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.
This “Absolutely Tireless” Researcher Made an Important Breakthrough for Cancer Patients
After months of looking at dead cells under a microscope, Theo Roth finally glimpsed what he had been hoping to see—flickers of green. His method was working.
"If we can go into the cell and add in new code and instructions, now we can give it whatever new functions we want."
When Roth joined the laboratory of Alex Marson at the University of California, San Francisco in June 2016, he set to work trying to figure out a new way to engineer human T cells, a type of white blood cell that's an important part of the immune system. If he succeeded, the resulting approach could make it easier and faster for scientists to develop and test cell and gene therapies, new treatments that involve genetically reprogramming the body's own cells.
For decades, researchers have been using engineered viruses to bestow human cells with new genetic characteristics. These so-called viral vectors "infect" human cells, transferring whatever new genetic material scientists put into them. The idea is that this new DNA could give T cells a boost to better fight diseases like cancer and HIV.
Several successful clinical trials have used virally-modified human T cells, and in fact, the U.S. Food and Drug Administration last year approved two such groundbreaking cancer gene therapies, Kymriah and Yescarta. But the process of genetically manipulating cells with viruses is expensive and time-consuming. In addition, viruses tend to randomly insert DNA with little predictability.
"What Theo wanted to do was to paste in big sequences of DNA at a targeted site without viruses," says Marson, an associate professor of microbiology and immunology. "That would have the benefit of being able to rewrite a specific site in the genome and do it flexibly and quickly without having to make a new virus for every site you want to manipulate."
Scientists have for a while been interested in non-viral engineering methods, but T cells are fragile and notoriously difficult to work with.
Previously, Marson's lab had collaborated with CRISPR pioneer Jennifer Doudna and her team at the University of California, Berkeley to use an electrical pulse together with CRISPR components to knock out certain genes. They also found some success with inserting very small pieces of DNA into a targeted site.
But Roth, a 27-year-old graduate student at UCSF pursuing MD and PhD degrees, was determined to figure out how to paste in much bigger sequences of genetic information. Marson says it was an "ambitious" goal. Scientists had tried before, but found that stuffing large chunks of DNA into T cells would quickly kill them.
"If we can go into the cell and add in new code and instructions, now we can give it whatever new functions we want," Roth says. "If you can add in new DNA sequences at the site that you want, then you have a much greater capacity to generate a cell that's going to be therapeutic or curative for a disease."
"He has already made his mark on the field."
So Roth began experimenting with hundreds of different variables a week, trying to find the right conditions to allow him to engineer T cells without the need for viruses. To know if the technique was working, Roth and his colleagues used a green fluorescent protein that would be expressed in cells that had successfully been modified.
"We went from having a lot of dead cells that didn't have any green to having maybe 1 percent of them being green," Roth says. "At that stage we got really excited."
After nearly a year of testing, he and collaborators found a combination of T cell ratios and DNA quantity mixed with CRISPR and zaps of electricity that seemed to work. These electrical pulses, called electroporation, deliver a jolt to cells that makes their membranes temporarily more permeable, allowing the CRISPR system to slip through. Once inside cells, CRISPR seeks out a specific place in the genome and makes a programmed, precise edit.
Roth and his colleagues used the approach to repair a genetic defect in T cells taken from children with a rare autoimmune disease and also to supercharge T cells so that they'd seek out and selectively kill human cancer cells while leaving healthy cells intact. In mice transplanted with human melanoma tissue, the edited T cells went to straight to the cancerous cells and attacked them. The findings were published in Nature in July.
Marson and Roth think even a relatively small number of modified T cells could be effective at treating some cancers, infections, and autoimmune diseases.
Roth is now working with the Parker Institute for Cancer Immunotherapy in San Francisco to engineer cells to treat a variety of cancers and hopefully commercialize his technique. Fred Ramsdell, vice president at the Parker Institute, says he's impressed by Roth's work. "He has already made his mark on the field."
Right now, there's a huge manufacturing backlog for viruses. If researchers want to start a clinical trial to test a new gene or cell therapy, they often have to wait a year to get the viruses they need.
"I think the biggest immediate impact is that it will lower the cost of a starting an early phase clinical trial."
Ramsdell says what Roth's findings allow researchers to do is engineer T cells quickly and more efficiently, cutting the time it takes to make them from several months to just a few weeks. That will allow researchers to develop and test several potential therapies in the lab at once.
"I think the biggest immediate impact is that it will lower the cost of a starting an early phase clinical trial," Roth says.
This isn't the first time Roth's work has been in the spotlight. As an undergraduate at Stanford University, he made significant contributions to traumatic brain injury research by developing a mouse model for observing the brain's cellular response to a concussion. He started the research, which was also published in Nature, the summer before entering college while he was an intern in Dorian McGavern's lab at the National Institutes of Health.
When Roth entered UCSF as a graduate student, his scientific interests shifted.
"It's definitely a big leap" from concussion research, says McGavern, who still keeps in touch with Roth. But he says he's not surprised about Roth's path. "He's absolutely tireless when it comes to the pursuit of science."
Roth says he's optimistic about the potential for gene and cell therapies to cure patients. "I want to try to figure out what one of the next therapies we should put into patients should be."
"Here's a question for you," I say to our dinner guests, dodging a knowing glance from my wife. "Imagine a future in which you could surgically replace your legs with robotic substitutes that had all the functionality and sensation of their biological counterparts. Let's say these new legs would allow you to run all day at 20 miles per hour without getting tired. Would you have the surgery?"
