Tony and Kelly Mantoan, with their boys Teddy and Fulton, who both suffer from SMA, a genetic disorder that makes walking, swallowing, and breathing progressively difficult.
Kelly Mantoan was nursing her newborn son, Teddy, in the NICU in a Philadelphia hospital when her doctor came in and silently laid a hand on her shoulder. Immediately, Kelly knew what the gesture meant and started to sob: Teddy, like his one-year-old brother, Fulton, had just tested positive for a neuromuscular condition called spinal muscular atrophy (SMA).
The boys were 8 and 10 when Kelly heard about an experimental new treatment, still being tested in clinical trials, called Spinraza.
"We knew that [SMA] was a genetic disorder, and we knew that we had a 1 in 4 chance of Teddy having SMA," Mantoan recalls. But the idea of having two children with the same severe disability seemed too unfair for Kelly and her husband, Tony, to imagine. "We had lots of well-meaning friends tell us, well, God won't do this to you twice," she says. Except that He, or a cruel trick of nature, had.
In part, the boys' diagnoses were so devastating because there was little that could be done at the time, back in 2009 and 2010, when the boys were diagnosed. Affecting an estimated 1 in 11,000 babies, SMA is a degenerative disease in which the body is deficient in survival motor neuron (SMN) protein, thanks to a genetic mutation or absence of the body's SNM1 gene. So muscles that control voluntary movement – such as walking, breathing, and swallowing – weaken and eventually cease to function altogether.
Babies diagnosed with SMA Type 1 rarely live past toddlerhood, while people diagnosed with SMA Types 2, 3, and 4 can live into adulthood, usually with assistance like ventilators and feeding tubes. Shortly after birth, both Teddy Mantoan and his brother, Fulton, were diagnosed with SMA Type 2.
The boys were 8 and 10 when Kelly heard about an experimental new treatment, still being tested in clinical trials, called Spinraza. Up until then, physical therapy was the only sanctioned treatment for SMA, and Kelly enrolled both her boys in weekly sessions to preserve some of their muscle strength as the disease marched forward. But Spinraza – a grueling regimen of lumbar punctures and injections designed to stimulate a backup survival motor neuron gene to produce more SMN protein – offered new hope.
In clinical trials, after just a few doses of Spinraza, babies with SMA Type 1 began meeting normal developmental milestones – holding up their heads, rolling over, and sitting up. In other trials, Spinraza treatment delayed the need for permanent ventilation, while patients on the placebo arm continued to lose function, and several died. Spinraza was such a success, and so well tolerated among patients, that clinical trials ended early and the drug was fast-tracked for FDA approval in 2016. In January 2017, when Kelly got the call that Fulton and Teddy had been approved by the hospital to start Spinraza infusions, Kelly dropped to her knees in the middle of the kitchen and screamed.
Spinraza, manufactured by Biogen, has been hailed as revolutionary, but it's also not without drawbacks: Priced per injection, just one dose of Spinraza costs $125,000, making it one of the most expensive drugs on the global market. What's worse, treatment requires a "loading dose" of four injections over a four-week period, and then periodic injections every four months, indefinitely. For the first year of treatment, Spinraza treatment costs $750,000 – and then $375,000 for every year thereafter.
Last week, a competitive treatment for SMA Type 1 manufactured by Novartis burst onto the market. The new treatment, called Zolgensma, is a one-time gene therapy intended to be given to infants and is currently priced at $2.125 million, or $425,000 annually for five years, making it the most expensive drug in the world. Like Spinraza, Zolgensma is currently raising challenging questions about how insurers and government payers like Medicaid will be able to afford these treatments without bankrupting an already-strained health care system.
To Biogen's credit, the company provides financial aid for Spinraza patients with private insurance who pay co-pays for treatment, as well as for those who have been denied by Medicaid and Medicare. But getting insurance companies to agree to pay for Spinraza can often be an ordeal in itself. Although Fulton and Teddy Mantoan were approved for treatment over two years ago, a lengthy insurance battle delayed treatment for another eight months – time that, for some SMA patients, can mean a significant loss of muscular function.
Kelly didn't notice anything in either boy – positive or negative – for the first few months of Spinraza injections. But one day in November 2017, as Teddy was lowered off his school bus in his wheelchair, he turned to say goodbye to his friends and "dab," – a dance move where one's arms are extended briefly across the chest and in the air. Normally, Teddy would dab by throwing his arms up in the air with momentum, striking a pose quickly before they fell down limp at his sides. But that day, Teddy held his arms rigid in the air. His classmates, along with Kelly, were stunned. "Teddy, look at your arms!" Kelly remembers shrieking. "You're holding them up – you're dabbing!"
