start to see that you can learn your risks for a rare monogenic condition, a common polygenic condition, a bad effect from a drug you might take in the future, or for having a child with a devastating recessive condition. Suddenly the information available in the genome of even an apparently healthy individual is looking more robust, and the prospect of preventive genomics is looking feasible.
Preventive Genomics Arrives in Clinical Medicine
There is still considerable evidence to gather before we can recommend genomic screening for the entire population. For example, it is important to make sure that families who learn about such risks do not suffer harms or waste resources from excessive medical attention. And many doctors don't yet have guidance on how to use such information with their patients. But our research is convincing many people that preventive genomics is coming and that it will save lives.
In fact, we recently launched a Preventive Genomics Clinic at Brigham and Women's Hospital where information-seeking adults can obtain predictive genomic testing with the highest quality interpretation and medical context, and be coached over time in light of their disease risks toward a healthier outcome. Insurance doesn't yet cover such testing, so patients must pay out of pocket for now, but they can choose from a menu of genetic screening tests, all of which are more comprehensive than consumer-facing products. Genetic counseling is available but optional. So far, this service is for adults only, but sequencing for children will surely follow soon.
As the costs of sequencing and other Omics technologies continue to decline, we will see both responsible and irresponsible marketing of genetic testing, and we will need to guard against unscientific claims. But at the same time, we must be far more imaginative and fast moving in mainstream medicine than we have been to date in order to claim the emerging benefits of preventive genomics where it is now clear that suffering can be averted, and lives can be saved. The future has arrived if we are bold enough to grasp it.
Funding and Disclosures:
Dr. Green's research is supported by the National Institutes of Health, the Department of Defense and through donations to The Franca Sozzani Fund for Preventive Genomics. Dr. Green receives compensation for advising the following companies: AIA, Applied Therapeutics, Helix, Ohana, OptraHealth, Prudential, Verily and Veritas; and is co-founder and advisor to Genome Medical, Inc, a technology and services company providing genetics expertise to patients, providers, employers and care systems.
Pregnant and Breastfeeding Women Might Have a New Reason to Ditch Artificial Sweeteners
Women considering pregnancy might have another reason to drop artificial sweeteners from their diet, if a new study of mice proves to apply to humans as well. It highlights "yet another potential health impact of zero-calorie sweeteners," according to lead author Stephanie Olivier-Van Stichelen.
The discovery was serendipitous, not part of the original study.
It found that commonly used artificial sweeteners consumed by female mice transfer to pups in the womb and later through milk, harming their development. The sweeteners affected the composition of bacteria in the gut of the pups, making them more vulnerable to developing diabetes, and greatly reduced the liver's capacity to neutralize toxins.
The discovery was serendipitous, not part of the original study, says John Hanover, the senior author and a cell biologist at the NIH National Institute of Diabetes and Digestive and Kidney Diseases. The main study looked at how a high sugar diet in the mother turns genes on and off in the developing offspring.
It compared them with mothers fed a low sugar diet, replacing sugar with a mix of sucralose and acesulfame-K (AK), two non-nutrient artificial sugars that are already used extensively in our food products and thought to be safe.
While the artificial sweeteners had little effect on the mothers, the trace amounts that were transferred through the placenta and milk had a profound effect on the pups. Hanover believes the molecules are changing gene expression during a crucial, short period of development.
"Somewhat to our surprise, we saw in the pups a really dramatic change in the microbiome" of those whose mothers were fed the artificial sweeteners, Hanover told leapsmag. "It looked like the neonates were much, much more sensitive than their mothers to the sucralose and AK." The unexpected discovery led them to publish a separate paper.
"The protective microbe Akkermansia was largely missing, and we saw a pretty dramatic shift in the ratio of two bacteria that are normally associated with metabolic disease," a precursor to diabetes, he explains. Akkermansia is a bacteria that feeds on mucus in the gut and helps remodel the tissue to an adult state over the first several months of life in a mouse. A similar process takes several years in humans, as the infant is weaned off of breast milk as the primary food source.
The good news is the body seems to remove these artificial sweeteners fairly quickly, probably within a week.
Another problem the researchers saw in the animals was "a particularly striking change in the metabolism of the detoxification systems" in the liver, says Hanover. A healthy liver is dark red, but a high dose of the artificial sweeteners turned it white, "which is a sign of massive problems."
The study was conducted in mice and Hanover cautions the findings may not apply to humans. "But in general, the microbiome changes that one sees in the rodent model mimics what we see in humans...[and] the genes that are turned on in the mouse and the human are very similar."
Hanover acknowledges the quantity of artificial sweeteners used in the study is on the high end of human consumption, roughly the equivalent of 20 cans of diet soda a day. But the sweeteners are so ubiquitous in consumer products, from foods to lipstick, and often not even mentioned on the label, that it is difficult to measure just how much a person consumes every day.
