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.
Like any life-threatening medical condition that affects children, food allergies can traumatize more than just the patient. My wife and I learned this one summer afternoon when our daughter was three years old.
Emergency room visits for anaphylaxis in children more than doubled from 2010 to 2016.
At an ice cream parlor, I gave Samantha a lick of my pistachio cone; within seconds, red blotches erupted on her skin, her lips began to swell, and she complained that her throat felt funny. We rushed her to the nearest emergency room, where a doctor injected her with epinephrine. Explaining that the reaction, known as anaphylaxis, could have been fatal if left unchecked, he advised us to have her tested for nut allergies—and to start carrying an injector of our own.
After an allergist confirmed Sam's vulnerability to tree nuts and peanuts, we figured that keeping her safe would be relatively simple. But food allergies often come in bunches. Over the next year, she wound up back in the ER after eating bread with sesame seeds at an Italian restaurant, and again after slurping buckwheat noodles at our neighborhood Japanese. She hated eggs, so we discovered that (less severe) allergy only when she vomited after eating a variety of products containing them.
In recent years, a growing number of families have had to grapple with such challenges. An estimated 32 million Americans have food allergies, or nearly 10 percent of the population—10 times the prevalence reported 35 years ago. The severity of symptoms seems to be increasing, too. According to a study released in January by Food Allergy Research & Education (FARE), a Virginia-based nonprofit, insurance claims for anaphylactic food reactions rose 377 percent in the U.S. from 2007 to 2016.
Because food allergies most commonly emerge in childhood, these trends are largely driven by the young. An insurance-industry study found that emergency room visits for anaphylaxis in children more than doubled from 2010 to 2016. Peanut allergies, once rare, tripled in kids between 1997 and 2008. "The first year, it was 1 in 250," says Scott Sicherer, chief of pediatric allergy and immunology at New York City's Mount Sinai Hospital, who led that study. "When we did the next round of research, in 2002, it was 1 in 125. I thought there must be a mistake. But by 2008, it was 1 in 70."
The forces behind these dire statistics—as well as similar numbers throughout the developed world—have yet to be positively identified. But the leading suspects are elements of our modern lifestyle that can throw the immune system out of whack, prompting potentially deadly overreactions to harmless proteins. Although parents can take a few steps that might lessen their children's risk, societal changes may be needed to brighten the larger epidemiological picture.
Meanwhile, scientists are racing to develop therapies that can induce patients' hyped-up immune defenses to chill. And lately, they've made some big strides toward that goal.
A Variety of Culprits
In the United States, about 90 percent of allergic reactions come from eight foods: milk, eggs, peanuts, tree nuts, soy, wheat, fish, and shellfish. The list varies from country to country, depending on dietary customs, but what the trigger foods all have in common is proteins that can survive breakdown in the stomach and enter the bloodstream more or less intact.
"When we were kids, we played in the dirt. Today, children tend to be on their screens, inside sealed buildings."
A food allergy results from a chain of biochemical misunderstandings. The first time the immune system encounters an allergen (as a protein that triggers an allergy is known), it mistakes the substance for a hostile invader—perhaps a parasite with a similar molecular profile. In response, it produces an antibody called immunoglobin E (IgE), which is designed to bind to a specific protein and flag it for attack. These antibodies circulate through the bloodstream and attach to immune-system foot soldiers known as mast cells and basophils, which congregate in the nose, throat, lungs, skin, and gastrointestinal tract.
The next time the person is exposed to the allergen, the IgE antibodies signal the warrior cells to blast the intruder with histamines and other chemical weapons. Tissues in the affected areas swell and leak fluid; blood pressure may fall. Depending on the strength of the reaction, collateral damage to the patient can range from unpleasant—itching, runny nose, nausea—to catastrophic.
This kind of immunological glitchiness runs in families. Genome-wide association studies have identified a dozen genes linked to allergies of all types, and twin studies suggest that about 80 percent of the risk of food allergies is heritable. But why one family member shows symptoms while another doesn't remains unknown. Nor can genetics explain why food allergy rates have skyrocketed in such a brief period. For that, we must turn to the environment.
First, it's important to note that rates of all allergies are rising—including skin and respiratory afflictions—though none as rapidly or with as much risk of anaphylaxis as those involving food. The takeoff was already underway in the late 1980s, when British epidemiologist David P. Strachan found that children in larger households had fewer instances of hay fever. The reason, he suggested, was that their immune systems were strengthened by exposure to their siblings' germs. Since then, other researchers have discerned more evidence for Strachan's "hygiene hypothesis": higher rates of allergy (as well as autoimmune disorders) in cities versus rural areas, in industrialized countries versus developing ones, in lab animals raised under sterile conditions versus those exposed to germs.