Teddy and Fulton Mantoan, who both suffer from spinal muscular atrophy, have seen life-changing results from Spinraza.
(Courtesy of Kelly Mantoan)
Not long after Teddy's dab, the Mantoans started seeing changes in Fulton as well. "With Fulton, we realized suddenly that he was no longer choking on his food during meals," Kelly said. "Almost every meal we'd have to stop and have him take a sip of water and make him slow down and take small bites so he wouldn't choke. But then we realized we hadn't had to do that in a long time. The nurses at school were like, 'it's not an issue anymore.'"
For the Mantoans, this was an enormous relief: Less choking meant less chance of aspiration pneumonia, a leading cause of death for people with SMA Types 1 and 2.
While Spinraza has been life-changing for the Mantoans, it remains painfully out of reach for many others. Thanks to Spinraza's enormous price tag, the threshold for who gets to use it is incredibly high: Adult and pediatric patients, particularly those with state-sponsored insurance, have reported multiple insurance denials, lengthy appeals processes, and endless bureaucracy from insurance and hospitals alike that stand in the way of treatment.
Kate Saldana, a 21-year-old woman with Type 2 SMA, is one of the many adult patients who have been lobbying for the drug. Saldana, who uses a ventilator 20 hours each day, says that Medicaid denied her Spinraza treatments because they mistakenly believed that she used a ventilator full-time. Saldana is currently in the process of appealing their decision, but knows she is fighting an uphill battle.
Kate Saldana, who suffers from Type 2 SMA, has been fighting unsuccessfully for Medicaid to cover Spinraza.
(Courtesy of Saldana)
"Originally, the treatments were studied and created for infants and children," Saldana said in an e-mail. "There is a plethora of data to support the effectiveness of Spinraza in those groups, but in adults it has not been studied as much. That makes it more difficult for insurance to approve it, because they are not sure if it will be as beneficial."
Saldana has been pursuing treatment unsuccessfully since last August – but others, like Kimberly Hill, a 32-year-old with SMA Type 2, have been waiting even longer. Hill, who lives in Oklahoma, has been fighting for treatment since Spinraza went on the U.S. market in December 2016. Because her mobility is limited to the use of her left thumb, Hill is eager to try anything that will enable her to keep working and finish a Master's degree in Fire and Emergency Management.
"Obviously, my family and I were elated with the approval of Spinraza," Hill said in an e-mail. "We thought I would finally have the chance to get a little stronger and healthier." But with Medicare and Medicaid, coverage and eligibility varies wildly by state. Earlier this year, Medicaid approved Spinraza for adult patients only if a clawback clause was attached to the approval, meaning that under certain conditions the Medicaid funds would need to be paid back. Because of the clawback clause, hospitals have been reluctant to take on Spinraza treatments, effectively barring adult Medicaid patients from accessing the drug altogether.
Hill's hospital is currently in negotiations with Medicaid to move forward with Spinraza treatment, but in the meantime, Hill is in limbo. "We keep being told there is nothing we can do, and we are devastated," Hill said.
"I felt extremely sad and honestly a bit forgotten, like adults [with SMA] don't matter."
Between Spinraza and its new competitor, Zolgensma, some are speculating that insurers will start to favor Zolgensma coverage instead, since the treatment is shorter and ultimately cheaper than Spinraza in the long term. But for some adults with SMA who can't access Spinraza and who don't qualify for Zolgensma treatment, the issue of what insurers will cover is moot.
"I was so excited when I heard that Zolgensma was approved by the FDA," said Annie Wilson, an adult SMA patient from Alameda, Calif. who has been fighting for Spinraza since 2017. "When I became aware that it was only being offered to children, I felt extremely sad and honestly a bit forgotten, like adults [with SMA] don't matter."
According to information from a Biogen representative, more than 7500 people worldwide have been treated with Spinraza to date, one third of whom are adults.
While Spinraza has been revolutionary for thousands of patients, it's unclear how many more lives state agencies and insurance companies will allow it to save.
Basecamp Research is using portable labs like this one to gather samples from ecosystems around the world.
Clark works for Basecamp Research, a biotech company headquartered in London, and his job is to collect samples from ecosystems around the world. By extracting DNA from soil, water, plants, microbes and other organisms, Basecamp is building an extensive database of the Earth’s proteins. While DNA itself isn’t a protein, the information stored in DNA is used to create proteins, so extracting, sequencing, and annotating DNA allows for the discovery of unique protein sequences.
Using what they’re finding in the middle of the Atlantic and beyond, Basecamp’s detailed database is constantly growing. The outputs could be essential for cleaning up the damage done by toxic chemicals and finding alternatives to these chemicals.
