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.
Podcast: New Solutions to Combat Gluten Sensitivities and Food Allergies
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.
This month, we talk Anat Binur, the CEO of Israeli/U.S.-based biotech company Ukko. Ukko is taking a revolutionary approach to the distressing problem of food allergies and gluten sensitivities: their scientists are designing and engineering proteins that keep the good biophysical properties of the original proteins, while removing the immune-triggering parts that can cause life-threatening allergies. The end goal is proteins that are safe for everyone. Ukko is focusing first on developing a new safe gluten protein for use in baking and a new peanut protein for use as a therapeutic. Their unique platform could theoretically be used for any protein-based allergy, including cats and bees. Hear more in this episode.
Watch the 60-second trailer
Listen to the whole episode
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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.
Can a Non-Invasive Magnetic Helmet Treat Brain Cancer?
Glioblastoma is an aggressive and deadly brain cancer, causing more than 10,000 deaths in the US per year. In the last 30 years there has only been limited improvement in the survival rate despite advances in radiation therapy and chemotherapy. Today the typical survival rate is just 14 months and that extra time is spent suffering from the adverse and often brutal effects of radiation and chemotherapy.
Scientists are trying to design more effective treatments for glioblastoma with fewer side effects, and a team at the Department of Neurosurgery at Houston Methodist Hospital has created a magnetic helmet-based treatment called oncomagnetic therapy: a promising non-invasive treatment for shrinking cancerous tumors. In the first patient tried, the device was able to reduce the tumor of a glioblastoma patient by 31%. The researchers caution, however, that much more research is needed to determine its safety and effectiveness.
How It Works
“The whole idea originally came from a conversation I had with General Norman Schwarzkopf, a supposedly brilliant military strategist,” says David Baskin, professor of neurosurgery and leader of the effort at Houston Methodist. “I asked him what is the secret to your success and he said, ‘Energy. Take out the power grid and the enemy can't communicate.’ So I thought about what supplies [energy to] cancer, especially brain cancer.”
Baskin came up with the idea of targeting the mitochondria, which process and produce energy for cancer cells.
"This is the most exciting thing in glioblastoma treatment I've seen since I've been a neurosurgeon, but it is very preliminary,” Baskin says.
The magnetic helmet creates a powerful oscillating magnetic field. At a set range of frequencies and timings, it disrupts the flow of electrons in the mitochondria of cancer cells. This leads to a release of certain chemicals called Reactive Oxygen Species, or ROS. In normal cells, this excess ROS is much lower, and it's neutralized by other chemicals called antioxidants.
However, cancer cells already have more ROS: they grow rapidly and uncontrollably, so their mitochondria need to produce more energy which in turn generates more ROS. By using the powerful magnetic field, levels of ROS get so high that the malignant cells are torn apart.
The biggest challenge was working out the specific range of frequencies and timing parameters they needed to use to kill cancer cells. It took skill, intuition, luck and lots of experiments. The helmet could theoretically be used to treat all types of glioblastoma.
Developing the magnetic helmet was a collaborative process. Santosh Helekar is a neuroscientist at Houston Methodist Research Institute and the director of oncomagnetics (magnetic cancer therapies) at the Peak Center in Houston Methodist Hospital. His previous invention with colleagues gave the team a starting point to build on. “About 7 years back I developed a portable brain magnetic stimulation device to conduct brain research,” Helekar says. “We [then] conducted a pilot clinical trial in stroke patients. The results were promising.”
Helekar presented his findings to neurosurgeons including Baskin. They decided to collaborate. With a team of scientists behind them, they modified the device to kill cancer cells.
The magnetic helmet studied for treatment of glioblastoma
Dr. David Baskin
Initial Results
After success in the lab, the team got FDA approval to conduct a compassionate trial in a 53-year-old man with end-stage glioblastoma. He had tried every other treatment available. But within 30 days of using the magnetic helmet his tumor shrank by 31%.
Sadly, 36 days into the treatment, the patient had an unrelated head injury due to a fall. The treatment was paused and he later died of the injury. Autopsy results of his brain highlighted the dramatic reduction in tumor cells.
Baskin says, “This is the most exciting thing in glioblastoma treatment I've seen since I've been a neurosurgeon, but it is very preliminary.”
The helmet is part of a growing number of non-invasive cancer treatments. One device that is currently being used by glioblastoma patients is Optune. It uses electric fields called tumor treating fields to slow down cell division and has been through a successful phase 3 clinical trial.
The magnetic helmet has the promise to be another useful non-invasive treatment according to Professor Gabriel Zada, a neurosurgeon and director of the USC Brain Tumor Center. “We're learning that various electromagnetic fields and tumor treating fields appear to play a role in glioblastoma. So there is some precedent for this though the tumor treating fields work a little differently. I think there is major potential for it to be effective but of course it will require some trials.”
Professor Jonathan Sherman, a neurosurgeon and director of neuro-oncology at West Virginia University, reiterates the need for further testing. “It sounds interesting but it’s too early to tell what kind of long-term efficacy you get. We do not have enough data. Also if you’re disrupting [the magnetic field] you could negatively impact a patient. You could be affecting the normal conduction of electromagnetic activity in the brain.”
The team is currently extending their research. They are now testing the treatment in two other patients with end-stage glioblastoma. The immediate challenge is getting FDA approval for those at an earlier stage of the disease who are more likely to benefit.
The Future
Baskin and the team are designing a clinical trial in the U.S., .U.K. and Germany. After positive results in cell cultures, they’re in negotiations to collaborate with other researchers in using the technology for lung and breast cancer. With breast cancer, the soft tissue is easier to access so a magnetic device could be worn over the breast.
“My hope is to develop a treatment to treat and hopefully cure glioblastoma without radiation or chemotherapy,” Baskin says. “We're onto a strategy that could make a huge difference for patients with this disease and probably for patients with many other forms of cancer.”