Fending off a variety of pathogens, experts theorize, helps train the immune system to better distinguish friend from foe, and to respond to threats in a more nuanced manner. In an era of increasing urbanization, shrinking family sizes, and more sheltered lifestyles, such conditioning may be harder to come by. "When we were kids, we played in the dirt," observes Cathryn R. Nagler, a professor and food allergy researcher at the University of Chicago. "Today, children tend to be on their screens, inside sealed buildings."
But other factors may be driving the allergy epidemic as well. More time indoors, for example, means less exposure to sunlight, which can lead to a deficiency in vitamin D—a nutrient crucial to immune system regulation. The growing popularity of processed foods filled with refined fats and sugars may play a role, along with rising rates of obesity, by promoting tissue inflammation that could increase some people's risk of immunological mayhem. And the surge in allergies also correlates with several trends that may be altering the human microbiome, the community of microbes (including bacteria, viruses, and fungi, among others) that inhabits our guts, skin, and bodily orifices.
The microbiome connection may be particularly relevant to food allergies. In 2014, a team led by Nagler published a landmark study showing that Clostridia, a common class of gut bacteria, protects against these allergies. When the researchers fed peanut allergens to germ-free mice (born and raised in sterile conditions) and to mice treated with antibiotics as newborns (reducing their gut bacteria), the animals showed a strong immunological response. This sensitization could be reversed, however, by reintroducing Clostridia—but not another class of bacteria, Bacteroides—into the mice. Further experiments revealed that Clostridia caused immune cells to produce high levels of interleukin-22 (IL-22), a signaling molecule known to decrease the permeability of the intestinal lining.
"In simple terms," Nagler says, "what we found is that these bacteria prevent food allergens from gaining access to the blood in an intact form that elicits an allergic reaction."
A growing body of evidence suggests that our eating habits are throwing our gut microbiota off-balance, in part by depriving helpful species of the dietary fiber they feed on. Our increasing exposure to antibiotics and antimicrobial compounds may be harming our beneficial bugs as well. These depletions could affect kids from the moment they enter the world: Because babies are seeded with their mothers' microbiota as they pass through the birth canal, they may be inheriting a less diverse microbiome than did previous generations. And the rising rate of caesarian deliveries may be further depriving our children of the bugs they need.
On expert suggests two measures worth a try: increasing consumption of fiber, and reducing use of antimicrobial agents, from antibacterial cleaners to antibiotics.
So which culprit is most responsible for the food allergy upsurge? "The illnesses that we're measuring are complex," says Sicherer. "There are multiple genetic inputs, which interact with one another, and there are multiple environmental inputs, which interact with each other and with the genes. There's not one single thing that's causing this. It's a conglomeration."
What Parents Can Do
For anyone hoping to reduce their child's or their own odds of developing a food allergy (rates of adult onset are also increasing), the current state of science offers few guideposts. As with many other areas of health research, it's hard to know when the data is solid enough to warrant a particular course of action. A case in point: the American Academy of Pediatrics once recommended that children at risk of allergy to peanuts (as evidenced by family history, other food allergies, or eczema) wait to eat them until age three; now, the AAP advises those parents to start their babies at four months, citing epidemiological evidence that early exposure may prevent peanut allergies.
And it's all too easy for a layperson to draw mistaken conclusions from media coverage of such research—inferring, for instance, that taking commercially available probiotics might have a protective effect. Unfortunately, says Nagler, none of those products even contain the relevant kind of bacteria.
Although, as a research scientist, she refrains from giving medical advice, Nagler does suggest (based on a large body of academic literature) that two measures are worth a try: increasing consumption of fiber, and reducing use of antimicrobial agents, from antibacterial cleaners to antibiotics. Yet she acknowledges that it's not always possible to avoid the suspected risk factors for food allergies. Sometimes an antibiotic is a lifesaving necessity, for example—and it's tough to avoid exposure to such drugs altogether, due to their use in animal feed and their consequent presence in many foods and in the water supply. If these chemicals are contributing to the food allergy epidemic, protecting ourselves will require action from farmers, doctors, manufacturers, and policymakers.
My family's experience illustrates the limits of healthy lifestyle choices in mitigating allergy risk. My daughter and son were born without C-sections; both were breastfed as well, receiving maximum microbial seeding from their mother. As a family, we eat exemplary diets, and no one could describe our home as excessively clean. Yet one child can't taste nuts, sesame, or buckwheat without becoming dangerously ill. "You can do everything right and still have allergies," says Ian A. Myles, a staff clinician at the National Institute of Allergy and Infectious Diseases. "You can do everything wrong and not have allergies. The two groups overlap."