Catalysts for change
Proteins provide structure and function in all living organisms. Some of these functional proteins are enzymes, which quite literally make things happen.
“Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development. Biocatalysis is providing advantages, both to make more complex drugs and to be more sustainable, reducing the pollution and toxicity of conventional chemistry," says Ahir Pushpanath, who heads partnerships for Basecamp.
“Enzymes are perfectly evolved catalysts,” says Ahir Pushpanath, a partnerships lead at Basecamp. ”Enzymes are essentially just a polymer, and polymers are made up of amino acids, which are nature’s building blocks.” He suggests thinking about it like Legos — if you have a bunch of Lego pieces and use them to build a structure that performs a function, “that’s basically how an enzyme works. In nature, these monuments have evolved to do life’s chemistry. If we didn’t have enzymes, we wouldn’t be alive.”
In our own bodies, enzymes catalyze everything from vision to digesting food to regrowing muscles, and these same types of enzymes are necessary in the pharmaceutical, agrochemical and fine chemical industries. But industrial conditions differ from those inside our bodies. So, when scientists need certain chemical reactions to create a particular product or substance, they make their own catalysts in their labs — generally through the use of petroleum and heavy metals.
These petrochemicals are effective and cost-efficient, but they’re wasteful and often hazardous. With growing concerns around sustainability and long-term public health, it's essential to find alternative solutions to toxic chemicals. “Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development,” Pushpanath says.
Basecamp is trying to replace lab-created catalysts with enzymes found in the wild. This concept is called biocatalysis, and in theory, all scientists have to do is find the right enzymes for their specific need. Yet, historically, researchers have struggled to find enzymes to replace petrochemicals. When they can’t identify a suitable match, they turn to what Pushpanath describes as “long, iterative, resource-intensive, directed evolution” in the laboratory to coax a protein into industrial adaptation. But the latest scientific advances have enabled these discoveries in nature instead.
Marlon Clark, a research scientist at Basecamp Research, looks for novel biochemistries in the Azores.
Glen Gowers
Enzyme hunters
Whether it’s Clark and a colleague setting off on an expedition, or a local, on-the-ground partner gathering and processing samples, there’s a lot to be learned from each collection. “Microbial genomes contain complete sets of information that define an organism — much like how letters are a code allowing us to form words, sentences, pages, and books that contain complex but digestible knowledge,” Clark says. He thinks of the environmental samples as biological libraries, filled with thousands of species, strains, and sequence variants. “It’s our job to glean genetic information from these samples.”
“We can actually dream up new proteins using generative AI," Pushpanath says.
Basecamp researchers manage this feat by sequencing the DNA and then assembling the information into a comprehensible structure. “We’re building the ‘stories’ of the biota,” Clark says. The more varied the samples, the more valuable insights his team gains into the characteristics of different organisms and their interactions with the environment. Sequencing allows scientists to examine the order of nucleotides — the organic molecules that form DNA — to identify genetic makeups and find changes within genomes. The process used to be too expensive, but the cost of sequencing has dropped from $10,000 a decade ago to as low as $100. Notably, biocatalysis isn’t a new concept — there have been waves of interest in using natural enzymes in catalysis for over a century, Pushpanath says. “But the technology just wasn’t there to make it cost effective,” he explains. “Sequencing has been the biggest boon.”
AI is probably the second biggest boon.
“We can actually dream up new proteins using generative AI,” Pushpanath says, which means that biocataylsis now has real potential to scale.
Glen Gowers, the co-founder of Basecamp, compares the company’s AI approach to that of social networks and streaming services. Consider how these platforms suggest connecting with the friends of your friends, or how watching one comedy film from the 1990s leads to a suggestion of three more.
“They’re thinking about data as networks of relationships as opposed to lists of items,” says Gowers. “By doing the same, we’re able to link the metadata of the proteins — by their relationships to each other, the environments in which they’re found, the way those proteins might look similar in sequence and structure, their surrounding genome context — really, this just comes down to creating a searchable network of proteins.”
On an Azores island, this volcanic opening may harbor organisms that can help scientists identify enzymes for biocatalysis to replace toxic chemicals.
Emma Bolton
Uwe Bornscheuer, professor at the Institute of Biochemistry at the University of Greifswald, and co-founder of Enzymicals, another biocatalysis company, says that the development of machine learning is a critical component of this work. “It’s a very hot topic, because the challenge in protein engineering is to predict which mutation at which position in the protein will make an enzyme suitable for certain applications,” Bornscheuer explains. These predictions are difficult for humans to make at all, let alone quickly. “It is clear that machine learning is a key technology.”
