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.
Scientists Just Started Testing a New Class of Drugs to Slow--and Even Reverse--Aging
Imagine reversing the processes of aging. It's an age-old quest, and now a study from the Mayo Clinic may be the first ray of light in the dawn of that new era.
The immune system can handle a certain amount of senescence, but that capacity declines with age.
The small preliminary report, just nine patients, primarily looked at the safety and tolerability of the compounds used. But it also showed that a new class of small molecules called senolytics, which has proven to reverse markers of aging in animal studies, can work in humans.
Aging is a relentless assault of chronic diseases including Alzheimer's, cardiovascular disease, diabetes, and frailty. Developing one chronic condition strongly predicts the rapid onset of another. They pile on top of each other and impede the body's ability to respond to the next challenge.
"Potentially, by targeting fundamental aging processes, it may be possible to delay or prevent or alleviate multiple age-related conditions and many diseases as a group, instead of one at a time," says James Kirkland, the Mayo Clinic physician who led the study and is a top researcher in the growing field of geroscience, the biology of aging.
Getting Rid of "Zombie" Cells
One element common to many of the diseases is senescence, a kind of limbo or zombie-like state where cells no longer divide or perform many regular functions, but they don't die. Senescence is thought to be beneficial in that it inhibits the cancerous proliferation of cells. But in aging, the senescent cells still produce molecules that create inflammation both locally and throughout the body. It is a cycle that feeds upon itself, slowly ratcheting down normal body function and health.
Disease and harmful stimuli like radiation to treat cancer can also generate senescence, which is why young cancer patients seem to experience earlier and more rapid aging. The immune system can handle a certain amount of senescence, but that capacity declines with age. There also appears to be a threshold effect, a tipping point where senescence becomes a dominant factor in aging.
Kirkland's team used an artificial intelligence approach called machine learning to look for cell signaling networks that keep senescent cells from dying. To date, researchers have identified at least eight such signaling networks, some of which seem to be unique to a particular type of cell or tissue, but others are shared or overlap.
Then a computer search identified molecules known to disrupt these signaling pathways "and allow cells that are fully senescent to kill themselves," he explains. The process is a bit like looking for the right weapons in a video game to wipe out lingering zombie cells. But instead of swords, guns, and grenades, the list of biological tools so far includes experimental molecules, approved drugs, and natural supplements.
Treatment
"We found early on that targeting single components of those networks will only kill a very small minority of senescent cells or senescent cell types," says Kirkland. "So instead of going after one drug-one target-one disease, we're going after networks with combinations of drugs or drugs that have multiple targets. And we're going after every age-related disease."
The FDA is grappling with guidance for researchers wanting to conduct clinical trials on something as broad as aging rather than a single disease.
The large number of potential senolytic (i.e. zombie-neutralizing) compounds they identified allowed Kirkland to be choosy, "purposefully selecting drugs where the side effects profile was good...and with short elimination half-lives." The hit and run approach meant they didn't have to worry about maintaining a steady state of drugs in the body for an extended period of time. Some of the compounds they selected need only a half hour exposure to trigger the dying process in senescent cells, which can then take several days.
Work in mice has already shown impressive results in reversing diabetes, weight gain, Alzheimer's, cardiovascular disease and other conditions using senolytic agents.
That led to Kirkland's pilot study in humans with diabetes-related kidney disease using a three-day regimen of dasatinib, a kinase inhibitor first approved in 2006 to treat some forms of blood cancer, and quercetin, a flavonoid found in many plants and sold as a food supplement.
The combination was safe and well tolerated; it reduced the number of senescent cells in the belly fat of patients and restored their normal function, according to results published in September in the journal EBioMedicine. This preliminary paper was based on 9 patients in an ongoing study of 30 patients.
Kirkland cautions that these are initial and incomplete findings looking primarily at safety issues, not effectiveness. There is still much to be learned about the use of senolytics, starting with proof that they actually provide clinical benefit, and against what chronic conditions. The drug combinations, doses, duration, and frequency, not to mention potential risks all must be worked out. Additional studies of other diseases are being developed.
What's Next
Ron Kohanski, a senior administrator at the NIH National Institute on Aging (NIA), says the field of senolytics is so new that there isn't even a consensus on how to identify a senescent cell, and the FDA is grappling with guidance for researchers wanting to conduct clinical trials on something as broad as aging rather than a single disease.
Intellectual property concerns may temper the pharmaceutical industry's interest in developing senolytics to treat chronic diseases of aging. It looks like many mix-and-match combinations are possible, and many of the potential molecules identified so far are found in nature or are drugs whose patents have or will soon expire. So the ability to set high prices for such future drugs, and hence the willingness to spend money on expensive clinical trials, may be limited.