The Latest Science Shows Promise
But while preventing all food allergies is clearly unrealistic, researchers are making remarkable progress in developing better treatments—therapies that, instead of combating symptoms after they've started (like epinephrine or antihistamines), aim to make patients less sensitive to allergens in the first place. One promising approach is oral immunotherapy (OIT), in which patients consume small but slowly increasing amounts of an allergen, gradually reducing their sensitivity. A study published last year in the New England Journal of Medicine showed that an experimental OIT called AR101, consisting of a standardized peanut powder mixed into food, enabled 67 percent of participants to tolerate a dose equivalent to two peanut kernels—a potential lifesaver if they were accidentally exposed to the real thing.
Because OIT itself can trigger troublesome reactions in some patients, however, it's not for everyone. Another experimental treatment, sublingual immunotherapy (SLIT) uses an allergen solution or dissolving tablet placed beneath the tongue; although its results are less robust than OIT's, it seems to generate milder side effects. Epicutaneous immunotherapy (EPIT) avoids the mouth entirely, using a technology similar to a nicotine patch to deliver allergens through the skin. Researchers are also exploring the use of medications known as biologics, aiming to speed up the action of immunotherapies by suppressing IgE or targeting other immune-system molecules.
These findings suggest that drugs based on microbial metabolites could help protect vulnerable individuals against a wide range of allergies.
One downside of the immunotherapy approach is that in most cases the allergen must be taken indefinitely to maintain desensitization. To provide a potentially permanent fix, scientists are working on vaccines that use DNA or peptides (protein fragments) from allergens to reset patients' immune systems.
Nagler is attacking the problem from a different angle—one that starts with the microbiome. In a recent study, a follow-up to her peanut-allergy investigation, she and her colleagues found that Clostridia bacteria protect mice against milk allergy as well; they also identified a particular species responsible, known as Anaerostipes caccae. The bugs, the team determined, produce a short-chain fatty acid called butyrate, which modulates many immune activities crucial to maintaining a well-sealed gut.
These findings suggest that drugs based on microbial metabolites could help protect vulnerable individuals against a wide range of allergies. Nagler has launched a company, ClostraBio, to develop biotherapeutics based on this notion; she expects its first product, using synthetic butyrate, to be ready for clinical trials within the next two years.
My daughter could well be a candidate for such a medication. Sam, now 15, is a vibrant, resilient kid who handles her allergies with confidence and humor. Thanks to vigilance and luck (on her part as well as her parents'), she hasn't had another food-related ER visit in more than a decade; she's never had to use her Epi-Pen. Still, she says, she would welcome the arrival of a pill that could reduce the danger. "I've learned how to watch out for myself," she says. "But it would be nice not to have to be so careful."
Imagine eating a slice of cake for breakfast. It's deliciously indulgent, but instead of your blood sugar spiking, your body processes all that sweetness as a healthy high-protein meal. It may sound like sci-fi, but this scenario is not necessarily far off.
"People with diabetes could especially benefit because sweet proteins don't trigger a need for insulin."
The Lowdown
An award-winning agtech startup called Amai is developing "sweet proteins," based on the molecular structure of naturally occuring exotic fruits. These new sugar substitutes could potentially replace artificial sweeteners and help people who are trying to curb their sugar intake. People with diabetes could especially benefit because sweet proteins don't trigger a need for insulin.
While there is a sweet protein currently on the market today called thaumatin, it's expensive, has a short shelf life, and is lacking in the taste department. But Amai's proteins taste 70 to 100 percent identical to the sweet ones found in nature. Once their molecular structure is designed through a sophisticated computing platform, they are made through fermentation, which is akin to brewing beer. These non-GMO proteins are over 10,000 times sweeter than sugar, which means much less needs to be produced and used.
Diseases like diabetes and heart disease, which are often linked to sugar overconsumption, have been on a major upswing over the last few decades, especially in the United States. According to the CDC, 100 million adults in the United States are now living with diabetes or prediabetes, which if not treated, often leads to type 2 diabetes within five years. By 2030, scientists predict cases of diabetes in the U.S. will increase by 54 percent. If sugar proteins like the type Amai is creating become widely available, these numbers could begin to decrease.
Next Up
Amai's sweet proteins are still in the research and development stage, but the Israeli startup is raising significant funding that should help expedite the process. They're also substantially upping their production ability by expanding their facilities.
Will consumers be comfortable ingesting a lab-designed food product?
And in March, the USDA and FDA announced plans to regulate cell-cultured foods, the category in which these sugar proteins would fall, so Amai researchers are hopeful they'll have an easier path to approval once their product is market ready.
Open Questions
All this progress may sound promising, but Amai still has a long way to go before the reality of healthy cake becomes tangible. Some questions to consider: Will consumers be comfortable ingesting a lab-designed food product? Will it taste enough like real sugar?
And if some products and brands begin to adopt it, will it ever overtake the real thing in popularity and make a dent in diseases like diabetes and obesity? Only time, more research, and a lot more money will tell, but in the meantime, feel free to daydream about eating entire pints of ice cream without needing to hit the gym.