Benefiting from nature’s bounty
Biodiversity commonly refers to plants and animals, but the term extends to all life, including microbial life, and some regions of the world are more biodiverse than others. Building relationships with global partners is another key element to Basecamp’s success. Doing so in accordance with the access and benefit sharing principles set forth by the Nagoya Protocol — an international agreement that seeks to ensure the benefits of using genetic resources are distributed in a fair and equitable way — is part of the company's ethos. “There's a lot of potential for us, and there’s a lot of potential for our partners to have exactly the same impact in building and discovering commercially relevant proteins and biochemistries from nature,” Clark says.
Bornscheuer points out that Basecamp is not the first company of its kind. A former San Diego company called Diversa went public in 2000 with similar work. “At that time, the Nagoya Protocol was not around, but Diversa also wanted to ensure that if a certain enzyme or microorganism from Costa Rica, for example, were used in an industrial process, then people in Costa Rica would somehow profit from this.”
An eventual merger turned Diversa into Verenium Corporation, which is now a part of the chemical producer BASF, but it laid important groundwork for modern companies like Basecamp to continue to scale with today’s technologies.
“To collect natural diversity is the key to identifying new catalysts for use in new applications,” Bornscheuer says. “Natural diversity is immense, and over the past 20 years we have gained the advantages that sequencing is no longer a cost or time factor.”
This has allowed Basecamp to rapidly grow its database, outperforming Universal Protein Resource or UniProt, which is the public repository of protein sequences most commonly used by researchers. Basecamp’s database is three times larger, totaling about 900 million sequences. (UniProt isn’t compliant with the Nagoya Protocol, because, as a public database, it doesn’t provide traceability of protein sequences. Some scientists, however, argue that Nagoya compliance hinders progress.)
“Eventually, this work will reduce chemical processes. We’ll have cleaner processes, more sustainable processes," says Uwe Bornscheuer, a professor at the University of Greifswald.
With so much information available, Basecamp’s AI has been trained on “the true dictionary of protein sequence life,” Pushpanath says, which makes it possible to design sequences for particular applications. “Through deep learning approaches, we’re able to find protein sequences directly from our database, without the need for further laboratory-directed evolution.”
Recently, a major chemical company was searching for a specific transaminase — an enzyme that catalyzes a transfer of amino groups. “They had already spent a year-and-a-half and nearly two million dollars to evolve a public-database enzyme, and still had not reached their goal,” Pushpanath says. “We used our AI approaches on our novel database to yield 10 candidates within a week, which, when validated by the client, achieved the desired target even better than their best-evolved candidate.”
Basecamp’s other huge potential is in bioremediation, where natural enzymes can help to undo the damage caused by toxic chemicals. “Biocatalysis impacts both sides,” says Gowers. “It reduces the usage of chemicals to make products, and at the same time, where contamination sites do exist from chemical spills, enzymes are also there to kind of mop those up.”
So far, Basecamp's round-the-world sampling has covered 50 percent of the 14 major biomes, or regions of the planet that can be distinguished by their flora, fauna, and climate, as defined by the World Wildlife Fund. The other half remains to be catalogued — a key milestone for understanding our planet’s protein diversity, Pushpanath notes.
There’s still a long road ahead to fully replace petrochemicals with natural enzymes, but biocatalysis is on an upward trajectory. "Eventually, this work will reduce chemical processes,” Bornscheuer says. “We’ll have cleaner processes, more sustainable processes.”
In an initial study, Canary analyzed speech recordings with AI and identified early stage Alzheimer’s with 96 percent accuracy.
Arnold was diagnosed sooner than many others. It's important to find out early, when interventions can make the most difference. One promising avenue is looking at how people talk. Research has shown that Alzheimer’s affects a part of the brain that controls speech, resulting in small changes before people show other signs of the disease.
Now, Canary Speech, a company based in Utah, is using AI to examine elements like the pitch of a person’s voice and their pauses. In an initial study, Canary analyzed speech recordings with AI and identified early stage Alzheimer’s with 96 percent accuracy.
Developing the AI model
Canary Speech’s CEO, Henry O’Connell, met cofounder Jeff Adams about 40 years before they started the company. Back when they first crossed paths, they were both living in Bethesda, Maryland; O’Connell was a research fellow at the National Institutes of Health studying rare neurological diseases, while Adams was working to decode spy messages. Later on, Adams would specialize in building mathematical models to analyze speech and sound as a team leader in developing Amazon's Alexa.
It wasn't until 2015 that they decided to make use of the fit between their backgrounds. ““We established Canary Speech in 2017 to build a product that could be used in multiple languages in clinical environments,” O'Connell says.