Still, Kohanski believes the field can move forward quickly because it often will include products that are already widely used and have a known safety profile. And approaches like Kirkland's hit and run strategy will minimize potential exposure and risk.
He says the NIA is going to support a number of clinical trials using these new approaches. Pharmaceutical companies may feel that they can develop a unique part of a senolytic combination regimen that will justify their investment. And if they don't, countries with socialized medicine may take the lead in supporting such research with the goal of reducing the costs of treating aging patients.
A New Test Aims to Objectively Measure Pain. It Could Help Legitimate Sufferers Access the Meds They Need.
"That throbbing you feel for the first minute after a door slams on your finger."
This is how Central Florida resident Bridgett Willkie describes the attacks of pain caused by her sickle cell anemia – a genetic blood disorder in which a patient's red blood cells become shaped like sickles and get stuck in blood vessels, thereby obstructing the flow of blood and oxygen.
"I found myself being labeled as an addict and I never was."
Willkie's lifelong battle with the condition has led to avascular necrosis in both of her shoulders, hips, knees and ankles. This means that her bone tissue is dying due to insufficient blood supply (sickle cell anemia is among the medical conditions that can decrease blood flow to one's bones).
"That adds to the pain significantly," she says. "Every time my heart beats, it hurts. And the pain moves. It follows the path of circulation. I liken it to a traffic jam in my veins."
For more than a decade, she received prescriptions for Oxycontin. Then, four years ago, her hematologist – who had been her doctor for 18 years – suffered a fatal heart attack. She says her longtime doctor's replacement lacked experience treating sickle cell patients and was uncomfortable writing her a prescription for opioids. What's more, this new doctor wanted to place her in a drug rehab facility.
"Because I refused to go, he stopped writing my scripts," she says. The ensuing three months were spent at home, detoxing. She describes the pain as unbearable. "Sometimes I just wanted to die."
One of the effects of the opioid epidemic is that many legitimate pain patients have seen their opioids significantly reduced or downright discontinued because of their doctors' fears of over-prescribing addictive medications.
"I found myself being labeled as an addict and I never was...Being treated like a drug-seeking patient is degrading and humiliating," says Willkie, who adds that when she is at the hospital, "it's exhausting arguing with the doctors...You dread them making their rounds because every day they come in talking about weaning you off your meds."
Situations such as these are fraught with tension between patients and doctors, who must remain wary about the risk of over-prescribing powerful and addictive medications. Adding to the complexity is that it can be very difficult to reliably assess a patient's level of physical pain.
However, this difficulty may soon decline, as Indiana University School of Medicine researchers, led by Dr. Alexander B. Niculescu, have reportedly devised a way to objectively assess physical pain by analyzing biomarkers in a patient's blood sample. The results of a study involving more than 300 participants were published earlier this year in the journal Molecular Psychiatry.
Niculescu – who is both a professor of psychiatry and medical neuroscience at the IU School of Medicine – explains that, when someone is in severe physical pain, a blood sample will show biomarkers related to intracellular adhesion and cell-signaling mechanisms. He adds that some of these biomarkers "have prior convergent evidence from animal or human studies for involvement in pain."
Aside from reliably measuring pain severity, Niculescu says blood biomarkers can measure the degree of one's response to treatment and also assess the risk of future recurrences of pain. He believes this new method's greatest benefit, however, might be the ability to identify a number of non-opioid medications that a particular patient is likely to respond to, based on his or her biomarker profile.
Clearly, such a method could be a gamechanger for pain patients and the professionals who treat them. As of yet, health workers have been forced to make crucial decisions based on their clinical impressions of patients; such impressions are invariably subjective. A method that enables people to prove the extent of their pain could remove the stigma that many legitimate pain patients face when seeking to obtain their needed medicine. It would also improve their chances of receiving sufficient treatment.
Niculescu says it's "theoretically possible" that there are some conditions which, despite being severe, might not reveal themselves through his testing method. But he also says that, "even if the same molecular markers that are involved in the pain process are not reflected in the blood, there are other indirect markers that should reflect the distress."
Niculescu expects his testing method will be available to the medical community at large within one to three years.
Willkie says she would welcome a reliable pain assessment method. Well-aware that she is not alone in her plight, she has more than 500 Facebook friends with sickle cell disease, and she says that "all of their opioid meds have been restricted or cut" as a result of the opioid crisis. Some now feel compelled to find their opioids "on the streets." She says she personally has never obtained opioids this way. Instead, she relies on marijuana to mitigate her pain.
Niculescu expects his testing method will be available to the medical community at large within one to three years: "It takes a while for things to translate from a lab setting to a commercial testing arena."
In the meantime, for Willkie and other patients, "we have to convince doctors and nurses that we're in pain."