The good news is the body seems to remove these artificial sweeteners fairly quickly, probably within a week. Until further studies provide a clearer picture, women who want to err on the side of caution can choose to reduce if not eliminate their exposure to artificial sweeteners during pregnancy and breastfeeding.
NASA Has the Technology to Save Us From an Asteroid Strike, But Congress Won’t Fund It
At the biannual Planetary Defense Conference earlier this year, NASA ran a simulation of an asteroid slamming into the center of Manhattan.
For several millennia now, we've been lucky, but our luck won't hold out forever.
The gathering of astronomers, planetary scientists, and FEMA disaster-response experts attempted a number of interventions that might be possible within a time window of eight years, the given warning period before impact.
Catastrophic asteroid crashes are not without precedent, and scientists say it's only a matter of time before another one occurs—that is, if we do nothing to prevent it. It's believed that a huge asteroid crash off the coast of Mexico's Yucatan Peninsula created a worldwide disaster that helped to speed the extinction of the dinosaurs 65 million years ago.
In 1908, a meteoroid less than 300 feet in diameter exploded in the air over the Tunguska region of Siberia, creating a shockwave that leveled trees for hundreds of square miles. It's a matter of sheer luck it didn't hit a major population center, where human casualties could have been enormous.
For several millennia now, we've been lucky, but our luck won't hold out forever. There are millions of asteroids circulating about in our solar system, some of them hundreds of miles across, and although the odds of a massive one crashing to Earth in the near future is statistically low, the devastation could be apocalyptic.
Back at the conference, the experts tried sending several spacecrafts to knock the asteroid off-course by slamming into it. They considered blasting it with nuclear weapons. They even considered painting it white so it absorbed less of the sun's energy, hoping that would shift the asteroid's trajectory. In the simulations, all of the interventions failed and the giant space rock crashed into Manhattan, killing 1.3 million people in a massive explosion that was 1,000 times more powerful than the Hiroshima bomb.
NEOCam is designed, tested, and ready to build, but the project is currently frozen because of a $40 million gap in NASA funding.
Given more time, the scientists said, they might have succeeded in preventing the disaster. However, with today's asteroid-hunting telescopes, it's not likely we would have more warning. Our current telescopes are not powerful enough to detect all the near-earth asteroids, nor are they positioned well enough for sufficient detection. As recently as last week, for example, an asteroid traveling 15 miles a second narrowly missed crashing into the Earth, and it was only noticed several days in advance.
Now for the good news: There is a new technology that could buy us the time we need, says MIT planetary sciences professor Richard P. Binzel and colleagues who attended the conference. The Near-Earth Object Camera, or NEOCam, designed by NASA's Jet Propulsion Laboratory, would detect more than 90 percent of nearby objects that are 420 feet across or larger, according to Binzel.
The powerful infrared telescope is designed to sit within the L1 Lagrange point, a stable location in space where the gravitational pulls of the Earth and the sun cancel each other out. From there, large space bodies could be detected early enough to give scientists decades of warning when an asteroid is heading for Earth. NEOCam is designed, tested, and ready to build, but the project is currently frozen because of a $40 million gap in NASA funding.
The status of NEOCam, according to Binzel, is a case-study in short-sightedness and a lack of leadership. Congress needs to raise NASA's Planetary Defense budget from its current $160 million to $200 million to get the telescope built and launched into space, a goal that would seem eminently doable within the strictures of 2020's $4.75 trillion government budget. But Binzel describes a current deadlock between NASA, Congress, and the Office of Management and Budget as a "cosmic game of chicken."
If we don't use our technology to defend the planet, "it would be the most epic failure in the history of science."
In an excruciatingly budget-conscious atmosphere, "No one wants to stick their neck out and take adult responsibility" for getting the funding allocated that would unfreeze the project, says Binzel. But, he adds, "We have a moral obligation to act."
NEOCam would not only spot the overwhelming majority of asteroids in Earth's vicinity, it would determine their size and pinpoint exactly where they are likely to strike the Earth. And it would allow us decades to act, according to Binzel. Repeated ramming by an international armada of specialized spacecraft could slightly change the trajectory of an asteroid, he says. Changing the trajectory only a tiny bit, given the scale of millions of miles and several decades for the course change to take effect, could cause an asteroid to miss the Earth altogether.
"So far we've been relying on luck," says Binzel, "but luck is not a plan." Now that we have the technology to discover what's careening through our space neighborhood, it's our ethical duty to deploy it. If we don't use our technology to gain the knowledge we need to defend the planet, Binzel concludes, "it would be the most epic failure in the history of science."
Should Congress green light the $40 million budget for the new asteroid-hunting telescope? @NASA #NASA #astroid— leapsmag (@leapsmag) 1564681293.0