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.
Its strength is in its lack of size.
Using materials on the minuscule scale of nanometers (billionths of a meter), nanomedicines have the ability to provide treatment more precise than any other form of medicine. Under optimal circumstances, they can target specific cells and perform feats like altering the expression of proteins in tumors so that the tumors shrink.
Another appealing concept about nanomedicine is that treatment on a nano-scale, which is smaller yet than individual cells, can greatly decrease exposure to parts of the body outside the target area, thereby mitigating side effects.
But this young field's huge potential has met with an ongoing obstacle: the recipient's immune system tends to regard incoming nanomedicines as a threat and launches a complement protein attack. These complement proteins, which act together through a wave of reactions to get rid of troubling microorganisms, have had more than 500 million years to refine their craft, so they are highly effective.
Seeking to overcome a half-billion-year disadvantage, nanomaterials engineers have tried such strategies as creating so-called stealth nanoparticles.
“All new technologies face technical barriers, and it is the job of innovators to engineer solutions to them,” Brenner says.
Despite these clever attempts, nanomedicines largely keep failing to arrive at their intended destinations. According to the most comprehensive meta-analysis of nanomedicines in oncology, fewer than 1 percent of nanoparticles manage to reach their targets. The remaining 99-plus percent are expelled to the liver, spleen, or lungs – thereby squandering their therapeutic potential. Though these numbers seem discouraging, systems biologist Jacob Brenner remains undaunted. “All new technologies face technical barriers, and it is the job of innovators to engineer solutions to them,” he says.
Brenner and his fellow researchers at the Perelman School of Medicine at the University of Pennsylvania have recently devised a method that, in a study published in late 2021 involving sepsis-afflicted mice, saw a longer half-life of nanoparticles in the bloodstream. This effect is crucial because “the longer our nanoparticles circulate, the more time they have to reach their target organs,” says Brenner, the study's co-principal investigator. He works as a critical care physician at the Hospital of the University of Pennsylvania, where he also serves as an assistant professor of medicine.
The method used by Brenner's lab involves coating nanoparticles with natural suppressors that safeguard against a complement attack from the recipient's immune system. For this idea, he credits bacteria. “They are so much smarter than us,” he says.
Brenner points out that many species of bacteria have learned to coat themselves in a natural complement suppressor known as Factor H in order to protect against a complement attack.
Humans also have Factor H, along with an additional suppressor called Factor I, both of which flow through our blood. These natural suppressors “are recruited to the surface of our own cells to prevent complement [proteins] from attacking our own cells,” says Brenner.
Coating nanoparticles with a natural suppressor is a “very creative approach that can help tone and improve the activity of nanotechnology medicines inside the body,” says Avi Schroeder, an associate professor at Technion - Israel Institute of Technology, where he also serves as Head of the Targeted Drug Delivery and Personalized Medicine Group.
Schroeder explains that “being able to tone [down] the immune response to nanoparticles enhances their circulation time and improves their targeting capacity to diseased organs inside the body.” He adds how the approach taken by the Penn Med researchers “shows that tailoring the surface of the nanoparticles can help control the interactions the nanoparticles undergo in the body, allowing wider and more accurate therapeutic activity.”
Brenner says he and his research team are “working on the engineering details” to streamline the process. Such improvements could further subdue the complement protein attacks which for decades have proven the bane of nanomedical engineers.
Though these attacks have limited nanomedicine's effectiveness, the field has managed some noteworthy successes, such as the chemotherapy drugs Abraxane and Doxil, the first FDA-approved nanomedicine.
And amid the COVID-19 pandemic, nanomedicines became almost universally relevant with the vast circulation of the Moderna and Pfizer-BioNTech vaccines, both of which consist of lipid nanoparticles. “Without the nanoparticle, the mRNA would not enter the cells effectively and would not carry out the therapeutic goal,” Schroeder explains.
These vaccines, though, are “just the start of the potential transformation that nanomedicine will bring to the world,” says Brenner. He relates how nanomedicine is “joining forces with a number of other technological innovations,” such as cell therapies in which nanoparticles aim to reprogram T-cells to attack cancer.
With a similar degree of optimism, Schroeder says, “We will see further growing impact of nanotechnologies in the clinic, mainly by enabling gene therapy for treating and even curing diseases that were incurable in the past.”
Brenner says that in the next 10 to 15 years, “nanomedicine is likely to impact patients” contending with a “huge diversity” of conditions. “I can't wait to see how it plays out.”
Podcast: A Nasal Spray COVID Booster Shot, With Dr. Akiko Iwasaki
The "Making Sense of Science" podcast features interviews with leading medical and scientific experts about the latest developments and the big ethical and societal questions they raise. This monthly podcast is hosted by journalist Kira Peikoff, founding editor of the award-winning science outlet Leaps.org.
Real-world data shows that protection against Covid-19 infection wanes a few months after two or three shots of mRNA vaccines (while protection against severe disease remains high). But what if there was another kind of booster that could shore up the immune response in your nose, the "door" to your body? Like bouncers at a club, a better prepared nasal defense system could stop the virus in its tracks -- mitigating illnesses as well as community spread. Dr. Akiko Iwasaki, an immunologist at Yale, is working on such a booster, with fantastic results recently reported in mice. In this episode, she shares the details of this important work.
Listen to episode
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.