The need is growing. About 55 million people worldwide currently live with Alzheimer’s, a number that is expected to double by 2050. Some scientists think the disease results from a buildup of plaque in the brain. It causes mild memory loss at first and, over time, this issue get worse while other symptoms, such as disorientation and hallucinations, can develop. Treatment to manage the disease is more effective in the earlier stages, but detection is difficult since mild symptoms are often attributed to the normal aging process.
O’Connell and Adams specialize in the complex ways that Alzheimer’s effects how people speak. Using AI, their mathematical model analyzes 15 million data points every minute, focusing on certain features of speech such as pitch, pauses and elongation of words. It also pays attention to how the vibrations of vocal cords change in different stages of the disease.
To create their model, the team used a type of machine learning called deep neural nets, which looks at multiple layers of data - in this case, the multiple features of a person’s speech patterns.
“Deep neural nets allow us to look at much, much larger data sets built out of millions of elements,” O’Connell explained. “Through machine learning and AI, we’ve identified features that are very sensitive to an Alzheimer’s patient versus [people without the disease] and also very sensitive to mild cognitive impairment, early stage and moderate Alzheimer's.” Based on their learnings, Canary is able to classify the disease stage very quickly, O’Connell said.
“When we’re listening to sublanguage elements, we’re really analyzing the direct result of changes in the brain in the physical body,” O’Connell said. “The brain controls your vocal cords: how fast they vibrate, the expansion of them, the contraction.” These factors, along with where people put their tongues when talking, function subconsciously and result in subtle changes in the sounds of speech.
Further testing is needed
In an initial trial, Canary analyzed speech recordings from phone calls to a large U.S. health insurer. They looked at the audio recordings of 651 policyholders who had early stage Alzheimer’s and 1018 who did not have the condition, aiming for a representative sample of age, gender and race. They used this data to create their first diagnostic model and found that it was 96 percent accurate in identifying Alzheimer’s.
Christian Herff, an assistant professor of neuroscience at Maastricht University in the Netherlands, praised this approach while adding that further testing is needed to assess its effectiveness.
“I think the general idea of identifying increased risk for cognitive impairment based on speech characteristics is very feasible, particularly when change in a user’s voice is monitored, for example, by recording speech every year,” Herff said. He noted that this can only be a first indication, not a full diagnosis. The accuracy still needs to be validated in studies that follows individuals over a period of time, he said.
Toby Walsh, a professor of artificial intelligence at the University of New South Wales, also thinks Canary’s tool has potential but highlights that Canary could diagnose some people who don’t really have the disease. “This is an interesting and promising application of AI,” he said, “but these tools need to be used carefully. Imagine the anxiety of being misdiagnosed with Alzheimer’s.”
As with many other AI tools, privacy and bias are additional issues to monitor closely, Walsh said.
Other languages
A related issue is that not everyone is fluent in English. Mahnaz Arvaneh, a senior lecturer in automatic control and systems engineering at the University of Sheffield, said this could be a blind spot.
“The system may not be very accurate for those who have English as their second language as their speaking patterns would be different, and any issue might be because of language deficiency rather than cognitive issues,” Arvaneh said.
The team is expanding to multiple languages starting with Japanese and Spanish. The elements of the model that make up the algorithm are very similar, but they need to be validated and retrained in a different language, which will require access to more data.
Recently, Canary analyzed the phone calls of 233 Japanese patients who had mild cognitive impairment and 704 healthy people. Using an English model they were able to identify the Japanese patients who had mild cognitive impairment with 78 percent accuracy. They also developed a model in Japanese that was 45 percent accurate, and they’re continuing to train it with more data.
The future
Canary is using their model to look at other diseases like Huntington’s and Parkinson’s. They’re also collaborating with pharmaceuticals to validate potential therapies for Alzheimer’s. By looking at speech patterns over time, Canary can get an indication of how well these drugs are working.
Dave Arnold and his wife dance at his nephew’s wedding in Rochester, New York, ten years ago, before his Alzheimer's diagnosis.
Dave Arnold
Ultimately, they want to integrate their tool into everyday life. “We want it to be used in a smartphone, or a teleconference call so that individuals could be examined in their home,” O’Connell said. “We could follow them over time and work with clinical teams and hospitals to improve the evaluation of patients and contribute towards an accurate diagnosis.”
Arnold, the patient with early stage Alzheimer’s, sees great promise. “The process of getting a diagnosis is already filled with so much anxiety,” he said. “Anything that can be done to make it easier and less stressful would be a good thing, as long as it’s proven accurate.”