Why are we so married to the arbitrary distinction between rehabilitating and augmenting?
Like most people I pose this question to, our guests respond with some variation on the theme of "no way"; the idea of undergoing a surgical procedure with the sole purpose of augmenting performance beyond traditional human limits borders on the unthinkable.
"Would your answer change if you had arthritis in your knees?" This is where things get interesting. People think differently about intervention when injury or illness is involved. The idea of a major surgery becomes more tractable to us in the setting of rehabilitation.
Consider the simplistic example of human walking speed. The average human walks at a baseline three miles per hour. If someone is only able to walk at one mile per hour, we do everything we can to increase their walking ability. However, to take a person who is already able to walk at three miles per hour and surgically alter their body so that they can walk twice as fast seems, to us, unreasonable.
What fascinates me about this is that the three-mile-per-hour baseline is set by arbitrary limitations of the healthy human body. If we ignore this reference point altogether, and consider that each case simply offers an improvement in walking ability, the line between augmentation and rehabilitation all but disappears. Why, then, are we so married to this arbitrary distinction between rehabilitating and augmenting? What makes us hold so tightly to baseline human function?
Where We Stand Now
As the functionality of advanced prosthetic devices continues to increase at an astounding rate, questions like these are becoming more relevant. Experimental prostheses, intended for the rehabilitation of people with amputation, are now able to replicate the motions of biological limbs with high fidelity. Neural interfacing technologies enable a person with amputation to control these devices with their brain and nervous system. Before long, synthetic body parts will outperform biological ones.
Our approach allows people to not only control a prosthesis with their brain, but also to feel its movements as if it were their own limb.
Against this backdrop, my colleagues and I developed a methodology to improve the connection between the biological body and a synthetic limb. Our approach, known as the agonist-antagonist myoneural interface ("AMI" for short), enables us to reflect joint movement sensations from a prosthetic limb onto the human nervous system. In other words, the AMI allows people to not only control a prosthesis with their brain, but also to feel its movements as if it were their own limb. The AMI involves a reimagining of the amputation surgery, so that the resultant residual limb is better suited to interact with a neurally-controlled prosthesis. In addition to increasing functionality, the AMI was designed with the primary goal of enabling adoption of a prosthetic limb as part of a patient's physical identity (known as "embodiment").
Early results have been remarkable. Patients with below-knee AMI amputation are better able to control an experimental prosthetic leg, compared to people who had their legs amputated in the traditional way. In addition, the AMI patients show increased evidence of embodiment. They identify with the device, and describe feeling as though it is part of them, part of self.
Where We're Going
True embodiment of robotic devices has the potential to fundamentally alter humankind's relationship with the built world. Throughout history, humans have excelled as tool builders. We innovate in ways that allow us to design and augment the world around us. However, tools for augmentation are typically external to our body identity; there is a clean line drawn between smart phone and self. As we advance our ability to integrate synthetic systems with physical identity, humanity will have the capacity to sculpt that very identity, rather than just the world in which it exists.
For this potential to be realized, we will need to let go of our reservations about surgery for augmentation. In reality, this shift has already begun. Consider the approximately 17.5 million surgical and minimally invasive cosmetic procedures performed in the United States in 2017 alone. Many of these represent patients with no demonstrated medical need, who have opted to undergo a surgical procedure for the sole purpose of synthetically enhancing their body. The ethical basis for such a procedure is built on the individual perception that the benefits of that procedure outweigh its costs.
At present, it seems absurd that amputation would ever reach this point. However, as robotic technology improves and becomes more integrated with self, the balance of cost and benefit will shift, lending a new perspective on what now seems like an unfathomable decision to electively amputate a healthy limb. When this barrier is crossed, we will collide head-on with the question of whether it is acceptable for a person to "upgrade" such an essential part of their body.
At a societal level, the potential benefits of physical augmentation are far-reaching. The world of robotic limb augmentation will be a world of experienced surgeons whose hands are perfectly steady, firefighters whose legs allow them to kick through walls, and athletes who never again have to worry about injury. It will be a world in which a teenage boy and his grandmother embark together on a four-hour sprint through the woods, for the sheer joy of it. It will be a world in which the human experience is fundamentally enriched, because our bodies, which play such a defining role in that experience, are truly malleable.
This is not to say that such societal benefits stand without potential costs. One justifiable concern is the misuse of augmentative technologies. We are all quite familiar with the proverbial supervillain whose nervous system has been fused to that of an all-powerful robot.
The world of robotic limb augmentation will be a world of experienced surgeons whose hands are perfectly steady.
In reality, misuse is likely to be both subtler and more insidious than this. As with all new technology, careful legislation will be necessary to work against those who would hijack physical augmentations for violent or oppressive purposes. It will also be important to ensure broad access to these technologies, to protect against further socioeconomic stratification. This particular issue is helped by the tendency of the cost of a technology to scale inversely with market size. It is my hope that when robotic augmentations are as ubiquitous as cell phones, the technology will serve to equalize, rather than to stratify.
In our future bodies, when we as a society decide that the benefits of augmentation outweigh the costs, it will no longer matter whether the base materials that make us up are biological or synthetic. When our AMI patients are connected to their experimental prosthesis, it is irrelevant to them that the leg is made of metal and carbon fiber; to them, it is simply their leg. After our first patient wore the experimental prosthesis for the first time, he sent me an email that provides a look at the immense possibility the future holds:
What transpired is still slowly sinking in. I keep trying to describe the sensation to people. Then this morning my daughter asked me if I felt like a cyborg. The answer was, "No, I felt like I had a foot."